From c9750a0cb53dd216eb088481c3fa7de92495f799 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 15:46:26 -0400 Subject: [PATCH 01/78] initial external status label impl Conflicts: src/main/java/propertyFiles/Bundle.properties --- .../harvard/iq/dataverse/DatasetVersion.java | 10 ++ .../harvard/iq/dataverse/MailServiceBean.java | 7 ++ .../iq/dataverse/UserNotification.java | 2 +- .../harvard/iq/dataverse/api/Datasets.java | 12 +++ .../providers/builtin/DataverseUserPage.java | 1 + .../impl/SetExternalStatusCommand.java | 91 +++++++++++++++++++ .../harvard/iq/dataverse/util/MailUtil.java | 2 + src/main/java/propertyFiles/Bundle.properties | 3 + src/main/webapp/dataset.xhtml | 1 + src/main/webapp/dataverseuser.xhtml | 10 ++ src/main/webapp/file.xhtml | 1 + 11 files changed, 139 insertions(+), 1 deletion(-) create mode 100644 src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java index 1f0467577a2..0eb516232f7 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java @@ -171,6 +171,8 @@ public enum License { @OneToMany(mappedBy = "datasetVersion", cascade={CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST}) private List workflowComments; + @Column(nullable=true) + private String externalStatusLabel; public Long getId() { return this.id; @@ -1952,4 +1954,12 @@ public String getLocaleLastUpdateTime() { return DateUtil.formatDate(new Timestamp(lastUpdateTime.getTime())); } + public String getExternalStatusLabel() { + return externalStatusLabel; + } + + public void setExternalStatusLabel(String externalStatusLabel) { + this.externalStatusLabel = externalStatusLabel; + } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java index 619f6577b61..ccf30f00ff7 100644 --- a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java @@ -522,6 +522,12 @@ public String getMessageTextBasedOnNotification(UserNotification userNotificatio String[] paramArrayWorkflowFailure = {version.getDataset().getDisplayName(), getDatasetLink(version.getDataset()), comment}; messageText += MessageFormat.format(pattern, paramArrayWorkflowFailure); return messageText; + case STATUSUPDATED: + version = (DatasetVersion) targetObject; + pattern = BundleUtil.getStringFromBundle("notification.email.status"); + String[] paramArrayStatus = {version.getDataset().getDisplayName(), version.getExternalStatusLabel()}; + messageText += MessageFormat.format(pattern, paramArrayStatus); + return messageText; case CREATEACC: InternetAddress systemAddress = getSystemAddress(); String accountCreatedMessage = BundleUtil.getStringFromBundle("notification.email.welcome", Arrays.asList( @@ -621,6 +627,7 @@ private Object getObjectOfNotification (UserNotification userNotification){ case RETURNEDDS: case WORKFLOW_SUCCESS: case WORKFLOW_FAILURE: + case STATUSUPDATED: return versionService.find(userNotification.getObjectId()); case CREATEACC: return userNotification.getUser(); diff --git a/src/main/java/edu/harvard/iq/dataverse/UserNotification.java b/src/main/java/edu/harvard/iq/dataverse/UserNotification.java index 78f8f38206b..8c0f7e3da16 100644 --- a/src/main/java/edu/harvard/iq/dataverse/UserNotification.java +++ b/src/main/java/edu/harvard/iq/dataverse/UserNotification.java @@ -30,7 +30,7 @@ public enum Type { ASSIGNROLE, REVOKEROLE, CREATEDV, CREATEDS, CREATEACC, SUBMITTEDDS, RETURNEDDS, PUBLISHEDDS, REQUESTFILEACCESS, GRANTFILEACCESS, REJECTFILEACCESS, FILESYSTEMIMPORT, CHECKSUMIMPORT, CHECKSUMFAIL, CONFIRMEMAIL, APIGENERATED, INGESTCOMPLETED, INGESTCOMPLETEDWITHERRORS, - PUBLISHFAILED_PIDREG, WORKFLOW_SUCCESS, WORKFLOW_FAILURE + PUBLISHFAILED_PIDREG, WORKFLOW_SUCCESS, WORKFLOW_FAILURE, STATUSUPDATED }; private static final long serialVersionUID = 1L; diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 226b4092078..42f6a74e847 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -69,6 +69,7 @@ import edu.harvard.iq.dataverse.engine.command.impl.RequestRsyncScriptCommand; import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand; import edu.harvard.iq.dataverse.engine.command.impl.SetDatasetCitationDateCommand; +import edu.harvard.iq.dataverse.engine.command.impl.SetExternalStatusCommand; import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand; import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand; import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetTargetURLCommand; @@ -1556,6 +1557,17 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo } } + @PUT + @Path("{id}/setExternalStatus") + public Response setExternalStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { + try { + execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); + return ok("External Status updated"); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } + @GET @Path("{id}/uploadsid") @Deprecated diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java index d050dbc0dbd..f38965ff28a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java @@ -492,6 +492,7 @@ public void displayNotification() { case RETURNEDDS: case WORKFLOW_SUCCESS: case WORKFLOW_FAILURE: + case STATUSUPDATED: userNotification.setTheObject(datasetVersionService.find(userNotification.getObjectId())); break; diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java new file mode 100644 index 00000000000..25d48b488ac --- /dev/null +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -0,0 +1,91 @@ +package edu.harvard.iq.dataverse.engine.command.impl; + +import edu.harvard.iq.dataverse.Dataset; +import edu.harvard.iq.dataverse.DatasetLock; +import edu.harvard.iq.dataverse.DatasetVersionUser; +import edu.harvard.iq.dataverse.UserNotification; +import edu.harvard.iq.dataverse.authorization.Permission; +import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser; +import edu.harvard.iq.dataverse.batch.util.LoggingUtil; +import edu.harvard.iq.dataverse.engine.command.AbstractCommand; +import edu.harvard.iq.dataverse.engine.command.CommandContext; +import edu.harvard.iq.dataverse.engine.command.DataverseRequest; +import edu.harvard.iq.dataverse.engine.command.RequiredPermissions; +import edu.harvard.iq.dataverse.engine.command.exception.CommandException; +import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; +import edu.harvard.iq.dataverse.util.BundleUtil; +import java.io.IOException; +import java.sql.Timestamp; +import java.util.Date; +import java.util.List; +import java.util.concurrent.Future; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +import org.apache.solr.client.solrj.SolrServerException; + +@RequiredPermissions(Permission.EditDataset) +public class SetExternalStatusCommand extends AbstractDatasetCommand { + + String label; + + public SetExternalStatusCommand(DataverseRequest aRequest, Dataset dataset, String label) { + super(aRequest, dataset); + this.label=label; + } + + @Override + public Dataset execute(CommandContext ctxt) throws CommandException { + + if (getDataset().getLatestVersion().isReleased()) { + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure.isReleased"), this); + } + Pattern pattern = Pattern.compile("/[\\w ]+/g"); + Matcher matcher = pattern.matcher(label); + if(!matcher.matches()) { + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure"), this); + } + getDataset().getLatestVersion().setExternalStatusLabel(label); + Dataset updatedDataset = save(ctxt); + + return updatedDataset; + } + + public Dataset save(CommandContext ctxt) throws CommandException { + + getDataset().getEditVersion().setLastUpdateTime(getTimestamp()); + getDataset().setModificationTime(getTimestamp()); + + Dataset savedDataset = ctxt.em().merge(getDataset()); + ctxt.em().flush(); + + updateDatasetUser(ctxt); + + AuthenticatedUser requestor = getUser().isAuthenticated() ? (AuthenticatedUser) getUser() : null; + + List authUsers = ctxt.permissions().getUsersWithPermissionOn(Permission.PublishDataset, savedDataset); + for (AuthenticatedUser au : authUsers) { + ctxt.notifications().sendNotification(au, new Timestamp(new Date().getTime()), UserNotification.Type.SUBMITTEDDS, savedDataset.getLatestVersion().getId(), "", requestor, false); + } + + // TODO: What should we do with the indexing result? Print it to the log? + return savedDataset; + } + + @Override + public boolean onSuccess(CommandContext ctxt, Object r) { + boolean retVal = true; + Dataset dataset = (Dataset) r; + + try { + Future indexString = ctxt.index().indexDataset(dataset, true); + } catch (IOException | SolrServerException e) { + String failureLogText = "Post submit for review indexing failed. You can kickoff a re-index of this dataset with: \r\n curl http://localhost:8080/api/admin/index/datasets/" + dataset.getId().toString(); + failureLogText += "\r\n" + e.getLocalizedMessage(); + LoggingUtil.writeOnSuccessFailureLog(this, failureLogText, dataset); + retVal = false; + } + return retVal; + } + +} diff --git a/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java index 7ca702cabbe..e776592b955 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java @@ -58,6 +58,8 @@ public static String getSubjectTextBasedOnNotification(UserNotification userNoti return BundleUtil.getStringFromBundle("notification.email.workflow.success.subject", rootDvNameAsList); case WORKFLOW_FAILURE: return BundleUtil.getStringFromBundle("notification.email.workflow.failure.subject", rootDvNameAsList); + case STATUSUPDATED: + return BundleUtil.getStringFromBundle("notification.email.status.change.subject", rootDvNameAsList); case CREATEACC: return BundleUtil.getStringFromBundle("notification.email.create.account.subject", rootDvNameAsList); case CHECKSUMFAIL: diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 77248d76ea8..afdf3e6b4d3 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -203,6 +203,7 @@ notification.wasPublished={0} was published in {1}. notification.publishFailedPidReg={0} in {1} could not be published due to a failure to register, or update the Global Identifier for the dataset or one of the files in it. Contact support if this continues to happen. notification.workflowFailed=An external workflow run on {0} in {1} has failed. Check your email and/or view the Dataset page which may have additional details. Contact support if this continues to happen. notification.workflowSucceeded=An external workflow run on {0} in {1} has succeeded. Check your email and/or view the Dataset page which may have additional details. +notification.statusUpdated=The status of dataset {0} has been updated to {1}. notification.ingestCompleted=Dataset {1} ingest has successfully finished. notification.ingestCompletedWithErrors=Dataset {1} ingest has finished with errors. @@ -681,6 +682,8 @@ notification.email.workflow.success.subject={0}: Your dataset has been processed notification.email.workflow.success=A workflow running on {0} (view at {1}) succeeded: {2} notification.email.workflow.failure.subject={0}: Failed to process your dataset notification.email.workflow.failure=A workflow running on {0} (view at {1}) failed: {2} +notification.email.status.change.subject={0}: Dataset Status Change +notification.email.status.change=The Status of the dataset ({0}) has changed to {1} notification.email.workflow.nullMessage=No additional message sent from the workflow. notification.email.create.account.subject={0}: Your account has been created notification.email.assign.role.subject={0}: You have been assigned a role diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 995d6188cc6..977ac704456 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -114,6 +114,7 @@ + diff --git a/src/main/webapp/dataverseuser.xhtml b/src/main/webapp/dataverseuser.xhtml index 3e48e16404c..c7c3873ef1f 100644 --- a/src/main/webapp/dataverseuser.xhtml +++ b/src/main/webapp/dataverseuser.xhtml @@ -334,6 +334,16 @@ + + + + + #{item.theObject.getDataset().getDisplayName()} + + + + + diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index 0e4931e7086..13e6e0b9440 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -68,6 +68,7 @@ + From 19dcce1c4fda90b8f9454451ff8c9750cdf85676 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 16:24:43 -0400 Subject: [PATCH 02/78] typos, update errors, change regexp Conflicts: src/main/java/propertyFiles/Bundle.properties --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 6 +++++- .../engine/command/impl/SetExternalStatusCommand.java | 6 +++++- src/main/java/propertyFiles/Bundle.properties | 2 ++ src/main/webapp/dataset.xhtml | 2 +- src/main/webapp/file.xhtml | 2 +- 5 files changed, 14 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 42f6a74e847..87f47efed05 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -86,6 +86,7 @@ import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter; import edu.harvard.iq.dataverse.dataaccess.S3AccessIO; import edu.harvard.iq.dataverse.engine.command.exception.CommandException; +import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; import edu.harvard.iq.dataverse.engine.command.exception.UnforcedCommandException; import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetStorageSizeCommand; import edu.harvard.iq.dataverse.engine.command.impl.RevokeRoleCommand; @@ -1560,11 +1561,14 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo @PUT @Path("{id}/setExternalStatus") public Response setExternalStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { + logger.info("Label is " + label); try { execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); return ok("External Status updated"); } catch (WrappedResponse wr) { - return wr.getResponse(); + //Just change to Bad Request and send + //ToDo - check in api call + return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index 25d48b488ac..b77b95bda86 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -19,6 +19,7 @@ import java.util.Date; import java.util.List; import java.util.concurrent.Future; +import java.util.logging.Logger; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -27,6 +28,8 @@ @RequiredPermissions(Permission.EditDataset) public class SetExternalStatusCommand extends AbstractDatasetCommand { + private static final Logger logger = Logger.getLogger(SetExternalStatusCommand.class.getName()); + String label; public SetExternalStatusCommand(DataverseRequest aRequest, Dataset dataset, String label) { @@ -40,9 +43,10 @@ public Dataset execute(CommandContext ctxt) throws CommandException { if (getDataset().getLatestVersion().isReleased()) { throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure.isReleased"), this); } - Pattern pattern = Pattern.compile("/[\\w ]+/g"); + Pattern pattern = Pattern.compile("(/^[\\w ]+$/"); Matcher matcher = pattern.matcher(label); if(!matcher.matches()) { + logger.info("Label rejected: " + label); throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure"), this); } getDataset().getLatestVersion().setExternalStatusLabel(label); diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index afdf3e6b4d3..32ebfed471e 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1329,6 +1329,8 @@ dataset.submit.failure=Dataset Submission Failed - {0} dataset.submit.failure.null=Can't submit for review. Dataset is null. dataset.submit.failure.isReleased=Latest version of dataset is already released. Only draft versions can be submitted for review. dataset.submit.failure.inReview=You cannot submit this dataset for review because it is already in review. +dataset.status.failure=Status update failed +dataset.status.failure.isReleased=Latest version of dataset is already released. Status can only be set on draft versions dataset.rejectMessage=Return this dataset to contributor for modification. dataset.rejectMessage.label=Return to Author Reason dataset.rejectWatermark=Please enter a reason for returning this dataset to its author(s). diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 977ac704456..b59ea71aaad 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -114,7 +114,7 @@ - + diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index 13e6e0b9440..b83511c23f2 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -68,7 +68,7 @@ - + From c5b215a4785820dee930c1149a403738563cc5a9 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 16:31:14 -0400 Subject: [PATCH 03/78] typo missing ) --- .../dataverse/engine/command/impl/SetExternalStatusCommand.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index b77b95bda86..30ac73f906d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -43,7 +43,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException { if (getDataset().getLatestVersion().isReleased()) { throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure.isReleased"), this); } - Pattern pattern = Pattern.compile("(/^[\\w ]+$/"); + Pattern pattern = Pattern.compile("(/^[\\w ]+$)/"); Matcher matcher = pattern.matcher(label); if(!matcher.matches()) { logger.info("Label rejected: " + label); From d0d996c5db18c6f9bce932b52e58077d8700c059 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 16:38:25 -0400 Subject: [PATCH 04/78] fix regexp, use new error msgs --- .../engine/command/impl/SetExternalStatusCommand.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index 30ac73f906d..8c01dacc519 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -41,13 +41,13 @@ public SetExternalStatusCommand(DataverseRequest aRequest, Dataset dataset, Stri public Dataset execute(CommandContext ctxt) throws CommandException { if (getDataset().getLatestVersion().isReleased()) { - throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure.isReleased"), this); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.isReleased"), this); } - Pattern pattern = Pattern.compile("(/^[\\w ]+$)/"); + Pattern pattern = Pattern.compile("(^[\\w ]+$)"); Matcher matcher = pattern.matcher(label); if(!matcher.matches()) { logger.info("Label rejected: " + label); - throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.submit.failure"), this); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure"), this); } getDataset().getLatestVersion().setExternalStatusLabel(label); Dataset updatedDataset = save(ctxt); From 044cbbc8b64033790d988b67b5e72901d3376519 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 16:55:24 -0400 Subject: [PATCH 05/78] allow delete, clear upon publication --- .../edu/harvard/iq/dataverse/api/Datasets.java | 14 ++++++++++++++ .../FinalizeDatasetPublicationCommand.java | 3 +++ .../command/impl/SetExternalStatusCommand.java | 18 +++++++++++------- 3 files changed, 28 insertions(+), 7 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 87f47efed05..ade41c3131a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -1572,6 +1572,20 @@ public Response setExternalStatus(@PathParam("id") String idSupplied, @QueryPara } } + @DELETE + @Path("{id}/setExternalStatus") + public Response deleteExternalStatus(@PathParam("id") String idSupplied) { + + try { + execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), null)); + return ok("External Status deleted"); + } catch (WrappedResponse wr) { + //Just change to Bad Request and send + //ToDo - check in api call + return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); + } + } + @GET @Path("{id}/uploadsid") @Deprecated diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java index 4fa07dedede..c33bf03f469 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java @@ -114,6 +114,9 @@ public Dataset execute(CommandContext ctxt) throws CommandException { theDataset.setPublicationDate(new Timestamp(new Date().getTime())); } + //Clear any external status + theDataset.getLatestVersion().setExternalStatusLabel(null); + // update metadata theDataset.getLatestVersion().setReleaseTime(getTimestamp()); theDataset.getLatestVersion().setLastUpdateTime(getTimestamp()); diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index 8c01dacc519..ccfdbe15751 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -43,13 +43,17 @@ public Dataset execute(CommandContext ctxt) throws CommandException { if (getDataset().getLatestVersion().isReleased()) { throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.isReleased"), this); } - Pattern pattern = Pattern.compile("(^[\\w ]+$)"); - Matcher matcher = pattern.matcher(label); - if(!matcher.matches()) { - logger.info("Label rejected: " + label); - throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure"), this); + if (label == null) { + getDataset().getLatestVersion().setExternalStatusLabel(label); + } else { + Pattern pattern = Pattern.compile("(^[\\w ]+$)"); + Matcher matcher = pattern.matcher(label); + if (!matcher.matches()) { + logger.info("Label rejected: " + label); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure"), this); + } + getDataset().getLatestVersion().setExternalStatusLabel(label); } - getDataset().getLatestVersion().setExternalStatusLabel(label); Dataset updatedDataset = save(ctxt); return updatedDataset; @@ -69,7 +73,7 @@ public Dataset save(CommandContext ctxt) throws CommandException { List authUsers = ctxt.permissions().getUsersWithPermissionOn(Permission.PublishDataset, savedDataset); for (AuthenticatedUser au : authUsers) { - ctxt.notifications().sendNotification(au, new Timestamp(new Date().getTime()), UserNotification.Type.SUBMITTEDDS, savedDataset.getLatestVersion().getId(), "", requestor, false); + ctxt.notifications().sendNotification(au, new Timestamp(new Date().getTime()), UserNotification.Type.STATUSUPDATED, savedDataset.getLatestVersion().getId(), "", requestor, false); } // TODO: What should we do with the indexing result? Print it to the log? From 149baa3f6700c6723f1be4e05dc6127524a9a446 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 17:12:31 -0400 Subject: [PATCH 06/78] typo --- src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java index ccf30f00ff7..e2d5fbded36 100644 --- a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java @@ -524,7 +524,7 @@ public String getMessageTextBasedOnNotification(UserNotification userNotificatio return messageText; case STATUSUPDATED: version = (DatasetVersion) targetObject; - pattern = BundleUtil.getStringFromBundle("notification.email.status"); + pattern = BundleUtil.getStringFromBundle("notification.email.status.change"); String[] paramArrayStatus = {version.getDataset().getDisplayName(), version.getExternalStatusLabel()}; messageText += MessageFormat.format(pattern, paramArrayStatus); return messageText; From 21efbb8ad896e996d88d41a15a3604938027b3ea Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 22 Jun 2021 17:21:41 -0400 Subject: [PATCH 07/78] don't say null in email --- src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java index e2d5fbded36..3760d1004f2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java @@ -525,7 +525,7 @@ public String getMessageTextBasedOnNotification(UserNotification userNotificatio case STATUSUPDATED: version = (DatasetVersion) targetObject; pattern = BundleUtil.getStringFromBundle("notification.email.status.change"); - String[] paramArrayStatus = {version.getDataset().getDisplayName(), version.getExternalStatusLabel()}; + String[] paramArrayStatus = {version.getDataset().getDisplayName(), (version.getExternalStatusLabel()==null) ? "" : version.getExternalStatusLabel()}; messageText += MessageFormat.format(pattern, paramArrayStatus); return messageText; case CREATEACC: From dac5389ad2ecb6840aae4823fa264c901c113f66 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 24 Jun 2021 14:27:04 -0400 Subject: [PATCH 08/78] fix: get the datasetversion --- src/main/webapp/file.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index b83511c23f2..481012eb021 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -68,7 +68,7 @@ - + From 346af0dd837161e4b0421873fac3c8405c3b6c1e Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 28 Jun 2021 13:19:17 -0400 Subject: [PATCH 09/78] require publish permission, add label list setting Conflicts: src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java src/main/java/propertyFiles/Bundle.properties --- .../impl/SetExternalStatusCommand.java | 22 +++++++++++++------ .../settings/SettingsServiceBean.java | 6 ++++- src/main/java/propertyFiles/Bundle.properties | 3 ++- 3 files changed, 22 insertions(+), 9 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index ccfdbe15751..f3f1b7f9021 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -13,9 +13,11 @@ import edu.harvard.iq.dataverse.engine.command.RequiredPermissions; import edu.harvard.iq.dataverse.engine.command.exception.CommandException; import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; +import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import edu.harvard.iq.dataverse.util.BundleUtil; import java.io.IOException; import java.sql.Timestamp; +import java.util.Arrays; import java.util.Date; import java.util.List; import java.util.concurrent.Future; @@ -25,7 +27,7 @@ import org.apache.solr.client.solrj.SolrServerException; -@RequiredPermissions(Permission.EditDataset) +@RequiredPermissions(Permission.PublishDataset) public class SetExternalStatusCommand extends AbstractDatasetCommand { private static final Logger logger = Logger.getLogger(SetExternalStatusCommand.class.getName()); @@ -46,13 +48,19 @@ public Dataset execute(CommandContext ctxt) throws CommandException { if (label == null) { getDataset().getLatestVersion().setExternalStatusLabel(label); } else { - Pattern pattern = Pattern.compile("(^[\\w ]+$)"); - Matcher matcher = pattern.matcher(label); - if (!matcher.matches()) { - logger.info("Label rejected: " + label); - throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure"), this); + String allowedLabels = ctxt.settings().getValueForKey(SettingsServiceBean.Key.AllowedCurationLabels, ""); + if (Arrays.asList(allowedLabels.split("\\s*,\\s*")).contains(label)) { + Pattern pattern = Pattern.compile("(^[\\w ]+$)"); + Matcher matcher = pattern.matcher(label); + if (!matcher.matches()) { + logger.info("Label rejected: " + label); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.badformat"), this); + } + getDataset().getLatestVersion().setExternalStatusLabel(label); + } else { + logger.info("Label not found: " + label); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.notallowed"), this); } - getDataset().getLatestVersion().setExternalStatusLabel(label); } Dataset updatedDataset = save(ctxt); diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java index 02637bfa8df..a48de83e558 100644 --- a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java @@ -433,7 +433,11 @@ Whether Harvesting (OAI) service is enabled * Installation Brand Name is always included (default/false) or is not included * when the Distributor field (citation metadatablock) is set (true) */ - ExportInstallationAsDistributorOnlyWhenNotSet + ExportInstallationAsDistributorOnlyWhenNotSet, + /** + * A comma separated list of the allowed labels. These should correspond to the states in an organizations curation process. + */ + AllowedCurationLabels ; @Override diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 32ebfed471e..4811bcdc821 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1329,7 +1329,8 @@ dataset.submit.failure=Dataset Submission Failed - {0} dataset.submit.failure.null=Can't submit for review. Dataset is null. dataset.submit.failure.isReleased=Latest version of dataset is already released. Only draft versions can be submitted for review. dataset.submit.failure.inReview=You cannot submit this dataset for review because it is already in review. -dataset.status.failure=Status update failed +dataset.status.failure.notallowed=Status update failed - label not allowed +dataset.status.failure.badformat=Status update failed - label can only include alphanumeric characters and internal spaces. dataset.status.failure.isReleased=Latest version of dataset is already released. Status can only be set on draft versions dataset.rejectMessage=Return this dataset to contributor for modification. dataset.rejectMessage.label=Return to Author Reason From 017254db0c18993238b1bdd92dd020008120ae6d Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 20 Jul 2021 17:51:59 -0400 Subject: [PATCH 10/78] add status label in search results --- src/main/webapp/search-include-fragment.xhtml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index f70b321cea4..07eecc087a0 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -590,6 +590,7 @@ + From cda78c266b17b6412aa967bfdffb0403ff6fded3 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 20 Jul 2021 18:25:20 -0400 Subject: [PATCH 11/78] make external status searchable/fix display in search --- conf/solr/8.8.1/schema.xml | 1 + .../iq/dataverse/search/IndexServiceBean.java | 3 +++ .../harvard/iq/dataverse/search/SearchFields.java | 2 ++ .../iq/dataverse/search/SearchServiceBean.java | 4 ++++ .../iq/dataverse/search/SolrSearchResult.java | 12 ++++++++++++ src/main/webapp/search-include-fragment.xhtml | 2 +- 6 files changed, 23 insertions(+), 1 deletion(-) diff --git a/conf/solr/8.8.1/schema.xml b/conf/solr/8.8.1/schema.xml index c6f6cd37cd6..3d46a8336be 100644 --- a/conf/solr/8.8.1/schema.xml +++ b/conf/solr/8.8.1/schema.xml @@ -162,6 +162,7 @@ + diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java index bfc2af2fcc4..2f6bcfbd394 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java @@ -781,6 +781,9 @@ private String addOrUpdateDataset(IndexableDataset indexableDataset, Set d if (datasetVersion.isInReview()) { solrInputDocument.addField(SearchFields.PUBLICATION_STATUS, IN_REVIEW_STRING); } + if(datasetVersion.getExternalStatusLabel()!=null) { + solrInputDocument.addField(SearchFields.EXTERNAL_STATUS, datasetVersion.getExternalStatusLabel()); + } for (DatasetField dsf : datasetVersion.getFlatDatasetFields()) { diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java index a14cac88f1e..422e74f2207 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java @@ -220,6 +220,8 @@ public class SearchFields { * i.e. "Unpublished", "Draft" (multivalued) */ public static final String PUBLICATION_STATUS = "publicationStatus"; + + public static final String EXTERNAL_STATUS = "externalStatus"; /** * @todo reconcile different with Solr schema.xml where type is Long rather * than String. diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java index 8969d7523cd..ceed424cbce 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java @@ -427,6 +427,10 @@ public SolrQueryResponse search(DataverseRequest dataverseRequest, List matchedFields; + //External Status Label (enabled via AllowedCurationLabels setting) + private String externalStatus; + /** * @todo: remove name? */ @@ -1205,4 +1208,13 @@ public String getNameOfDataverse() { public void setNameOfDataverse(String id) { this.nameOfDataverse = id; } + + public String getExternalStatus() { + return externalStatus; + } + + public void setExternalStatus(String externalStatus) { + this.externalStatus = externalStatus; + + } } diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index 07eecc087a0..59bf368fa57 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -590,7 +590,7 @@ - + From 62166f2412ca1a77983953cf101e32b70dd353c5 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 20 Jul 2021 20:35:42 -0400 Subject: [PATCH 12/78] add to dataset card --- src/main/webapp/search-include-fragment.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index 59bf368fa57..1b21f0ebd70 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -525,6 +525,7 @@ +
@@ -590,7 +591,6 @@ -
From 7ceef90eb777c4cad7a616bed635359a3fc0db63 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 10:36:21 -0400 Subject: [PATCH 13/78] add curation status menu Conflicts: src/main/webapp/dataset.xhtml --- .../edu/harvard/iq/dataverse/DatasetPage.java | 13 +++ .../harvard/iq/dataverse/SettingsWrapper.java | 9 ++ src/main/java/propertyFiles/Bundle.properties | 4 + src/main/webapp/dataset.xhtml | 101 ++++++++++-------- 4 files changed, 83 insertions(+), 44 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index d441faf7ec6..f8f18756f17 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -100,6 +100,7 @@ import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetResult; import edu.harvard.iq.dataverse.engine.command.impl.RestrictFileCommand; import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand; +import edu.harvard.iq.dataverse.engine.command.impl.SetExternalStatusCommand; import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand; import edu.harvard.iq.dataverse.externaltools.ExternalTool; import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean; @@ -5477,4 +5478,16 @@ public boolean isFileDeleted (DataFile dataFile) { return dataFile.getDeleted(); } + + public void setExternalStatus(String status) { + try { + commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); + JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.externalstatus.header"), + BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); + } catch (CommandException ex) { + String msg = BundleUtil.getStringFromBundle("dataset.externalstatus.cantchange"); + logger.warning("Unable to change external status to " + status + " for dataset id " + dataset.getId() + ". Message to user: " + msg + " Exception: " + ex); + JsfHelper.addErrorMessage(msg); + } + } } diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index eb4527f2aaa..739ce99f426 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -276,5 +276,14 @@ public boolean displayChronologicalDateFacets() { } + List allowedExternalStatuses = null; + + public List getAllowedExternalStatuses() { + String names = get(SettingsServiceBean.Key.AllowedCurationLabels.toString(), ""); + if (allowedExternalStatuses == null) { + allowedExternalStatuses.addAll(Arrays.asList(names.split(",\\s"))); + } + return allowedExternalStatuses; + } } diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 4811bcdc821..f129b97551b 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1278,6 +1278,7 @@ dataset.shareBtn=Share dataset.publishBtn=Publish Dataset dataset.editBtn=Edit Dataset +dataset.changestatus=Change Curation Status dataset.editBtn.itemLabel.upload=Files (Upload) dataset.editBtn.itemLabel.metadata=Metadata dataset.editBtn.itemLabel.terms=Terms @@ -1515,6 +1516,9 @@ dataset.privateurl.roleassigeeTitle=Private URL Enabled dataset.privateurl.createdSuccess=Success! dataset.privateurl.disabledSuccess=You have successfully disabled the Private URL for this unpublished dataset. dataset.privateurl.noPermToCreate=To create a Private URL you must have the following permissions: {0}. +dataset.externalstatus.header=Curation Status Changed +dataset.externalstatus.info=Curation Status is now {0} +dataset.externalstatus.cantchange=Unable to change Curation Status. Please contact the administrator. file.display.label=Change View file.display.table=Table file.display.tree=Tree diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index b59ea71aaad..4f9d9ea6f82 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -279,51 +279,64 @@ - -
-
- - - - - - - - - - - - - #{bundle['dataset.publishBtn']} - - -
    -
  • - - - #{bundle['dataset.publish.btn']} - -
    • -
  • - - - #{bundle['dataset.rejectBtn']} - -
    • -
  • - - - #{DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn']} - + +
    +
    + + + + + + + + + + + + + #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} + + +
      +
    • + + + #{bundle['dataset.publish.btn']} + +
      • +
    • + + + #{DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn']} + +
      • +
    • + + + #{bundle['dataset.rejectBtn']} + +
      • + +
    • + #{bundle['dataset.changestatus']} +
        + +
      • + + #{status} + +
        • +         +
      • -
    -
    + +
From 2c5ae21db837fd2bb5139613b703bce1405fb210 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 10:45:28 -0400 Subject: [PATCH 14/78] handle nulls --- src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index 739ce99f426..aac5523f756 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -280,7 +280,8 @@ public boolean displayChronologicalDateFacets() { public List getAllowedExternalStatuses() { String names = get(SettingsServiceBean.Key.AllowedCurationLabels.toString(), ""); - if (allowedExternalStatuses == null) { + if (names != null && allowedExternalStatuses == null) { + allowedExternalStatuses = new ArrayList(); allowedExternalStatuses.addAll(Arrays.asList(names.split(",\\s"))); } return allowedExternalStatuses; From 6dbc26a64409de6207866e10da35bb5c733a9be4 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 10:52:17 -0400 Subject: [PATCH 15/78] fix update --- src/main/webapp/dataset.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 4f9d9ea6f82..927a7627a8d 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -328,7 +328,7 @@
  • - + #{status}
    • From b3a224fa2447e0aead8c725643fc9e6727593e0a Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 11:02:51 -0400 Subject: [PATCH 16/78] add remove status --- src/main/java/propertyFiles/Bundle.properties | 1 + src/main/webapp/dataset.xhtml | 6 ++++++ 2 files changed, 7 insertions(+) diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index f129b97551b..3df2f38ec22 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1279,6 +1279,7 @@ dataset.publishBtn=Publish Dataset dataset.editBtn=Edit Dataset dataset.changestatus=Change Curation Status +dataset.changestatus=Remove Current Status dataset.editBtn.itemLabel.upload=Files (Upload) dataset.editBtn.itemLabel.metadata=Metadata dataset.editBtn.itemLabel.terms=Terms diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 927a7627a8d..37a8258a102 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -332,6 +332,12 @@ #{status} + +
  • + + #{dataset.removestatus} + +
From 1648080d55a6f87f86093c4484bafa4376262889 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 11:10:42 -0400 Subject: [PATCH 17/78] typo getting bundled string --- src/main/webapp/dataset.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 37a8258a102..60c6536fbf8 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -335,7 +335,7 @@
  • - #{dataset.removestatus} + #{bundle['dataset.removestatus']}
    • From b3a20c390b7a10b514abd52d04e16c6585dad0b5 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 11:21:26 -0400 Subject: [PATCH 18/78] bundle typo, move remove outside repeat --- src/main/java/propertyFiles/Bundle.properties | 2 +- src/main/webapp/dataset.xhtml | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 3df2f38ec22..08dd70b68d7 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1279,7 +1279,7 @@ dataset.publishBtn=Publish Dataset dataset.editBtn=Edit Dataset dataset.changestatus=Change Curation Status -dataset.changestatus=Remove Current Status +dataset.removestatus=Remove Current Status dataset.editBtn.itemLabel.upload=Files (Upload) dataset.editBtn.itemLabel.metadata=Metadata dataset.editBtn.itemLabel.terms=Terms diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 60c6536fbf8..50a9e13eb72 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -332,13 +332,13 @@ #{status} - -
  • - - #{bundle['dataset.removestatus']} - -
    • + +
  • + + #{bundle['dataset.removestatus']} + +
    • From 74e36229b06d361012d9b0736246ee6153b74581 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 13:16:33 -0400 Subject: [PATCH 19/78] update dataset after status change --- src/main/java/edu/harvard/iq/dataverse/DatasetPage.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index f8f18756f17..2287e63ce7b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5481,9 +5481,9 @@ public boolean isFileDeleted (DataFile dataFile) { public void setExternalStatus(String status) { try { - commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); + dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.externalstatus.header"), - BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); + status==null ? "" : BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); } catch (CommandException ex) { String msg = BundleUtil.getStringFromBundle("dataset.externalstatus.cantchange"); logger.warning("Unable to change external status to " + status + " for dataset id " + dataset.getId() + ". Message to user: " + msg + " Exception: " + ex); From 25dbdc1c08c7b3621c17f8cb596ed215b783615c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 15:23:40 -0400 Subject: [PATCH 20/78] debug publish button --- src/main/webapp/dataset.xhtml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 50a9e13eb72..25442a751f4 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -283,6 +283,9 @@
    + + + From 839bc34231c2befce3085c7b79beadca08b086a4 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 15:35:31 -0400 Subject: [PATCH 21/78] show menu when enabled --- src/main/webapp/dataset.xhtml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 25442a751f4..6a999d16c5c 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -283,15 +283,12 @@
    - - - - + - + From 250cb2ccc44757c111bf79e114f81d8a7ce66df9 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 15:49:54 -0400 Subject: [PATCH 22/78] fix carat --- src/main/webapp/dataset.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 6a999d16c5c..6818e64d12f 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -294,7 +294,7 @@ - #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} + #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])}
      From f7c61d0a3bc529fdb38369f645a7f9bbe924b20c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 15:50:08 -0400 Subject: [PATCH 23/78] handle empty and null status --- src/main/java/edu/harvard/iq/dataverse/DatasetPage.java | 2 +- .../engine/command/impl/SetExternalStatusCommand.java | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 2287e63ce7b..f3bf877dc1e 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5483,7 +5483,7 @@ public void setExternalStatus(String status) { try { dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.externalstatus.header"), - status==null ? "" : BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); + (status == null || status.isEmpty()) ? "" : BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); } catch (CommandException ex) { String msg = BundleUtil.getStringFromBundle("dataset.externalstatus.cantchange"); logger.warning("Unable to change external status to " + status + " for dataset id " + dataset.getId() + ". Message to user: " + msg + " Exception: " + ex); diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index f3f1b7f9021..df0cfc51d55 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -27,6 +27,9 @@ import org.apache.solr.client.solrj.SolrServerException; +import com.beust.jcommander.Strings; +import com.google.api.LabelDescriptor; + @RequiredPermissions(Permission.PublishDataset) public class SetExternalStatusCommand extends AbstractDatasetCommand { @@ -45,7 +48,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException { if (getDataset().getLatestVersion().isReleased()) { throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.isReleased"), this); } - if (label == null) { + if (label==null || label.isEmpty()) { getDataset().getLatestVersion().setExternalStatusLabel(label); } else { String allowedLabels = ctxt.settings().getValueForKey(SettingsServiceBean.Key.AllowedCurationLabels, ""); From 0c91b18c4e43839062046d40e0bdc4cefbb9a80d Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 21 Jul 2021 16:14:11 -0400 Subject: [PATCH 24/78] handle trailing space(s), update messaging --- src/main/java/edu/harvard/iq/dataverse/DatasetPage.java | 8 ++++++-- .../java/edu/harvard/iq/dataverse/SettingsWrapper.java | 2 +- src/main/java/propertyFiles/Bundle.properties | 3 ++- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index f3bf877dc1e..6729aef38a2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5482,8 +5482,12 @@ public boolean isFileDeleted (DataFile dataFile) { public void setExternalStatus(String status) { try { dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); - JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.externalstatus.header"), - (status == null || status.isEmpty()) ? "" : BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); + if (status == null || status.isEmpty()) { + JsfHelper.addInfoMessage(BundleUtil.getStringFromBundle("dataset.externalstatus.removed")); + } else { + JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.externalstatus.header"), BundleUtil.getStringFromBundle("dataset.externalstatus.info", Arrays.asList(status))); + } + } catch (CommandException ex) { String msg = BundleUtil.getStringFromBundle("dataset.externalstatus.cantchange"); logger.warning("Unable to change external status to " + status + " for dataset id " + dataset.getId() + ". Message to user: " + msg + " Exception: " + ex); diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index aac5523f756..879a6a195ac 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -282,7 +282,7 @@ public List getAllowedExternalStatuses() { String names = get(SettingsServiceBean.Key.AllowedCurationLabels.toString(), ""); if (names != null && allowedExternalStatuses == null) { allowedExternalStatuses = new ArrayList(); - allowedExternalStatuses.addAll(Arrays.asList(names.split(",\\s"))); + allowedExternalStatuses.addAll(Arrays.asList(names.split("\\s*,\\s*"))); } return allowedExternalStatuses; } diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 08dd70b68d7..ab83fc2b3f7 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1518,7 +1518,8 @@ dataset.privateurl.createdSuccess=Success! dataset.privateurl.disabledSuccess=You have successfully disabled the Private URL for this unpublished dataset. dataset.privateurl.noPermToCreate=To create a Private URL you must have the following permissions: {0}. dataset.externalstatus.header=Curation Status Changed -dataset.externalstatus.info=Curation Status is now {0} +dataset.externalstatus.removed=Curation Status Removed +dataset.externalstatus.info=Curation Status is now "{0}" dataset.externalstatus.cantchange=Unable to change Curation Status. Please contact the administrator. file.display.label=Change View file.display.table=Table From 6551af4e1188027b276ebdcf3dab1d4fcb1c91de Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 22 Jul 2021 11:12:53 -0400 Subject: [PATCH 25/78] add status flyway --- src/main/resources/db/migration/V5.5.0.4--externalstatus.sql | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 src/main/resources/db/migration/V5.5.0.4--externalstatus.sql diff --git a/src/main/resources/db/migration/V5.5.0.4--externalstatus.sql b/src/main/resources/db/migration/V5.5.0.4--externalstatus.sql new file mode 100644 index 00000000000..eae6b46c3ef --- /dev/null +++ b/src/main/resources/db/migration/V5.5.0.4--externalstatus.sql @@ -0,0 +1,2 @@ +ALTER TABLE datasetversion ADD COLUMN IF NOT EXISTS externalstatuslabel varchar(32); + From c37ad7c59e4150d619df62fee612fee5a20a1222 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 22 Jul 2021 11:24:03 -0400 Subject: [PATCH 26/78] bad script name --- ...{V5.5.0.4--externalstatus.sql => V5.5.0.4__externalstatus.sql} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/main/resources/db/migration/{V5.5.0.4--externalstatus.sql => V5.5.0.4__externalstatus.sql} (100%) diff --git a/src/main/resources/db/migration/V5.5.0.4--externalstatus.sql b/src/main/resources/db/migration/V5.5.0.4__externalstatus.sql similarity index 100% rename from src/main/resources/db/migration/V5.5.0.4--externalstatus.sql rename to src/main/resources/db/migration/V5.5.0.4__externalstatus.sql From 5d7eaeaab0df7757152ccd6ac6281426a344ad60 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 22 Jul 2021 15:31:53 -0400 Subject: [PATCH 27/78] change to label-info to adjust color --- src/main/webapp/dataset.xhtml | 2 +- src/main/webapp/file.xhtml | 2 +- src/main/webapp/search-include-fragment.xhtml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 6818e64d12f..03064c12a1c 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -114,7 +114,7 @@ - + diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index 481012eb021..ed435eb7cc8 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -68,7 +68,7 @@ - + diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index 1b21f0ebd70..fecac6ec99f 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -525,7 +525,7 @@ - +
    From 47637629a959bb0ece02eb13a02e215de556a34d Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 26 Jul 2021 16:11:53 -0400 Subject: [PATCH 28/78] restrict ext status label visibility to those who can publish --- src/main/java/edu/harvard/iq/dataverse/FilePage.java | 4 ++++ .../harvard/iq/dataverse/search/SearchIncludeFragment.java | 4 ++++ src/main/webapp/dataset.xhtml | 2 +- src/main/webapp/file.xhtml | 2 +- src/main/webapp/search-include-fragment.xhtml | 2 +- 5 files changed, 11 insertions(+), 3 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/FilePage.java b/src/main/java/edu/harvard/iq/dataverse/FilePage.java index 045ac1f934a..f3488d950db 100644 --- a/src/main/java/edu/harvard/iq/dataverse/FilePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/FilePage.java @@ -238,6 +238,10 @@ public String init() { private boolean canViewUnpublishedDataset() { return permissionsWrapper.canViewUnpublishedDataset( dvRequestService.getDataverseRequest(), fileMetadata.getDatasetVersion().getDataset()); } + + public boolean canPublishDataset(){ + return permissionsWrapper.canIssuePublishDatasetCommand(fileMetadata.getDatasetVersion().getDataset()); + } public FileMetadata getFileMetadata() { diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java index 09ab372c687..81adef74c57 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java @@ -1249,6 +1249,10 @@ public String dataFileSizeDisplay(DataFile datafile) { } + public boolean canPublishDataset(long datasetId){ + return permissionsWrapper.canIssuePublishDatasetCommand(dvObjectService.findDvObject(datasetId)); + } + public void setDisplayCardValues() { Set harvestedDatasetIds = null; diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index b647387eef3..b7836dc6004 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -114,7 +114,7 @@ - + diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml index e238a66a8a5..8669f683c78 100644 --- a/src/main/webapp/file.xhtml +++ b/src/main/webapp/file.xhtml @@ -68,7 +68,7 @@ - + diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index fecac6ec99f..d84096d8b83 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -525,7 +525,7 @@ - +
    From 2bf2686f82af2e9518b847fcd4b1830c22fffed4 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 26 Jul 2021 18:15:26 -0400 Subject: [PATCH 29/78] handle string conversion --- .../iq/dataverse/search/SearchIncludeFragment.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java index 81adef74c57..79e430c81c6 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java @@ -1249,8 +1249,15 @@ public String dataFileSizeDisplay(DataFile datafile) { } - public boolean canPublishDataset(long datasetId){ + public boolean canPublishDataset(String id){ + try { + //Should only be called with a valid id (set during indexing) but catch/log any exception. + Long datasetId = Long.parseLong(id); return permissionsWrapper.canIssuePublishDatasetCommand(dvObjectService.findDvObject(datasetId)); + } catch (NumberFormatException nfe) { + logger.warning("canPublishDataset called with dataset id: " + id); + return false; + } } public void setDisplayCardValues() { From 25cfbac30b79da200efa4772a6a2d467315c1475 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 26 Jul 2021 18:29:49 -0400 Subject: [PATCH 30/78] use entityId directly Conflicts: src/main/webapp/search-include-fragment.xhtml --- .../iq/dataverse/search/SearchIncludeFragment.java | 9 +-------- src/main/webapp/search-include-fragment.xhtml | 2 +- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java index 79e430c81c6..f4e97a3842a 100644 --- a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java +++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java @@ -1249,15 +1249,8 @@ public String dataFileSizeDisplay(DataFile datafile) { } - public boolean canPublishDataset(String id){ - try { - //Should only be called with a valid id (set during indexing) but catch/log any exception. - Long datasetId = Long.parseLong(id); + public boolean canPublishDataset(Long datasetId){ return permissionsWrapper.canIssuePublishDatasetCommand(dvObjectService.findDvObject(datasetId)); - } catch (NumberFormatException nfe) { - logger.warning("canPublishDataset called with dataset id: " + id); - return false; - } } public void setDisplayCardValues() { diff --git a/src/main/webapp/search-include-fragment.xhtml b/src/main/webapp/search-include-fragment.xhtml index d84096d8b83..cb542ec776d 100644 --- a/src/main/webapp/search-include-fragment.xhtml +++ b/src/main/webapp/search-include-fragment.xhtml @@ -525,7 +525,7 @@ - +
    From 448e212e673cc0b470931de1ed6743cabb1aa051 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 29 Jul 2021 09:53:31 -0400 Subject: [PATCH 31/78] update flyway --- ...{V5.5.0.4__externalstatus.sql => V5.5.0.6__externalstatus.sql} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/main/resources/db/migration/{V5.5.0.4__externalstatus.sql => V5.5.0.6__externalstatus.sql} (100%) diff --git a/src/main/resources/db/migration/V5.5.0.4__externalstatus.sql b/src/main/resources/db/migration/V5.5.0.6__externalstatus.sql similarity index 100% rename from src/main/resources/db/migration/V5.5.0.4__externalstatus.sql rename to src/main/resources/db/migration/V5.5.0.6__externalstatus.sql From 11e45a2aedde1f210bc3dc6d5b316995e5b70c85 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Fri, 30 Jul 2021 10:34:14 -0400 Subject: [PATCH 32/78] update workingVersion after status change --- src/main/java/edu/harvard/iq/dataverse/DatasetPage.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index c29f4561e76..14a66addd8b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5492,6 +5492,7 @@ public boolean isFileDeleted (DataFile dataFile) { public void setExternalStatus(String status) { try { dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); + workingVersion=dataset.getLatestVersion(); if (status == null || status.isEmpty()) { JsfHelper.addInfoMessage(BundleUtil.getStringFromBundle("dataset.externalstatus.removed")); } else { From d4b2d8d922fddfc7aeb5ae1e3da17742ddbc3916 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Fri, 30 Jul 2021 15:34:52 -0400 Subject: [PATCH 33/78] missing
    and spacing --- src/main/webapp/dataset.xhtml | 123 +++++++++++++++++----------------- 1 file changed, 62 insertions(+), 61 deletions(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index b7836dc6004..a261e9c28ea 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -280,70 +280,71 @@
    - -
    -
    - - - - - - - - - - - - - #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} - - -
      -
    • - - - #{bundle['dataset.publish.btn']} - -
      • -
    • - - - #{DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn']} - -
      • -
    • - - - #{bundle['dataset.rejectBtn']} - -
      • - -
    • - #{bundle['dataset.changestatus']} -
        - + +
        +
        + + + + + + + + + + + + + #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} + + +
          +
        • + + + #{bundle['dataset.publish.btn']} + +
          • +
        • + + + #{DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn']} + +
          • +
        • + + + #{bundle['dataset.rejectBtn']} + +
          • + +
        • + #{bundle['dataset.changestatus']} +
            + +
          • + + #{status} + +
            • +             +
          • - - #{status} + + #{bundle['dataset.removestatus']}
            • - - -
          • - - #{bundle['dataset.removestatus']} - -
            • -
          -
          • -           -
        +
      +
      • +       +
    +
    From b135cdcee0c6cae3033810cd44ce8968a32ca46c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Fri, 30 Jul 2021 15:35:07 -0400 Subject: [PATCH 34/78] don't create list if empty --- src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index 1bf99749e12..11cd4def44d 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -296,7 +296,7 @@ public boolean shouldBeAnonymized(DatasetField df) { public List getAllowedExternalStatuses() { String names = get(SettingsServiceBean.Key.AllowedCurationLabels.toString(), ""); - if (names != null && allowedExternalStatuses == null) { + if (!names.isEmpty() && allowedExternalStatuses == null) { allowedExternalStatuses = new ArrayList(); allowedExternalStatuses.addAll(Arrays.asList(names.split("\\s*,\\s*"))); } From cb876cb6caa7de766f7e483878c39d2685ab4896 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Fri, 30 Jul 2021 17:35:31 -0400 Subject: [PATCH 35/78] fix menu/button logic --- src/main/webapp/dataset.xhtml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index a261e9c28ea..318df88f5ee 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -285,17 +285,17 @@
    - + - + - #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} + #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])}
      From 9368f553f3c20c2d17df05572b84e083e416c165 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 4 Aug 2021 18:14:13 -0400 Subject: [PATCH 36/78] update flyway numbering --- ...{V5.5.0.6__externalstatus.sql => V5.6.0.1__externalstatus.sql} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/main/resources/db/migration/{V5.5.0.6__externalstatus.sql => V5.6.0.1__externalstatus.sql} (100%) diff --git a/src/main/resources/db/migration/V5.5.0.6__externalstatus.sql b/src/main/resources/db/migration/V5.6.0.1__externalstatus.sql similarity index 100% rename from src/main/resources/db/migration/V5.5.0.6__externalstatus.sql rename to src/main/resources/db/migration/V5.6.0.1__externalstatus.sql From c304f094e8136b4ee4d86c119e7c072792c18d8c Mon Sep 17 00:00:00 2001 From: qqmyers Date: Thu, 12 Aug 2021 17:42:40 -0400 Subject: [PATCH 37/78] docs --- doc/release-notes/7967-curation-labels.md | 3 +++ doc/sphinx-guides/source/installation/config.rst | 11 +++++++++++ .../iq/dataverse/settings/SettingsServiceBean.java | 9 ++++++++- 3 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 doc/release-notes/7967-curation-labels.md diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md new file mode 100644 index 00000000000..861d7c60921 --- /dev/null +++ b/doc/release-notes/7967-curation-labels.md @@ -0,0 +1,3 @@ +### Support for external curation processes + +Dataverse can now be configured, via the :AllowedCurationLabels setting, to support arbitrary short labels (e.g. "Author contacted", "Privacy Review", "Awaiting paper publication") on draft datasets that indicate the status/state of the dataset with respect to some externally defined curation process. Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. \ No newline at end of file diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index 2b2ef8dadad..896cbbdba1b 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -2333,3 +2333,14 @@ A comma-separated list of field type names that should be 'withheld' when datase A suggested minimum includes author, datasetContact, and contributor, but additional fields such as depositor, grantNumber, and publication might also need to be included. ``curl -X PUT -d 'author, datasetContact, contributor, depositor, grantNumber, publication' http://localhost:8080/api/admin/settings/:AnonymizedFieldTypeNames`` + +:AllowedCurationLabels + +A comma separated list of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. +These should correspond to the states in an organizations curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. +A dataset may only have one label at a time and if a label is set, it will be removed at publication time. +This functionality is disabled when this setting is empty/not set. + +Dataverse can now be configured, via the :AllowedCurationLabels setting, to support arbitrary short labels (e.g. "Author contacted", "Privacy Review", "Awaiting paper publication") on draft datasets that indicate the status/state of the dataset with respect to some externally defined curation process. Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. + +``curl -X PUT -d 'Author contacted, Privacy Review, Awaiting paper publication, Final Approval' http://localhost:8080/api/admin/settings/:AllowedCurationLabels`` \ No newline at end of file diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java index 3439b233771..af7cffdebb8 100644 --- a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java @@ -458,7 +458,14 @@ Whether Harvesting (OAI) service is enabled */ MetadataLanguages, /** - * A comma separated list of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. These should correspond to the states in an organizations curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. A dataset may only have one label at a time and if a label is set, it will be removed at publication time. This functionality is disabled when this setting is empty/not set. + * A comma separated list of allowed labels (up to 32 characters, spaces + * allowed) that can be set, via API or UI by users with the permission to + * publish a dataset. These should correspond to the states in an organizations + * curation process and are intended to help users/curators track the progress + * of a dataset through an externally defined curation process. A dataset may + * only have one label at a time and if a label is set, it will be removed at + * publication time. This functionality is disabled when this setting is + * empty/not set. */ AllowedCurationLabels ; From 039d239f8ca94b3bd560cd7a5919750d286dde9c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 18 Aug 2021 17:12:55 -0400 Subject: [PATCH 38/78] fix error on submit for review Conflicts: src/main/webapp/dataset.xhtml --- src/main/webapp/dataset.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 90b3fb4c548..92f3bacfbc8 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -323,7 +323,7 @@ #{bundle['dataset.rejectBtn']} - +
    • #{bundle['dataset.changestatus']}
        From effe3bf95c1f2b46c2047ce8c1b162be4b14f4b6 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 19 Aug 2021 16:45:19 -0400 Subject: [PATCH 39/78] add a curation status report api call --- .../iq/dataverse/DatasetServiceBean.java | 5 ++ .../harvard/iq/dataverse/api/Datasets.java | 49 +++++++++++++++++++ src/main/java/propertyFiles/Bundle.properties | 3 ++ 3 files changed, 57 insertions(+) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java index 2cf1f0d094f..288575d5462 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java @@ -198,6 +198,11 @@ public List findAllUnindexed() { return em.createQuery("SELECT o.id FROM Dataset o WHERE o.indexTime IS null ORDER BY o.id DESC", Long.class).getResultList(); } + //Used in datasets listcurationstatus API + public List findAllUnpublished() { + return em.createQuery("SELECT object(o) FROM Dataset o, DvObject d WHERE d.id=o.id and d.publicationDate IS null ORDER BY o.id ASC", Dataset.class).getResultList(); + } + /** * For docs, see the equivalent method on the DataverseServiceBean. * @param numPartitions diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 6219aea65e1..ba39195e864 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -122,6 +122,7 @@ import java.io.StringReader; import java.sql.Timestamp; import java.text.MessageFormat; +import java.text.SimpleDateFormat; import java.time.LocalDateTime; import java.time.ZoneId; import java.time.format.DateTimeFormatter; @@ -2734,4 +2735,52 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, return addFileHelper.addFiles(jsonData, dataset, authUser); } + + + /** QDR + * + * API to find curation assignements and statuses + * + * @return + * @throws WrappedResponse + */ + @GET + @Path("/listCurationStatuses") + @Produces("text/csv") + public Response getCurationStatuses() throws WrappedResponse { + + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + + StringBuilder csvSB = new StringBuilder(String.join(",", + BundleUtil.getStringFromBundle("dataset"), + BundleUtil.getStringFromBundle("datasets.api.creationdate"), + BundleUtil.getStringFromBundle("datasets.api.modificationdate"), + BundleUtil.getStringFromBundle("datasets.api.curationstatus"))); + for (Dataset dataset : datasetSvc.findAllUnpublished()) { + List ras = permissionService.assignmentsOn(dataset); + String assignee = null; + for (RoleAssignment ra : ras) { + if (ra.getRole().getName().equals("Assignee")) { + assignee = ra.getAssigneeIdentifier(); + break; + } + } + String name = dataset.getCurrentName().replace("\"","\"\""); + String status = dataset.getLatestVersion().getExternalStatusLabel(); + String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); + String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); + String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); + String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; + csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, assignee==null ? "":assignee, status==null ? "": status)); + } + csvSB.append("\n"); + return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); + } } diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index cf29f8ad707..c92451c2f61 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -2401,6 +2401,9 @@ datasets.api.privateurl.error.datasetnotfound=Could not find dataset. datasets.api.privateurl.error.alreadyexists=Private URL already exists for this dataset. datasets.api.privateurl.error.notdraft=Can't create Private URL because the latest version of this dataset is not a draft. datasets.api.privateurl.anonymized.error.released=Can't create a URL for anonymized access because this dataset has been published. +datasets.api.creationdate=Date Created +datasets.api.modificationdate=Last Modified Date +datasets.api.curationstatus=Curation Status #Dataverses.java From 702df0e88bdce489d5e312e642d50f47436b7961 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 20 Sep 2021 15:52:58 -0400 Subject: [PATCH 40/78] allow config of curation labels per collection Conflicts: src/main/java/edu/harvard/iq/dataverse/DataversePage.java src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java src/main/java/propertyFiles/Bundle.properties --- .../harvard/iq/dataverse/DataversePage.java | 42 +++++++++++++++++++ .../iq/dataverse/DvObjectContainer.java | 32 +++++++++++++- .../iq/dataverse/util/SystemConfig.java | 38 +++++++++++++++++ src/main/java/propertyFiles/Bundle.properties | 2 + src/main/webapp/dataverse.xhtml | 13 ++++++ 5 files changed, 126 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index c6731d26503..7571e6a2953 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -36,6 +36,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; +import java.util.HashSet; import java.util.Map; import java.util.Map.Entry; import java.util.Set; @@ -1210,4 +1211,45 @@ public Set> getMetadataLanguages() { return settingsWrapper.getMetadataLanguages(this.dataverse).entrySet(); } + public Set getCurationLabelSetOptions() { + Set setNames = new HashSet(); + Set allowedSetNames = systemConfig.getCurationLabels().keySet(); + if (allowedSetNames.size() > 0) { + // Add an entry for the default (inherited from an ancestor or the system + // default) + String inheritedLabelSet = getCurationLabelSetName(); + if (!StringUtils.isBlank(inheritedLabelSet)) { + setNames.add(inheritedLabelSet); + } + // Add an entry for disabled + setNames.add(SystemConfig.CURATIONLABELSDISABLED); + setNames.addAll(allowedSetNames); + } + return setNames; + } + + public String getCurationLabelSetName() { + Dataverse parent = dataverse.getOwner(); + String setName = null; + boolean fromAncestor = false; + if (parent != null) { + setName = parent.getEffectiveCurationLabelSetName(); + // recurse dataverse chain to root and if any have a curation label set name set, + // fromAncestor is true + while (parent != null) { + if (!parent.getCurationLabelSetName().equals(SystemConfig.DEFAULTCURATIONLABELSET)) { + fromAncestor = true; + break; + } + parent = parent.getOwner(); + } + } + if (fromAncestor) { + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); + } else { + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); + } + return setName; + } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java index 87206020e36..a31571a28d7 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java +++ b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java @@ -1,8 +1,8 @@ package edu.harvard.iq.dataverse; import edu.harvard.iq.dataverse.dataaccess.DataAccess; +import edu.harvard.iq.dataverse.util.SystemConfig; import java.util.Locale; - import javax.persistence.MappedSuperclass; import org.apache.commons.lang3.StringUtils; @@ -95,4 +95,34 @@ public void setMetadataLanguage(String ml) { } } + + + /* Dataverse collections can be configured to allow use of Curation labels and have this inheritable value to decide which set of labels to use. + * This mechanism is similar to that for the storageDriver except that there is an addition option to disable use of labels. + */ + private String curationLabelSetName = null; + + public String getEffectiveCurationLabelSetName() { + String setName = curationLabelSetName; + if (StringUtils.isBlank(setName) || setName.equals(SystemConfig.defaultCurationLabelSet)) { + if (this.getOwner() != null) { + setName = this.getOwner().getEffectiveCurationLabelSetName(); + } else { + setName = SystemConfig.CURATIONLABELSDISABLED; + } + } + return setName; + } + + public String getCurationLabelSetName() { + if (curationLabelSetName == null) { + return SystemConfig.defaultCurationLabelSet; + } + return curationLabelSetName; + } + + public void setCurationLabelSetName(String setName) { + this.curationLabelSetName = setName; + } + } diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java index b0548d0ffe6..d1f9c2aabdd 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java @@ -9,6 +9,8 @@ import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean; import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProvider; import edu.harvard.iq.dataverse.authorization.providers.oauth2.AbstractOAuth2AuthenticationProvider; +import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; + import static edu.harvard.iq.dataverse.datasetutility.FileSizeChecker.bytesToHumanReadable; import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import edu.harvard.iq.dataverse.validation.PasswordValidatorUtil; @@ -29,6 +31,9 @@ import java.util.Properties; import java.util.ResourceBundle; import java.util.logging.Logger; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + import javax.ejb.EJB; import javax.ejb.Stateless; import javax.inject.Named; @@ -117,6 +122,9 @@ public class SystemConfig { private static final long DEFAULT_GUESTBOOK_RESPONSES_DISPLAY_LIMIT = 5000L; + public final static String DEFAULTCURATIONLABELSET = "DEFAULT"; + public final static String CURATIONLABELSDISABLED = "DISABLED"; + public String getVersion() { return getVersion(false); } @@ -1082,4 +1090,34 @@ public String getDataCiteRestApiUrlString() { return System.getProperty("doi.dataciterestapiurlstring", System.getProperty("doi.mdcbaseurlstring", "https://api.datacite.org")); } + public Map getCurationLabels() { + Map labelMap = new HashMap(); + + try { + JsonReader jsonReader = Json.createReader(new StringReader(settingsService.getValueForKey(SettingsServiceBean.Key.AllowedCurationLabels, ""))); + + Pattern pattern = Pattern.compile("(^[\\w ]+$)"); // alphanumeric, underscore and whitespace allowed + + JsonObject labelSets = jsonReader.readObject(); + for (String key : labelSets.keySet()) { + JsonArray labels = (JsonArray) labelSets.getJsonArray(key); + boolean allLabelsOK = true; + String[] labelArray = labels.toArray(String[]::new); + for (String label : labelArray) { + Matcher matcher = pattern.matcher(label); + if (!matcher.matches()) { + logger.warning("Label rejected: " + label + ", Label set " + key + " ignored."); + allLabelsOK = false; + break; + } + } + if (allLabelsOK) { + labelMap.put(key, labelArray); + } + } + } catch (Exception e) { + logger.warning("Unable to parse " + SettingsServiceBean.Key.AllowedCurationLabels.name()); + } + return labelMap; + } } diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index c92451c2f61..ca1f8b22d8b 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -40,6 +40,7 @@ institution=Institution position=Position affiliation=Affiliation storage=Storage +curationLabels=Curation Labels metadataLanguage=Dataset Metadata Language createDataverse=Create Dataverse remove=Remove @@ -739,6 +740,7 @@ dataverse.identifier.title=Short name used for the URL of this dataverse. dataverse.affiliation.title=The organization with which this dataverse is affiliated. dataverse.storage.title=A storage service to be used for datasets in this dataverse. dataverse.metadatalanguage.title=Metadata entered for datasets in this dataverse will be assumed to be in the selected language. +dataverse.curationLabels.title=A set of curation labels that can be used for datasets in this collection. dataverse.category=Category dataverse.category.title=The type that most closely reflects this dataverse. dataverse.type.selectTab.top=Select one... diff --git a/src/main/webapp/dataverse.xhtml b/src/main/webapp/dataverse.xhtml index c14e872278d..b980cb3b4f1 100644 --- a/src/main/webapp/dataverse.xhtml +++ b/src/main/webapp/dataverse.xhtml @@ -160,6 +160,19 @@
    +
    + + #{bundle.curationLabels} + + +
    + + + + +
    +
    From b24e77565d056077ba3f45a493976f6486f5af5e Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 20 Sep 2021 15:57:13 -0400 Subject: [PATCH 41/78] failed refactor fix --- src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java index a31571a28d7..be8c4912d80 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java +++ b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java @@ -104,7 +104,7 @@ public void setMetadataLanguage(String ml) { public String getEffectiveCurationLabelSetName() { String setName = curationLabelSetName; - if (StringUtils.isBlank(setName) || setName.equals(SystemConfig.defaultCurationLabelSet)) { + if (StringUtils.isBlank(setName) || setName.equals(SystemConfig.DEFAULTCURATIONLABELSET)) { if (this.getOwner() != null) { setName = this.getOwner().getEffectiveCurationLabelSetName(); } else { @@ -116,7 +116,7 @@ public String getEffectiveCurationLabelSetName() { public String getCurationLabelSetName() { if (curationLabelSetName == null) { - return SystemConfig.defaultCurationLabelSet; + return SystemConfig.DEFAULTCURATIONLABELSET; } return curationLabelSetName; } From db4e136b07b7d8fdcf01b20996293dbd54faac4a Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 20 Sep 2021 17:04:31 -0400 Subject: [PATCH 42/78] sql script update --- .../edu/harvard/iq/dataverse/DvObjectContainer.java | 10 +++++----- .../db/migration/V5.6.0.1__curationlabels.sql | 4 ++++ 2 files changed, 9 insertions(+), 5 deletions(-) create mode 100644 src/main/resources/db/migration/V5.6.0.1__curationlabels.sql diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java index be8c4912d80..8bde808252f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java +++ b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java @@ -100,10 +100,10 @@ public void setMetadataLanguage(String ml) { /* Dataverse collections can be configured to allow use of Curation labels and have this inheritable value to decide which set of labels to use. * This mechanism is similar to that for the storageDriver except that there is an addition option to disable use of labels. */ - private String curationLabelSetName = null; + private String externalLabelSetName = null; public String getEffectiveCurationLabelSetName() { - String setName = curationLabelSetName; + String setName = externalLabelSetName; if (StringUtils.isBlank(setName) || setName.equals(SystemConfig.DEFAULTCURATIONLABELSET)) { if (this.getOwner() != null) { setName = this.getOwner().getEffectiveCurationLabelSetName(); @@ -115,14 +115,14 @@ public String getEffectiveCurationLabelSetName() { } public String getCurationLabelSetName() { - if (curationLabelSetName == null) { + if (externalLabelSetName == null) { return SystemConfig.DEFAULTCURATIONLABELSET; } - return curationLabelSetName; + return externalLabelSetName; } public void setCurationLabelSetName(String setName) { - this.curationLabelSetName = setName; + this.externalLabelSetName = setName; } } diff --git a/src/main/resources/db/migration/V5.6.0.1__curationlabels.sql b/src/main/resources/db/migration/V5.6.0.1__curationlabels.sql new file mode 100644 index 00000000000..0f2c799482a --- /dev/null +++ b/src/main/resources/db/migration/V5.6.0.1__curationlabels.sql @@ -0,0 +1,4 @@ +ALTER TABLE datasetversion ADD COLUMN IF NOT EXISTS externalstatuslabel varchar(32); +ALTER TABLE dataverse ADD COLUMN IF NOT EXISTS externallabelsetname varchar(32); +ALTER TABLE dataset ADD COLUMN IF NOT EXISTS externallabelsetname varchar(32); + From c6c5604041d8a0d4d24c1bc9109bca137432f7da Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 20 Sep 2021 22:24:41 -0400 Subject: [PATCH 43/78] more debug info --- src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java index d1f9c2aabdd..1cab5881866 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java @@ -1116,7 +1116,8 @@ public Map getCurationLabels() { } } } catch (Exception e) { - logger.warning("Unable to parse " + SettingsServiceBean.Key.AllowedCurationLabels.name()); + logger.warning("Unable to parse " + SettingsServiceBean.Key.AllowedCurationLabels.name() + ": " + e.getLocalizedMessage()); + e.printStackTrace(); } return labelMap; } From a45b2e744cadd9d13ad11a71df078ec74931558c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 20 Sep 2021 22:43:11 -0400 Subject: [PATCH 44/78] change loop --- .../edu/harvard/iq/dataverse/util/SystemConfig.java | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java index 1cab5881866..c190f6f3cde 100644 --- a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java +++ b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java @@ -23,6 +23,7 @@ import java.time.Year; import java.util.Arrays; import java.util.HashMap; +import java.util.Iterator; import java.util.List; import java.util.Locale; import java.util.Map; @@ -1101,15 +1102,21 @@ public Map getCurationLabels() { JsonObject labelSets = jsonReader.readObject(); for (String key : labelSets.keySet()) { JsonArray labels = (JsonArray) labelSets.getJsonArray(key); + String[] labelArray = new String[labels.size()]; + boolean allLabelsOK = true; - String[] labelArray = labels.toArray(String[]::new); - for (String label : labelArray) { + Iterator iter = labels.iterator(); + int i=0; + while(iter.hasNext()) { + String label = ((JsonString)iter.next()).getString(); Matcher matcher = pattern.matcher(label); if (!matcher.matches()) { logger.warning("Label rejected: " + label + ", Label set " + key + " ignored."); allLabelsOK = false; break; } + labelArray[i] = label; + i++; } if (allLabelsOK) { labelMap.put(key, labelArray); From fa4a6715f48bf5ff980916bf43f9acd0a553cab4 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 09:23:57 -0400 Subject: [PATCH 45/78] fix default, update label setting menu and command Conflicts: src/main/java/edu/harvard/iq/dataverse/DataversePage.java src/main/java/propertyFiles/Bundle.properties src/main/webapp/dataset.xhtml --- .../edu/harvard/iq/dataverse/DatasetPage.java | 4 +++ .../harvard/iq/dataverse/DataversePage.java | 18 +++++------ .../harvard/iq/dataverse/SettingsWrapper.java | 13 ++++---- .../impl/SetExternalStatusCommand.java | 30 ++++++++++++------- src/main/java/propertyFiles/Bundle.properties | 2 +- src/main/webapp/dataset.xhtml | 8 ++--- src/main/webapp/dataverse.xhtml | 2 +- 7 files changed, 45 insertions(+), 32 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 94139c570b1..fa7f6280ac3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5533,4 +5533,8 @@ public void setExternalStatus(String status) { JsfHelper.addErrorMessage(msg); } } + + public List getAllowedExternalStatuses() { + return settingsWrapper.getAllowedExternalStatuses(dataset); + } } diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 7571e6a2953..0c18bfe48a4 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -1211,24 +1211,24 @@ public Set> getMetadataLanguages() { return settingsWrapper.getMetadataLanguages(this.dataverse).entrySet(); } - public Set getCurationLabelSetOptions() { - Set setNames = new HashSet(); + public Set> getCurationLabelSetOptions() { + HashMap setNames = new HashMap(); Set allowedSetNames = systemConfig.getCurationLabels().keySet(); if (allowedSetNames.size() > 0) { // Add an entry for the default (inherited from an ancestor or the system // default) - String inheritedLabelSet = getCurationLabelSetName(); + String inheritedLabelSet = getCurationLabelSetNameLabel(); if (!StringUtils.isBlank(inheritedLabelSet)) { - setNames.add(inheritedLabelSet); + setNames.put(inheritedLabelSet,SystemConfig.DEFAULTCURATIONLABELSET); } // Add an entry for disabled - setNames.add(SystemConfig.CURATIONLABELSDISABLED); - setNames.addAll(allowedSetNames); + setNames.put(SystemConfig.CURATIONLABELSDISABLED, SystemConfig.CURATIONLABELSDISABLED); + allowedSetNames.forEach(name -> {setNames.put(name, name);}); } - return setNames; + return setNames.entrySet(); } - public String getCurationLabelSetName() { + public String getCurationLabelSetNameLabel() { Dataverse parent = dataverse.getOwner(); String setName = null; boolean fromAncestor = false; @@ -1244,7 +1244,7 @@ public String getCurationLabelSetName() { parent = parent.getOwner(); } } - if (fromAncestor) { + if (fromAncestor && setName!=null) { setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); } else { setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index 5aec24a1947..c874fdcf0e8 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -6,6 +6,7 @@ package edu.harvard.iq.dataverse; import edu.harvard.iq.dataverse.branding.BrandingUtil; +import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; import edu.harvard.iq.dataverse.settings.Setting; import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key; @@ -375,13 +376,13 @@ public String getDefaultMetadataLanguage() { List allowedExternalStatuses = null; - public List getAllowedExternalStatuses() { - String names = get(SettingsServiceBean.Key.AllowedCurationLabels.toString(), ""); - if (!names.isEmpty() && allowedExternalStatuses == null) { - allowedExternalStatuses = new ArrayList(); - allowedExternalStatuses.addAll(Arrays.asList(names.split("\\s*,\\s*"))); + public List getAllowedExternalStatuses(Dataset d) { + String setName = d.getEffectiveCurationLabelSetName(); + if(setName.equals(SystemConfig.CURATIONLABELSDISABLED)) { + return new ArrayList(); } - return allowedExternalStatuses; + String[] labelArray = systemConfig.getCurationLabels().get(setName); + return Arrays.asList(labelArray); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java index df0cfc51d55..97bbfae91f4 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java @@ -15,6 +15,8 @@ import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; import edu.harvard.iq.dataverse.settings.SettingsServiceBean; import edu.harvard.iq.dataverse.util.BundleUtil; +import edu.harvard.iq.dataverse.util.SystemConfig; + import java.io.IOException; import java.sql.Timestamp; import java.util.Arrays; @@ -49,19 +51,25 @@ public Dataset execute(CommandContext ctxt) throws CommandException { throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.isReleased"), this); } if (label==null || label.isEmpty()) { - getDataset().getLatestVersion().setExternalStatusLabel(label); + getDataset().getLatestVersion().setExternalStatusLabel(null); } else { - String allowedLabels = ctxt.settings().getValueForKey(SettingsServiceBean.Key.AllowedCurationLabels, ""); - if (Arrays.asList(allowedLabels.split("\\s*,\\s*")).contains(label)) { - Pattern pattern = Pattern.compile("(^[\\w ]+$)"); - Matcher matcher = pattern.matcher(label); - if (!matcher.matches()) { - logger.info("Label rejected: " + label); - throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.badformat"), this); + String setName = getDataset().getEffectiveCurationLabelSetName(); + if(setName.equals(SystemConfig.CURATIONLABELSDISABLED)) { + logger.info("External status labeling disbaled for dataset id: " + getDataset().getId()); + throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.disabled"), this); + + } + String[] labelArray = ctxt.systemConfig().getCurationLabels().get(setName); + boolean found = false; + for(String name: labelArray) { + if(name.equals(label)) { + found=true; + getDataset().getLatestVersion().setExternalStatusLabel(label); + break; } - getDataset().getLatestVersion().setExternalStatusLabel(label); - } else { - logger.info("Label not found: " + label); + } + if(!found) { + logger.info("Label not found: " + label + " in set " + setName); throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.notallowed"), this); } } diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index ca1f8b22d8b..cab1d123c3e 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -1340,7 +1340,7 @@ dataset.submit.failure.null=Can't submit for review. Dataset is null. dataset.submit.failure.isReleased=Latest version of dataset is already released. Only draft versions can be submitted for review. dataset.submit.failure.inReview=You cannot submit this dataset for review because it is already in review. dataset.status.failure.notallowed=Status update failed - label not allowed -dataset.status.failure.badformat=Status update failed - label can only include alphanumeric characters and internal spaces. +dataset.status.failure.disabled=Status labeling disabled for this dataset dataset.status.failure.isReleased=Latest version of dataset is already released. Status can only be set on draft versions dataset.rejectMessage=Return this dataset to contributor for modification. dataset.rejectMessage.label=Return to Author Reason diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index 92f3bacfbc8..b0aec04b22c 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -285,17 +285,17 @@
    - + - + - #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])} + #{showPublishLink ? bundle['dataset.publishBtn'] : (DatasetPage.dataset.latestVersion.inReview ? bundle['dataset.disabledSubmittedBtn'] : bundle['dataset.submitBtn'])}
      @@ -323,7 +323,7 @@ #{bundle['dataset.rejectBtn']} - +
    • #{bundle['dataset.changestatus']}
        diff --git a/src/main/webapp/dataverse.xhtml b/src/main/webapp/dataverse.xhtml index b980cb3b4f1..cc1a1e8ed59 100644 --- a/src/main/webapp/dataverse.xhtml +++ b/src/main/webapp/dataverse.xhtml @@ -168,7 +168,7 @@
        - +
        From 20cf1afa138011ef52ea57244e288526ed926474 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 09:50:36 -0400 Subject: [PATCH 46/78] debug/ handle null --- .../java/edu/harvard/iq/dataverse/SettingsWrapper.java | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index c874fdcf0e8..b08a988a8e0 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -23,6 +23,8 @@ import java.util.List; import java.util.Locale; import java.util.Map; +import java.util.logging.Logger; + import javax.ejb.EJB; import javax.faces.view.ViewScoped; import javax.inject.Named; @@ -35,6 +37,7 @@ import org.json.JSONArray; import org.json.JSONException; import org.json.JSONObject; +import org.omnifaces.el.functions.Strings; /** * @@ -43,6 +46,8 @@ @ViewScoped @Named public class SettingsWrapper implements java.io.Serializable { + + private static final Logger logger = Logger.getLogger(SettingsWrapper.class.getCanonicalName()); @EJB SettingsServiceBean settingsService; @@ -378,10 +383,15 @@ public String getDefaultMetadataLanguage() { public List getAllowedExternalStatuses(Dataset d) { String setName = d.getEffectiveCurationLabelSetName(); + logger.info("Set name: " + setName); if(setName.equals(SystemConfig.CURATIONLABELSDISABLED)) { return new ArrayList(); } + logger.info(Strings.concat(",", systemConfig.getCurationLabels().keySet())); String[] labelArray = systemConfig.getCurationLabels().get(setName); + if(labelArray==null) { + return new ArrayList(); + } return Arrays.asList(labelArray); } } From df3fac7dd83e9ed64a8c7c3604a7ad6148cd7b9f Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 10:01:36 -0400 Subject: [PATCH 47/78] fix no parent logic --- .../java/edu/harvard/iq/dataverse/DataversePage.java | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 0c18bfe48a4..62b9e4f1d27 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -1244,10 +1244,12 @@ public String getCurationLabelSetNameLabel() { parent = parent.getOwner(); } } - if (fromAncestor && setName!=null) { - setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); - } else { - setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); + if (setName != null) { + if (fromAncestor) { + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); + } else { + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); + } } return setName; } From eade0066585b3511ccb9adbc1cea1d1f4d8caf37 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 12:50:19 -0400 Subject: [PATCH 48/78] add apis and docs --- .../source/admin/dataverses-datasets.rst | 42 +++++++++ .../source/installation/config.rst | 10 +- .../edu/harvard/iq/dataverse/api/Admin.java | 94 +++++++++++++++++++ .../harvard/iq/dataverse/api/Datasets.java | 84 +++++++++++++++++ 4 files changed, 225 insertions(+), 5 deletions(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index a18204588c2..c72cc7c0c48 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -61,6 +61,29 @@ The available drivers can be listed with:: (Individual datasets can be configured to use specific file stores as well. See the "Datasets" section below.) +Configure a Dataverse Collection to allow use of a given Curation Label Set +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: + + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSet http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet + +The current driver can be seen using:: + + curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet + +and can be reset to the default store with:: + + curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet + +The available curation label sets can be listed with:: + + curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSet + +If the :AllowedCurationLabels setting has a value, one of the available values will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset + +(Individual datasets can be configured to use specific file stores as well. See the "Datasets" section below.) + Datasets -------- @@ -153,4 +176,23 @@ The available drivers can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/storageDrivers +Configure a Dataset to allow use of a Curation Label Set +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Configure a dataset to allow use of labels from a given Curation Label Set (as defined with the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting) This API can only be used by a superuser. :: + + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSet http://$SERVER/api/datasets/$dataset-id/curationLabelSet + +The current driver can be seen using:: + + curl http://$SERVER/api/datasets/$dataset-id/curationLabelSet + +It can be reset to the default store as follows (only a superuser can do this) :: + + curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/datasets/$dataset-id/curationLabelSet + +The available drivers can be listed with:: + curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSets + +If the :AllowedCurationLabels setting has a value, one of the available values will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index 58831f26e8e..7659530063c 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -2387,12 +2387,12 @@ Scripts that implement this association for specific service protocols are maint :AllowedCurationLabels -A comma separated list of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. -These should correspond to the states in an organizations curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. +A JSON Object containing lists of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. The set of labels allowed +for datasets can be selected via the Dataverse collection page (Edit/General Info) or set via API call. +The labels in a set should correspond to the states in an organization's curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. A dataset may only have one label at a time and if a label is set, it will be removed at publication time. This functionality is disabled when this setting is empty/not set. +Each set of labels is identified by a title and a JSON Array of the labels allowed in that set. -Dataverse can now be configured, via the :AllowedCurationLabels setting, to support arbitrary short labels (e.g. "Author contacted", "Privacy Review", "Awaiting paper publication") on draft datasets that indicate the status/state of the dataset with respect to some externally defined curation process. Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. - -``curl -X PUT -d 'Author contacted, Privacy Review, Awaiting paper publication, Final Approval' http://localhost:8080/api/admin/settings/:AllowedCurationLabels`` +``curl -X PUT -d '{"Standard Process":["Author contacted", "Privacy Review", "Awaiting paper publication", "Final Approval"], "Alternate Process":["State 1","State 2","State 3"]}' http://localhost:8080/api/admin/settings/:AllowedCurationLabels`` diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java index 1df51137969..c8af541502f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java @@ -72,6 +72,7 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.omnifaces.el.functions.Strings; import java.util.List; import edu.harvard.iq.dataverse.authorization.AuthTestDataServiceBean; @@ -96,6 +97,8 @@ import edu.harvard.iq.dataverse.util.ArchiverUtil; import edu.harvard.iq.dataverse.util.BundleUtil; import edu.harvard.iq.dataverse.util.FileUtil; +import edu.harvard.iq.dataverse.util.SystemConfig; + import java.io.IOException; import java.io.OutputStream; @@ -1896,6 +1899,97 @@ public Response listStorageDrivers() throws WrappedResponse { return ok(bld); } + @GET + @Path("/dataverse/{alias}/curationLabelSet") + public Response getCurationLabelSet(@PathParam("alias") String alias) throws WrappedResponse { + Dataverse dataverse = dataverseSvc.findByAlias(alias); + if (dataverse == null) { + return error(Response.Status.NOT_FOUND, "Could not find dataverse based on alias supplied: " + alias + "."); + } + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + // Note that this returns what's set directly on this dataverse. If + // null/SystemConfig.DEFAULTCURATIONLABELSET, the user would have to recurse the + // chain of parents to find the effective curationLabelSet + return ok(dataverse.getCurationLabelSetName()); + } + + @PUT + @Path("/dataverse/{alias}/curationLabelSet") + public Response setCurationLabelSet(@PathParam("alias") String alias, String label) throws WrappedResponse { + Dataverse dataverse = dataverseSvc.findByAlias(alias); + if (dataverse == null) { + return error(Response.Status.NOT_FOUND, "Could not find dataverse based on alias supplied: " + alias + "."); + } + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + if (SystemConfig.CURATIONLABELSDISABLED.equals(label) || SystemConfig.DEFAULTCURATIONLABELSET.equals(label)) { + dataverse.setCurationLabelSetName(label); + return ok("Curation Label Set Name set to: " + label); + } else { + for (String setName : systemConfig.getCurationLabels().keySet()) { + if (setName.equals(label)) { + dataverse.setCurationLabelSetName(label); + return ok("Curation Label Set Name set to: " + setName); + } + } + } + return error(Response.Status.BAD_REQUEST, + "No Curation Label Set found for : " + label); + } + + @DELETE + @Path("/dataverse/{alias}/curationLabelSet") + public Response resetCurationLabelSet(@PathParam("alias") String alias) throws WrappedResponse { + Dataverse dataverse = dataverseSvc.findByAlias(alias); + if (dataverse == null) { + return error(Response.Status.NOT_FOUND, "Could not find dataverse based on alias supplied: " + alias + "."); + } + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + dataverse.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); + return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); + } + + @GET + @Path("/dataverse/curationLabelSets") + public Response listCurationLabelSets() throws WrappedResponse { + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + JsonObjectBuilder bld = Json.createObjectBuilder(); + + systemConfig.getCurationLabels().entrySet().forEach(s -> { + JsonArrayBuilder labels = Json.createArrayBuilder(); + Arrays.asList(s.getValue()).forEach(l -> labels.add(l)); + bld.add(s.getKey(), labels); + }); + return ok(bld); + } + @POST @Path("/bannerMessage") public Response addBannerMessage(JsonObject jsonObject) throws WrappedResponse { diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index ba39195e864..c2f820fbf84 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2595,6 +2595,90 @@ public Response resetFileStore(@PathParam("identifier") String dvIdtf, return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); } + @GET + @Path("{identifier}/curationLabelSet") + public Response getCurationLabelSet(@PathParam("identifier") String dvIdtf, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + Dataset dataset; + + try { + dataset = findDatasetOrDie(dvIdtf); + } catch (WrappedResponse ex) { + return error(Response.Status.NOT_FOUND, "No such dataset"); + } + + return response(req -> ok(dataset.getEffectiveCurationLabelSetName())); + } + + @PUT + @Path("{identifier}/curationLabelSet") + public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, + String curationLabelSet, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + // Superuser-only: + AuthenticatedUser user; + try { + user = findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + return error(Response.Status.BAD_REQUEST, "Authentication is required."); + } + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + + Dataset dataset; + + try { + dataset = findDatasetOrDie(dvIdtf); + } catch (WrappedResponse ex) { + return error(Response.Status.NOT_FOUND, "No such dataset"); + } + if (SystemConfig.CURATIONLABELSDISABLED.equals(curationLabelSet) || SystemConfig.DEFAULTCURATIONLABELSET.equals(curationLabelSet)) { + dataset.setCurationLabelSetName(curationLabelSet); + return ok("Curation Label Set Name set to: " + curationLabelSet); + } else { + for (String setName : systemConfig.getCurationLabels().keySet()) { + if (setName.equals(curationLabelSet)) { + dataset.setCurationLabelSetName(curationLabelSet); + return ok("Curation Label Set Name set to: " + setName); + } + } + } + return error(Response.Status.BAD_REQUEST, + "No Such Curation Label Set"); + } + + @DELETE + @Path("{identifier}/curationLabelSet") + public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + // Superuser-only: + AuthenticatedUser user; + try { + user = findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + return error(Response.Status.BAD_REQUEST, "Authentication is required."); + } + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + + Dataset dataset; + + try { + dataset = findDatasetOrDie(dvIdtf); + } catch (WrappedResponse ex) { + return error(Response.Status.NOT_FOUND, "No such dataset"); + } + + dataset.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); + datasetService.merge(dataset); + return ok("Curation Label Set reset to default: " + SystemConfig.DEFAULTCURATIONLABELSET); + } + @GET @Path("{identifier}/timestamps") @Produces(MediaType.APPLICATION_JSON) From 10996d679b08c8933d5c20d25a9ff9ae7b30788d Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 13:08:08 -0400 Subject: [PATCH 49/78] cleanup --- doc/release-notes/7967-curation-labels.md | 6 ++-- .../source/installation/config.rst | 2 ++ .../edu/harvard/iq/dataverse/DatasetPage.java | 33 +++++++++---------- .../harvard/iq/dataverse/api/Datasets.java | 14 ++++---- ....6.0.1__7967_external-curation-labels.sql} | 0 .../db/migration/V5.6.0.1__externalstatus.sql | 2 -- 6 files changed, 28 insertions(+), 29 deletions(-) rename src/main/resources/db/migration/{V5.6.0.1__curationlabels.sql => V5.6.0.1__7967_external-curation-labels.sql} (100%) delete mode 100644 src/main/resources/db/migration/V5.6.0.1__externalstatus.sql diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index 861d7c60921..1bff954362f 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -1,3 +1,5 @@ -### Support for external curation processes +### External Curation Status Labels -Dataverse can now be configured, via the :AllowedCurationLabels setting, to support arbitrary short labels (e.g. "Author contacted", "Privacy Review", "Awaiting paper publication") on draft datasets that indicate the status/state of the dataset with respect to some externally defined curation process. Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. \ No newline at end of file +A new :AllowedCurationLabels setting allows an administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to an externally defined curation process. + +Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index 7659530063c..f7ec9312322 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -2385,6 +2385,8 @@ Scripts that implement this association for specific service protocols are maint ``curl -X PUT --upload-file cvoc-conf.json http://localhost:8080/api/admin/settings/:CVocConf`` +.. _:AllowedCurationLabels: + :AllowedCurationLabels A JSON Object containing lists of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. The set of labels allowed diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 37767d55aaf..25b1e10e76f 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -5532,7 +5532,22 @@ public String getLocaleDisplayName(String code) { return displayName; } -<<<<<<< HEAD + public Map getCVocConf() { + //Cache this in the view + if(cachedCvocMap==null) { + cachedCvocMap = fieldService.getCVocConf(false); + } + return cachedCvocMap; + } + + public List getVocabScripts() { + return fieldService.getVocabScripts(getCVocConf()); + } + + public String getFieldLanguage(String languages) { + return fieldService.getFieldLanguage(languages,session.getLocaleCode()); + } + public void setExternalStatus(String status) { try { dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); @@ -5552,21 +5567,5 @@ public void setExternalStatus(String status) { public List getAllowedExternalStatuses() { return settingsWrapper.getAllowedExternalStatuses(dataset); -======= - public Map getCVocConf() { - //Cache this in the view - if(cachedCvocMap==null) { - cachedCvocMap = fieldService.getCVocConf(false); - } - return cachedCvocMap; - } - - public List getVocabScripts() { - return fieldService.getVocabScripts(getCVocConf()); - } - - public String getFieldLanguage(String languages) { - return fieldService.getFieldLanguage(languages,session.getLocaleCode()); ->>>>>>> refs/remotes/IQSS/develop } } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index c2f820fbf84..dc96f10a0d3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -1756,29 +1756,27 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo } @PUT - @Path("{id}/setExternalStatus") - public Response setExternalStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { + @Path("{id}/setExternalCurationStatus") + public Response setExternalCurationStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { logger.info("Label is " + label); try { execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); - return ok("External Status updated"); + return ok("External Curation Status updated"); } catch (WrappedResponse wr) { //Just change to Bad Request and send - //ToDo - check in api call return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } @DELETE - @Path("{id}/setExternalStatus") - public Response deleteExternalStatus(@PathParam("id") String idSupplied) { + @Path("{id}/setExternalCurationStatus") + public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) { try { execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), null)); - return ok("External Status deleted"); + return ok("External Curation Status deleted"); } catch (WrappedResponse wr) { //Just change to Bad Request and send - //ToDo - check in api call return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } diff --git a/src/main/resources/db/migration/V5.6.0.1__curationlabels.sql b/src/main/resources/db/migration/V5.6.0.1__7967_external-curation-labels.sql similarity index 100% rename from src/main/resources/db/migration/V5.6.0.1__curationlabels.sql rename to src/main/resources/db/migration/V5.6.0.1__7967_external-curation-labels.sql diff --git a/src/main/resources/db/migration/V5.6.0.1__externalstatus.sql b/src/main/resources/db/migration/V5.6.0.1__externalstatus.sql deleted file mode 100644 index eae6b46c3ef..00000000000 --- a/src/main/resources/db/migration/V5.6.0.1__externalstatus.sql +++ /dev/null @@ -1,2 +0,0 @@ -ALTER TABLE datasetversion ADD COLUMN IF NOT EXISTS externalstatuslabel varchar(32); - From d266bb31169f22576620002b716c6c918191faaa Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 13:47:45 -0400 Subject: [PATCH 50/78] make role reporting generic Conflicts: src/main/java/edu/harvard/iq/dataverse/api/Datasets.java --- .../harvard/iq/dataverse/api/Datasets.java | 34 +++++++++++++------ 1 file changed, 23 insertions(+), 11 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index dc96f10a0d3..2da116f5f65 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -13,6 +13,7 @@ import edu.harvard.iq.dataverse.DatasetVersion; import edu.harvard.iq.dataverse.Dataverse; import edu.harvard.iq.dataverse.DataverseRequestServiceBean; +import edu.harvard.iq.dataverse.DataverseRoleServiceBean; import edu.harvard.iq.dataverse.DataverseServiceBean; import edu.harvard.iq.dataverse.DataverseSession; import edu.harvard.iq.dataverse.DvObject; @@ -129,6 +130,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Date; +import java.util.HashMap; import java.util.HashSet; import java.util.LinkedList; import java.util.List; @@ -184,7 +186,7 @@ public class Datasets extends AbstractApiBean { private static final Logger logger = Logger.getLogger(Datasets.class.getCanonicalName()); - @Inject DataverseSession session; + @Inject DataverseSession session; @EJB DatasetServiceBean datasetService; @@ -240,6 +242,9 @@ public class Datasets extends AbstractApiBean { @Inject WorkflowServiceBean wfService; + + @Inject + DataverseRoleServiceBean dataverseRoleService; /** * Used to consolidate the way we parse and handle dataset versions. @@ -2819,17 +2824,16 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, } - /** QDR - * + /** * API to find curation assignements and statuses * * @return * @throws WrappedResponse */ @GET - @Path("/listCurationStatuses") + @Path("/listCurationStates") @Produces("text/csv") - public Response getCurationStatuses() throws WrappedResponse { + public Response getCurationStates() throws WrappedResponse { try { AuthenticatedUser user = findAuthenticatedUserOrDie(); @@ -2840,18 +2844,24 @@ public Response getCurationStatuses() throws WrappedResponse { return wr.getResponse(); } + List allRoles = dataverseRoleService.findAll(); + List curationRoles = new ArrayList(); + allRoles.forEach(r -> {if(r.permissions().contains(Permission.PublishDataset)) curationRoles.add(r);}); + HashMap> assignees = new HashMap>(); + curationRoles.forEach(r-> {assignees.put(r.getAlias(), null);}); + StringBuilder csvSB = new StringBuilder(String.join(",", BundleUtil.getStringFromBundle("dataset"), BundleUtil.getStringFromBundle("datasets.api.creationdate"), BundleUtil.getStringFromBundle("datasets.api.modificationdate"), - BundleUtil.getStringFromBundle("datasets.api.curationstatus"))); + BundleUtil.getStringFromBundle("datasets.api.curationstatus"), + String.join(",", assignees.keySet()))); for (Dataset dataset : datasetSvc.findAllUnpublished()) { List ras = permissionService.assignmentsOn(dataset); - String assignee = null; + curationRoles.forEach(r-> {assignees.put(r.getAlias(), new HashSet());}); for (RoleAssignment ra : ras) { - if (ra.getRole().getName().equals("Assignee")) { - assignee = ra.getAssigneeIdentifier(); - break; + if (curationRoles.contains(ra.getRole())) { + assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); } } String name = dataset.getCurrentName().replace("\"","\"\""); @@ -2860,7 +2870,9 @@ public Response getCurationStatuses() throws WrappedResponse { String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; - csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, assignee==null ? "":assignee, status==null ? "": status)); + List sList = new ArrayList(); + assignees.entrySet().forEach(e-> sList.add(e.getValue().size()==0 ? "": String.join(";", e.getValue()))); + csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status==null ? "": status, String.join(",", sList))); } csvSB.append("\n"); return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); From 56fd065a1675449925d0426558aa007bf0a299e7 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Tue, 21 Sep 2021 14:37:57 -0400 Subject: [PATCH 51/78] style fixes --- .../harvard/iq/dataverse/DataversePage.java | 17 +- .../harvard/iq/dataverse/api/Datasets.java | 1620 +++++++++-------- 2 files changed, 828 insertions(+), 809 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 62b9e4f1d27..4d1a189c488 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -7,6 +7,7 @@ import edu.harvard.iq.dataverse.dataaccess.DataAccess; import edu.harvard.iq.dataverse.dataverse.DataverseUtil; import edu.harvard.iq.dataverse.engine.command.Command; +import edu.harvard.iq.dataverse.engine.command.DataverseRequest; import edu.harvard.iq.dataverse.engine.command.exception.CommandException; import edu.harvard.iq.dataverse.engine.command.impl.CreateDataverseCommand; import edu.harvard.iq.dataverse.engine.command.impl.CreateSavedSearchCommand; @@ -16,6 +17,7 @@ import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseCommand; import edu.harvard.iq.dataverse.search.FacetCategory; import edu.harvard.iq.dataverse.search.IndexServiceBean; +import edu.harvard.iq.dataverse.search.SearchException; import edu.harvard.iq.dataverse.search.SearchFields; import edu.harvard.iq.dataverse.search.SearchIncludeFragment; import edu.harvard.iq.dataverse.search.SearchServiceBean; @@ -30,9 +32,12 @@ import javax.ejb.EJB; import javax.faces.application.FacesMessage; import javax.faces.context.FacesContext; +import javax.faces.event.ActionEvent; import javax.faces.view.ViewScoped; import javax.inject.Inject; import javax.inject.Named; + +import java.util.AbstractMap; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -1200,17 +1205,13 @@ public String getDefaultStorageDriverLabel() { } String label = DataAccess.getStorageDriverLabelFor(storageDriverId); if(fromAncestor) { - label = label + " " + BundleUtil.getStringFromBundle("dataverse.inherited"); + label = label + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); } else { - label = label + " " + BundleUtil.getStringFromBundle("dataverse.default"); + label = label + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); } return label; } - public Set> getMetadataLanguages() { - return settingsWrapper.getMetadataLanguages(this.dataverse).entrySet(); - } - public Set> getCurationLabelSetOptions() { HashMap setNames = new HashMap(); Set allowedSetNames = systemConfig.getCurationLabels().keySet(); @@ -1223,7 +1224,9 @@ public Set> getCurationLabelSetOptions() { } // Add an entry for disabled setNames.put(SystemConfig.CURATIONLABELSDISABLED, SystemConfig.CURATIONLABELSDISABLED); - allowedSetNames.forEach(name -> {setNames.put(name, name);}); + allowedSetNames.forEach(name -> { + setNames.put(name, name); + }); } return setNames.entrySet(); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 2da116f5f65..a9b73171678 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -185,30 +185,31 @@ public class Datasets extends AbstractApiBean { private static final Logger logger = Logger.getLogger(Datasets.class.getCanonicalName()); - - @Inject DataverseSession session; + + @Inject + DataverseSession session; @EJB DatasetServiceBean datasetService; @EJB DataverseServiceBean dataverseService; - + @EJB UserNotificationServiceBean userNotificationService; - + @EJB PermissionServiceBean permissionService; - + @EJB AuthenticationServiceBean authenticationServiceBean; - + @EJB DDIExportServiceBean ddiExportService; - + @EJB MetadataBlockServiceBean metadataBlockService; - + @EJB DataFileServiceBean fileService; @@ -217,71 +218,77 @@ public class Datasets extends AbstractApiBean { @EJB EjbDataverseEngine commandEngine; - + @EJB IndexServiceBean indexService; @EJB S3PackageImporter s3PackageImporter; - + @EJB SettingsServiceBean settingsService; // TODO: Move to AbstractApiBean @EJB DatasetMetricsServiceBean datasetMetricsSvc; - + @EJB DatasetExternalCitationsServiceBean datasetExternalCitationsService; - + @Inject MakeDataCountLoggingServiceBean mdcLogService; - + @Inject DataverseRequestServiceBean dvRequestService; - + @Inject WorkflowServiceBean wfService; - + @Inject DataverseRoleServiceBean dataverseRoleService; /** * Used to consolidate the way we parse and handle dataset versions. - * @param + * + * @param */ public interface DsVersionHandler { T handleLatest(); + T handleDraft(); - T handleSpecific( long major, long minor ); + + T handleSpecific(long major, long minor); + T handleLatestPublished(); } - + @GET @Path("{id}") public Response getDataset(@PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { - return response( req -> { + return response(req -> { final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id))); final DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(req, retrieved)); final JsonObjectBuilder jsonbuilder = json(retrieved); - //Report MDC if this is a released version (could be draft if user has access, or user may not have access at all and is not getting metadata beyond the minimum) - if((latest != null) && latest.isReleased()) { + // Report MDC if this is a released version (could be draft if user has access, + // or user may not have access at all and is not getting metadata beyond the + // minimum) + if ((latest != null) && latest.isReleased()) { MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, retrieved); mdcLogService.logEntry(entry); } return ok(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null)); }); } - - // TODO: - // This API call should, ideally, call findUserOrDie() and the GetDatasetCommand + + // TODO: + // This API call should, ideally, call findUserOrDie() and the GetDatasetCommand // to obtain the dataset that we are trying to export - which would handle - // Auth in the process... For now, Auth isn't necessary - since export ONLY + // Auth in the process... For now, Auth isn't necessary - since export ONLY // WORKS on published datasets, which are open to the world. -- L.A. 4.5 - + @GET @Path("/export") - @Produces({"application/xml", "application/json", "application/html" }) + @Produces({ "application/xml", "application/json", "application/html" }) public Response exportDataset(@QueryParam("persistentId") String persistentId, @QueryParam("exporter") String exporter, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { try { @@ -289,20 +296,20 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ if (dataset == null) { return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); } - + ExportService instance = ExportService.getInstance(); - + InputStream is = instance.getExport(dataset, exporter); - + String mediaType = instance.getMediaType(exporter); - //Export is only possible for released (non-draft) dataset versions so we can log without checking to see if this is a request for a draft + // Export is only possible for released (non-draft) dataset versions so we can + // log without checking to see if this is a request for a draft MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, dataset); mdcLogService.logEntry(entry); - + return Response.ok() .entity(is) - .type(mediaType). - build(); + .type(mediaType).build(); } catch (Exception wr) { return error(Response.Status.FORBIDDEN, "Export Failed"); } @@ -310,23 +317,25 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ @DELETE @Path("{id}") - public Response deleteDataset( @PathParam("id") String id) { - // Internally, "DeleteDatasetCommand" simply redirects to "DeleteDatasetVersionCommand" + public Response deleteDataset(@PathParam("id") String id) { + // Internally, "DeleteDatasetCommand" simply redirects to + // "DeleteDatasetVersionCommand" // (and there's a comment that says "TODO: remove this command") - // do we need an exposed API call for it? - // And DeleteDatasetVersionCommand further redirects to DestroyDatasetCommand, - // if the dataset only has 1 version... In other words, the functionality - // currently provided by this API is covered between the "deleteDraftVersion" and - // "destroyDataset" API calls. - // (The logic below follows the current implementation of the underlying + // do we need an exposed API call for it? + // And DeleteDatasetVersionCommand further redirects to DestroyDatasetCommand, + // if the dataset only has 1 version... In other words, the functionality + // currently provided by this API is covered between the "deleteDraftVersion" + // and + // "destroyDataset" API calls. + // (The logic below follows the current implementation of the underlying // commands!) - - return response( req -> { + + return response(req -> { Dataset doomed = findDatasetOrDie(id); DatasetVersion doomedVersion = doomed.getLatestVersion(); User u = findUserOrDie(); boolean destroy = false; - + if (doomed.getVersions().size() == 1) { if (doomed.isReleased() && (!(u instanceof AuthenticatedUser) || !u.isSuperuser())) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Only superusers can delete published datasets")); @@ -337,26 +346,26 @@ public Response deleteDataset( @PathParam("id") String id) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is a published dataset with multiple versions. This API can only delete the latest version if it is a DRAFT")); } } - - // Gather the locations of the physical files that will need to be + + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomedVersion, destroy); - - execCommand( new DeleteDatasetCommand(req, findDatasetOrDie(id))); - - // If we have gotten this far, the destroy command has succeeded, + + execCommand(new DeleteDatasetCommand(req, findDatasetOrDie(id))); + + // If we have gotten this far, the destroy command has succeeded, // so we can finalize it by permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); } - + return ok("Dataset " + id + " deleted"); }); } - + @DELETE @Path("{id}/destroy") public Response destroyDataset(@PathParam("id") String id) { @@ -370,16 +379,16 @@ public Response destroyDataset(@PathParam("id") String id) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Destroy can only be called by superusers.")); } - // Gather the locations of the physical files that will need to be + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed); execCommand(new DestroyDatasetCommand(doomed, req)); - // If we have gotten this far, the destroy command has succeeded, + // If we have gotten this far, the destroy command has succeeded, // so we can finalize permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); @@ -388,59 +397,59 @@ public Response destroyDataset(@PathParam("id") String id) { return ok("Dataset " + id + " destroyed"); }); } - + @DELETE @Path("{id}/versions/{versionId}") - public Response deleteDraftVersion( @PathParam("id") String id, @PathParam("versionId") String versionId ){ - if ( ! ":draft".equals(versionId) ) { + public Response deleteDraftVersion(@PathParam("id") String id, @PathParam("versionId") String versionId) { + if (!":draft".equals(versionId)) { return badRequest("Only the :draft version can be deleted"); } - return response( req -> { + return response(req -> { Dataset dataset = findDatasetOrDie(id); DatasetVersion doomed = dataset.getLatestVersion(); - + if (!doomed.isDraft()) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is NOT a DRAFT version")); } - - // Gather the locations of the physical files that will need to be + + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: - + Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed); - - execCommand( new DeleteDatasetVersionCommand(req, dataset)); - - // If we have gotten this far, the delete command has succeeded - - // by either deleting the Draft version of a published dataset, - // or destroying an unpublished one. + + execCommand(new DeleteDatasetVersionCommand(req, dataset)); + + // If we have gotten this far, the delete command has succeeded - + // by either deleting the Draft version of a published dataset, + // or destroying an unpublished one. // This means we can finalize permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); } - + return ok("Draft version of dataset " + id + " deleted"); }); } - + @DELETE @Path("{datasetId}/deleteLink/{linkedDataverseId}") - public Response deleteDatasetLinkingDataverse( @PathParam("datasetId") String datasetId, @PathParam("linkedDataverseId") String linkedDataverseId) { - boolean index = true; + public Response deleteDatasetLinkingDataverse(@PathParam("datasetId") String datasetId, @PathParam("linkedDataverseId") String linkedDataverseId) { + boolean index = true; return response(req -> { execCommand(new DeleteDatasetLinkingDataverseCommand(req, findDatasetOrDie(datasetId), findDatasetLinkingDataverseOrDie(datasetId, linkedDataverseId), index)); return ok("Link from Dataset " + datasetId + " to linked Dataverse " + linkedDataverseId + " deleted"); }); } - + @PUT @Path("{id}/citationdate") - public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) { - return response( req -> { - if ( dsfTypeName.trim().isEmpty() ){ + public Response setCitationDate(@PathParam("id") String id, String dsfTypeName) { + return response(req -> { + if (dsfTypeName.trim().isEmpty()) { return badRequest("Please provide a dataset field type in the requst body."); } DatasetFieldType dsfType = null; @@ -454,124 +463,121 @@ public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), dsfType)); return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); }); - } - + } + @DELETE @Path("{id}/citationdate") - public Response useDefaultCitationDate( @PathParam("id") String id) { - return response( req -> { + public Response useDefaultCitationDate(@PathParam("id") String id) { + return response(req -> { execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), null)); return ok("Citation Date for dataset " + id + " set to default"); }); - } - + } + @GET @Path("{id}/versions") - public Response listVersions( @PathParam("id") String id ) { - return response( req -> - ok( execCommand( new ListVersionsCommand(req, findDatasetOrDie(id)) ) - .stream() - .map( d -> json(d) ) - .collect(toJsonArray()))); - } - + public Response listVersions(@PathParam("id") String id) { + return response(req -> ok(execCommand(new ListVersionsCommand(req, findDatasetOrDie(id))) + .stream() + .map(d -> json(d)) + .collect(toJsonArray()))); + } + @GET @Path("{id}/versions/{versionId}") - public Response getVersion( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response( req -> { - DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); + public Response getVersion(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response(req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found") - : ok(json(dsv)); + : ok(json(dsv)); }); } - + @GET @Path("{id}/versions/{versionId}/files") - public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response( req -> ok( jsonFileMetadatas( - getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas()))); + public Response getVersionFiles(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response(req -> ok(jsonFileMetadatas( + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas()))); } - + @GET @Path("{id}/dirindex") @Produces("text/html") public Response getFileAccessFolderView(@PathParam("id") String datasetId, @QueryParam("version") String versionId, @QueryParam("folder") String folderName, @QueryParam("original") Boolean originals, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { folderName = folderName == null ? "" : folderName; - versionId = versionId == null ? ":latest-published" : versionId; - - DatasetVersion version; + versionId = versionId == null ? ":latest-published" : versionId; + + DatasetVersion version; try { DataverseRequest req = createDataverseRequest(findUserOrDie()); version = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); } catch (WrappedResponse wr) { return wr.getResponse(); } - + String output = FileUtil.formatFolderListingHtml(folderName, version, "", originals != null && originals); - + // return "NOT FOUND" if there is no such folder in the dataset version: - + if ("".equals(output)) { return notFound("Folder " + folderName + " does not exist"); } - - + String indexFileName = folderName.equals("") ? ".index.html" : ".index-" + folderName.replace('/', '_') + ".html"; response.setHeader("Content-disposition", "filename=\"" + indexFileName + "\""); - return Response.ok() .entity(output) - //.type("application/html"). + // .type("application/html"). .build(); } - + @GET @Path("{id}/versions/{versionId}/metadata") - public Response getVersionMetadata( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response( req -> ok( - jsonByBlocks( - getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers ) + public Response getVersionMetadata(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response(req -> ok( + jsonByBlocks( + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers) .getDatasetFields()))); } - + @GET @Path("{id}/versions/{versionNumber}/metadata/{block}") - public Response getVersionMetadataBlock( @PathParam("id") String datasetId, - @PathParam("versionNumber") String versionNumber, - @PathParam("block") String blockName, - @Context UriInfo uriInfo, - @Context HttpHeaders headers ) { - - return response( req -> { - DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo, headers ); - + public Response getVersionMetadataBlock(@PathParam("id") String datasetId, + @PathParam("versionNumber") String versionNumber, + @PathParam("block") String blockName, + @Context UriInfo uriInfo, + @Context HttpHeaders headers) { + + return response(req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo, headers); + Map> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields()); - for ( Map.Entry> p : fieldsByBlock.entrySet() ) { - if ( p.getKey().getName().equals(blockName) ) { + for (Map.Entry> p : fieldsByBlock.entrySet()) { + if (p.getKey().getName().equals(blockName)) { return ok(json(p.getKey(), p.getValue())); } } return notFound("metadata block named " + blockName + " not found"); }); } - + @GET @Path("{id}/modifyRegistration") - public Response updateDatasetTargetURL(@PathParam("id") String id ) { - return response( req -> { + public Response updateDatasetTargetURL(@PathParam("id") String id) { + return response(req -> { execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), req)); return ok("Dataset " + id + " target url updated"); }); } - + @POST @Path("/modifyRegistrationAll") public Response updateDatasetTargetURLAll() { - return response( req -> { - datasetService.findAll().forEach( ds -> { + return response(req -> { + datasetService.findAll().forEach(ds -> { try { execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(ds.getId().toString()), req)); } catch (WrappedResponse ex) { @@ -581,7 +587,7 @@ public Response updateDatasetTargetURLAll() { return ok("Update All Dataset target url completed"); }); } - + @POST @Path("{id}/modifyRegistrationMetadata") public Response updateDatasetPIDMetadata(@PathParam("id") String id) { @@ -601,37 +607,37 @@ public Response updateDatasetPIDMetadata(@PathParam("id") String id) { return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.single.dataset", args)); }); } - + @GET @Path("/modifyRegistrationPIDMetadataAll") public Response updateDatasetPIDMetadataAll() { - return response( req -> { - datasetService.findAll().forEach( ds -> { + return response(req -> { + datasetService.findAll().forEach(ds -> { try { execCommand(new UpdateDvObjectPIDMetadataCommand(findDatasetOrDie(ds.getId().toString()), req)); } catch (WrappedResponse ex) { Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex); } - }); + }); return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.update.all")); }); } - + @PUT @Path("{id}/versions/{versionId}") @Consumes(MediaType.APPLICATION_JSON) - public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId ){ - - if ( ! ":draft".equals(versionId) ) { - return error( Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); + public Response updateDraftVersion(String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId) { + + if (!":draft".equals(versionId)) { + return error(Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); } - - try ( StringReader rdr = new StringReader(jsonBody) ) { + + try (StringReader rdr = new StringReader(jsonBody)) { DataverseRequest req = createDataverseRequest(findUserOrDie()); Dataset ds = findDatasetOrDie(id); JsonObject json = Json.createReader(rdr).readObject(); DatasetVersion incomingVersion = jsonParser().parseDatasetVersion(json); - + // clear possibly stale fields from the incoming dataset version. // creation and modification dates are updated by the commands. incomingVersion.setId(null); @@ -641,38 +647,38 @@ public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, incomingVersion.setDataset(ds); incomingVersion.setCreateTime(null); incomingVersion.setLastUpdateTime(null); - - if (!incomingVersion.getFileMetadatas().isEmpty()){ - return error( Response.Status.BAD_REQUEST, "You may not add files via this api."); + + if (!incomingVersion.getFileMetadatas().isEmpty()) { + return error(Response.Status.BAD_REQUEST, "You may not add files via this api."); } - + boolean updateDraft = ds.getLatestVersion().isDraft(); - + DatasetVersion managedVersion; - if ( updateDraft ) { + if (updateDraft) { final DatasetVersion editVersion = ds.getEditVersion(); editVersion.setDatasetFields(incomingVersion.getDatasetFields()); - editVersion.setTermsOfUseAndAccess( incomingVersion.getTermsOfUseAndAccess() ); + editVersion.setTermsOfUseAndAccess(incomingVersion.getTermsOfUseAndAccess()); Dataset managedDataset = execCommand(new UpdateDatasetVersionCommand(ds, req)); managedVersion = managedDataset.getEditVersion(); } else { managedVersion = execCommand(new CreateDatasetVersionCommand(req, ds, incomingVersion)); } -// DatasetVersion managedVersion = execCommand( updateDraft -// ? new UpdateDatasetVersionCommand(req, incomingVersion) -// : new CreateDatasetVersionCommand(req, ds, incomingVersion)); - return ok( json(managedVersion) ); - + // DatasetVersion managedVersion = execCommand( updateDraft + // ? new UpdateDatasetVersionCommand(req, incomingVersion) + // : new CreateDatasetVersionCommand(req, ds, incomingVersion)); + return ok(json(managedVersion)); + } catch (JsonParseException ex) { logger.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex); - return error( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() ); - + return error(Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage()); + } catch (WrappedResponse ex) { return ex.getResponse(); - + } } - + @GET @Path("{id}/versions/{versionId}/metadata") @Produces("application/ld+json, application/json-ld") @@ -700,7 +706,7 @@ public Response getVersionJsonLDMetadata(@PathParam("id") String id, @PathParam( public Response getVersionJsonLDMetadata(@PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers) { return getVersionJsonLDMetadata(id, ":draft", uriInfo, headers); } - + @PUT @Path("{id}/metadata") @Consumes("application/ld+json, application/json-ld") @@ -712,7 +718,7 @@ public Response updateVersionMetadata(String jsonLDBody, @PathParam("id") String DatasetVersion dsv = ds.getEditVersion(); boolean updateDraft = ds.getLatestVersion().isDraft(); dsv = JSONLDUtil.updateDatasetVersionMDFromJsonLD(dsv, jsonLDBody, metadataBlockService, datasetFieldSvc, !replaceTerms, false); - + DatasetVersion managedVersion; if (updateDraft) { Dataset managedDataset = execCommand(new UpdateDatasetVersionCommand(ds, req)); @@ -730,7 +736,7 @@ public Response updateVersionMetadata(String jsonLDBody, @PathParam("id") String return error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage()); } } - + @PUT @Path("{id}/metadata/delete") @Consumes("application/ld+json, application/json-ld") @@ -760,7 +766,7 @@ public Response deleteMetadata(String jsonLDBody, @PathParam("id") String id) { return error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage()); } } - + @PUT @Path("{id}/deleteMetadata") public Response deleteVersionMetadata(String jsonBody, @PathParam("id") String id) throws WrappedResponse { @@ -798,7 +804,7 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav boolean found = false; for (DatasetField dsf : dsv.getDatasetFields()) { if (dsf.getDatasetFieldType().equals(updateField.getDatasetFieldType())) { - if (dsf.getDatasetFieldType().isAllowMultiples()) { + if (dsf.getDatasetFieldType().isAllowMultiples()) { if (updateField.getDatasetFieldType().isControlledVocabulary()) { if (dsf.getDatasetFieldType().isAllowMultiples()) { for (ControlledVocabularyValue cvv : updateField.getControlledVocabularyValues()) { @@ -863,7 +869,7 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav datasetFieldCompoundValueItemsToRemove.forEach((remove) -> { dsf.getDatasetFieldCompoundValues().remove(remove); }); - if (!found) { + if (!found) { logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found."); return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found."); } @@ -878,17 +884,15 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav break; } } - if (!found){ + if (!found) { String displayValue = !updateField.getDisplayValue().isEmpty() ? updateField.getDisplayValue() : updateField.getCompoundDisplayValue(); - logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." ); - return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." ); + logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found."); + return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found."); } - } - + } - boolean updateDraft = ds.getLatestVersion().isDraft(); - DatasetVersion managedVersion = updateDraft + DatasetVersion managedVersion = updateDraft ? execCommand(new UpdateDatasetVersionCommand(ds, req)).getEditVersion() : execCommand(new CreateDatasetVersionCommand(req, ds, dsv)); return ok(json(managedVersion)); @@ -902,21 +906,21 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav return ex.getResponse(); } - + } - - private String getCompoundDisplayValue (DatasetFieldCompoundValue dscv){ + + private String getCompoundDisplayValue(DatasetFieldCompoundValue dscv) { String returnString = ""; - for (DatasetField dsf : dscv.getChildDatasetFields()) { - for (String value : dsf.getValues()) { - if (!(value == null)) { - returnString += (returnString.isEmpty() ? "" : "; ") + value.trim(); - } + for (DatasetField dsf : dscv.getChildDatasetFields()) { + for (String value : dsf.getValues()) { + if (!(value == null)) { + returnString += (returnString.isEmpty() ? "" : "; ") + value.trim(); } } + } return returnString; } - + @PUT @Path("{id}/editMetadata") public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, @QueryParam("replace") Boolean replace) { @@ -924,7 +928,7 @@ public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, Boolean replaceData = replace != null; DataverseRequest req = null; try { - req = createDataverseRequest(findUserOrDie()); + req = createDataverseRequest(findUserOrDie()); } catch (WrappedResponse ex) { logger.log(Level.SEVERE, "Edit metdata error: " + ex.getMessage(), ex); return ex.getResponse(); @@ -932,26 +936,24 @@ public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, return processDatasetUpdate(jsonBody, id, req, replaceData); } - - - private Response processDatasetUpdate(String jsonBody, String id, DataverseRequest req, Boolean replaceData){ + + private Response processDatasetUpdate(String jsonBody, String id, DataverseRequest req, Boolean replaceData) { try (StringReader rdr = new StringReader(jsonBody)) { - + Dataset ds = findDatasetOrDie(id); JsonObject json = Json.createReader(rdr).readObject(); DatasetVersion dsv = ds.getEditVersion(); - + List fields = new LinkedList<>(); - DatasetField singleField = null; - + DatasetField singleField = null; + JsonArray fieldsJson = json.getJsonArray("fields"); - if( fieldsJson == null ){ - singleField = jsonParser().parseField(json, Boolean.FALSE); + if (fieldsJson == null) { + singleField = jsonParser().parseField(json, Boolean.FALSE); fields.add(singleField); - } else{ + } else { fields = jsonParser().parseMultipleFields(json); } - String valdationErrors = validateDatasetFieldValues(fields); @@ -962,10 +964,10 @@ private Response processDatasetUpdate(String jsonBody, String id, DataverseReque dsv.setVersionState(DatasetVersion.VersionState.DRAFT); - //loop through the update fields - // and compare to the version fields - //if exist add/replace values - //if not add entire dsf + // loop through the update fields + // and compare to the version fields + // if exist add/replace values + // if not add entire dsf for (DatasetField updateField : fields) { boolean found = false; for (DatasetField dsf : dsv.getDatasetFields()) { @@ -1061,7 +1063,7 @@ private Response processDatasetUpdate(String jsonBody, String id, DataverseReque } } - + private String validateDatasetFieldValues(List fields) { StringBuilder error = new StringBuilder(); @@ -1079,14 +1081,15 @@ private String validateDatasetFieldValues(List fields) { } return ""; } - + /** - * @deprecated This was shipped as a GET but should have been a POST, see https://github.com/IQSS/dataverse/issues/2431 + * @deprecated This was shipped as a GET but should have been a POST, see + * https://github.com/IQSS/dataverse/issues/2431 */ @GET @Path("{id}/actions/:publish") @Deprecated - public Response publishDataseUsingGetDeprecated( @PathParam("id") String id, @QueryParam("type") String type ) { + public Response publishDataseUsingGetDeprecated(@PathParam("id") String id, @QueryParam("type") String type) { logger.info("publishDataseUsingGetDeprecated called on id " + id + ". Encourage use of POST rather than GET, which is deprecated."); return publishDataset(id, type, false); } @@ -1098,25 +1101,25 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S if (type == null) { return error(Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major','minor', or 'updatecurrent')."); } - boolean updateCurrent=false; + boolean updateCurrent = false; AuthenticatedUser user = findAuthenticatedUserOrDie(); type = type.toLowerCase(); - boolean isMinor=false; + boolean isMinor = false; switch (type) { - case "minor": - isMinor = true; - break; - case "major": - isMinor = false; - break; + case "minor": + isMinor = true; + break; + case "major": + isMinor = false; + break; case "updatecurrent": - if(user.isSuperuser()) { - updateCurrent=true; + if (user.isSuperuser()) { + updateCurrent = true; } else { - return error(Response.Status.FORBIDDEN, "Only superusers can update the current version"); + return error(Response.Status.FORBIDDEN, "Only superusers can update the current version"); } break; - default: + default: return error(Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major', 'minor', or 'updatecurrent'."); } @@ -1139,8 +1142,8 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S * error is returned. * */ - if ((ds.getModificationTime()!=null && (ds.getIndexTime() == null || (ds.getIndexTime().compareTo(ds.getModificationTime()) <= 0))) || - (ds.getPermissionModificationTime()!=null && (ds.getPermissionIndexTime() == null || (ds.getPermissionIndexTime().compareTo(ds.getPermissionModificationTime()) <= 0)))) { + if ((ds.getModificationTime() != null && (ds.getIndexTime() == null || (ds.getIndexTime().compareTo(ds.getModificationTime()) <= 0))) || + (ds.getPermissionModificationTime() != null && (ds.getPermissionIndexTime() == null || (ds.getPermissionIndexTime().compareTo(ds.getPermissionModificationTime()) <= 0)))) { return error(Response.Status.CONFLICT, "Dataset is awaiting indexing"); } } @@ -1201,20 +1204,20 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S .build(); } } else { - PublishDatasetResult res = execCommand(new PublishDatasetCommand(ds, + PublishDatasetResult res = execCommand(new PublishDatasetCommand(ds, createDataverseRequest(user), - isMinor)); - return res.isWorkflow() ? accepted(json(res.getDataset())) : ok(json(res.getDataset())); + isMinor)); + return res.isWorkflow() ? accepted(json(res.getDataset())) : ok(json(res.getDataset())); } } catch (WrappedResponse ex) { return ex.getResponse(); } } - + @POST @Path("{id}/actions/:releasemigrated") @Consumes("application/ld+json, application/json-ld") - public Response publishMigratedDataset(String jsonldBody, @PathParam("id") String id, @DefaultValue("false") @QueryParam ("updatepidatprovider") boolean contactPIDProvider) { + public Response publishMigratedDataset(String jsonldBody, @PathParam("id") String id, @DefaultValue("false") @QueryParam("updatepidatprovider") boolean contactPIDProvider) { try { AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { @@ -1227,10 +1230,10 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin String pubDate = metadata.getString(JsonLDTerm.schemaOrg("datePublished").getUrl()); logger.fine("Submitted date: " + pubDate); LocalDateTime dateTime = null; - if(!StringUtils.isEmpty(pubDate)) { + if (!StringUtils.isEmpty(pubDate)) { dateTime = JSONLDUtil.getDateTimeFrom(pubDate); final Timestamp time = Timestamp.valueOf(dateTime); - //Set version release date + // Set version release date ds.getLatestVersion().setReleaseTime(new Date(time.getTime())); } // dataset.getPublicationDateFormattedYYYYMMDD()) @@ -1250,10 +1253,10 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin ds.getLatestVersion().setMinorVersionNumber(Long.valueOf(0)); } } - if(ds.getLatestVersion().getVersionNumber()==1 && ds.getLatestVersion().getMinorVersionNumber()==0) { - //Also set publication date if this is the first - if(dateTime != null) { - ds.setPublicationDate(Timestamp.valueOf(dateTime)); + if (ds.getLatestVersion().getVersionNumber() == 1 && ds.getLatestVersion().getMinorVersionNumber() == 0) { + // Also set publication date if this is the first + if (dateTime != null) { + ds.setPublicationDate(Timestamp.valueOf(dateTime)); } // Release User is only set in FinalizeDatasetPublicationCommand if the pub date // is null, so set it here. @@ -1289,7 +1292,7 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin errorMsg = BundleUtil.getStringFromBundle("datasetversion.update.failure") + " - " + ex.toString(); logger.severe(ex.getMessage()); } - + if (errorMsg != null) { return error(Response.Status.INTERNAL_SERVER_ERROR, errorMsg); } else { @@ -1300,21 +1303,20 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin return ex.getResponse(); } } - + @POST @Path("{id}/move/{targetDataverseAlias}") public Response moveDataset(@PathParam("id") String id, @PathParam("targetDataverseAlias") String targetDataverseAlias, @QueryParam("forceMove") Boolean force) { try { - User u = findUserOrDie(); + User u = findUserOrDie(); Dataset ds = findDatasetOrDie(id); Dataverse target = dataverseService.findByAlias(targetDataverseAlias); if (target == null) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("datasets.api.moveDataset.error.targetDataverseNotFound")); } - //Command requires Super user - it will be tested by the command + // Command requires Super user - it will be tested by the command execCommand(new MoveDatasetCommand( - createDataverseRequest(u), ds, target, force - )); + createDataverseRequest(u), ds, target, force)); return ok(BundleUtil.getStringFromBundle("datasets.api.moveDataset.success")); } catch (WrappedResponse ex) { if (ex.getCause() instanceof UnforcedCommandException) { @@ -1324,32 +1326,31 @@ public Response moveDataset(@PathParam("id") String id, @PathParam("targetDatave } } } - + @PUT - @Path("{linkedDatasetId}/link/{linkingDataverseAlias}") - public Response linkDataset(@PathParam("linkedDatasetId") String linkedDatasetId, @PathParam("linkingDataverseAlias") String linkingDataverseAlias) { - try{ - User u = findUserOrDie(); + @Path("{linkedDatasetId}/link/{linkingDataverseAlias}") + public Response linkDataset(@PathParam("linkedDatasetId") String linkedDatasetId, @PathParam("linkingDataverseAlias") String linkingDataverseAlias) { + try { + User u = findUserOrDie(); Dataset linked = findDatasetOrDie(linkedDatasetId); Dataverse linking = findDataverseOrDie(linkingDataverseAlias); - if (linked == null){ + if (linked == null) { return error(Response.Status.BAD_REQUEST, "Linked Dataset not found."); - } - if (linking == null){ + } + if (linking == null) { return error(Response.Status.BAD_REQUEST, "Linking Dataverse not found."); - } + } execCommand(new LinkDatasetCommand( - createDataverseRequest(u), linking, linked - )); + createDataverseRequest(u), linking, linked)); return ok("Dataset " + linked.getId() + " linked successfully to " + linking.getAlias()); } catch (WrappedResponse ex) { return ex.getResponse(); } } - + @GET @Path("{id}/links") - public Response getLinks(@PathParam("id") String idSupplied ) { + public Response getLinks(@PathParam("id") String idSupplied) { try { User u = findUserOrDie(); if (!u.isSuperuser()) { @@ -1373,8 +1374,11 @@ public Response getLinks(@PathParam("id") String idSupplied ) { /** * Add a given assignment to a given user or group - * @param ra role assignment DTO - * @param id dataset id + * + * @param ra + * role assignment DTO + * @param id + * dataset id * @param apiKey */ @POST @@ -1382,12 +1386,12 @@ public Response getLinks(@PathParam("id") String idSupplied ) { public Response createAssignment(RoleAssignmentDTO ra, @PathParam("identifier") String id, @QueryParam("key") String apiKey) { try { Dataset dataset = findDatasetOrDie(id); - + RoleAssignee assignee = findAssignee(ra.getAssignee()); if (assignee == null) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("datasets.api.grant.role.assignee.not.found.error")); - } - + } + DataverseRole theRole; Dataverse dv = dataset.getOwner(); theRole = null; @@ -1415,7 +1419,7 @@ public Response createAssignment(RoleAssignmentDTO ra, @PathParam("identifier") } } - + @DELETE @Path("{identifier}/assignments/{id}") public Response deleteAssignment(@PathParam("id") long assignmentId, @PathParam("identifier") String dsId) { @@ -1438,37 +1442,35 @@ public Response deleteAssignment(@PathParam("id") long assignmentId, @PathParam( @GET @Path("{identifier}/assignments") public Response getAssignments(@PathParam("identifier") String id) { - return response( req -> - ok( execCommand( - new ListRoleAssignments(req, findDatasetOrDie(id))) - .stream().map(ra->json(ra)).collect(toJsonArray())) ); + return response(req -> ok(execCommand( + new ListRoleAssignments(req, findDatasetOrDie(id))) + .stream().map(ra -> json(ra)).collect(toJsonArray()))); } @GET @Path("{id}/privateUrl") public Response getPrivateUrlData(@PathParam("id") String idSupplied) { - return response( req -> { + return response(req -> { PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, findDatasetOrDie(idSupplied))); - return (privateUrl != null) ? ok(json(privateUrl)) - : error(Response.Status.NOT_FOUND, "Private URL not found."); + return (privateUrl != null) ? ok(json(privateUrl)) + : error(Response.Status.NOT_FOUND, "Private URL not found."); }); } @POST @Path("{id}/privateUrl") - public Response createPrivateUrl(@PathParam("id") String idSupplied,@DefaultValue("false") @QueryParam ("anonymizedAccess") boolean anonymizedAccess) { - if(anonymizedAccess && settingsSvc.getValueForKey(SettingsServiceBean.Key.AnonymizedFieldTypeNames)==null) { + public Response createPrivateUrl(@PathParam("id") String idSupplied, @DefaultValue("false") @QueryParam("anonymizedAccess") boolean anonymizedAccess) { + if (anonymizedAccess && settingsSvc.getValueForKey(SettingsServiceBean.Key.AnonymizedFieldTypeNames) == null) { throw new NotAcceptableException("Anonymized Access not enabled"); } - return response( req -> - ok(json(execCommand( + return response(req -> ok(json(execCommand( new CreatePrivateUrlCommand(req, findDatasetOrDie(idSupplied), anonymizedAccess))))); } @DELETE @Path("{id}/privateUrl") public Response deletePrivateUrl(@PathParam("id") String idSupplied) { - return response( req -> { + return response(req -> { Dataset dataset = findDatasetOrDie(idSupplied); PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, dataset)); if (privateUrl != null) { @@ -1516,13 +1518,13 @@ public Response getDatasetThumbnailCandidates(@PathParam("id") String idSupplied } @GET - @Produces({"image/png"}) + @Produces({ "image/png" }) @Path("{id}/thumbnail") public Response getDatasetThumbnail(@PathParam("id") String idSupplied) { try { Dataset dataset = findDatasetOrDie(idSupplied); InputStream is = DatasetUtil.getThumbnailAsInputStream(dataset, ImageThumbConverter.DEFAULT_CARDIMAGE_SIZE); - if(is == null) { + if (is == null) { return notFound("Thumbnail not available"); } return Response.ok(is).build(); @@ -1531,7 +1533,8 @@ public Response getDatasetThumbnail(@PathParam("id") String idSupplied) { } } - // TODO: Rather than only supporting looking up files by their database IDs (dataFileIdSupplied), consider supporting persistent identifiers. + // TODO: Rather than only supporting looking up files by their database IDs + // (dataFileIdSupplied), consider supporting persistent identifiers. @POST @Path("{id}/thumbnail/{dataFileId}") public Response setDataFileAsThumbnail(@PathParam("id") String idSupplied, @PathParam("dataFileId") long dataFileIdSupplied) { @@ -1546,8 +1549,7 @@ public Response setDataFileAsThumbnail(@PathParam("id") String idSupplied, @Path @POST @Path("{id}/thumbnail") @Consumes(MediaType.MULTIPART_FORM_DATA) - public Response uploadDatasetLogo(@PathParam("id") String idSupplied, @FormDataParam("file") InputStream inputStream - ) { + public Response uploadDatasetLogo(@PathParam("id") String idSupplied, @FormDataParam("file") InputStream inputStream) { try { DatasetThumbnail datasetThumbnail = execCommand(new UpdateDatasetThumbnailCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), UpdateDatasetThumbnailCommand.UserIntent.setNonDatasetFileAsThumbnail, null, inputStream)); return ok("Thumbnail is now " + datasetThumbnail.getBase64image()); @@ -1570,7 +1572,8 @@ public Response removeDatasetLogo(@PathParam("id") String idSupplied) { @GET @Path("{identifier}/dataCaptureModule/rsync") public Response getRsync(@PathParam("identifier") String id) { - //TODO - does it make sense to switch this to dataset identifier for consistency with the rest of the DCM APIs? + // TODO - does it make sense to switch this to dataset identifier for + // consistency with the rest of the DCM APIs? if (!DataCaptureModuleUtil.rsyncSupportEnabled(settingsSvc.getValueForKey(SettingsServiceBean.Key.UploadMethods))) { return error(Response.Status.METHOD_NOT_ALLOWED, SettingsServiceBean.Key.UploadMethods + " does not contain " + SystemConfig.FileUploadMethods.RSYNC + "."); } @@ -1579,11 +1582,11 @@ public Response getRsync(@PathParam("identifier") String id) { dataset = findDatasetOrDie(id); AuthenticatedUser user = findAuthenticatedUserOrDie(); ScriptRequestResponse scriptRequestResponse = execCommand(new RequestRsyncScriptCommand(createDataverseRequest(user), dataset)); - + DatasetLock lock = datasetService.addDatasetLock(dataset.getId(), DatasetLock.Reason.DcmUpload, user.getId(), "script downloaded"); if (lock == null) { logger.log(Level.WARNING, "Failed to lock the dataset (dataset id={0})", dataset.getId()); - return error(Response.Status.FORBIDDEN, "Failed to lock the dataset (dataset id="+dataset.getId()+")"); + return error(Response.Status.FORBIDDEN, "Failed to lock the dataset (dataset id=" + dataset.getId() + ")"); } return ok(scriptRequestResponse.getScript(), MediaType.valueOf(MediaType.TEXT_PLAIN), null); } catch (WrappedResponse wr) { @@ -1592,19 +1595,23 @@ public Response getRsync(@PathParam("identifier") String id) { return error(Response.Status.INTERNAL_SERVER_ERROR, "Something went wrong attempting to download rsync script: " + EjbUtil.ejbExceptionToString(ex)); } } - + /** - * This api endpoint triggers the creation of a "package" file in a dataset - * after that package has been moved onto the same filesystem via the Data Capture Module. - * The package is really just a way that Dataverse interprets a folder created by DCM, seeing it as just one file. - * The "package" can be downloaded over RSAL. + * This api endpoint triggers the creation of a "package" file in a dataset + * after that package has been moved onto the same filesystem via the Data + * Capture Module. The package is really just a way that Dataverse interprets a + * folder created by DCM, seeing it as just one file. The "package" can be + * downloaded over RSAL. * - * This endpoint currently supports both posix file storage and AWS s3 storage in Dataverse, and depending on which one is active acts accordingly. + * This endpoint currently supports both posix file storage and AWS s3 storage + * in Dataverse, and depending on which one is active acts accordingly. * - * The initial design of the DCM/Dataverse interaction was not to use packages, but to allow import of all individual files natively into Dataverse. - * But due to the possibly immense number of files (millions) the package approach was taken. - * This is relevant because the posix ("file") code contains many remnants of that development work. - * The s3 code was written later and is set to only support import as packages. It takes a lot from FileRecordWriter. + * The initial design of the DCM/Dataverse interaction was not to use packages, + * but to allow import of all individual files natively into Dataverse. But due + * to the possibly immense number of files (millions) the package approach was + * taken. This is relevant because the posix ("file") code contains many + * remnants of that development work. The s3 code was written later and is set + * to only support import as packages. It takes a lot from FileRecordWriter. * -MAD 4.9.1 */ @POST @@ -1624,13 +1631,13 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String try { Dataset dataset = findDatasetOrDie(id); if ("validation passed".equals(statusMessageFromDcm)) { - logger.log(Level.INFO, "Checksum Validation passed for DCM."); + logger.log(Level.INFO, "Checksum Validation passed for DCM."); String storageDriver = dataset.getDataverseContext().getEffectiveStorageDriverId(); String uploadFolder = jsonFromDcm.getString("uploadFolder"); int totalSize = jsonFromDcm.getInt("totalSize"); String storageDriverType = System.getProperty("dataverse.file." + storageDriver + ".type"); - + if (storageDriverType.equals("file")) { logger.log(Level.INFO, "File storage driver used for (dataset id={0})", dataset.getId()); @@ -1647,15 +1654,16 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String String message = wr.getMessage(); return error(Response.Status.INTERNAL_SERVER_ERROR, "Uploaded files have passed checksum validation but something went wrong while attempting to put the files into Dataverse. Message was '" + message + "'."); } - } else if(storageDriverType.equals("s3")) { - + } else if (storageDriverType.equals("s3")) { + logger.log(Level.INFO, "S3 storage driver used for DCM (dataset id={0})", dataset.getId()); try { - - //Where the lifting is actually done, moving the s3 files over and having dataverse know of the existance of the package + + // Where the lifting is actually done, moving the s3 files over and having + // dataverse know of the existance of the package s3PackageImporter.copyFromS3(dataset, uploadFolder); DataFile packageFile = s3PackageImporter.createPackageDataFile(dataset, uploadFolder, new Long(totalSize)); - + if (packageFile == null) { logger.log(Level.SEVERE, "S3 File package import failed."); return error(Response.Status.INTERNAL_SERVER_ERROR, "S3 File package import failed."); @@ -1667,8 +1675,9 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String datasetService.removeDatasetLocks(dataset, DatasetLock.Reason.DcmUpload); dataset.removeLock(dcmLock); } - - // update version using the command engine to enforce user permissions and constraints + + // update version using the command engine to enforce user permissions and + // constraints if (dataset.getVersions().size() == 1 && dataset.getLatestVersion().getVersionState() == DatasetVersion.VersionState.DRAFT) { try { Command cmd; @@ -1685,11 +1694,11 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String JsonObjectBuilder job = Json.createObjectBuilder(); return ok(job); - - } catch (IOException e) { + + } catch (IOException e) { String message = e.getMessage(); return error(Response.Status.INTERNAL_SERVER_ERROR, "Uploaded files have passed checksum validation but something went wrong while attempting to move the files into Dataverse. Message was '" + message + "'."); - } + } } else { return error(Response.Status.INTERNAL_SERVER_ERROR, "Invalid storage driver in Dataverse, not compatible with dcm"); } @@ -1712,7 +1721,6 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String return ex.getResponse(); } } - @POST @Path("{id}/submitForReview") @@ -1720,9 +1728,9 @@ public Response submitForReview(@PathParam("id") String idSupplied) { try { Dataset updatedDataset = execCommand(new SubmitDatasetForReviewCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied))); JsonObjectBuilder result = Json.createObjectBuilder(); - + boolean inReview = updatedDataset.isLockedFor(DatasetLock.Reason.InReview); - + result.add("inReview", inReview); result.add("message", "Dataset id " + updatedDataset.getId() + " has been submitted for review."); return ok(result); @@ -1734,7 +1742,7 @@ public Response submitForReview(@PathParam("id") String idSupplied) { @POST @Path("{id}/returnToAuthor") public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBody) { - + if (jsonBody == null || jsonBody.isEmpty()) { return error(Response.Status.BAD_REQUEST, "You must supply JSON to this API endpoint and it must contain a reason for returning the dataset (field: reasonForReturn)."); } @@ -1742,14 +1750,16 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo JsonObject json = Json.createReader(rdr).readObject(); try { Dataset dataset = findDatasetOrDie(idSupplied); - String reasonForReturn = null; + String reasonForReturn = null; reasonForReturn = json.getString("reasonForReturn"); - // TODO: Once we add a box for the curator to type into, pass the reason for return to the ReturnDatasetToAuthorCommand and delete this check and call to setReturnReason on the API side. + // TODO: Once we add a box for the curator to type into, pass the reason for + // return to the ReturnDatasetToAuthorCommand and delete this check and call to + // setReturnReason on the API side. if (reasonForReturn == null || reasonForReturn.isEmpty()) { return error(Response.Status.BAD_REQUEST, "You must enter a reason for returning a dataset to the author(s)."); } AuthenticatedUser authenticatedUser = findAuthenticatedUserOrDie(); - Dataset updatedDataset = execCommand(new ReturnDatasetToAuthorCommand(createDataverseRequest(authenticatedUser), dataset, reasonForReturn )); + Dataset updatedDataset = execCommand(new ReturnDatasetToAuthorCommand(createDataverseRequest(authenticatedUser), dataset, reasonForReturn)); JsonObjectBuilder result = Json.createObjectBuilder(); result.add("inReview", false); @@ -1768,11 +1778,11 @@ public Response setExternalCurationStatus(@PathParam("id") String idSupplied, @Q execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); return ok("External Curation Status updated"); } catch (WrappedResponse wr) { - //Just change to Bad Request and send + // Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } - + @DELETE @Path("{id}/setExternalCurationStatus") public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) { @@ -1781,222 +1791,222 @@ public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), null)); return ok("External Curation Status deleted"); } catch (WrappedResponse wr) { - //Just change to Bad Request and send + // Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } - -@GET -@Path("{id}/uploadsid") -@Deprecated -public Response getUploadUrl(@PathParam("id") String idSupplied) { - try { - Dataset dataset = findDatasetOrDie(idSupplied); - - boolean canUpdateDataset = false; - try { - canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset).canIssue(UpdateDatasetVersionCommand.class); - } catch (WrappedResponse ex) { - logger.info("Exception thrown while trying to figure out permissions while getting upload URL for dataset id " + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - if (!canUpdateDataset) { - return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); - } - S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); - if(s3io == null) { - return error(Response.Status.NOT_FOUND,"Direct upload not supported for files in this dataset: " + dataset.getId()); - } - String url = null; - String storageIdentifier = null; - try { - url = s3io.generateTemporaryS3UploadUrl(); - storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); - } catch (IOException io) { - logger.warning(io.getMessage()); - throw new WrappedResponse(io, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); - } - - JsonObjectBuilder response = Json.createObjectBuilder() - .add("url", url) - .add("storageIdentifier", storageIdentifier ); - return ok(response); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } -} -@GET -@Path("{id}/uploadurls") -public Response getMPUploadUrls(@PathParam("id") String idSupplied, @QueryParam("size") long fileSize) { - try { - Dataset dataset = findDatasetOrDie(idSupplied); - - boolean canUpdateDataset = false; - try { - canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions while getting upload URLs for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - if (!canUpdateDataset) { - return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); - } - S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); - if (s3io == null) { - return error(Response.Status.NOT_FOUND, - "Direct upload not supported for files in this dataset: " + dataset.getId()); - } - JsonObjectBuilder response = null; - String storageIdentifier = null; - try { - storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); - response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize); - - } catch (IOException io) { - logger.warning(io.getMessage()); - throw new WrappedResponse(io, - error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); - } - - response.add("storageIdentifier", storageIdentifier); - return ok(response); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } -} + @GET + @Path("{id}/uploadsid") + @Deprecated + public Response getUploadUrl(@PathParam("id") String idSupplied) { + try { + Dataset dataset = findDatasetOrDie(idSupplied); -@DELETE -@Path("mpupload") -public Response abortMPUpload(@QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { - try { - Dataset dataset = datasetSvc.findByGlobalId(idSupplied); - //Allow the API to be used within a session (e.g. for direct upload in the UI) - User user =session.getUser(); - if (!user.isAuthenticated()) { - try { - user = findAuthenticatedUserOrDie(); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions while getting aborting upload for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - } - boolean allowed = false; - if (dataset != null) { - allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } else { - /* - * The only legitimate case where a global id won't correspond to a dataset is - * for uploads during creation. Given that this call will still fail unless all - * three parameters correspond to an active multipart upload, it should be safe - * to allow the attempt for an authenticated user. If there are concerns about - * permissions, one could check with the current design that the user is allowed - * to create datasets in some dataverse that is configured to use the storage - * provider specified in the storageidentifier, but testing for the ability to - * create a dataset in a specific dataverse would requiring changing the design - * somehow (e.g. adding the ownerId to this call). - */ - allowed = true; - } - if (!allowed) { - return error(Response.Status.FORBIDDEN, - "You are not permitted to abort file uploads with the supplied parameters."); - } - try { - S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); - } catch (IOException io) { - logger.warning("Multipart upload abort failed for uploadId: " + uploadId + " storageidentifier=" - + storageidentifier + " dataset Id: " + dataset.getId()); - logger.warning(io.getMessage()); - throw new WrappedResponse(io, - error(Response.Status.INTERNAL_SERVER_ERROR, "Could not abort multipart upload")); - } - return Response.noContent().build(); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } -} + boolean canUpdateDataset = false; + try { + canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset).canIssue(UpdateDatasetVersionCommand.class); + } catch (WrappedResponse ex) { + logger.info("Exception thrown while trying to figure out permissions while getting upload URL for dataset id " + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + if (!canUpdateDataset) { + return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); + } + S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); + if (s3io == null) { + return error(Response.Status.NOT_FOUND, "Direct upload not supported for files in this dataset: " + dataset.getId()); + } + String url = null; + String storageIdentifier = null; + try { + url = s3io.generateTemporaryS3UploadUrl(); + storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); + } catch (IOException io) { + logger.warning(io.getMessage()); + throw new WrappedResponse(io, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); + } -@PUT -@Path("mpupload") -public Response completeMPUpload(String partETagBody, @QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { - try { - Dataset dataset = datasetSvc.findByGlobalId(idSupplied); - //Allow the API to be used within a session (e.g. for direct upload in the UI) - User user =session.getUser(); - if (!user.isAuthenticated()) { - try { - user=findAuthenticatedUserOrDie(); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions to complete mpupload for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - } - boolean allowed = false; - if (dataset != null) { - allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } else { - /* - * The only legitimate case where a global id won't correspond to a dataset is - * for uploads during creation. Given that this call will still fail unless all - * three parameters correspond to an active multipart upload, it should be safe - * to allow the attempt for an authenticated user. If there are concerns about - * permissions, one could check with the current design that the user is allowed - * to create datasets in some dataverse that is configured to use the storage - * provider specified in the storageidentifier, but testing for the ability to - * create a dataset in a specific dataverse would requiring changing the design - * somehow (e.g. adding the ownerId to this call). - */ - allowed = true; - } - if (!allowed) { - return error(Response.Status.FORBIDDEN, - "You are not permitted to complete file uploads with the supplied parameters."); - } - List eTagList = new ArrayList(); - logger.info("Etags: " + partETagBody); - try { - JsonReader jsonReader = Json.createReader(new StringReader(partETagBody)); - JsonObject object = jsonReader.readObject(); - jsonReader.close(); - for(String partNo : object.keySet()) { - eTagList.add(new PartETag(Integer.parseInt(partNo), object.getString(partNo))); - } - for(PartETag et: eTagList) { - logger.info("Part: " + et.getPartNumber() + " : " + et.getETag()); - } - } catch (JsonException je) { - logger.info("Unable to parse eTags from: " + partETagBody); - throw new WrappedResponse(je, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); - } - try { - S3AccessIO.completeMultipartUpload(idSupplied, storageidentifier, uploadId, eTagList); - } catch (IOException io) { - logger.warning("Multipart upload completion failed for uploadId: " + uploadId +" storageidentifier=" + storageidentifier + " globalId: " + idSupplied); - logger.warning(io.getMessage()); - try { - S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); - } catch (IOException e) { - logger.severe("Also unable to abort the upload (and release the space on S3 for uploadId: " + uploadId +" storageidentifier=" + storageidentifier + " globalId: " + idSupplied); - logger.severe(io.getMessage()); - } - - throw new WrappedResponse(io, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); - } - return ok("Multipart Upload completed"); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } -} + JsonObjectBuilder response = Json.createObjectBuilder() + .add("url", url) + .add("storageIdentifier", storageIdentifier); + return ok(response); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } + + @GET + @Path("{id}/uploadurls") + public Response getMPUploadUrls(@PathParam("id") String idSupplied, @QueryParam("size") long fileSize) { + try { + Dataset dataset = findDatasetOrDie(idSupplied); + + boolean canUpdateDataset = false; + try { + canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions while getting upload URLs for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + if (!canUpdateDataset) { + return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); + } + S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); + if (s3io == null) { + return error(Response.Status.NOT_FOUND, + "Direct upload not supported for files in this dataset: " + dataset.getId()); + } + JsonObjectBuilder response = null; + String storageIdentifier = null; + try { + storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); + response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize); + + } catch (IOException io) { + logger.warning(io.getMessage()); + throw new WrappedResponse(io, + error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); + } + + response.add("storageIdentifier", storageIdentifier); + return ok(response); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } + + @DELETE + @Path("mpupload") + public Response abortMPUpload(@QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { + try { + Dataset dataset = datasetSvc.findByGlobalId(idSupplied); + // Allow the API to be used within a session (e.g. for direct upload in the UI) + User user = session.getUser(); + if (!user.isAuthenticated()) { + try { + user = findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions while getting aborting upload for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + } + boolean allowed = false; + if (dataset != null) { + allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } else { + /* + * The only legitimate case where a global id won't correspond to a dataset is + * for uploads during creation. Given that this call will still fail unless all + * three parameters correspond to an active multipart upload, it should be safe + * to allow the attempt for an authenticated user. If there are concerns about + * permissions, one could check with the current design that the user is allowed + * to create datasets in some dataverse that is configured to use the storage + * provider specified in the storageidentifier, but testing for the ability to + * create a dataset in a specific dataverse would requiring changing the design + * somehow (e.g. adding the ownerId to this call). + */ + allowed = true; + } + if (!allowed) { + return error(Response.Status.FORBIDDEN, + "You are not permitted to abort file uploads with the supplied parameters."); + } + try { + S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); + } catch (IOException io) { + logger.warning("Multipart upload abort failed for uploadId: " + uploadId + " storageidentifier=" + + storageidentifier + " dataset Id: " + dataset.getId()); + logger.warning(io.getMessage()); + throw new WrappedResponse(io, + error(Response.Status.INTERNAL_SERVER_ERROR, "Could not abort multipart upload")); + } + return Response.noContent().build(); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } + + @PUT + @Path("mpupload") + public Response completeMPUpload(String partETagBody, @QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { + try { + Dataset dataset = datasetSvc.findByGlobalId(idSupplied); + // Allow the API to be used within a session (e.g. for direct upload in the UI) + User user = session.getUser(); + if (!user.isAuthenticated()) { + try { + user = findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions to complete mpupload for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + } + boolean allowed = false; + if (dataset != null) { + allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } else { + /* + * The only legitimate case where a global id won't correspond to a dataset is + * for uploads during creation. Given that this call will still fail unless all + * three parameters correspond to an active multipart upload, it should be safe + * to allow the attempt for an authenticated user. If there are concerns about + * permissions, one could check with the current design that the user is allowed + * to create datasets in some dataverse that is configured to use the storage + * provider specified in the storageidentifier, but testing for the ability to + * create a dataset in a specific dataverse would requiring changing the design + * somehow (e.g. adding the ownerId to this call). + */ + allowed = true; + } + if (!allowed) { + return error(Response.Status.FORBIDDEN, + "You are not permitted to complete file uploads with the supplied parameters."); + } + List eTagList = new ArrayList(); + logger.info("Etags: " + partETagBody); + try { + JsonReader jsonReader = Json.createReader(new StringReader(partETagBody)); + JsonObject object = jsonReader.readObject(); + jsonReader.close(); + for (String partNo : object.keySet()) { + eTagList.add(new PartETag(Integer.parseInt(partNo), object.getString(partNo))); + } + for (PartETag et : eTagList) { + logger.info("Part: " + et.getPartNumber() + " : " + et.getETag()); + } + } catch (JsonException je) { + logger.info("Unable to parse eTags from: " + partETagBody); + throw new WrappedResponse(je, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); + } + try { + S3AccessIO.completeMultipartUpload(idSupplied, storageidentifier, uploadId, eTagList); + } catch (IOException io) { + logger.warning("Multipart upload completion failed for uploadId: " + uploadId + " storageidentifier=" + storageidentifier + " globalId: " + idSupplied); + logger.warning(io.getMessage()); + try { + S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); + } catch (IOException e) { + logger.severe("Also unable to abort the upload (and release the space on S3 for uploadId: " + uploadId + " storageidentifier=" + storageidentifier + " globalId: " + idSupplied); + logger.severe(io.getMessage()); + } + + throw new WrappedResponse(io, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); + } + return ok("Multipart Upload completed"); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } /** * Add a File to an existing Dataset @@ -2006,17 +2016,16 @@ public Response completeMPUpload(String partETagBody, @QueryParam("globalid") St * @param fileInputStream * @param contentDispositionHeader * @param formDataBodyPart - * @return + * @return */ @POST @Path("{id}/add") @Consumes(MediaType.MULTIPART_FORM_DATA) public Response addFileToDataset(@PathParam("id") String idSupplied, - @FormDataParam("jsonData") String jsonData, - @FormDataParam("file") InputStream fileInputStream, - @FormDataParam("file") FormDataContentDisposition contentDispositionHeader, - @FormDataParam("file") final FormDataBodyPart formDataBodyPart - ){ + @FormDataParam("jsonData") String jsonData, + @FormDataParam("file") InputStream fileInputStream, + @FormDataParam("file") FormDataContentDisposition contentDispositionHeader, + @FormDataParam("file") final FormDataBodyPart formDataBodyPart) { if (!systemConfig.isHTTPUpload()) { return error(Response.Status.SERVICE_UNAVAILABLE, BundleUtil.getStringFromBundle("file.api.httpDisabled")); @@ -2030,114 +2039,106 @@ public Response addFileToDataset(@PathParam("id") String idSupplied, authUser = findUserOrDie(); } catch (WrappedResponse ex) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.addreplace.error.auth") - ); + BundleUtil.getStringFromBundle("file.addreplace.error.auth")); } - - + // ------------------------------------- // (2) Get the Dataset Id - // + // // ------------------------------------- Dataset dataset; - + try { dataset = findDatasetOrDie(idSupplied); } catch (WrappedResponse wr) { - return wr.getResponse(); + return wr.getResponse(); } - - //------------------------------------ + + // ------------------------------------ // (2a) Make sure dataset does not have package file // // -------------------------------------- - + for (DatasetVersion dv : dataset.getVersions()) { if (dv.isHasPackageFile()) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile") - ); + BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile")); } } // (2a) Load up optional params via JSON - //--------------------------------------- + // --------------------------------------- OptionalFileParams optionalFileParams = null; - msgt("(api) jsonData: " + jsonData); + msgt("(api) jsonData: " + jsonData); try { optionalFileParams = new OptionalFileParams(jsonData); } catch (DataFileTagException ex) { - return error( Response.Status.BAD_REQUEST, ex.getMessage()); - } - catch (ClassCastException | com.google.gson.JsonParseException ex) { + return error(Response.Status.BAD_REQUEST, ex.getMessage()); + } catch (ClassCastException | com.google.gson.JsonParseException ex) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("file.addreplace.error.parsing")); } - + // ------------------------------------- // (3) Get the file name and content type // ------------------------------------- String newFilename = null; String newFileContentType = null; String newStorageIdentifier = null; - if (null == contentDispositionHeader) { - if (optionalFileParams.hasStorageIdentifier()) { - newStorageIdentifier = optionalFileParams.getStorageIdentifier(); - // ToDo - check that storageIdentifier is valid - if (optionalFileParams.hasFileName()) { - newFilename = optionalFileParams.getFileName(); - if (optionalFileParams.hasMimetype()) { - newFileContentType = optionalFileParams.getMimeType(); - } - } - } else { - return error(BAD_REQUEST, - "You must upload a file or provide a storageidentifier, filename, and mimetype."); - } - } else { - newFilename = contentDispositionHeader.getFileName(); - newFileContentType = formDataBodyPart.getMediaType().toString(); - } - - - //------------------- + if (null == contentDispositionHeader) { + if (optionalFileParams.hasStorageIdentifier()) { + newStorageIdentifier = optionalFileParams.getStorageIdentifier(); + // ToDo - check that storageIdentifier is valid + if (optionalFileParams.hasFileName()) { + newFilename = optionalFileParams.getFileName(); + if (optionalFileParams.hasMimetype()) { + newFileContentType = optionalFileParams.getMimeType(); + } + } + } else { + return error(BAD_REQUEST, + "You must upload a file or provide a storageidentifier, filename, and mimetype."); + } + } else { + newFilename = contentDispositionHeader.getFileName(); + newFileContentType = formDataBodyPart.getMediaType().toString(); + } + + // ------------------- // (3) Create the AddReplaceFileHelper object - //------------------- + // ------------------- msg("ADD!"); DataverseRequest dvRequest2 = createDataverseRequest(authUser); AddReplaceFileHelper addFileHelper = new AddReplaceFileHelper(dvRequest2, - ingestService, - datasetService, - fileService, - permissionSvc, - commandEngine, - systemConfig); - - - //------------------- + ingestService, + datasetService, + fileService, + permissionSvc, + commandEngine, + systemConfig); + + // ------------------- // (4) Run "runAddFileByDatasetId" - //------------------- + // ------------------- addFileHelper.runAddFileByDataset(dataset, - newFilename, - newFileContentType, - newStorageIdentifier, - fileInputStream, - optionalFileParams); + newFilename, + newFileContentType, + newStorageIdentifier, + fileInputStream, + optionalFileParams); - - if (addFileHelper.hasError()){ + if (addFileHelper.hasError()) { return error(addFileHelper.getHttpErrorCode(), addFileHelper.getErrorMessagesAsString("\n")); - }else{ + } else { String successMsg = BundleUtil.getStringFromBundle("file.addreplace.success.add"); try { - //msgt("as String: " + addFileHelper.getSuccessResult()); + // msgt("as String: " + addFileHelper.getSuccessResult()); /** - * @todo We need a consistent, sane way to communicate a human - * readable message to an API client suitable for human - * consumption. Imagine if the UI were built in Angular or React - * and we want to return a message from the API as-is to the - * user. Human readable. + * @todo We need a consistent, sane way to communicate a human readable message + * to an API client suitable for human consumption. Imagine if the UI were + * built in Angular or React and we want to return a message from the API + * as-is to the user. Human readable. */ logger.fine("successMsg: " + successMsg); String duplicateWarning = addFileHelper.getDuplicateFileWarning(); @@ -2146,79 +2147,83 @@ public Response addFileToDataset(@PathParam("id") String idSupplied, } else { return ok(addFileHelper.getSuccessResultAsJsonObjectBuilder()); } - - //"Look at that! You added a file! (hey hey, it may have worked)"); + + // "Look at that! You added a file! (hey hey, it may have worked)"); } catch (NoFilesException ex) { Logger.getLogger(Files.class.getName()).log(Level.SEVERE, null, ex); return error(Response.Status.BAD_REQUEST, "NoFileException! Serious Error! See administrator!"); } } - - } // end: addFileToDataset + } // end: addFileToDataset - - private void msg(String m){ - //System.out.println(m); + private void msg(String m) { + // System.out.println(m); logger.fine(m); } - private void dashes(){ + + private void dashes() { msg("----------------"); } - private void msgt(String m){ - dashes(); msg(m); dashes(); + + private void msgt(String m) { + dashes(); + msg(m); + dashes(); } - - - public static T handleVersion( String versionId, DsVersionHandler hdl ) - throws WrappedResponse { + + public static T handleVersion(String versionId, DsVersionHandler hdl) + throws WrappedResponse { switch (versionId) { - case ":latest": return hdl.handleLatest(); - case ":draft": return hdl.handleDraft(); - case ":latest-published": return hdl.handleLatestPublished(); - default: - try { - String[] versions = versionId.split("\\."); - switch (versions.length) { - case 1: - return hdl.handleSpecific(Long.parseLong(versions[0]), (long)0.0); - case 2: - return hdl.handleSpecific( Long.parseLong(versions[0]), Long.parseLong(versions[1]) ); - default: - throw new WrappedResponse(error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); - } - } catch ( NumberFormatException nfe ) { - throw new WrappedResponse( error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); + case ":latest": + return hdl.handleLatest(); + case ":draft": + return hdl.handleDraft(); + case ":latest-published": + return hdl.handleLatestPublished(); + default: + try { + String[] versions = versionId.split("\\."); + switch (versions.length) { + case 1: + return hdl.handleSpecific(Long.parseLong(versions[0]), (long) 0.0); + case 2: + return hdl.handleSpecific(Long.parseLong(versions[0]), Long.parseLong(versions[1])); + default: + throw new WrappedResponse(error(Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); } + } catch (NumberFormatException nfe) { + throw new WrappedResponse(error(Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); + } } } - - private DatasetVersion getDatasetVersionOrDie( final DataverseRequest req, String versionNumber, final Dataset ds, UriInfo uriInfo, HttpHeaders headers) throws WrappedResponse { - DatasetVersion dsv = execCommand( handleVersion(versionNumber, new DsVersionHandler>(){ - @Override - public Command handleLatest() { - return new GetLatestAccessibleDatasetVersionCommand(req, ds); - } + private DatasetVersion getDatasetVersionOrDie(final DataverseRequest req, String versionNumber, final Dataset ds, UriInfo uriInfo, HttpHeaders headers) throws WrappedResponse { + DatasetVersion dsv = execCommand(handleVersion(versionNumber, new DsVersionHandler>() { - @Override - public Command handleDraft() { - return new GetDraftDatasetVersionCommand(req, ds); - } - - @Override - public Command handleSpecific(long major, long minor) { - return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); - } + @Override + public Command handleLatest() { + return new GetLatestAccessibleDatasetVersionCommand(req, ds); + } - @Override - public Command handleLatestPublished() { - return new GetLatestPublishedDatasetVersionCommand(req, ds); - } - })); - if ( dsv == null || dsv.getId() == null ) { - throw new WrappedResponse( notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found") ); + @Override + public Command handleDraft() { + return new GetDraftDatasetVersionCommand(req, ds); + } + + @Override + public Command handleSpecific(long major, long minor) { + return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); + } + + @Override + public Command handleLatestPublished() { + return new GetLatestPublishedDatasetVersionCommand(req, ds); + } + })); + if (dsv == null || dsv.getId() == null) { + throw new WrappedResponse(notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found")); } if (dsv.isReleased()) { MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, ds); @@ -2226,7 +2231,7 @@ public Command handleLatestPublished() { } return dsv; } - + @GET @Path("{identifier}/locks") public Response getLocks(@PathParam("identifier") String id, @QueryParam("type") DatasetLock.Reason lockType) { @@ -2234,26 +2239,26 @@ public Response getLocks(@PathParam("identifier") String id, @QueryParam("type") Dataset dataset = null; try { dataset = findDatasetOrDie(id); - Set locks; + Set locks; if (lockType == null) { locks = dataset.getLocks(); } else { // request for a specific type lock: DatasetLock lock = dataset.getLockFor(lockType); - locks = new HashSet<>(); + locks = new HashSet<>(); if (lock != null) { locks.add(lock); } } - + return ok(locks.stream().map(lock -> json(lock)).collect(toJsonArray())); } catch (WrappedResponse wr) { return wr.getResponse(); - } - } - + } + } + @DELETE @Path("{identifier}/locks") public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("type") DatasetLock.Reason lockType) { @@ -2265,7 +2270,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ return error(Response.Status.FORBIDDEN, "This API end point can be used by superusers only."); } Dataset dataset = findDatasetOrDie(id); - + if (lockType == null) { Set locks = new HashSet<>(); for (DatasetLock lock : dataset.getLocks()) { @@ -2277,7 +2282,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ // refresh the dataset: dataset = findDatasetOrDie(id); } - // kick of dataset reindexing, in case the locks removed + // kick of dataset reindexing, in case the locks removed // affected the search card: try { indexService.indexDataset(dataset, true); @@ -2297,7 +2302,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ execCommand(new RemoveLockCommand(req, dataset, lock.getReason())); // refresh the dataset: dataset = findDatasetOrDie(id); - // ... and kick of dataset reindexing, in case the lock removed + // ... and kick of dataset reindexing, in case the lock removed // affected the search card: try { indexService.indexDataset(dataset, true); @@ -2317,7 +2322,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ }); } - + @POST @Path("{identifier}/lock/{type}") public Response lockDataset(@PathParam("identifier") String id, @PathParam("type") DatasetLock.Reason lockType) { @@ -2326,7 +2331,7 @@ public Response lockDataset(@PathParam("identifier") String id, @PathParam("type AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "This API end point can be used by superusers only."); - } + } Dataset dataset = findDatasetOrDie(id); DatasetLock lock = dataset.getLockFor(lockType); if (lock != null) { @@ -2353,29 +2358,28 @@ public Response lockDataset(@PathParam("identifier") String id, @PathParam("type }); } - + @GET @Path("{id}/makeDataCount/citations") public Response getMakeDataCountCitations(@PathParam("id") String idSupplied) { - + try { Dataset dataset = findDatasetOrDie(idSupplied); JsonArrayBuilder datasetsCitations = Json.createArrayBuilder(); List externalCitations = datasetExternalCitationsService.getDatasetExternalCitationsByDataset(dataset); - for (DatasetExternalCitations citation : externalCitations ){ + for (DatasetExternalCitations citation : externalCitations) { JsonObjectBuilder candidateObj = Json.createObjectBuilder(); /** - * In the future we can imagine storing and presenting more - * information about the citation such as the title of the paper - * and the names of the authors. For now, we'll at least give - * the URL of the citation so people can click and find out more - * about the citation. + * In the future we can imagine storing and presenting more information about + * the citation such as the title of the paper and the names of the authors. For + * now, we'll at least give the URL of the citation so people can click and find + * out more about the citation. */ candidateObj.add("citationUrl", citation.getCitedByUrl()); datasetsCitations.add(candidateObj); - } - return ok(datasetsCitations); - + } + return ok(datasetsCitations); + } catch (WrappedResponse wr) { return wr.getResponse(); } @@ -2388,23 +2392,23 @@ public Response getMakeDataCountMetricCurrentMonth(@PathParam("id") String idSup String nullCurrentMonth = null; return getMakeDataCountMetric(idSupplied, metricSupplied, nullCurrentMonth, country); } - + @GET @Path("{identifier}/storagesize") - public Response getStorageSize(@PathParam("identifier") String dvIdtf, @QueryParam("includeCached") boolean includeCached, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + public Response getStorageSize(@PathParam("identifier") String dvIdtf, @QueryParam("includeCached") boolean includeCached, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + return response(req -> ok(MessageFormat.format(BundleUtil.getStringFromBundle("datasets.api.datasize.storage"), - execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), includeCached,GetDatasetStorageSizeCommand.Mode.STORAGE, null))))); + execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), includeCached, GetDatasetStorageSizeCommand.Mode.STORAGE, null))))); } - + @GET @Path("{identifier}/versions/{versionId}/downloadsize") - public Response getDownloadSize(@PathParam("identifier") String dvIdtf, @PathParam("versionId") String version, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + public Response getDownloadSize(@PathParam("identifier") String dvIdtf, @PathParam("versionId") String version, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + return response(req -> ok(MessageFormat.format(BundleUtil.getStringFromBundle("datasets.api.datasize.download"), - execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), false, GetDatasetStorageSizeCommand.Mode.DOWNLOAD, getDatasetVersionOrDie(req, version , findDatasetOrDie(dvIdtf), uriInfo, headers)))))); + execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), false, GetDatasetStorageSizeCommand.Mode.DOWNLOAD, getDatasetVersionOrDie(req, version, findDatasetOrDie(dvIdtf), uriInfo, headers)))))); } @GET @@ -2421,8 +2425,10 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path } String monthYear = null; if (yyyymm != null) { - // We add "-01" because we store "2018-05-01" rather than "2018-05" in the "monthyear" column. - // Dates come to us as "2018-05-01" in the SUSHI JSON ("begin-date") and we decided to store them as-is. + // We add "-01" because we store "2018-05-01" rather than "2018-05" in the + // "monthyear" column. + // Dates come to us as "2018-05-01" in the SUSHI JSON ("begin-date") and we + // decided to store them as-is. monthYear = MetricsUtil.sanitizeYearMonthUserInput(yyyymm) + "-01"; } if (country != null) { @@ -2450,50 +2456,50 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path Long downloadsTotal = null; Long downloadsUnique = null; switch (metricSupplied) { - case "viewsTotal": - viewsTotal = datasetMetrics.getViewsTotal(); - break; - case "viewsTotalRegular": - viewsTotalRegular = datasetMetrics.getViewsTotalRegular(); - break; - case "viewsTotalMachine": - viewsTotalMachine = datasetMetrics.getViewsTotalMachine(); - break; - case "viewsUnique": - viewsUnique = datasetMetrics.getViewsUnique(); - break; - case "viewsUniqueRegular": - viewsUniqueRegular = datasetMetrics.getViewsUniqueRegular(); - break; - case "viewsUniqueMachine": - viewsUniqueMachine = datasetMetrics.getViewsUniqueMachine(); - break; - case "downloadsTotal": - downloadsTotal = datasetMetrics.getDownloadsTotal(); - break; - case "downloadsTotalRegular": - downloadsTotalRegular = datasetMetrics.getDownloadsTotalRegular(); - break; - case "downloadsTotalMachine": - downloadsTotalMachine = datasetMetrics.getDownloadsTotalMachine(); - break; - case "downloadsUnique": - downloadsUnique = datasetMetrics.getDownloadsUnique(); - break; - case "downloadsUniqueRegular": - downloadsUniqueRegular = datasetMetrics.getDownloadsUniqueRegular(); - break; - case "downloadsUniqueMachine": - downloadsUniqueMachine = datasetMetrics.getDownloadsUniqueMachine(); - break; - default: - break; + case "viewsTotal": + viewsTotal = datasetMetrics.getViewsTotal(); + break; + case "viewsTotalRegular": + viewsTotalRegular = datasetMetrics.getViewsTotalRegular(); + break; + case "viewsTotalMachine": + viewsTotalMachine = datasetMetrics.getViewsTotalMachine(); + break; + case "viewsUnique": + viewsUnique = datasetMetrics.getViewsUnique(); + break; + case "viewsUniqueRegular": + viewsUniqueRegular = datasetMetrics.getViewsUniqueRegular(); + break; + case "viewsUniqueMachine": + viewsUniqueMachine = datasetMetrics.getViewsUniqueMachine(); + break; + case "downloadsTotal": + downloadsTotal = datasetMetrics.getDownloadsTotal(); + break; + case "downloadsTotalRegular": + downloadsTotalRegular = datasetMetrics.getDownloadsTotalRegular(); + break; + case "downloadsTotalMachine": + downloadsTotalMachine = datasetMetrics.getDownloadsTotalMachine(); + break; + case "downloadsUnique": + downloadsUnique = datasetMetrics.getDownloadsUnique(); + break; + case "downloadsUniqueRegular": + downloadsUniqueRegular = datasetMetrics.getDownloadsUniqueRegular(); + break; + case "downloadsUniqueMachine": + downloadsUniqueMachine = datasetMetrics.getDownloadsUniqueMachine(); + break; + default: + break; } /** * TODO: Think more about the JSON output and the API design. - * getDatasetMetricsByDatasetMonthCountry returns a single row right - * now, by country. We could return multiple metrics (viewsTotal, - * viewsUnique, downloadsTotal, and downloadsUnique) by country. + * getDatasetMetricsByDatasetMonthCountry returns a single row right now, by + * country. We could return multiple metrics (viewsTotal, viewsUnique, + * downloadsTotal, and downloadsUnique) by country. */ jsonObjectBuilder.add("viewsTotalRegular", viewsTotalRegular); jsonObjectBuilder.add("viewsUniqueRegular", viewsUniqueRegular); @@ -2511,33 +2517,33 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path } catch (WrappedResponse wr) { return wr.getResponse(); } catch (Exception e) { - //bad date - caught in sanitize call + // bad date - caught in sanitize call return error(BAD_REQUEST, e.getMessage()); } } - + @GET @Path("{identifier}/storageDriver") public Response getFileStore(@PathParam("identifier") String dvIdtf, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - - Dataset dataset; - + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + return response(req -> ok(dataset.getEffectiveStorageDriverId())); } - + @PUT @Path("{identifier}/storageDriver") public Response setFileStore(@PathParam("identifier") String dvIdtf, String storageDriverLabel, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2547,17 +2553,17 @@ public Response setFileStore(@PathParam("identifier") String dvIdtf, } if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); - } - - Dataset dataset; - + } + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - - // We don't want to allow setting this to a store id that does not exist: + + // We don't want to allow setting this to a store id that does not exist: for (Entry store : DataAccess.getStorageDriverLabels().entrySet()) { if (store.getKey().equals(storageDriverLabel)) { dataset.setStorageDriverId(store.getValue()); @@ -2565,15 +2571,15 @@ public Response setFileStore(@PathParam("identifier") String dvIdtf, return ok("Storage driver set to: " + store.getKey() + "/" + store.getValue()); } } - return error(Response.Status.BAD_REQUEST, - "No Storage Driver found for : " + storageDriverLabel); + return error(Response.Status.BAD_REQUEST, + "No Storage Driver found for : " + storageDriverLabel); } - + @DELETE @Path("{identifier}/storageDriver") public Response resetFileStore(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2583,43 +2589,43 @@ public Response resetFileStore(@PathParam("identifier") String dvIdtf, } if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); - } - - Dataset dataset; - + } + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + dataset.setStorageDriverId(null); datasetService.merge(dataset); - return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); + return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); } @GET @Path("{identifier}/curationLabelSet") public Response getCurationLabelSet(@PathParam("identifier") String dvIdtf, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - - Dataset dataset; - + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + return response(req -> ok(dataset.getEffectiveCurationLabelSetName())); } - + @PUT @Path("{identifier}/curationLabelSet") public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, String curationLabelSet, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2630,9 +2636,9 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); } - - Dataset dataset; - + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { @@ -2650,14 +2656,14 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, } } return error(Response.Status.BAD_REQUEST, - "No Such Curation Label Set"); + "No Such Curation Label Set"); } - + @DELETE @Path("{identifier}/curationLabelSet") public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2668,15 +2674,15 @@ public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); } - - Dataset dataset; - + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + dataset.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); datasetService.merge(dataset); return ok("Curation Label Set reset to default: " + SystemConfig.DEFAULTCURATIONLABELSET); @@ -2718,7 +2724,8 @@ public Response getTimestamps(@PathParam("identifier") String id) { dataset.getMostRecentMajorVersionReleaseDate().toInstant().atZone(ZoneId.systemDefault()))); } // If the modification/permissionmodification time is - // set and the index time is null or is before the mod time, the relevant index is stale + // set and the index time is null or is before the mod time, the relevant index + // is stale timestamps.add("hasStaleIndex", (dataset.getModificationTime() != null && (dataset.getIndexTime() == null || (dataset.getIndexTime().compareTo(dataset.getModificationTime()) <= 0))) ? true @@ -2754,7 +2761,6 @@ public Response getTimestamps(@PathParam("identifier") String id) { } } - /** * Add multiple Files to an existing Dataset * @@ -2766,7 +2772,7 @@ public Response getTimestamps(@PathParam("identifier") String id) { @Path("{id}/addFiles") @Consumes(MediaType.MULTIPART_FORM_DATA) public Response addFilesToDataset(@PathParam("id") String idSupplied, - @FormDataParam("jsonData") String jsonData) { + @FormDataParam("jsonData") String jsonData) { if (!systemConfig.isHTTPUpload()) { return error(Response.Status.SERVICE_UNAVAILABLE, BundleUtil.getStringFromBundle("file.api.httpDisabled")); @@ -2779,8 +2785,7 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, try { authUser = findUserOrDie(); } catch (WrappedResponse ex) { - return error(Response.Status.FORBIDDEN, BundleUtil.getStringFromBundle("file.addreplace.error.auth") - ); + return error(Response.Status.FORBIDDEN, BundleUtil.getStringFromBundle("file.addreplace.error.auth")); } // ------------------------------------- @@ -2794,16 +2799,14 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, return wr.getResponse(); } - - //------------------------------------ + // ------------------------------------ // (2a) Make sure dataset does not have package file // -------------------------------------- for (DatasetVersion dv : dataset.getVersions()) { if (dv.isHasPackageFile()) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile") - ); + BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile")); } } @@ -2816,18 +2819,24 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, this.fileService, this.permissionSvc, this.commandEngine, - this.systemConfig - ); + this.systemConfig); return addFileHelper.addFiles(jsonData, dataset, authUser); } - - - /** - * API to find curation assignements and statuses + + /** + * API to list dataset creation and modification dates, curation status, and + * direct curator role assignments * - * @return + * Curation Status is a label from the :AllowedCurationLabels setting The + * returned table/csv file also lists the users with any assignments on this + * dataset that allow publication. These would be most relevant in uses cases + * where local role assignments are used to identify responsible party(ies) who + * have been given roles in movign the dataset through the defined curation + * process. + * + * @return a CSV table with headings * @throws WrappedResponse */ @GET @@ -2843,38 +2852,45 @@ public Response getCurationStates() throws WrappedResponse { } catch (WrappedResponse wr) { return wr.getResponse(); } - + List allRoles = dataverseRoleService.findAll(); List curationRoles = new ArrayList(); - allRoles.forEach(r -> {if(r.permissions().contains(Permission.PublishDataset)) curationRoles.add(r);}); + allRoles.forEach(r -> { + if (r.permissions().contains(Permission.PublishDataset)) + curationRoles.add(r); + }); HashMap> assignees = new HashMap>(); - curationRoles.forEach(r-> {assignees.put(r.getAlias(), null);}); - - StringBuilder csvSB = new StringBuilder(String.join(",", - BundleUtil.getStringFromBundle("dataset"), - BundleUtil.getStringFromBundle("datasets.api.creationdate"), - BundleUtil.getStringFromBundle("datasets.api.modificationdate"), + curationRoles.forEach(r -> { + assignees.put(r.getAlias(), null); + }); + + StringBuilder csvSB = new StringBuilder(String.join(",", + BundleUtil.getStringFromBundle("dataset"), + BundleUtil.getStringFromBundle("datasets.api.creationdate"), + BundleUtil.getStringFromBundle("datasets.api.modificationdate"), BundleUtil.getStringFromBundle("datasets.api.curationstatus"), String.join(",", assignees.keySet()))); for (Dataset dataset : datasetSvc.findAllUnpublished()) { - List ras = permissionService.assignmentsOn(dataset); - curationRoles.forEach(r-> {assignees.put(r.getAlias(), new HashSet());}); - for (RoleAssignment ra : ras) { - if (curationRoles.contains(ra.getRole())) { - assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); - } + List ras = permissionService.assignmentsOn(dataset); + curationRoles.forEach(r -> { + assignees.put(r.getAlias(), new HashSet()); + }); + for (RoleAssignment ra : ras) { + if (curationRoles.contains(ra.getRole())) { + assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); } - String name = dataset.getCurrentName().replace("\"","\"\""); - String status = dataset.getLatestVersion().getExternalStatusLabel(); - String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); - String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); - String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); - String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; - List sList = new ArrayList(); - assignees.entrySet().forEach(e-> sList.add(e.getValue().size()==0 ? "": String.join(";", e.getValue()))); - csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status==null ? "": status, String.join(",", sList))); + } + String name = dataset.getCurrentName().replace("\"", "\"\""); + String status = dataset.getLatestVersion().getExternalStatusLabel(); + String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); + String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); + String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); + String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; + List sList = new ArrayList(); + assignees.entrySet().forEach(e -> sList.add(e.getValue().size() == 0 ? "" : String.join(";", e.getValue()))); + csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status == null ? "" : status, String.join(",", sList))); } csvSB.append("\n"); - return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); + return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); } } From bc066f76e0b0ccd55013ed1cba22cf680e534290 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 27 Sep 2021 14:57:49 -0400 Subject: [PATCH 52/78] merge issue --- src/main/java/edu/harvard/iq/dataverse/DataversePage.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 4d1a189c488..01fe715abfd 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -1205,13 +1205,17 @@ public String getDefaultStorageDriverLabel() { } String label = DataAccess.getStorageDriverLabelFor(storageDriverId); if(fromAncestor) { - label = label + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); + label = label + " " + BundleUtil.getStringFromBundle("dataverse.inherited"); } else { - label = label + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); + label = label + " " + BundleUtil.getStringFromBundle("dataverse.default"); } return label; } + public Set> getMetadataLanguages() { + return settingsWrapper.getMetadataLanguages(this.dataverse).entrySet(); + } + public Set> getCurationLabelSetOptions() { HashMap setNames = new HashMap(); Set allowedSetNames = systemConfig.getCurationLabels().keySet(); From 8f8531a23b5156f0093e32272ed683c692e27f7f Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 27 Sep 2021 16:32:36 -0400 Subject: [PATCH 53/78] Revert "style fixes" This reverts commit 56fd065a1675449925d0426558aa007bf0a299e7. --- .../harvard/iq/dataverse/DataversePage.java | 9 +- .../harvard/iq/dataverse/api/Datasets.java | 1620 ++++++++--------- 2 files changed, 803 insertions(+), 826 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 01fe715abfd..62b9e4f1d27 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -7,7 +7,6 @@ import edu.harvard.iq.dataverse.dataaccess.DataAccess; import edu.harvard.iq.dataverse.dataverse.DataverseUtil; import edu.harvard.iq.dataverse.engine.command.Command; -import edu.harvard.iq.dataverse.engine.command.DataverseRequest; import edu.harvard.iq.dataverse.engine.command.exception.CommandException; import edu.harvard.iq.dataverse.engine.command.impl.CreateDataverseCommand; import edu.harvard.iq.dataverse.engine.command.impl.CreateSavedSearchCommand; @@ -17,7 +16,6 @@ import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseCommand; import edu.harvard.iq.dataverse.search.FacetCategory; import edu.harvard.iq.dataverse.search.IndexServiceBean; -import edu.harvard.iq.dataverse.search.SearchException; import edu.harvard.iq.dataverse.search.SearchFields; import edu.harvard.iq.dataverse.search.SearchIncludeFragment; import edu.harvard.iq.dataverse.search.SearchServiceBean; @@ -32,12 +30,9 @@ import javax.ejb.EJB; import javax.faces.application.FacesMessage; import javax.faces.context.FacesContext; -import javax.faces.event.ActionEvent; import javax.faces.view.ViewScoped; import javax.inject.Inject; import javax.inject.Named; - -import java.util.AbstractMap; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -1228,9 +1223,7 @@ public Set> getCurationLabelSetOptions() { } // Add an entry for disabled setNames.put(SystemConfig.CURATIONLABELSDISABLED, SystemConfig.CURATIONLABELSDISABLED); - allowedSetNames.forEach(name -> { - setNames.put(name, name); - }); + allowedSetNames.forEach(name -> {setNames.put(name, name);}); } return setNames.entrySet(); } diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index a9b73171678..2da116f5f65 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -185,31 +185,30 @@ public class Datasets extends AbstractApiBean { private static final Logger logger = Logger.getLogger(Datasets.class.getCanonicalName()); - - @Inject - DataverseSession session; + + @Inject DataverseSession session; @EJB DatasetServiceBean datasetService; @EJB DataverseServiceBean dataverseService; - + @EJB UserNotificationServiceBean userNotificationService; - + @EJB PermissionServiceBean permissionService; - + @EJB AuthenticationServiceBean authenticationServiceBean; - + @EJB DDIExportServiceBean ddiExportService; - + @EJB MetadataBlockServiceBean metadataBlockService; - + @EJB DataFileServiceBean fileService; @@ -218,77 +217,71 @@ public class Datasets extends AbstractApiBean { @EJB EjbDataverseEngine commandEngine; - + @EJB IndexServiceBean indexService; @EJB S3PackageImporter s3PackageImporter; - + @EJB SettingsServiceBean settingsService; // TODO: Move to AbstractApiBean @EJB DatasetMetricsServiceBean datasetMetricsSvc; - + @EJB DatasetExternalCitationsServiceBean datasetExternalCitationsService; - + @Inject MakeDataCountLoggingServiceBean mdcLogService; - + @Inject DataverseRequestServiceBean dvRequestService; - + @Inject WorkflowServiceBean wfService; - + @Inject DataverseRoleServiceBean dataverseRoleService; /** * Used to consolidate the way we parse and handle dataset versions. - * - * @param + * @param */ public interface DsVersionHandler { T handleLatest(); - T handleDraft(); - - T handleSpecific(long major, long minor); - + T handleSpecific( long major, long minor ); T handleLatestPublished(); } - + @GET @Path("{id}") public Response getDataset(@PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { - return response(req -> { + return response( req -> { final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id))); final DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(req, retrieved)); final JsonObjectBuilder jsonbuilder = json(retrieved); - // Report MDC if this is a released version (could be draft if user has access, - // or user may not have access at all and is not getting metadata beyond the - // minimum) - if ((latest != null) && latest.isReleased()) { + //Report MDC if this is a released version (could be draft if user has access, or user may not have access at all and is not getting metadata beyond the minimum) + if((latest != null) && latest.isReleased()) { MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, retrieved); mdcLogService.logEntry(entry); } return ok(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null)); }); } - - // TODO: - // This API call should, ideally, call findUserOrDie() and the GetDatasetCommand + + // TODO: + // This API call should, ideally, call findUserOrDie() and the GetDatasetCommand // to obtain the dataset that we are trying to export - which would handle - // Auth in the process... For now, Auth isn't necessary - since export ONLY + // Auth in the process... For now, Auth isn't necessary - since export ONLY // WORKS on published datasets, which are open to the world. -- L.A. 4.5 - + @GET @Path("/export") - @Produces({ "application/xml", "application/json", "application/html" }) + @Produces({"application/xml", "application/json", "application/html" }) public Response exportDataset(@QueryParam("persistentId") String persistentId, @QueryParam("exporter") String exporter, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { try { @@ -296,20 +289,20 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ if (dataset == null) { return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found."); } - + ExportService instance = ExportService.getInstance(); - + InputStream is = instance.getExport(dataset, exporter); - + String mediaType = instance.getMediaType(exporter); - // Export is only possible for released (non-draft) dataset versions so we can - // log without checking to see if this is a request for a draft + //Export is only possible for released (non-draft) dataset versions so we can log without checking to see if this is a request for a draft MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, dataset); mdcLogService.logEntry(entry); - + return Response.ok() .entity(is) - .type(mediaType).build(); + .type(mediaType). + build(); } catch (Exception wr) { return error(Response.Status.FORBIDDEN, "Export Failed"); } @@ -317,25 +310,23 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @ @DELETE @Path("{id}") - public Response deleteDataset(@PathParam("id") String id) { - // Internally, "DeleteDatasetCommand" simply redirects to - // "DeleteDatasetVersionCommand" + public Response deleteDataset( @PathParam("id") String id) { + // Internally, "DeleteDatasetCommand" simply redirects to "DeleteDatasetVersionCommand" // (and there's a comment that says "TODO: remove this command") - // do we need an exposed API call for it? - // And DeleteDatasetVersionCommand further redirects to DestroyDatasetCommand, - // if the dataset only has 1 version... In other words, the functionality - // currently provided by this API is covered between the "deleteDraftVersion" - // and - // "destroyDataset" API calls. - // (The logic below follows the current implementation of the underlying + // do we need an exposed API call for it? + // And DeleteDatasetVersionCommand further redirects to DestroyDatasetCommand, + // if the dataset only has 1 version... In other words, the functionality + // currently provided by this API is covered between the "deleteDraftVersion" and + // "destroyDataset" API calls. + // (The logic below follows the current implementation of the underlying // commands!) - - return response(req -> { + + return response( req -> { Dataset doomed = findDatasetOrDie(id); DatasetVersion doomedVersion = doomed.getLatestVersion(); User u = findUserOrDie(); boolean destroy = false; - + if (doomed.getVersions().size() == 1) { if (doomed.isReleased() && (!(u instanceof AuthenticatedUser) || !u.isSuperuser())) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Only superusers can delete published datasets")); @@ -346,26 +337,26 @@ public Response deleteDataset(@PathParam("id") String id) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is a published dataset with multiple versions. This API can only delete the latest version if it is a DRAFT")); } } - - // Gather the locations of the physical files that will need to be + + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomedVersion, destroy); - - execCommand(new DeleteDatasetCommand(req, findDatasetOrDie(id))); - - // If we have gotten this far, the destroy command has succeeded, + + execCommand( new DeleteDatasetCommand(req, findDatasetOrDie(id))); + + // If we have gotten this far, the destroy command has succeeded, // so we can finalize it by permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); } - + return ok("Dataset " + id + " deleted"); }); } - + @DELETE @Path("{id}/destroy") public Response destroyDataset(@PathParam("id") String id) { @@ -379,16 +370,16 @@ public Response destroyDataset(@PathParam("id") String id) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Destroy can only be called by superusers.")); } - // Gather the locations of the physical files that will need to be + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed); execCommand(new DestroyDatasetCommand(doomed, req)); - // If we have gotten this far, the destroy command has succeeded, + // If we have gotten this far, the destroy command has succeeded, // so we can finalize permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); @@ -397,59 +388,59 @@ public Response destroyDataset(@PathParam("id") String id) { return ok("Dataset " + id + " destroyed"); }); } - + @DELETE @Path("{id}/versions/{versionId}") - public Response deleteDraftVersion(@PathParam("id") String id, @PathParam("versionId") String versionId) { - if (!":draft".equals(versionId)) { + public Response deleteDraftVersion( @PathParam("id") String id, @PathParam("versionId") String versionId ){ + if ( ! ":draft".equals(versionId) ) { return badRequest("Only the :draft version can be deleted"); } - return response(req -> { + return response( req -> { Dataset dataset = findDatasetOrDie(id); DatasetVersion doomed = dataset.getLatestVersion(); - + if (!doomed.isDraft()) { throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is NOT a DRAFT version")); } - - // Gather the locations of the physical files that will need to be + + // Gather the locations of the physical files that will need to be // deleted once the destroy command execution has been finalized: - + Map deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed); - - execCommand(new DeleteDatasetVersionCommand(req, dataset)); - - // If we have gotten this far, the delete command has succeeded - - // by either deleting the Draft version of a published dataset, - // or destroying an unpublished one. + + execCommand( new DeleteDatasetVersionCommand(req, dataset)); + + // If we have gotten this far, the delete command has succeeded - + // by either deleting the Draft version of a published dataset, + // or destroying an unpublished one. // This means we can finalize permanently deleting the physical files: - // (DataFileService will double-check that the datafiles no - // longer exist in the database, before attempting to delete + // (DataFileService will double-check that the datafiles no + // longer exist in the database, before attempting to delete // the physical files) if (!deleteStorageLocations.isEmpty()) { fileService.finalizeFileDeletes(deleteStorageLocations); } - + return ok("Draft version of dataset " + id + " deleted"); }); } - + @DELETE @Path("{datasetId}/deleteLink/{linkedDataverseId}") - public Response deleteDatasetLinkingDataverse(@PathParam("datasetId") String datasetId, @PathParam("linkedDataverseId") String linkedDataverseId) { - boolean index = true; + public Response deleteDatasetLinkingDataverse( @PathParam("datasetId") String datasetId, @PathParam("linkedDataverseId") String linkedDataverseId) { + boolean index = true; return response(req -> { execCommand(new DeleteDatasetLinkingDataverseCommand(req, findDatasetOrDie(datasetId), findDatasetLinkingDataverseOrDie(datasetId, linkedDataverseId), index)); return ok("Link from Dataset " + datasetId + " to linked Dataverse " + linkedDataverseId + " deleted"); }); } - + @PUT @Path("{id}/citationdate") - public Response setCitationDate(@PathParam("id") String id, String dsfTypeName) { - return response(req -> { - if (dsfTypeName.trim().isEmpty()) { + public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) { + return response( req -> { + if ( dsfTypeName.trim().isEmpty() ){ return badRequest("Please provide a dataset field type in the requst body."); } DatasetFieldType dsfType = null; @@ -463,121 +454,124 @@ public Response setCitationDate(@PathParam("id") String id, String dsfTypeName) execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), dsfType)); return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default")); }); - } - + } + @DELETE @Path("{id}/citationdate") - public Response useDefaultCitationDate(@PathParam("id") String id) { - return response(req -> { + public Response useDefaultCitationDate( @PathParam("id") String id) { + return response( req -> { execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), null)); return ok("Citation Date for dataset " + id + " set to default"); }); - } - + } + @GET @Path("{id}/versions") - public Response listVersions(@PathParam("id") String id) { - return response(req -> ok(execCommand(new ListVersionsCommand(req, findDatasetOrDie(id))) - .stream() - .map(d -> json(d)) - .collect(toJsonArray()))); - } - + public Response listVersions( @PathParam("id") String id ) { + return response( req -> + ok( execCommand( new ListVersionsCommand(req, findDatasetOrDie(id)) ) + .stream() + .map( d -> json(d) ) + .collect(toJsonArray()))); + } + @GET @Path("{id}/versions/{versionId}") - public Response getVersion(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response(req -> { - DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); + public Response getVersion( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response( req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found") - : ok(json(dsv)); + : ok(json(dsv)); }); } - + @GET @Path("{id}/versions/{versionId}/files") - public Response getVersionFiles(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response(req -> ok(jsonFileMetadatas( - getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas()))); + public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response( req -> ok( jsonFileMetadatas( + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas()))); } - + @GET @Path("{id}/dirindex") @Produces("text/html") public Response getFileAccessFolderView(@PathParam("id") String datasetId, @QueryParam("version") String versionId, @QueryParam("folder") String folderName, @QueryParam("original") Boolean originals, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) { folderName = folderName == null ? "" : folderName; - versionId = versionId == null ? ":latest-published" : versionId; - - DatasetVersion version; + versionId = versionId == null ? ":latest-published" : versionId; + + DatasetVersion version; try { DataverseRequest req = createDataverseRequest(findUserOrDie()); version = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers); } catch (WrappedResponse wr) { return wr.getResponse(); } - + String output = FileUtil.formatFolderListingHtml(folderName, version, "", originals != null && originals); - + // return "NOT FOUND" if there is no such folder in the dataset version: - + if ("".equals(output)) { return notFound("Folder " + folderName + " does not exist"); } - + + String indexFileName = folderName.equals("") ? ".index.html" : ".index-" + folderName.replace('/', '_') + ".html"; response.setHeader("Content-disposition", "filename=\"" + indexFileName + "\""); + return Response.ok() .entity(output) - // .type("application/html"). + //.type("application/html"). .build(); } - + @GET @Path("{id}/versions/{versionId}/metadata") - public Response getVersionMetadata(@PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { - return response(req -> ok( - jsonByBlocks( - getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers) + public Response getVersionMetadata( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) { + return response( req -> ok( + jsonByBlocks( + getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers ) .getDatasetFields()))); } - + @GET @Path("{id}/versions/{versionNumber}/metadata/{block}") - public Response getVersionMetadataBlock(@PathParam("id") String datasetId, - @PathParam("versionNumber") String versionNumber, - @PathParam("block") String blockName, - @Context UriInfo uriInfo, - @Context HttpHeaders headers) { - - return response(req -> { - DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo, headers); - + public Response getVersionMetadataBlock( @PathParam("id") String datasetId, + @PathParam("versionNumber") String versionNumber, + @PathParam("block") String blockName, + @Context UriInfo uriInfo, + @Context HttpHeaders headers ) { + + return response( req -> { + DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo, headers ); + Map> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields()); - for (Map.Entry> p : fieldsByBlock.entrySet()) { - if (p.getKey().getName().equals(blockName)) { + for ( Map.Entry> p : fieldsByBlock.entrySet() ) { + if ( p.getKey().getName().equals(blockName) ) { return ok(json(p.getKey(), p.getValue())); } } return notFound("metadata block named " + blockName + " not found"); }); } - + @GET @Path("{id}/modifyRegistration") - public Response updateDatasetTargetURL(@PathParam("id") String id) { - return response(req -> { + public Response updateDatasetTargetURL(@PathParam("id") String id ) { + return response( req -> { execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), req)); return ok("Dataset " + id + " target url updated"); }); } - + @POST @Path("/modifyRegistrationAll") public Response updateDatasetTargetURLAll() { - return response(req -> { - datasetService.findAll().forEach(ds -> { + return response( req -> { + datasetService.findAll().forEach( ds -> { try { execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(ds.getId().toString()), req)); } catch (WrappedResponse ex) { @@ -587,7 +581,7 @@ public Response updateDatasetTargetURLAll() { return ok("Update All Dataset target url completed"); }); } - + @POST @Path("{id}/modifyRegistrationMetadata") public Response updateDatasetPIDMetadata(@PathParam("id") String id) { @@ -607,37 +601,37 @@ public Response updateDatasetPIDMetadata(@PathParam("id") String id) { return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.single.dataset", args)); }); } - + @GET @Path("/modifyRegistrationPIDMetadataAll") public Response updateDatasetPIDMetadataAll() { - return response(req -> { - datasetService.findAll().forEach(ds -> { + return response( req -> { + datasetService.findAll().forEach( ds -> { try { execCommand(new UpdateDvObjectPIDMetadataCommand(findDatasetOrDie(ds.getId().toString()), req)); } catch (WrappedResponse ex) { Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex); } - }); + }); return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.update.all")); }); } - + @PUT @Path("{id}/versions/{versionId}") @Consumes(MediaType.APPLICATION_JSON) - public Response updateDraftVersion(String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId) { - - if (!":draft".equals(versionId)) { - return error(Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); + public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId ){ + + if ( ! ":draft".equals(versionId) ) { + return error( Response.Status.BAD_REQUEST, "Only the :draft version can be updated"); } - - try (StringReader rdr = new StringReader(jsonBody)) { + + try ( StringReader rdr = new StringReader(jsonBody) ) { DataverseRequest req = createDataverseRequest(findUserOrDie()); Dataset ds = findDatasetOrDie(id); JsonObject json = Json.createReader(rdr).readObject(); DatasetVersion incomingVersion = jsonParser().parseDatasetVersion(json); - + // clear possibly stale fields from the incoming dataset version. // creation and modification dates are updated by the commands. incomingVersion.setId(null); @@ -647,38 +641,38 @@ public Response updateDraftVersion(String jsonBody, @PathParam("id") String id, incomingVersion.setDataset(ds); incomingVersion.setCreateTime(null); incomingVersion.setLastUpdateTime(null); - - if (!incomingVersion.getFileMetadatas().isEmpty()) { - return error(Response.Status.BAD_REQUEST, "You may not add files via this api."); + + if (!incomingVersion.getFileMetadatas().isEmpty()){ + return error( Response.Status.BAD_REQUEST, "You may not add files via this api."); } - + boolean updateDraft = ds.getLatestVersion().isDraft(); - + DatasetVersion managedVersion; - if (updateDraft) { + if ( updateDraft ) { final DatasetVersion editVersion = ds.getEditVersion(); editVersion.setDatasetFields(incomingVersion.getDatasetFields()); - editVersion.setTermsOfUseAndAccess(incomingVersion.getTermsOfUseAndAccess()); + editVersion.setTermsOfUseAndAccess( incomingVersion.getTermsOfUseAndAccess() ); Dataset managedDataset = execCommand(new UpdateDatasetVersionCommand(ds, req)); managedVersion = managedDataset.getEditVersion(); } else { managedVersion = execCommand(new CreateDatasetVersionCommand(req, ds, incomingVersion)); } - // DatasetVersion managedVersion = execCommand( updateDraft - // ? new UpdateDatasetVersionCommand(req, incomingVersion) - // : new CreateDatasetVersionCommand(req, ds, incomingVersion)); - return ok(json(managedVersion)); - +// DatasetVersion managedVersion = execCommand( updateDraft +// ? new UpdateDatasetVersionCommand(req, incomingVersion) +// : new CreateDatasetVersionCommand(req, ds, incomingVersion)); + return ok( json(managedVersion) ); + } catch (JsonParseException ex) { logger.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex); - return error(Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage()); - + return error( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() ); + } catch (WrappedResponse ex) { return ex.getResponse(); - + } } - + @GET @Path("{id}/versions/{versionId}/metadata") @Produces("application/ld+json, application/json-ld") @@ -706,7 +700,7 @@ public Response getVersionJsonLDMetadata(@PathParam("id") String id, @PathParam( public Response getVersionJsonLDMetadata(@PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers) { return getVersionJsonLDMetadata(id, ":draft", uriInfo, headers); } - + @PUT @Path("{id}/metadata") @Consumes("application/ld+json, application/json-ld") @@ -718,7 +712,7 @@ public Response updateVersionMetadata(String jsonLDBody, @PathParam("id") String DatasetVersion dsv = ds.getEditVersion(); boolean updateDraft = ds.getLatestVersion().isDraft(); dsv = JSONLDUtil.updateDatasetVersionMDFromJsonLD(dsv, jsonLDBody, metadataBlockService, datasetFieldSvc, !replaceTerms, false); - + DatasetVersion managedVersion; if (updateDraft) { Dataset managedDataset = execCommand(new UpdateDatasetVersionCommand(ds, req)); @@ -736,7 +730,7 @@ public Response updateVersionMetadata(String jsonLDBody, @PathParam("id") String return error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage()); } } - + @PUT @Path("{id}/metadata/delete") @Consumes("application/ld+json, application/json-ld") @@ -766,7 +760,7 @@ public Response deleteMetadata(String jsonLDBody, @PathParam("id") String id) { return error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage()); } } - + @PUT @Path("{id}/deleteMetadata") public Response deleteVersionMetadata(String jsonBody, @PathParam("id") String id) throws WrappedResponse { @@ -804,7 +798,7 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav boolean found = false; for (DatasetField dsf : dsv.getDatasetFields()) { if (dsf.getDatasetFieldType().equals(updateField.getDatasetFieldType())) { - if (dsf.getDatasetFieldType().isAllowMultiples()) { + if (dsf.getDatasetFieldType().isAllowMultiples()) { if (updateField.getDatasetFieldType().isControlledVocabulary()) { if (dsf.getDatasetFieldType().isAllowMultiples()) { for (ControlledVocabularyValue cvv : updateField.getControlledVocabularyValues()) { @@ -869,7 +863,7 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav datasetFieldCompoundValueItemsToRemove.forEach((remove) -> { dsf.getDatasetFieldCompoundValues().remove(remove); }); - if (!found) { + if (!found) { logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found."); return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found."); } @@ -884,15 +878,17 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav break; } } - if (!found) { + if (!found){ String displayValue = !updateField.getDisplayValue().isEmpty() ? updateField.getDisplayValue() : updateField.getCompoundDisplayValue(); - logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found."); - return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found."); + logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." ); + return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." ); } - } + } + + boolean updateDraft = ds.getLatestVersion().isDraft(); - DatasetVersion managedVersion = updateDraft + DatasetVersion managedVersion = updateDraft ? execCommand(new UpdateDatasetVersionCommand(ds, req)).getEditVersion() : execCommand(new CreateDatasetVersionCommand(req, ds, dsv)); return ok(json(managedVersion)); @@ -906,21 +902,21 @@ private Response processDatasetFieldDataDelete(String jsonBody, String id, Datav return ex.getResponse(); } - + } - - private String getCompoundDisplayValue(DatasetFieldCompoundValue dscv) { + + private String getCompoundDisplayValue (DatasetFieldCompoundValue dscv){ String returnString = ""; - for (DatasetField dsf : dscv.getChildDatasetFields()) { - for (String value : dsf.getValues()) { - if (!(value == null)) { - returnString += (returnString.isEmpty() ? "" : "; ") + value.trim(); + for (DatasetField dsf : dscv.getChildDatasetFields()) { + for (String value : dsf.getValues()) { + if (!(value == null)) { + returnString += (returnString.isEmpty() ? "" : "; ") + value.trim(); + } } } - } return returnString; } - + @PUT @Path("{id}/editMetadata") public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, @QueryParam("replace") Boolean replace) { @@ -928,7 +924,7 @@ public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, Boolean replaceData = replace != null; DataverseRequest req = null; try { - req = createDataverseRequest(findUserOrDie()); + req = createDataverseRequest(findUserOrDie()); } catch (WrappedResponse ex) { logger.log(Level.SEVERE, "Edit metdata error: " + ex.getMessage(), ex); return ex.getResponse(); @@ -936,24 +932,26 @@ public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, return processDatasetUpdate(jsonBody, id, req, replaceData); } - - private Response processDatasetUpdate(String jsonBody, String id, DataverseRequest req, Boolean replaceData) { + + + private Response processDatasetUpdate(String jsonBody, String id, DataverseRequest req, Boolean replaceData){ try (StringReader rdr = new StringReader(jsonBody)) { - + Dataset ds = findDatasetOrDie(id); JsonObject json = Json.createReader(rdr).readObject(); DatasetVersion dsv = ds.getEditVersion(); - + List fields = new LinkedList<>(); - DatasetField singleField = null; - + DatasetField singleField = null; + JsonArray fieldsJson = json.getJsonArray("fields"); - if (fieldsJson == null) { - singleField = jsonParser().parseField(json, Boolean.FALSE); + if( fieldsJson == null ){ + singleField = jsonParser().parseField(json, Boolean.FALSE); fields.add(singleField); - } else { + } else{ fields = jsonParser().parseMultipleFields(json); } + String valdationErrors = validateDatasetFieldValues(fields); @@ -964,10 +962,10 @@ private Response processDatasetUpdate(String jsonBody, String id, DataverseReque dsv.setVersionState(DatasetVersion.VersionState.DRAFT); - // loop through the update fields - // and compare to the version fields - // if exist add/replace values - // if not add entire dsf + //loop through the update fields + // and compare to the version fields + //if exist add/replace values + //if not add entire dsf for (DatasetField updateField : fields) { boolean found = false; for (DatasetField dsf : dsv.getDatasetFields()) { @@ -1063,7 +1061,7 @@ private Response processDatasetUpdate(String jsonBody, String id, DataverseReque } } - + private String validateDatasetFieldValues(List fields) { StringBuilder error = new StringBuilder(); @@ -1081,15 +1079,14 @@ private String validateDatasetFieldValues(List fields) { } return ""; } - + /** - * @deprecated This was shipped as a GET but should have been a POST, see - * https://github.com/IQSS/dataverse/issues/2431 + * @deprecated This was shipped as a GET but should have been a POST, see https://github.com/IQSS/dataverse/issues/2431 */ @GET @Path("{id}/actions/:publish") @Deprecated - public Response publishDataseUsingGetDeprecated(@PathParam("id") String id, @QueryParam("type") String type) { + public Response publishDataseUsingGetDeprecated( @PathParam("id") String id, @QueryParam("type") String type ) { logger.info("publishDataseUsingGetDeprecated called on id " + id + ". Encourage use of POST rather than GET, which is deprecated."); return publishDataset(id, type, false); } @@ -1101,25 +1098,25 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S if (type == null) { return error(Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major','minor', or 'updatecurrent')."); } - boolean updateCurrent = false; + boolean updateCurrent=false; AuthenticatedUser user = findAuthenticatedUserOrDie(); type = type.toLowerCase(); - boolean isMinor = false; + boolean isMinor=false; switch (type) { - case "minor": - isMinor = true; - break; - case "major": - isMinor = false; - break; + case "minor": + isMinor = true; + break; + case "major": + isMinor = false; + break; case "updatecurrent": - if (user.isSuperuser()) { - updateCurrent = true; + if(user.isSuperuser()) { + updateCurrent=true; } else { - return error(Response.Status.FORBIDDEN, "Only superusers can update the current version"); + return error(Response.Status.FORBIDDEN, "Only superusers can update the current version"); } break; - default: + default: return error(Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major', 'minor', or 'updatecurrent'."); } @@ -1142,8 +1139,8 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S * error is returned. * */ - if ((ds.getModificationTime() != null && (ds.getIndexTime() == null || (ds.getIndexTime().compareTo(ds.getModificationTime()) <= 0))) || - (ds.getPermissionModificationTime() != null && (ds.getPermissionIndexTime() == null || (ds.getPermissionIndexTime().compareTo(ds.getPermissionModificationTime()) <= 0)))) { + if ((ds.getModificationTime()!=null && (ds.getIndexTime() == null || (ds.getIndexTime().compareTo(ds.getModificationTime()) <= 0))) || + (ds.getPermissionModificationTime()!=null && (ds.getPermissionIndexTime() == null || (ds.getPermissionIndexTime().compareTo(ds.getPermissionModificationTime()) <= 0)))) { return error(Response.Status.CONFLICT, "Dataset is awaiting indexing"); } } @@ -1204,20 +1201,20 @@ public Response publishDataset(@PathParam("id") String id, @QueryParam("type") S .build(); } } else { - PublishDatasetResult res = execCommand(new PublishDatasetCommand(ds, + PublishDatasetResult res = execCommand(new PublishDatasetCommand(ds, createDataverseRequest(user), - isMinor)); - return res.isWorkflow() ? accepted(json(res.getDataset())) : ok(json(res.getDataset())); + isMinor)); + return res.isWorkflow() ? accepted(json(res.getDataset())) : ok(json(res.getDataset())); } } catch (WrappedResponse ex) { return ex.getResponse(); } } - + @POST @Path("{id}/actions/:releasemigrated") @Consumes("application/ld+json, application/json-ld") - public Response publishMigratedDataset(String jsonldBody, @PathParam("id") String id, @DefaultValue("false") @QueryParam("updatepidatprovider") boolean contactPIDProvider) { + public Response publishMigratedDataset(String jsonldBody, @PathParam("id") String id, @DefaultValue("false") @QueryParam ("updatepidatprovider") boolean contactPIDProvider) { try { AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { @@ -1230,10 +1227,10 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin String pubDate = metadata.getString(JsonLDTerm.schemaOrg("datePublished").getUrl()); logger.fine("Submitted date: " + pubDate); LocalDateTime dateTime = null; - if (!StringUtils.isEmpty(pubDate)) { + if(!StringUtils.isEmpty(pubDate)) { dateTime = JSONLDUtil.getDateTimeFrom(pubDate); final Timestamp time = Timestamp.valueOf(dateTime); - // Set version release date + //Set version release date ds.getLatestVersion().setReleaseTime(new Date(time.getTime())); } // dataset.getPublicationDateFormattedYYYYMMDD()) @@ -1253,10 +1250,10 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin ds.getLatestVersion().setMinorVersionNumber(Long.valueOf(0)); } } - if (ds.getLatestVersion().getVersionNumber() == 1 && ds.getLatestVersion().getMinorVersionNumber() == 0) { - // Also set publication date if this is the first - if (dateTime != null) { - ds.setPublicationDate(Timestamp.valueOf(dateTime)); + if(ds.getLatestVersion().getVersionNumber()==1 && ds.getLatestVersion().getMinorVersionNumber()==0) { + //Also set publication date if this is the first + if(dateTime != null) { + ds.setPublicationDate(Timestamp.valueOf(dateTime)); } // Release User is only set in FinalizeDatasetPublicationCommand if the pub date // is null, so set it here. @@ -1292,7 +1289,7 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin errorMsg = BundleUtil.getStringFromBundle("datasetversion.update.failure") + " - " + ex.toString(); logger.severe(ex.getMessage()); } - + if (errorMsg != null) { return error(Response.Status.INTERNAL_SERVER_ERROR, errorMsg); } else { @@ -1303,20 +1300,21 @@ public Response publishMigratedDataset(String jsonldBody, @PathParam("id") Strin return ex.getResponse(); } } - + @POST @Path("{id}/move/{targetDataverseAlias}") public Response moveDataset(@PathParam("id") String id, @PathParam("targetDataverseAlias") String targetDataverseAlias, @QueryParam("forceMove") Boolean force) { try { - User u = findUserOrDie(); + User u = findUserOrDie(); Dataset ds = findDatasetOrDie(id); Dataverse target = dataverseService.findByAlias(targetDataverseAlias); if (target == null) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("datasets.api.moveDataset.error.targetDataverseNotFound")); } - // Command requires Super user - it will be tested by the command + //Command requires Super user - it will be tested by the command execCommand(new MoveDatasetCommand( - createDataverseRequest(u), ds, target, force)); + createDataverseRequest(u), ds, target, force + )); return ok(BundleUtil.getStringFromBundle("datasets.api.moveDataset.success")); } catch (WrappedResponse ex) { if (ex.getCause() instanceof UnforcedCommandException) { @@ -1326,31 +1324,32 @@ public Response moveDataset(@PathParam("id") String id, @PathParam("targetDatave } } } - + @PUT - @Path("{linkedDatasetId}/link/{linkingDataverseAlias}") - public Response linkDataset(@PathParam("linkedDatasetId") String linkedDatasetId, @PathParam("linkingDataverseAlias") String linkingDataverseAlias) { - try { - User u = findUserOrDie(); + @Path("{linkedDatasetId}/link/{linkingDataverseAlias}") + public Response linkDataset(@PathParam("linkedDatasetId") String linkedDatasetId, @PathParam("linkingDataverseAlias") String linkingDataverseAlias) { + try{ + User u = findUserOrDie(); Dataset linked = findDatasetOrDie(linkedDatasetId); Dataverse linking = findDataverseOrDie(linkingDataverseAlias); - if (linked == null) { + if (linked == null){ return error(Response.Status.BAD_REQUEST, "Linked Dataset not found."); - } - if (linking == null) { + } + if (linking == null){ return error(Response.Status.BAD_REQUEST, "Linking Dataverse not found."); - } + } execCommand(new LinkDatasetCommand( - createDataverseRequest(u), linking, linked)); + createDataverseRequest(u), linking, linked + )); return ok("Dataset " + linked.getId() + " linked successfully to " + linking.getAlias()); } catch (WrappedResponse ex) { return ex.getResponse(); } } - + @GET @Path("{id}/links") - public Response getLinks(@PathParam("id") String idSupplied) { + public Response getLinks(@PathParam("id") String idSupplied ) { try { User u = findUserOrDie(); if (!u.isSuperuser()) { @@ -1374,11 +1373,8 @@ public Response getLinks(@PathParam("id") String idSupplied) { /** * Add a given assignment to a given user or group - * - * @param ra - * role assignment DTO - * @param id - * dataset id + * @param ra role assignment DTO + * @param id dataset id * @param apiKey */ @POST @@ -1386,12 +1382,12 @@ public Response getLinks(@PathParam("id") String idSupplied) { public Response createAssignment(RoleAssignmentDTO ra, @PathParam("identifier") String id, @QueryParam("key") String apiKey) { try { Dataset dataset = findDatasetOrDie(id); - + RoleAssignee assignee = findAssignee(ra.getAssignee()); if (assignee == null) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("datasets.api.grant.role.assignee.not.found.error")); - } - + } + DataverseRole theRole; Dataverse dv = dataset.getOwner(); theRole = null; @@ -1419,7 +1415,7 @@ public Response createAssignment(RoleAssignmentDTO ra, @PathParam("identifier") } } - + @DELETE @Path("{identifier}/assignments/{id}") public Response deleteAssignment(@PathParam("id") long assignmentId, @PathParam("identifier") String dsId) { @@ -1442,35 +1438,37 @@ public Response deleteAssignment(@PathParam("id") long assignmentId, @PathParam( @GET @Path("{identifier}/assignments") public Response getAssignments(@PathParam("identifier") String id) { - return response(req -> ok(execCommand( - new ListRoleAssignments(req, findDatasetOrDie(id))) - .stream().map(ra -> json(ra)).collect(toJsonArray()))); + return response( req -> + ok( execCommand( + new ListRoleAssignments(req, findDatasetOrDie(id))) + .stream().map(ra->json(ra)).collect(toJsonArray())) ); } @GET @Path("{id}/privateUrl") public Response getPrivateUrlData(@PathParam("id") String idSupplied) { - return response(req -> { + return response( req -> { PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, findDatasetOrDie(idSupplied))); - return (privateUrl != null) ? ok(json(privateUrl)) - : error(Response.Status.NOT_FOUND, "Private URL not found."); + return (privateUrl != null) ? ok(json(privateUrl)) + : error(Response.Status.NOT_FOUND, "Private URL not found."); }); } @POST @Path("{id}/privateUrl") - public Response createPrivateUrl(@PathParam("id") String idSupplied, @DefaultValue("false") @QueryParam("anonymizedAccess") boolean anonymizedAccess) { - if (anonymizedAccess && settingsSvc.getValueForKey(SettingsServiceBean.Key.AnonymizedFieldTypeNames) == null) { + public Response createPrivateUrl(@PathParam("id") String idSupplied,@DefaultValue("false") @QueryParam ("anonymizedAccess") boolean anonymizedAccess) { + if(anonymizedAccess && settingsSvc.getValueForKey(SettingsServiceBean.Key.AnonymizedFieldTypeNames)==null) { throw new NotAcceptableException("Anonymized Access not enabled"); } - return response(req -> ok(json(execCommand( + return response( req -> + ok(json(execCommand( new CreatePrivateUrlCommand(req, findDatasetOrDie(idSupplied), anonymizedAccess))))); } @DELETE @Path("{id}/privateUrl") public Response deletePrivateUrl(@PathParam("id") String idSupplied) { - return response(req -> { + return response( req -> { Dataset dataset = findDatasetOrDie(idSupplied); PrivateUrl privateUrl = execCommand(new GetPrivateUrlCommand(req, dataset)); if (privateUrl != null) { @@ -1518,13 +1516,13 @@ public Response getDatasetThumbnailCandidates(@PathParam("id") String idSupplied } @GET - @Produces({ "image/png" }) + @Produces({"image/png"}) @Path("{id}/thumbnail") public Response getDatasetThumbnail(@PathParam("id") String idSupplied) { try { Dataset dataset = findDatasetOrDie(idSupplied); InputStream is = DatasetUtil.getThumbnailAsInputStream(dataset, ImageThumbConverter.DEFAULT_CARDIMAGE_SIZE); - if (is == null) { + if(is == null) { return notFound("Thumbnail not available"); } return Response.ok(is).build(); @@ -1533,8 +1531,7 @@ public Response getDatasetThumbnail(@PathParam("id") String idSupplied) { } } - // TODO: Rather than only supporting looking up files by their database IDs - // (dataFileIdSupplied), consider supporting persistent identifiers. + // TODO: Rather than only supporting looking up files by their database IDs (dataFileIdSupplied), consider supporting persistent identifiers. @POST @Path("{id}/thumbnail/{dataFileId}") public Response setDataFileAsThumbnail(@PathParam("id") String idSupplied, @PathParam("dataFileId") long dataFileIdSupplied) { @@ -1549,7 +1546,8 @@ public Response setDataFileAsThumbnail(@PathParam("id") String idSupplied, @Path @POST @Path("{id}/thumbnail") @Consumes(MediaType.MULTIPART_FORM_DATA) - public Response uploadDatasetLogo(@PathParam("id") String idSupplied, @FormDataParam("file") InputStream inputStream) { + public Response uploadDatasetLogo(@PathParam("id") String idSupplied, @FormDataParam("file") InputStream inputStream + ) { try { DatasetThumbnail datasetThumbnail = execCommand(new UpdateDatasetThumbnailCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), UpdateDatasetThumbnailCommand.UserIntent.setNonDatasetFileAsThumbnail, null, inputStream)); return ok("Thumbnail is now " + datasetThumbnail.getBase64image()); @@ -1572,8 +1570,7 @@ public Response removeDatasetLogo(@PathParam("id") String idSupplied) { @GET @Path("{identifier}/dataCaptureModule/rsync") public Response getRsync(@PathParam("identifier") String id) { - // TODO - does it make sense to switch this to dataset identifier for - // consistency with the rest of the DCM APIs? + //TODO - does it make sense to switch this to dataset identifier for consistency with the rest of the DCM APIs? if (!DataCaptureModuleUtil.rsyncSupportEnabled(settingsSvc.getValueForKey(SettingsServiceBean.Key.UploadMethods))) { return error(Response.Status.METHOD_NOT_ALLOWED, SettingsServiceBean.Key.UploadMethods + " does not contain " + SystemConfig.FileUploadMethods.RSYNC + "."); } @@ -1582,11 +1579,11 @@ public Response getRsync(@PathParam("identifier") String id) { dataset = findDatasetOrDie(id); AuthenticatedUser user = findAuthenticatedUserOrDie(); ScriptRequestResponse scriptRequestResponse = execCommand(new RequestRsyncScriptCommand(createDataverseRequest(user), dataset)); - + DatasetLock lock = datasetService.addDatasetLock(dataset.getId(), DatasetLock.Reason.DcmUpload, user.getId(), "script downloaded"); if (lock == null) { logger.log(Level.WARNING, "Failed to lock the dataset (dataset id={0})", dataset.getId()); - return error(Response.Status.FORBIDDEN, "Failed to lock the dataset (dataset id=" + dataset.getId() + ")"); + return error(Response.Status.FORBIDDEN, "Failed to lock the dataset (dataset id="+dataset.getId()+")"); } return ok(scriptRequestResponse.getScript(), MediaType.valueOf(MediaType.TEXT_PLAIN), null); } catch (WrappedResponse wr) { @@ -1595,23 +1592,19 @@ public Response getRsync(@PathParam("identifier") String id) { return error(Response.Status.INTERNAL_SERVER_ERROR, "Something went wrong attempting to download rsync script: " + EjbUtil.ejbExceptionToString(ex)); } } - + /** - * This api endpoint triggers the creation of a "package" file in a dataset - * after that package has been moved onto the same filesystem via the Data - * Capture Module. The package is really just a way that Dataverse interprets a - * folder created by DCM, seeing it as just one file. The "package" can be - * downloaded over RSAL. + * This api endpoint triggers the creation of a "package" file in a dataset + * after that package has been moved onto the same filesystem via the Data Capture Module. + * The package is really just a way that Dataverse interprets a folder created by DCM, seeing it as just one file. + * The "package" can be downloaded over RSAL. * - * This endpoint currently supports both posix file storage and AWS s3 storage - * in Dataverse, and depending on which one is active acts accordingly. + * This endpoint currently supports both posix file storage and AWS s3 storage in Dataverse, and depending on which one is active acts accordingly. * - * The initial design of the DCM/Dataverse interaction was not to use packages, - * but to allow import of all individual files natively into Dataverse. But due - * to the possibly immense number of files (millions) the package approach was - * taken. This is relevant because the posix ("file") code contains many - * remnants of that development work. The s3 code was written later and is set - * to only support import as packages. It takes a lot from FileRecordWriter. + * The initial design of the DCM/Dataverse interaction was not to use packages, but to allow import of all individual files natively into Dataverse. + * But due to the possibly immense number of files (millions) the package approach was taken. + * This is relevant because the posix ("file") code contains many remnants of that development work. + * The s3 code was written later and is set to only support import as packages. It takes a lot from FileRecordWriter. * -MAD 4.9.1 */ @POST @@ -1631,13 +1624,13 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String try { Dataset dataset = findDatasetOrDie(id); if ("validation passed".equals(statusMessageFromDcm)) { - logger.log(Level.INFO, "Checksum Validation passed for DCM."); + logger.log(Level.INFO, "Checksum Validation passed for DCM."); String storageDriver = dataset.getDataverseContext().getEffectiveStorageDriverId(); String uploadFolder = jsonFromDcm.getString("uploadFolder"); int totalSize = jsonFromDcm.getInt("totalSize"); String storageDriverType = System.getProperty("dataverse.file." + storageDriver + ".type"); - + if (storageDriverType.equals("file")) { logger.log(Level.INFO, "File storage driver used for (dataset id={0})", dataset.getId()); @@ -1654,16 +1647,15 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String String message = wr.getMessage(); return error(Response.Status.INTERNAL_SERVER_ERROR, "Uploaded files have passed checksum validation but something went wrong while attempting to put the files into Dataverse. Message was '" + message + "'."); } - } else if (storageDriverType.equals("s3")) { - + } else if(storageDriverType.equals("s3")) { + logger.log(Level.INFO, "S3 storage driver used for DCM (dataset id={0})", dataset.getId()); try { - - // Where the lifting is actually done, moving the s3 files over and having - // dataverse know of the existance of the package + + //Where the lifting is actually done, moving the s3 files over and having dataverse know of the existance of the package s3PackageImporter.copyFromS3(dataset, uploadFolder); DataFile packageFile = s3PackageImporter.createPackageDataFile(dataset, uploadFolder, new Long(totalSize)); - + if (packageFile == null) { logger.log(Level.SEVERE, "S3 File package import failed."); return error(Response.Status.INTERNAL_SERVER_ERROR, "S3 File package import failed."); @@ -1675,9 +1667,8 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String datasetService.removeDatasetLocks(dataset, DatasetLock.Reason.DcmUpload); dataset.removeLock(dcmLock); } - - // update version using the command engine to enforce user permissions and - // constraints + + // update version using the command engine to enforce user permissions and constraints if (dataset.getVersions().size() == 1 && dataset.getLatestVersion().getVersionState() == DatasetVersion.VersionState.DRAFT) { try { Command cmd; @@ -1694,11 +1685,11 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String JsonObjectBuilder job = Json.createObjectBuilder(); return ok(job); - - } catch (IOException e) { + + } catch (IOException e) { String message = e.getMessage(); return error(Response.Status.INTERNAL_SERVER_ERROR, "Uploaded files have passed checksum validation but something went wrong while attempting to move the files into Dataverse. Message was '" + message + "'."); - } + } } else { return error(Response.Status.INTERNAL_SERVER_ERROR, "Invalid storage driver in Dataverse, not compatible with dcm"); } @@ -1721,6 +1712,7 @@ public Response receiveChecksumValidationResults(@PathParam("identifier") String return ex.getResponse(); } } + @POST @Path("{id}/submitForReview") @@ -1728,9 +1720,9 @@ public Response submitForReview(@PathParam("id") String idSupplied) { try { Dataset updatedDataset = execCommand(new SubmitDatasetForReviewCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied))); JsonObjectBuilder result = Json.createObjectBuilder(); - + boolean inReview = updatedDataset.isLockedFor(DatasetLock.Reason.InReview); - + result.add("inReview", inReview); result.add("message", "Dataset id " + updatedDataset.getId() + " has been submitted for review."); return ok(result); @@ -1742,7 +1734,7 @@ public Response submitForReview(@PathParam("id") String idSupplied) { @POST @Path("{id}/returnToAuthor") public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBody) { - + if (jsonBody == null || jsonBody.isEmpty()) { return error(Response.Status.BAD_REQUEST, "You must supply JSON to this API endpoint and it must contain a reason for returning the dataset (field: reasonForReturn)."); } @@ -1750,16 +1742,14 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo JsonObject json = Json.createReader(rdr).readObject(); try { Dataset dataset = findDatasetOrDie(idSupplied); - String reasonForReturn = null; + String reasonForReturn = null; reasonForReturn = json.getString("reasonForReturn"); - // TODO: Once we add a box for the curator to type into, pass the reason for - // return to the ReturnDatasetToAuthorCommand and delete this check and call to - // setReturnReason on the API side. + // TODO: Once we add a box for the curator to type into, pass the reason for return to the ReturnDatasetToAuthorCommand and delete this check and call to setReturnReason on the API side. if (reasonForReturn == null || reasonForReturn.isEmpty()) { return error(Response.Status.BAD_REQUEST, "You must enter a reason for returning a dataset to the author(s)."); } AuthenticatedUser authenticatedUser = findAuthenticatedUserOrDie(); - Dataset updatedDataset = execCommand(new ReturnDatasetToAuthorCommand(createDataverseRequest(authenticatedUser), dataset, reasonForReturn)); + Dataset updatedDataset = execCommand(new ReturnDatasetToAuthorCommand(createDataverseRequest(authenticatedUser), dataset, reasonForReturn )); JsonObjectBuilder result = Json.createObjectBuilder(); result.add("inReview", false); @@ -1778,11 +1768,11 @@ public Response setExternalCurationStatus(@PathParam("id") String idSupplied, @Q execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); return ok("External Curation Status updated"); } catch (WrappedResponse wr) { - // Just change to Bad Request and send + //Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } - + @DELETE @Path("{id}/setExternalCurationStatus") public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) { @@ -1791,222 +1781,222 @@ public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), null)); return ok("External Curation Status deleted"); } catch (WrappedResponse wr) { - // Just change to Bad Request and send + //Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } + +@GET +@Path("{id}/uploadsid") +@Deprecated +public Response getUploadUrl(@PathParam("id") String idSupplied) { + try { + Dataset dataset = findDatasetOrDie(idSupplied); + + boolean canUpdateDataset = false; + try { + canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset).canIssue(UpdateDatasetVersionCommand.class); + } catch (WrappedResponse ex) { + logger.info("Exception thrown while trying to figure out permissions while getting upload URL for dataset id " + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + if (!canUpdateDataset) { + return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); + } + S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); + if(s3io == null) { + return error(Response.Status.NOT_FOUND,"Direct upload not supported for files in this dataset: " + dataset.getId()); + } + String url = null; + String storageIdentifier = null; + try { + url = s3io.generateTemporaryS3UploadUrl(); + storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); + } catch (IOException io) { + logger.warning(io.getMessage()); + throw new WrappedResponse(io, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); + } + + JsonObjectBuilder response = Json.createObjectBuilder() + .add("url", url) + .add("storageIdentifier", storageIdentifier ); + return ok(response); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } +} - @GET - @Path("{id}/uploadsid") - @Deprecated - public Response getUploadUrl(@PathParam("id") String idSupplied) { - try { - Dataset dataset = findDatasetOrDie(idSupplied); - - boolean canUpdateDataset = false; - try { - canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset).canIssue(UpdateDatasetVersionCommand.class); - } catch (WrappedResponse ex) { - logger.info("Exception thrown while trying to figure out permissions while getting upload URL for dataset id " + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - if (!canUpdateDataset) { - return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); - } - S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); - if (s3io == null) { - return error(Response.Status.NOT_FOUND, "Direct upload not supported for files in this dataset: " + dataset.getId()); - } - String url = null; - String storageIdentifier = null; - try { - url = s3io.generateTemporaryS3UploadUrl(); - storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); - } catch (IOException io) { - logger.warning(io.getMessage()); - throw new WrappedResponse(io, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); - } - - JsonObjectBuilder response = Json.createObjectBuilder() - .add("url", url) - .add("storageIdentifier", storageIdentifier); - return ok(response); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } - } - - @GET - @Path("{id}/uploadurls") - public Response getMPUploadUrls(@PathParam("id") String idSupplied, @QueryParam("size") long fileSize) { - try { - Dataset dataset = findDatasetOrDie(idSupplied); - - boolean canUpdateDataset = false; - try { - canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions while getting upload URLs for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - if (!canUpdateDataset) { - return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); - } - S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); - if (s3io == null) { - return error(Response.Status.NOT_FOUND, - "Direct upload not supported for files in this dataset: " + dataset.getId()); - } - JsonObjectBuilder response = null; - String storageIdentifier = null; - try { - storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); - response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize); - - } catch (IOException io) { - logger.warning(io.getMessage()); - throw new WrappedResponse(io, - error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); - } - - response.add("storageIdentifier", storageIdentifier); - return ok(response); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } - } - - @DELETE - @Path("mpupload") - public Response abortMPUpload(@QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { - try { - Dataset dataset = datasetSvc.findByGlobalId(idSupplied); - // Allow the API to be used within a session (e.g. for direct upload in the UI) - User user = session.getUser(); - if (!user.isAuthenticated()) { - try { - user = findAuthenticatedUserOrDie(); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions while getting aborting upload for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - } - boolean allowed = false; - if (dataset != null) { - allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } else { - /* - * The only legitimate case where a global id won't correspond to a dataset is - * for uploads during creation. Given that this call will still fail unless all - * three parameters correspond to an active multipart upload, it should be safe - * to allow the attempt for an authenticated user. If there are concerns about - * permissions, one could check with the current design that the user is allowed - * to create datasets in some dataverse that is configured to use the storage - * provider specified in the storageidentifier, but testing for the ability to - * create a dataset in a specific dataverse would requiring changing the design - * somehow (e.g. adding the ownerId to this call). - */ - allowed = true; - } - if (!allowed) { - return error(Response.Status.FORBIDDEN, - "You are not permitted to abort file uploads with the supplied parameters."); - } - try { - S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); - } catch (IOException io) { - logger.warning("Multipart upload abort failed for uploadId: " + uploadId + " storageidentifier=" - + storageidentifier + " dataset Id: " + dataset.getId()); - logger.warning(io.getMessage()); - throw new WrappedResponse(io, - error(Response.Status.INTERNAL_SERVER_ERROR, "Could not abort multipart upload")); - } - return Response.noContent().build(); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } - } +@GET +@Path("{id}/uploadurls") +public Response getMPUploadUrls(@PathParam("id") String idSupplied, @QueryParam("size") long fileSize) { + try { + Dataset dataset = findDatasetOrDie(idSupplied); + + boolean canUpdateDataset = false; + try { + canUpdateDataset = permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions while getting upload URLs for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + if (!canUpdateDataset) { + return error(Response.Status.FORBIDDEN, "You are not permitted to upload files to this dataset."); + } + S3AccessIO s3io = FileUtil.getS3AccessForDirectUpload(dataset); + if (s3io == null) { + return error(Response.Status.NOT_FOUND, + "Direct upload not supported for files in this dataset: " + dataset.getId()); + } + JsonObjectBuilder response = null; + String storageIdentifier = null; + try { + storageIdentifier = FileUtil.getStorageIdentifierFromLocation(s3io.getStorageLocation()); + response = s3io.generateTemporaryS3UploadUrls(dataset.getGlobalId().asString(), storageIdentifier, fileSize); + + } catch (IOException io) { + logger.warning(io.getMessage()); + throw new WrappedResponse(io, + error(Response.Status.INTERNAL_SERVER_ERROR, "Could not create process direct upload request")); + } + + response.add("storageIdentifier", storageIdentifier); + return ok(response); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } +} - @PUT - @Path("mpupload") - public Response completeMPUpload(String partETagBody, @QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { - try { - Dataset dataset = datasetSvc.findByGlobalId(idSupplied); - // Allow the API to be used within a session (e.g. for direct upload in the UI) - User user = session.getUser(); - if (!user.isAuthenticated()) { - try { - user = findAuthenticatedUserOrDie(); - } catch (WrappedResponse ex) { - logger.info( - "Exception thrown while trying to figure out permissions to complete mpupload for dataset id " - + dataset.getId() + ": " + ex.getLocalizedMessage()); - throw ex; - } - } - boolean allowed = false; - if (dataset != null) { - allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) - .canIssue(UpdateDatasetVersionCommand.class); - } else { - /* - * The only legitimate case where a global id won't correspond to a dataset is - * for uploads during creation. Given that this call will still fail unless all - * three parameters correspond to an active multipart upload, it should be safe - * to allow the attempt for an authenticated user. If there are concerns about - * permissions, one could check with the current design that the user is allowed - * to create datasets in some dataverse that is configured to use the storage - * provider specified in the storageidentifier, but testing for the ability to - * create a dataset in a specific dataverse would requiring changing the design - * somehow (e.g. adding the ownerId to this call). - */ - allowed = true; - } - if (!allowed) { - return error(Response.Status.FORBIDDEN, - "You are not permitted to complete file uploads with the supplied parameters."); - } - List eTagList = new ArrayList(); - logger.info("Etags: " + partETagBody); - try { - JsonReader jsonReader = Json.createReader(new StringReader(partETagBody)); - JsonObject object = jsonReader.readObject(); - jsonReader.close(); - for (String partNo : object.keySet()) { - eTagList.add(new PartETag(Integer.parseInt(partNo), object.getString(partNo))); - } - for (PartETag et : eTagList) { - logger.info("Part: " + et.getPartNumber() + " : " + et.getETag()); - } - } catch (JsonException je) { - logger.info("Unable to parse eTags from: " + partETagBody); - throw new WrappedResponse(je, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); - } - try { - S3AccessIO.completeMultipartUpload(idSupplied, storageidentifier, uploadId, eTagList); - } catch (IOException io) { - logger.warning("Multipart upload completion failed for uploadId: " + uploadId + " storageidentifier=" + storageidentifier + " globalId: " + idSupplied); - logger.warning(io.getMessage()); - try { - S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); - } catch (IOException e) { - logger.severe("Also unable to abort the upload (and release the space on S3 for uploadId: " + uploadId + " storageidentifier=" + storageidentifier + " globalId: " + idSupplied); - logger.severe(io.getMessage()); - } +@DELETE +@Path("mpupload") +public Response abortMPUpload(@QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { + try { + Dataset dataset = datasetSvc.findByGlobalId(idSupplied); + //Allow the API to be used within a session (e.g. for direct upload in the UI) + User user =session.getUser(); + if (!user.isAuthenticated()) { + try { + user = findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions while getting aborting upload for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + } + boolean allowed = false; + if (dataset != null) { + allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } else { + /* + * The only legitimate case where a global id won't correspond to a dataset is + * for uploads during creation. Given that this call will still fail unless all + * three parameters correspond to an active multipart upload, it should be safe + * to allow the attempt for an authenticated user. If there are concerns about + * permissions, one could check with the current design that the user is allowed + * to create datasets in some dataverse that is configured to use the storage + * provider specified in the storageidentifier, but testing for the ability to + * create a dataset in a specific dataverse would requiring changing the design + * somehow (e.g. adding the ownerId to this call). + */ + allowed = true; + } + if (!allowed) { + return error(Response.Status.FORBIDDEN, + "You are not permitted to abort file uploads with the supplied parameters."); + } + try { + S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); + } catch (IOException io) { + logger.warning("Multipart upload abort failed for uploadId: " + uploadId + " storageidentifier=" + + storageidentifier + " dataset Id: " + dataset.getId()); + logger.warning(io.getMessage()); + throw new WrappedResponse(io, + error(Response.Status.INTERNAL_SERVER_ERROR, "Could not abort multipart upload")); + } + return Response.noContent().build(); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } +} - throw new WrappedResponse(io, error(Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); - } - return ok("Multipart Upload completed"); - } catch (WrappedResponse wr) { - return wr.getResponse(); - } - } +@PUT +@Path("mpupload") +public Response completeMPUpload(String partETagBody, @QueryParam("globalid") String idSupplied, @QueryParam("storageidentifier") String storageidentifier, @QueryParam("uploadid") String uploadId) { + try { + Dataset dataset = datasetSvc.findByGlobalId(idSupplied); + //Allow the API to be used within a session (e.g. for direct upload in the UI) + User user =session.getUser(); + if (!user.isAuthenticated()) { + try { + user=findAuthenticatedUserOrDie(); + } catch (WrappedResponse ex) { + logger.info( + "Exception thrown while trying to figure out permissions to complete mpupload for dataset id " + + dataset.getId() + ": " + ex.getLocalizedMessage()); + throw ex; + } + } + boolean allowed = false; + if (dataset != null) { + allowed = permissionSvc.requestOn(createDataverseRequest(user), dataset) + .canIssue(UpdateDatasetVersionCommand.class); + } else { + /* + * The only legitimate case where a global id won't correspond to a dataset is + * for uploads during creation. Given that this call will still fail unless all + * three parameters correspond to an active multipart upload, it should be safe + * to allow the attempt for an authenticated user. If there are concerns about + * permissions, one could check with the current design that the user is allowed + * to create datasets in some dataverse that is configured to use the storage + * provider specified in the storageidentifier, but testing for the ability to + * create a dataset in a specific dataverse would requiring changing the design + * somehow (e.g. adding the ownerId to this call). + */ + allowed = true; + } + if (!allowed) { + return error(Response.Status.FORBIDDEN, + "You are not permitted to complete file uploads with the supplied parameters."); + } + List eTagList = new ArrayList(); + logger.info("Etags: " + partETagBody); + try { + JsonReader jsonReader = Json.createReader(new StringReader(partETagBody)); + JsonObject object = jsonReader.readObject(); + jsonReader.close(); + for(String partNo : object.keySet()) { + eTagList.add(new PartETag(Integer.parseInt(partNo), object.getString(partNo))); + } + for(PartETag et: eTagList) { + logger.info("Part: " + et.getPartNumber() + " : " + et.getETag()); + } + } catch (JsonException je) { + logger.info("Unable to parse eTags from: " + partETagBody); + throw new WrappedResponse(je, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); + } + try { + S3AccessIO.completeMultipartUpload(idSupplied, storageidentifier, uploadId, eTagList); + } catch (IOException io) { + logger.warning("Multipart upload completion failed for uploadId: " + uploadId +" storageidentifier=" + storageidentifier + " globalId: " + idSupplied); + logger.warning(io.getMessage()); + try { + S3AccessIO.abortMultipartUpload(idSupplied, storageidentifier, uploadId); + } catch (IOException e) { + logger.severe("Also unable to abort the upload (and release the space on S3 for uploadId: " + uploadId +" storageidentifier=" + storageidentifier + " globalId: " + idSupplied); + logger.severe(io.getMessage()); + } + + throw new WrappedResponse(io, error( Response.Status.INTERNAL_SERVER_ERROR, "Could not complete multipart upload")); + } + return ok("Multipart Upload completed"); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } +} /** * Add a File to an existing Dataset @@ -2016,16 +2006,17 @@ public Response completeMPUpload(String partETagBody, @QueryParam("globalid") St * @param fileInputStream * @param contentDispositionHeader * @param formDataBodyPart - * @return + * @return */ @POST @Path("{id}/add") @Consumes(MediaType.MULTIPART_FORM_DATA) public Response addFileToDataset(@PathParam("id") String idSupplied, - @FormDataParam("jsonData") String jsonData, - @FormDataParam("file") InputStream fileInputStream, - @FormDataParam("file") FormDataContentDisposition contentDispositionHeader, - @FormDataParam("file") final FormDataBodyPart formDataBodyPart) { + @FormDataParam("jsonData") String jsonData, + @FormDataParam("file") InputStream fileInputStream, + @FormDataParam("file") FormDataContentDisposition contentDispositionHeader, + @FormDataParam("file") final FormDataBodyPart formDataBodyPart + ){ if (!systemConfig.isHTTPUpload()) { return error(Response.Status.SERVICE_UNAVAILABLE, BundleUtil.getStringFromBundle("file.api.httpDisabled")); @@ -2039,106 +2030,114 @@ public Response addFileToDataset(@PathParam("id") String idSupplied, authUser = findUserOrDie(); } catch (WrappedResponse ex) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.addreplace.error.auth")); + BundleUtil.getStringFromBundle("file.addreplace.error.auth") + ); } - + + // ------------------------------------- // (2) Get the Dataset Id - // + // // ------------------------------------- Dataset dataset; - + try { dataset = findDatasetOrDie(idSupplied); } catch (WrappedResponse wr) { - return wr.getResponse(); + return wr.getResponse(); } - - // ------------------------------------ + + //------------------------------------ // (2a) Make sure dataset does not have package file // // -------------------------------------- - + for (DatasetVersion dv : dataset.getVersions()) { if (dv.isHasPackageFile()) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile")); + BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile") + ); } } // (2a) Load up optional params via JSON - // --------------------------------------- + //--------------------------------------- OptionalFileParams optionalFileParams = null; - msgt("(api) jsonData: " + jsonData); + msgt("(api) jsonData: " + jsonData); try { optionalFileParams = new OptionalFileParams(jsonData); } catch (DataFileTagException ex) { - return error(Response.Status.BAD_REQUEST, ex.getMessage()); - } catch (ClassCastException | com.google.gson.JsonParseException ex) { + return error( Response.Status.BAD_REQUEST, ex.getMessage()); + } + catch (ClassCastException | com.google.gson.JsonParseException ex) { return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("file.addreplace.error.parsing")); } - + // ------------------------------------- // (3) Get the file name and content type // ------------------------------------- String newFilename = null; String newFileContentType = null; String newStorageIdentifier = null; - if (null == contentDispositionHeader) { - if (optionalFileParams.hasStorageIdentifier()) { - newStorageIdentifier = optionalFileParams.getStorageIdentifier(); - // ToDo - check that storageIdentifier is valid - if (optionalFileParams.hasFileName()) { - newFilename = optionalFileParams.getFileName(); - if (optionalFileParams.hasMimetype()) { - newFileContentType = optionalFileParams.getMimeType(); - } - } - } else { - return error(BAD_REQUEST, - "You must upload a file or provide a storageidentifier, filename, and mimetype."); - } - } else { - newFilename = contentDispositionHeader.getFileName(); - newFileContentType = formDataBodyPart.getMediaType().toString(); - } - - // ------------------- + if (null == contentDispositionHeader) { + if (optionalFileParams.hasStorageIdentifier()) { + newStorageIdentifier = optionalFileParams.getStorageIdentifier(); + // ToDo - check that storageIdentifier is valid + if (optionalFileParams.hasFileName()) { + newFilename = optionalFileParams.getFileName(); + if (optionalFileParams.hasMimetype()) { + newFileContentType = optionalFileParams.getMimeType(); + } + } + } else { + return error(BAD_REQUEST, + "You must upload a file or provide a storageidentifier, filename, and mimetype."); + } + } else { + newFilename = contentDispositionHeader.getFileName(); + newFileContentType = formDataBodyPart.getMediaType().toString(); + } + + + //------------------- // (3) Create the AddReplaceFileHelper object - // ------------------- + //------------------- msg("ADD!"); DataverseRequest dvRequest2 = createDataverseRequest(authUser); AddReplaceFileHelper addFileHelper = new AddReplaceFileHelper(dvRequest2, - ingestService, - datasetService, - fileService, - permissionSvc, - commandEngine, - systemConfig); - - // ------------------- + ingestService, + datasetService, + fileService, + permissionSvc, + commandEngine, + systemConfig); + + + //------------------- // (4) Run "runAddFileByDatasetId" - // ------------------- + //------------------- addFileHelper.runAddFileByDataset(dataset, - newFilename, - newFileContentType, - newStorageIdentifier, - fileInputStream, - optionalFileParams); + newFilename, + newFileContentType, + newStorageIdentifier, + fileInputStream, + optionalFileParams); - if (addFileHelper.hasError()) { + + if (addFileHelper.hasError()){ return error(addFileHelper.getHttpErrorCode(), addFileHelper.getErrorMessagesAsString("\n")); - } else { + }else{ String successMsg = BundleUtil.getStringFromBundle("file.addreplace.success.add"); try { - // msgt("as String: " + addFileHelper.getSuccessResult()); + //msgt("as String: " + addFileHelper.getSuccessResult()); /** - * @todo We need a consistent, sane way to communicate a human readable message - * to an API client suitable for human consumption. Imagine if the UI were - * built in Angular or React and we want to return a message from the API - * as-is to the user. Human readable. + * @todo We need a consistent, sane way to communicate a human + * readable message to an API client suitable for human + * consumption. Imagine if the UI were built in Angular or React + * and we want to return a message from the API as-is to the + * user. Human readable. */ logger.fine("successMsg: " + successMsg); String duplicateWarning = addFileHelper.getDuplicateFileWarning(); @@ -2147,83 +2146,79 @@ public Response addFileToDataset(@PathParam("id") String idSupplied, } else { return ok(addFileHelper.getSuccessResultAsJsonObjectBuilder()); } - - // "Look at that! You added a file! (hey hey, it may have worked)"); + + //"Look at that! You added a file! (hey hey, it may have worked)"); } catch (NoFilesException ex) { Logger.getLogger(Files.class.getName()).log(Level.SEVERE, null, ex); return error(Response.Status.BAD_REQUEST, "NoFileException! Serious Error! See administrator!"); } } - + } // end: addFileToDataset - private void msg(String m) { - // System.out.println(m); + + + private void msg(String m){ + //System.out.println(m); logger.fine(m); } - - private void dashes() { + private void dashes(){ msg("----------------"); } - - private void msgt(String m) { - dashes(); - msg(m); - dashes(); + private void msgt(String m){ + dashes(); msg(m); dashes(); } - - public static T handleVersion(String versionId, DsVersionHandler hdl) - throws WrappedResponse { + + + public static T handleVersion( String versionId, DsVersionHandler hdl ) + throws WrappedResponse { switch (versionId) { - case ":latest": - return hdl.handleLatest(); - case ":draft": - return hdl.handleDraft(); - case ":latest-published": - return hdl.handleLatestPublished(); - default: - try { - String[] versions = versionId.split("\\."); - switch (versions.length) { - case 1: - return hdl.handleSpecific(Long.parseLong(versions[0]), (long) 0.0); - case 2: - return hdl.handleSpecific(Long.parseLong(versions[0]), Long.parseLong(versions[1])); - default: - throw new WrappedResponse(error(Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); + case ":latest": return hdl.handleLatest(); + case ":draft": return hdl.handleDraft(); + case ":latest-published": return hdl.handleLatestPublished(); + default: + try { + String[] versions = versionId.split("\\."); + switch (versions.length) { + case 1: + return hdl.handleSpecific(Long.parseLong(versions[0]), (long)0.0); + case 2: + return hdl.handleSpecific( Long.parseLong(versions[0]), Long.parseLong(versions[1]) ); + default: + throw new WrappedResponse(error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); + } + } catch ( NumberFormatException nfe ) { + throw new WrappedResponse( error( Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'") ); } - } catch (NumberFormatException nfe) { - throw new WrappedResponse(error(Response.Status.BAD_REQUEST, "Illegal version identifier '" + versionId + "'")); - } } } + + private DatasetVersion getDatasetVersionOrDie( final DataverseRequest req, String versionNumber, final Dataset ds, UriInfo uriInfo, HttpHeaders headers) throws WrappedResponse { + DatasetVersion dsv = execCommand( handleVersion(versionNumber, new DsVersionHandler>(){ - private DatasetVersion getDatasetVersionOrDie(final DataverseRequest req, String versionNumber, final Dataset ds, UriInfo uriInfo, HttpHeaders headers) throws WrappedResponse { - DatasetVersion dsv = execCommand(handleVersion(versionNumber, new DsVersionHandler>() { - - @Override - public Command handleLatest() { - return new GetLatestAccessibleDatasetVersionCommand(req, ds); - } - - @Override - public Command handleDraft() { - return new GetDraftDatasetVersionCommand(req, ds); - } + @Override + public Command handleLatest() { + return new GetLatestAccessibleDatasetVersionCommand(req, ds); + } - @Override - public Command handleSpecific(long major, long minor) { - return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); - } + @Override + public Command handleDraft() { + return new GetDraftDatasetVersionCommand(req, ds); + } + + @Override + public Command handleSpecific(long major, long minor) { + return new GetSpecificPublishedDatasetVersionCommand(req, ds, major, minor); + } - @Override - public Command handleLatestPublished() { - return new GetLatestPublishedDatasetVersionCommand(req, ds); - } - })); - if (dsv == null || dsv.getId() == null) { - throw new WrappedResponse(notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found")); + @Override + public Command handleLatestPublished() { + return new GetLatestPublishedDatasetVersionCommand(req, ds); + } + })); + if ( dsv == null || dsv.getId() == null ) { + throw new WrappedResponse( notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found") ); } if (dsv.isReleased()) { MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, ds); @@ -2231,7 +2226,7 @@ public Command handleLatestPublished() { } return dsv; } - + @GET @Path("{identifier}/locks") public Response getLocks(@PathParam("identifier") String id, @QueryParam("type") DatasetLock.Reason lockType) { @@ -2239,26 +2234,26 @@ public Response getLocks(@PathParam("identifier") String id, @QueryParam("type") Dataset dataset = null; try { dataset = findDatasetOrDie(id); - Set locks; + Set locks; if (lockType == null) { locks = dataset.getLocks(); } else { // request for a specific type lock: DatasetLock lock = dataset.getLockFor(lockType); - locks = new HashSet<>(); + locks = new HashSet<>(); if (lock != null) { locks.add(lock); } } - + return ok(locks.stream().map(lock -> json(lock)).collect(toJsonArray())); } catch (WrappedResponse wr) { return wr.getResponse(); - } - } - + } + } + @DELETE @Path("{identifier}/locks") public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("type") DatasetLock.Reason lockType) { @@ -2270,7 +2265,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ return error(Response.Status.FORBIDDEN, "This API end point can be used by superusers only."); } Dataset dataset = findDatasetOrDie(id); - + if (lockType == null) { Set locks = new HashSet<>(); for (DatasetLock lock : dataset.getLocks()) { @@ -2282,7 +2277,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ // refresh the dataset: dataset = findDatasetOrDie(id); } - // kick of dataset reindexing, in case the locks removed + // kick of dataset reindexing, in case the locks removed // affected the search card: try { indexService.indexDataset(dataset, true); @@ -2302,7 +2297,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ execCommand(new RemoveLockCommand(req, dataset, lock.getReason())); // refresh the dataset: dataset = findDatasetOrDie(id); - // ... and kick of dataset reindexing, in case the lock removed + // ... and kick of dataset reindexing, in case the lock removed // affected the search card: try { indexService.indexDataset(dataset, true); @@ -2322,7 +2317,7 @@ public Response deleteLocks(@PathParam("identifier") String id, @QueryParam("typ }); } - + @POST @Path("{identifier}/lock/{type}") public Response lockDataset(@PathParam("identifier") String id, @PathParam("type") DatasetLock.Reason lockType) { @@ -2331,7 +2326,7 @@ public Response lockDataset(@PathParam("identifier") String id, @PathParam("type AuthenticatedUser user = findAuthenticatedUserOrDie(); if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "This API end point can be used by superusers only."); - } + } Dataset dataset = findDatasetOrDie(id); DatasetLock lock = dataset.getLockFor(lockType); if (lock != null) { @@ -2358,28 +2353,29 @@ public Response lockDataset(@PathParam("identifier") String id, @PathParam("type }); } - + @GET @Path("{id}/makeDataCount/citations") public Response getMakeDataCountCitations(@PathParam("id") String idSupplied) { - + try { Dataset dataset = findDatasetOrDie(idSupplied); JsonArrayBuilder datasetsCitations = Json.createArrayBuilder(); List externalCitations = datasetExternalCitationsService.getDatasetExternalCitationsByDataset(dataset); - for (DatasetExternalCitations citation : externalCitations) { + for (DatasetExternalCitations citation : externalCitations ){ JsonObjectBuilder candidateObj = Json.createObjectBuilder(); /** - * In the future we can imagine storing and presenting more information about - * the citation such as the title of the paper and the names of the authors. For - * now, we'll at least give the URL of the citation so people can click and find - * out more about the citation. + * In the future we can imagine storing and presenting more + * information about the citation such as the title of the paper + * and the names of the authors. For now, we'll at least give + * the URL of the citation so people can click and find out more + * about the citation. */ candidateObj.add("citationUrl", citation.getCitedByUrl()); datasetsCitations.add(candidateObj); - } - return ok(datasetsCitations); - + } + return ok(datasetsCitations); + } catch (WrappedResponse wr) { return wr.getResponse(); } @@ -2392,23 +2388,23 @@ public Response getMakeDataCountMetricCurrentMonth(@PathParam("id") String idSup String nullCurrentMonth = null; return getMakeDataCountMetric(idSupplied, metricSupplied, nullCurrentMonth, country); } - + @GET @Path("{identifier}/storagesize") - public Response getStorageSize(@PathParam("identifier") String dvIdtf, @QueryParam("includeCached") boolean includeCached, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + public Response getStorageSize(@PathParam("identifier") String dvIdtf, @QueryParam("includeCached") boolean includeCached, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + return response(req -> ok(MessageFormat.format(BundleUtil.getStringFromBundle("datasets.api.datasize.storage"), - execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), includeCached, GetDatasetStorageSizeCommand.Mode.STORAGE, null))))); + execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), includeCached,GetDatasetStorageSizeCommand.Mode.STORAGE, null))))); } - + @GET @Path("{identifier}/versions/{versionId}/downloadsize") - public Response getDownloadSize(@PathParam("identifier") String dvIdtf, @PathParam("versionId") String version, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + public Response getDownloadSize(@PathParam("identifier") String dvIdtf, @PathParam("versionId") String version, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + return response(req -> ok(MessageFormat.format(BundleUtil.getStringFromBundle("datasets.api.datasize.download"), - execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), false, GetDatasetStorageSizeCommand.Mode.DOWNLOAD, getDatasetVersionOrDie(req, version, findDatasetOrDie(dvIdtf), uriInfo, headers)))))); + execCommand(new GetDatasetStorageSizeCommand(req, findDatasetOrDie(dvIdtf), false, GetDatasetStorageSizeCommand.Mode.DOWNLOAD, getDatasetVersionOrDie(req, version , findDatasetOrDie(dvIdtf), uriInfo, headers)))))); } @GET @@ -2425,10 +2421,8 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path } String monthYear = null; if (yyyymm != null) { - // We add "-01" because we store "2018-05-01" rather than "2018-05" in the - // "monthyear" column. - // Dates come to us as "2018-05-01" in the SUSHI JSON ("begin-date") and we - // decided to store them as-is. + // We add "-01" because we store "2018-05-01" rather than "2018-05" in the "monthyear" column. + // Dates come to us as "2018-05-01" in the SUSHI JSON ("begin-date") and we decided to store them as-is. monthYear = MetricsUtil.sanitizeYearMonthUserInput(yyyymm) + "-01"; } if (country != null) { @@ -2456,50 +2450,50 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path Long downloadsTotal = null; Long downloadsUnique = null; switch (metricSupplied) { - case "viewsTotal": - viewsTotal = datasetMetrics.getViewsTotal(); - break; - case "viewsTotalRegular": - viewsTotalRegular = datasetMetrics.getViewsTotalRegular(); - break; - case "viewsTotalMachine": - viewsTotalMachine = datasetMetrics.getViewsTotalMachine(); - break; - case "viewsUnique": - viewsUnique = datasetMetrics.getViewsUnique(); - break; - case "viewsUniqueRegular": - viewsUniqueRegular = datasetMetrics.getViewsUniqueRegular(); - break; - case "viewsUniqueMachine": - viewsUniqueMachine = datasetMetrics.getViewsUniqueMachine(); - break; - case "downloadsTotal": - downloadsTotal = datasetMetrics.getDownloadsTotal(); - break; - case "downloadsTotalRegular": - downloadsTotalRegular = datasetMetrics.getDownloadsTotalRegular(); - break; - case "downloadsTotalMachine": - downloadsTotalMachine = datasetMetrics.getDownloadsTotalMachine(); - break; - case "downloadsUnique": - downloadsUnique = datasetMetrics.getDownloadsUnique(); - break; - case "downloadsUniqueRegular": - downloadsUniqueRegular = datasetMetrics.getDownloadsUniqueRegular(); - break; - case "downloadsUniqueMachine": - downloadsUniqueMachine = datasetMetrics.getDownloadsUniqueMachine(); - break; - default: - break; + case "viewsTotal": + viewsTotal = datasetMetrics.getViewsTotal(); + break; + case "viewsTotalRegular": + viewsTotalRegular = datasetMetrics.getViewsTotalRegular(); + break; + case "viewsTotalMachine": + viewsTotalMachine = datasetMetrics.getViewsTotalMachine(); + break; + case "viewsUnique": + viewsUnique = datasetMetrics.getViewsUnique(); + break; + case "viewsUniqueRegular": + viewsUniqueRegular = datasetMetrics.getViewsUniqueRegular(); + break; + case "viewsUniqueMachine": + viewsUniqueMachine = datasetMetrics.getViewsUniqueMachine(); + break; + case "downloadsTotal": + downloadsTotal = datasetMetrics.getDownloadsTotal(); + break; + case "downloadsTotalRegular": + downloadsTotalRegular = datasetMetrics.getDownloadsTotalRegular(); + break; + case "downloadsTotalMachine": + downloadsTotalMachine = datasetMetrics.getDownloadsTotalMachine(); + break; + case "downloadsUnique": + downloadsUnique = datasetMetrics.getDownloadsUnique(); + break; + case "downloadsUniqueRegular": + downloadsUniqueRegular = datasetMetrics.getDownloadsUniqueRegular(); + break; + case "downloadsUniqueMachine": + downloadsUniqueMachine = datasetMetrics.getDownloadsUniqueMachine(); + break; + default: + break; } /** * TODO: Think more about the JSON output and the API design. - * getDatasetMetricsByDatasetMonthCountry returns a single row right now, by - * country. We could return multiple metrics (viewsTotal, viewsUnique, - * downloadsTotal, and downloadsUnique) by country. + * getDatasetMetricsByDatasetMonthCountry returns a single row right + * now, by country. We could return multiple metrics (viewsTotal, + * viewsUnique, downloadsTotal, and downloadsUnique) by country. */ jsonObjectBuilder.add("viewsTotalRegular", viewsTotalRegular); jsonObjectBuilder.add("viewsUniqueRegular", viewsUniqueRegular); @@ -2517,33 +2511,33 @@ public Response getMakeDataCountMetric(@PathParam("id") String idSupplied, @Path } catch (WrappedResponse wr) { return wr.getResponse(); } catch (Exception e) { - // bad date - caught in sanitize call + //bad date - caught in sanitize call return error(BAD_REQUEST, e.getMessage()); } } - + @GET @Path("{identifier}/storageDriver") public Response getFileStore(@PathParam("identifier") String dvIdtf, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - - Dataset dataset; - + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + return response(req -> ok(dataset.getEffectiveStorageDriverId())); } - + @PUT @Path("{identifier}/storageDriver") public Response setFileStore(@PathParam("identifier") String dvIdtf, String storageDriverLabel, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2553,17 +2547,17 @@ public Response setFileStore(@PathParam("identifier") String dvIdtf, } if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); - } - - Dataset dataset; - + } + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - - // We don't want to allow setting this to a store id that does not exist: + + // We don't want to allow setting this to a store id that does not exist: for (Entry store : DataAccess.getStorageDriverLabels().entrySet()) { if (store.getKey().equals(storageDriverLabel)) { dataset.setStorageDriverId(store.getValue()); @@ -2571,15 +2565,15 @@ public Response setFileStore(@PathParam("identifier") String dvIdtf, return ok("Storage driver set to: " + store.getKey() + "/" + store.getValue()); } } - return error(Response.Status.BAD_REQUEST, - "No Storage Driver found for : " + storageDriverLabel); + return error(Response.Status.BAD_REQUEST, + "No Storage Driver found for : " + storageDriverLabel); } - + @DELETE @Path("{identifier}/storageDriver") public Response resetFileStore(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2589,43 +2583,43 @@ public Response resetFileStore(@PathParam("identifier") String dvIdtf, } if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); - } - - Dataset dataset; - + } + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + dataset.setStorageDriverId(null); datasetService.merge(dataset); - return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); + return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); } @GET @Path("{identifier}/curationLabelSet") public Response getCurationLabelSet(@PathParam("identifier") String dvIdtf, - @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - - Dataset dataset; - + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + return response(req -> ok(dataset.getEffectiveCurationLabelSetName())); } - + @PUT @Path("{identifier}/curationLabelSet") public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, String curationLabelSet, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2636,9 +2630,9 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); } - - Dataset dataset; - + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { @@ -2656,14 +2650,14 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, } } return error(Response.Status.BAD_REQUEST, - "No Such Curation Label Set"); + "No Such Curation Label Set"); } - + @DELETE @Path("{identifier}/curationLabelSet") public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + // Superuser-only: AuthenticatedUser user; try { @@ -2674,15 +2668,15 @@ public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); } - - Dataset dataset; - + + Dataset dataset; + try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { return error(Response.Status.NOT_FOUND, "No such dataset"); } - + dataset.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); datasetService.merge(dataset); return ok("Curation Label Set reset to default: " + SystemConfig.DEFAULTCURATIONLABELSET); @@ -2724,8 +2718,7 @@ public Response getTimestamps(@PathParam("identifier") String id) { dataset.getMostRecentMajorVersionReleaseDate().toInstant().atZone(ZoneId.systemDefault()))); } // If the modification/permissionmodification time is - // set and the index time is null or is before the mod time, the relevant index - // is stale + // set and the index time is null or is before the mod time, the relevant index is stale timestamps.add("hasStaleIndex", (dataset.getModificationTime() != null && (dataset.getIndexTime() == null || (dataset.getIndexTime().compareTo(dataset.getModificationTime()) <= 0))) ? true @@ -2761,6 +2754,7 @@ public Response getTimestamps(@PathParam("identifier") String id) { } } + /** * Add multiple Files to an existing Dataset * @@ -2772,7 +2766,7 @@ public Response getTimestamps(@PathParam("identifier") String id) { @Path("{id}/addFiles") @Consumes(MediaType.MULTIPART_FORM_DATA) public Response addFilesToDataset(@PathParam("id") String idSupplied, - @FormDataParam("jsonData") String jsonData) { + @FormDataParam("jsonData") String jsonData) { if (!systemConfig.isHTTPUpload()) { return error(Response.Status.SERVICE_UNAVAILABLE, BundleUtil.getStringFromBundle("file.api.httpDisabled")); @@ -2785,7 +2779,8 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, try { authUser = findUserOrDie(); } catch (WrappedResponse ex) { - return error(Response.Status.FORBIDDEN, BundleUtil.getStringFromBundle("file.addreplace.error.auth")); + return error(Response.Status.FORBIDDEN, BundleUtil.getStringFromBundle("file.addreplace.error.auth") + ); } // ------------------------------------- @@ -2799,14 +2794,16 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, return wr.getResponse(); } - // ------------------------------------ + + //------------------------------------ // (2a) Make sure dataset does not have package file // -------------------------------------- for (DatasetVersion dv : dataset.getVersions()) { if (dv.isHasPackageFile()) { return error(Response.Status.FORBIDDEN, - BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile")); + BundleUtil.getStringFromBundle("file.api.alreadyHasPackageFile") + ); } } @@ -2819,24 +2816,18 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, this.fileService, this.permissionSvc, this.commandEngine, - this.systemConfig); + this.systemConfig + ); return addFileHelper.addFiles(jsonData, dataset, authUser); } - - /** - * API to list dataset creation and modification dates, curation status, and - * direct curator role assignments - * - * Curation Status is a label from the :AllowedCurationLabels setting The - * returned table/csv file also lists the users with any assignments on this - * dataset that allow publication. These would be most relevant in uses cases - * where local role assignments are used to identify responsible party(ies) who - * have been given roles in movign the dataset through the defined curation - * process. + + + /** + * API to find curation assignements and statuses * - * @return a CSV table with headings + * @return * @throws WrappedResponse */ @GET @@ -2852,45 +2843,38 @@ public Response getCurationStates() throws WrappedResponse { } catch (WrappedResponse wr) { return wr.getResponse(); } - + List allRoles = dataverseRoleService.findAll(); List curationRoles = new ArrayList(); - allRoles.forEach(r -> { - if (r.permissions().contains(Permission.PublishDataset)) - curationRoles.add(r); - }); + allRoles.forEach(r -> {if(r.permissions().contains(Permission.PublishDataset)) curationRoles.add(r);}); HashMap> assignees = new HashMap>(); - curationRoles.forEach(r -> { - assignees.put(r.getAlias(), null); - }); - - StringBuilder csvSB = new StringBuilder(String.join(",", - BundleUtil.getStringFromBundle("dataset"), - BundleUtil.getStringFromBundle("datasets.api.creationdate"), - BundleUtil.getStringFromBundle("datasets.api.modificationdate"), + curationRoles.forEach(r-> {assignees.put(r.getAlias(), null);}); + + StringBuilder csvSB = new StringBuilder(String.join(",", + BundleUtil.getStringFromBundle("dataset"), + BundleUtil.getStringFromBundle("datasets.api.creationdate"), + BundleUtil.getStringFromBundle("datasets.api.modificationdate"), BundleUtil.getStringFromBundle("datasets.api.curationstatus"), String.join(",", assignees.keySet()))); for (Dataset dataset : datasetSvc.findAllUnpublished()) { - List ras = permissionService.assignmentsOn(dataset); - curationRoles.forEach(r -> { - assignees.put(r.getAlias(), new HashSet()); - }); - for (RoleAssignment ra : ras) { - if (curationRoles.contains(ra.getRole())) { - assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); + List ras = permissionService.assignmentsOn(dataset); + curationRoles.forEach(r-> {assignees.put(r.getAlias(), new HashSet());}); + for (RoleAssignment ra : ras) { + if (curationRoles.contains(ra.getRole())) { + assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); + } } - } - String name = dataset.getCurrentName().replace("\"", "\"\""); - String status = dataset.getLatestVersion().getExternalStatusLabel(); - String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); - String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); - String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); - String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; - List sList = new ArrayList(); - assignees.entrySet().forEach(e -> sList.add(e.getValue().size() == 0 ? "" : String.join(";", e.getValue()))); - csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status == null ? "" : status, String.join(",", sList))); + String name = dataset.getCurrentName().replace("\"","\"\""); + String status = dataset.getLatestVersion().getExternalStatusLabel(); + String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); + String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); + String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); + String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; + List sList = new ArrayList(); + assignees.entrySet().forEach(e-> sList.add(e.getValue().size()==0 ? "": String.join(";", e.getValue()))); + csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status==null ? "": status, String.join(",", sList))); } csvSB.append("\n"); - return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); + return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); } } From 20cf55d5d7603145ddc40caf6b9d0631ccdefd6a Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 27 Sep 2021 16:42:33 -0400 Subject: [PATCH 54/78] cleanup --- .../harvard/iq/dataverse/DataversePage.java | 8 ++- .../harvard/iq/dataverse/api/Datasets.java | 59 ++++++++++--------- 2 files changed, 37 insertions(+), 30 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 62b9e4f1d27..46c2cab9044 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -1223,7 +1223,9 @@ public Set> getCurationLabelSetOptions() { } // Add an entry for disabled setNames.put(SystemConfig.CURATIONLABELSDISABLED, SystemConfig.CURATIONLABELSDISABLED); - allowedSetNames.forEach(name -> {setNames.put(name, name);}); + allowedSetNames.forEach(name -> { + setNames.put(name, name); + }); } return setNames.entrySet(); } @@ -1246,9 +1248,9 @@ public String getCurationLabelSetNameLabel() { } if (setName != null) { if (fromAncestor) { - setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.inherited"); + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.inherited"); } else { - setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.storage.default"); + setName = setName + " " + BundleUtil.getStringFromBundle("dataverse.default"); } } return setName; diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 2da116f5f65..fb3f87cc19b 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -86,7 +86,6 @@ import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter; import edu.harvard.iq.dataverse.dataaccess.S3AccessIO; import edu.harvard.iq.dataverse.engine.command.exception.CommandException; -import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException; import edu.harvard.iq.dataverse.engine.command.exception.UnforcedCommandException; import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetStorageSizeCommand; import edu.harvard.iq.dataverse.engine.command.impl.RevokeRoleCommand; @@ -2823,9 +2822,8 @@ public Response addFilesToDataset(@PathParam("id") String idSupplied, } - /** - * API to find curation assignements and statuses + * API to find curation assignments and statuses * * @return * @throws WrappedResponse @@ -2843,38 +2841,45 @@ public Response getCurationStates() throws WrappedResponse { } catch (WrappedResponse wr) { return wr.getResponse(); } - + List allRoles = dataverseRoleService.findAll(); List curationRoles = new ArrayList(); - allRoles.forEach(r -> {if(r.permissions().contains(Permission.PublishDataset)) curationRoles.add(r);}); + allRoles.forEach(r -> { + if (r.permissions().contains(Permission.PublishDataset)) + curationRoles.add(r); + }); HashMap> assignees = new HashMap>(); - curationRoles.forEach(r-> {assignees.put(r.getAlias(), null);}); - - StringBuilder csvSB = new StringBuilder(String.join(",", - BundleUtil.getStringFromBundle("dataset"), - BundleUtil.getStringFromBundle("datasets.api.creationdate"), - BundleUtil.getStringFromBundle("datasets.api.modificationdate"), + curationRoles.forEach(r -> { + assignees.put(r.getAlias(), null); + }); + + StringBuilder csvSB = new StringBuilder(String.join(",", + BundleUtil.getStringFromBundle("dataset"), + BundleUtil.getStringFromBundle("datasets.api.creationdate"), + BundleUtil.getStringFromBundle("datasets.api.modificationdate"), BundleUtil.getStringFromBundle("datasets.api.curationstatus"), String.join(",", assignees.keySet()))); for (Dataset dataset : datasetSvc.findAllUnpublished()) { - List ras = permissionService.assignmentsOn(dataset); - curationRoles.forEach(r-> {assignees.put(r.getAlias(), new HashSet());}); - for (RoleAssignment ra : ras) { - if (curationRoles.contains(ra.getRole())) { - assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); - } + List ras = permissionService.assignmentsOn(dataset); + curationRoles.forEach(r -> { + assignees.put(r.getAlias(), new HashSet()); + }); + for (RoleAssignment ra : ras) { + if (curationRoles.contains(ra.getRole())) { + assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); } - String name = dataset.getCurrentName().replace("\"","\"\""); - String status = dataset.getLatestVersion().getExternalStatusLabel(); - String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); - String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); - String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); - String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; - List sList = new ArrayList(); - assignees.entrySet().forEach(e-> sList.add(e.getValue().size()==0 ? "": String.join(";", e.getValue()))); - csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status==null ? "": status, String.join(",", sList))); + } + String name = dataset.getCurrentName().replace("\"", "\"\""); + String status = dataset.getLatestVersion().getExternalStatusLabel(); + String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); + String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); + String modDate = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getModificationTime()); + String hyperlink = "\"=HYPERLINK(\"\"" + url + "\"\",\"\"" + name + "\"\")\""; + List sList = new ArrayList(); + assignees.entrySet().forEach(e -> sList.add(e.getValue().size() == 0 ? "" : String.join(";", e.getValue()))); + csvSB.append("\n").append(String.join(",", hyperlink, date, modDate, status == null ? "" : status, String.join(",", sList))); } csvSB.append("\n"); - return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); + return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv"); } } From 38b8baa6c3b0f5d3878037c506d6f055380385a0 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 29 Sep 2021 15:28:46 -0400 Subject: [PATCH 55/78] addressing review feedback --- doc/release-notes/7967-curation-labels.md | 7 +- .../source/admin/dataverses-datasets.rst | 32 +++--- .../source/developers/curation-label-api.rst | 95 ++++++++++++++++++ .../source/installation/config.rst | 5 +- .../edu/harvard/iq/dataverse/DatasetPage.java | 4 +- .../harvard/iq/dataverse/DataversePage.java | 2 +- .../harvard/iq/dataverse/SettingsWrapper.java | 2 - .../edu/harvard/iq/dataverse/api/Admin.java | 16 +-- .../harvard/iq/dataverse/api/Datasets.java | 97 ++++++++++++++++--- ...and.java => SetCurationStatusCommand.java} | 10 +- .../settings/SettingsServiceBean.java | 19 ++-- src/main/java/propertyFiles/Bundle.properties | 3 +- .../harvard/iq/dataverse/api/DatasetsIT.java | 58 ++++++++++- .../edu/harvard/iq/dataverse/api/UtilIT.java | 21 ++++ 14 files changed, 310 insertions(+), 61 deletions(-) create mode 100644 doc/sphinx-guides/source/developers/curation-label-api.rst rename src/main/java/edu/harvard/iq/dataverse/engine/command/impl/{SetExternalStatusCommand.java => SetCurationStatusCommand.java} (91%) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index 1bff954362f..fddca33d0cd 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -1,5 +1,8 @@ ### External Curation Status Labels -A new :AllowedCurationLabels setting allows an administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to an externally defined curation process. +A new :AllowedCurationLabels setting allows a site administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to an externally defined curation process. -Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Anyone who can publish the dataset (e.g. curators) can set/change/remove labels from the defined set via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. +Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Site admins can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. + + +The solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index c72cc7c0c48..560de3445c9 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -40,7 +40,7 @@ Recursively assigns the users and groups having a role(s),that are in the set co curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/$dataverse-alias/addRoleAssignmentsToChildren -Configure a Dataverse Collection to store all new files in a specific file store +Configure a Dataverse Collection to Store All New Files in a Specific File Store ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To direct new files (uploaded when datasets are created or edited) for all datasets in a given Dataverse collection, the store can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: @@ -64,15 +64,19 @@ The available drivers can be listed with:: Configure a Dataverse Collection to allow use of a given Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: +Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: + +The curationLabelSet to use within a given collection can be set by specifying its name using:: curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSet http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet -The current driver can be seen using:: +The reserved word "DISABLED" can be used to disable this feature within a given Dataverse collection. + +The name of the current curationLabelSet can be seen using:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet -and can be reset to the default store with:: +and can be reset to the default (inherited from the parent collection or DISABLED for the root collection) with:: curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet @@ -80,9 +84,9 @@ The available curation label sets can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSet -If the :AllowedCurationLabels setting has a value, one of the available values will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset +If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset -(Individual datasets can be configured to use specific file stores as well. See the "Datasets" section below.) +(Individual datasets can be configured to use specific curationLabelSets as well. See the "Datasets" section below.) Datasets @@ -157,7 +161,7 @@ Diagnose Constraint Violations Issues in Datasets To identify invalid data values in specific datasets (if, for example, an attempt to edit a dataset results in a ConstraintViolationException in the server log), or to check all the datasets in the Dataverse installation for constraint violations, see :ref:`Dataset Validation ` in the :doc:`/api/native-api` section of the User Guide. -Configure a Dataset to store all new files in a specific file store +Configure a Dataset to Store All New Files in a Specific File Store ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Configure a dataset to use a specific file store (this API can only be used by a superuser) :: @@ -181,18 +185,22 @@ Configure a Dataset to allow use of a Curation Label Set Configure a dataset to allow use of labels from a given Curation Label Set (as defined with the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting) This API can only be used by a superuser. :: - curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSet http://$SERVER/api/datasets/$dataset-id/curationLabelSet + The curationLabelSet to use within a given dataset can be set by specifying its name using:: + + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSetName http://$SERVER/api/datasets/$dataset-id/curationLabelSet -The current driver can be seen using:: +The reserved word "DISABLED" can be used to disable this feature within a given Dataverse collection. + +The name of the current curationLabelSet can be seen using:: curl http://$SERVER/api/datasets/$dataset-id/curationLabelSet -It can be reset to the default store as follows (only a superuser can do this) :: +and can be reset to the default (inherited from the parent collection) with (only a superuser can do this) :: curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE http://$SERVER/api/datasets/$dataset-id/curationLabelSet -The available drivers can be listed with:: +The available curationLabelSets can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSets -If the :AllowedCurationLabels setting has a value, one of the available values will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset +If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset diff --git a/doc/sphinx-guides/source/developers/curation-label-api.rst b/doc/sphinx-guides/source/developers/curation-label-api.rst new file mode 100644 index 00000000000..cb68a8fadef --- /dev/null +++ b/doc/sphinx-guides/source/developers/curation-label-api.rst @@ -0,0 +1,95 @@ +Dataset Curation Label API +========================== + +When the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting has been used to define Curation Labels, this API can be used to set these labels on draft datasets. +Superusers can define which set of labels are allowed for a given datasets in a collection/an individual dataset using the api described in the :doc:`dataverses-datasets` section. +The API here can be used by curators/those who have permission to publish the dataset to get/set/change/delete the label currently assigned to a draft dataset. + +This functionality is intended as a mechanism to integrate the Dataverse software with an external curation process/application: it is a way to make the state of a draft dataset, +as defined in the external process, visible within Dataverse. These labels have no other effect in Dataverse and are only visible to curators/those with permission to publish the dataset. +Any curation label assigned to a draft dataset will be removed upon publication. + +Get a Draft Dataset's Curation Label +------------------------------------ + +.. code-block:: bash + + export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx + export DATASET_ID='12345' + export DATASET_PID='doi:10.5072/FK2A1B2C3' + export SERVER_URL=https://demo.dataverse.org + + Example 1: Get the label using the DATASET ID + + curl -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/$DATASET_ID/curationStatus" + + Example 2: Get the label using the DATASET PID + + curl -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/:persistentId/curationStatus?persistentId=$DATASET_PID" + +You should expect a 200 ("OK") response and the draft dataset's curation status label contained in a JSON 'data' object. + + +Set a Draft Dataset's Curation Label +------------------------------------ + +To add a curation label for a draft Dataset, specify the Dataset ID (DATASET_ID) or Persistent identifier (DATASET_PID) and the label desired. + +.. code-block:: bash + + export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx + export DATASET_ID='12345' + export DATASET_PID='doi:10.5072/FK2A1B2C3' + export LABEL='Author contacted' + export SERVER_URL=https://demo.dataverse.org + + Example: Add the label using the DATASET ID + + curl -X PUT -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/$DATASET_ID/curationStatus?label=$LABEL" + + Example 2: Add a description using the DATASET PID + + curl -X PUT -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/:persistentId/curationStatus?label=$LABEL&persistentId=$DATASET_PID" + +You should expect a 200 ("OK") response indicating that the label has been set. 403/Forbidden and 400/Bad Request responses are also possible, i.e. if you don't have permission to make this change or are trying to add a label that isn't in the allowed set or to add a label to a dataset with no draft version. + + +Delete a Draft Dataset's Curation Label +--------------------------------------- + +To delete the curation label on a draft Datasetspecify the Dataset ID (DATASET_ID) or Persistent identifier (DATASET_PID). + +.. code-block:: bash + + export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx + export DATASET_PID='doi:10.5072/FK2A1B2C3' + export SERVER_URL=https://demo.dataverse.org + + Example: Delete the label using the DATASET PID + + curl -X DELETE -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/:persistentId/curationStatus?persistentId=$DATASET_PID" + +You should expect a 200 ("OK") response indicating the label has been removed. + + +Get the Set of Allowed Labels for a Dataset +------------------------------------------- + +To get the list of allowed curation labels allowed for a given Dataset + +.. code-block:: bash + + export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx + export DATASET_ID='12345' + export DATASET_PID='doi:10.5072/FK2A1B2C3' + export SERVER_URL=https://demo.dataverse.org + + Example 1: Get the label using the DATASET ID + + curl -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/$DATASET_ID/allowedCurationLabels" + + Example 2: Get the label using the DATASET PID + + curl -H X-Dataverse-key:$API_TOKEN "$SERVER_URL/api/datasets/:persistentId/allowedCurationLabels?persistentId=$DATASET_PID" + +You should expect a 200 ("OK") response with a comma-separated list of allowed labels contained in a JSON 'data' object. diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index f7ec9312322..56207a3cf6f 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -2388,13 +2388,14 @@ Scripts that implement this association for specific service protocols are maint .. _:AllowedCurationLabels: :AllowedCurationLabels +++++++++++++++++++++++ A JSON Object containing lists of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. The set of labels allowed -for datasets can be selected via the Dataverse collection page (Edit/General Info) or set via API call. +for datasets can be selected by a superuser - via the Dataverse collection page (Edit/General Info) or set via API call. The labels in a set should correspond to the states in an organization's curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. A dataset may only have one label at a time and if a label is set, it will be removed at publication time. This functionality is disabled when this setting is empty/not set. -Each set of labels is identified by a title and a JSON Array of the labels allowed in that set. +Each set of labels is identified by a curationLabelSet name and a JSON Array of the labels allowed in that set. ``curl -X PUT -d '{"Standard Process":["Author contacted", "Privacy Review", "Awaiting paper publication", "Final Approval"], "Alternate Process":["State 1","State 2","State 3"]}' http://localhost:8080/api/admin/settings/:AllowedCurationLabels`` diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java index 25b1e10e76f..6523e564be1 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java @@ -107,7 +107,7 @@ import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetResult; import edu.harvard.iq.dataverse.engine.command.impl.RestrictFileCommand; import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand; -import edu.harvard.iq.dataverse.engine.command.impl.SetExternalStatusCommand; +import edu.harvard.iq.dataverse.engine.command.impl.SetCurationStatusCommand; import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand; import edu.harvard.iq.dataverse.externaltools.ExternalTool; import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean; @@ -5550,7 +5550,7 @@ public String getFieldLanguage(String languages) { public void setExternalStatus(String status) { try { - dataset = commandEngine.submit(new SetExternalStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); + dataset = commandEngine.submit(new SetCurationStatusCommand(dvRequestService.getDataverseRequest(), dataset, status)); workingVersion=dataset.getLatestVersion(); if (status == null || status.isEmpty()) { JsfHelper.addInfoMessage(BundleUtil.getStringFromBundle("dataset.externalstatus.removed")); diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java index 46c2cab9044..18886ce41a2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java +++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java @@ -1222,7 +1222,7 @@ public Set> getCurationLabelSetOptions() { setNames.put(inheritedLabelSet,SystemConfig.DEFAULTCURATIONLABELSET); } // Add an entry for disabled - setNames.put(SystemConfig.CURATIONLABELSDISABLED, SystemConfig.CURATIONLABELSDISABLED); + setNames.put(BundleUtil.getStringFromBundle("dataverse.curationLabels.disabled"), SystemConfig.CURATIONLABELSDISABLED); allowedSetNames.forEach(name -> { setNames.put(name, name); }); diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java index b08a988a8e0..73ffeb73ee6 100644 --- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java +++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java @@ -383,11 +383,9 @@ public String getDefaultMetadataLanguage() { public List getAllowedExternalStatuses(Dataset d) { String setName = d.getEffectiveCurationLabelSetName(); - logger.info("Set name: " + setName); if(setName.equals(SystemConfig.CURATIONLABELSDISABLED)) { return new ArrayList(); } - logger.info(Strings.concat(",", systemConfig.getCurationLabels().keySet())); String[] labelArray = systemConfig.getCurationLabels().get(setName); if(labelArray==null) { return new ArrayList(); diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java index c8af541502f..335454053e0 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java @@ -1922,7 +1922,7 @@ public Response getCurationLabelSet(@PathParam("alias") String alias) throws Wra @PUT @Path("/dataverse/{alias}/curationLabelSet") - public Response setCurationLabelSet(@PathParam("alias") String alias, String label) throws WrappedResponse { + public Response setCurationLabelSet(@PathParam("alias") String alias, @QueryParam("name") String name) throws WrappedResponse { Dataverse dataverse = dataverseSvc.findByAlias(alias); if (dataverse == null) { return error(Response.Status.NOT_FOUND, "Could not find dataverse based on alias supplied: " + alias + "."); @@ -1935,19 +1935,19 @@ public Response setCurationLabelSet(@PathParam("alias") String alias, String lab } catch (WrappedResponse wr) { return wr.getResponse(); } - if (SystemConfig.CURATIONLABELSDISABLED.equals(label) || SystemConfig.DEFAULTCURATIONLABELSET.equals(label)) { - dataverse.setCurationLabelSetName(label); - return ok("Curation Label Set Name set to: " + label); + if (SystemConfig.CURATIONLABELSDISABLED.equals(name) || SystemConfig.DEFAULTCURATIONLABELSET.equals(name)) { + dataverse.setCurationLabelSetName(name); + return ok("Curation Label Set Name set to: " + name); } else { for (String setName : systemConfig.getCurationLabels().keySet()) { - if (setName.equals(label)) { - dataverse.setCurationLabelSetName(label); + if (setName.equals(name)) { + dataverse.setCurationLabelSetName(name); return ok("Curation Label Set Name set to: " + setName); } } } return error(Response.Status.BAD_REQUEST, - "No Curation Label Set found for : " + label); + "No Curation Label Set found for : " + name); } @DELETE @@ -1966,7 +1966,7 @@ public Response resetCurationLabelSet(@PathParam("alias") String alias) throws W return wr.getResponse(); } dataverse.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); - return ok("Storage reset to default: " + DataAccess.DEFAULT_STORAGE_DRIVER_IDENTIFIER); + return ok("Curation Label Set reset to default: " + SystemConfig.DEFAULTCURATIONLABELSET); } @GET diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index fb3f87cc19b..8ef1fcefa11 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -70,7 +70,7 @@ import edu.harvard.iq.dataverse.engine.command.impl.RequestRsyncScriptCommand; import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand; import edu.harvard.iq.dataverse.engine.command.impl.SetDatasetCitationDateCommand; -import edu.harvard.iq.dataverse.engine.command.impl.SetExternalStatusCommand; +import edu.harvard.iq.dataverse.engine.command.impl.SetCurationStatusCommand; import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand; import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand; import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetTargetURLCommand; @@ -177,6 +177,7 @@ import org.glassfish.jersey.media.multipart.FormDataBodyPart; import org.glassfish.jersey.media.multipart.FormDataContentDisposition; import org.glassfish.jersey.media.multipart.FormDataParam; +import org.omnifaces.el.functions.Strings; import com.amazonaws.services.s3.model.PartETag; @@ -1759,26 +1760,56 @@ public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBo } } + @GET + @Path("{id}/curationStatus") + public Response getCurationStatus(@PathParam("id") String idSupplied) { + try { + Dataset ds = findDatasetOrDie(idSupplied); + DatasetVersion dsv = ds.getLatestVersion(); + if (dsv.isDraft() && permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), ds).has(Permission.PublishDataset)) { + return response(req -> ok(dsv.getExternalStatusLabel())); + } else { + return error(Response.Status.FORBIDDEN, "You are not permitted to view the curation status of this dataset."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + } + @PUT - @Path("{id}/setExternalCurationStatus") - public Response setExternalCurationStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { - logger.info("Label is " + label); + @Path("{id}/curationStatus") + public Response setCurationStatus(@PathParam("id") String idSupplied, @QueryParam("label") String label) { + Dataset ds = null; + User u = null; try { - execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), label)); - return ok("External Curation Status updated"); + ds = findDatasetOrDie(idSupplied); + u = findUserOrDie(); } catch (WrappedResponse wr) { - //Just change to Bad Request and send + return wr.getResponse(); + } + try { + execCommand(new SetCurationStatusCommand(createDataverseRequest(u), ds, label)); + return ok("Curation Status updated"); + } catch (WrappedResponse wr) { + // Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); } } @DELETE - @Path("{id}/setExternalCurationStatus") - public Response deleteExternalCurationStatus(@PathParam("id") String idSupplied) { - + @Path("{id}/curationStatus") + public Response deleteCurationStatus(@PathParam("id") String idSupplied) { + Dataset ds = null; + User u = null; try { - execCommand(new SetExternalStatusCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied), null)); - return ok("External Curation Status deleted"); + ds = findDatasetOrDie(idSupplied); + u = findUserOrDie(); + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + try { + execCommand(new SetCurationStatusCommand(createDataverseRequest(u), ds, null)); + return ok("Curation Status deleted"); } catch (WrappedResponse wr) { //Just change to Bad Request and send return Response.fromResponse(wr.getResponse()).status(Response.Status.BAD_REQUEST).build(); @@ -2602,12 +2633,21 @@ public Response resetFileStore(@PathParam("identifier") String dvIdtf, public Response getCurationLabelSet(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + Dataset dataset; try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { - return error(Response.Status.NOT_FOUND, "No such dataset"); + return ex.getResponse(); } return response(req -> ok(dataset.getEffectiveCurationLabelSetName())); @@ -2635,7 +2675,7 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { - return error(Response.Status.NOT_FOUND, "No such dataset"); + return ex.getResponse(); } if (SystemConfig.CURATIONLABELSDISABLED.equals(curationLabelSet) || SystemConfig.DEFAULTCURATIONLABELSET.equals(curationLabelSet)) { dataset.setCurationLabelSetName(curationLabelSet); @@ -2673,7 +2713,7 @@ public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, try { dataset = findDatasetOrDie(dvIdtf); } catch (WrappedResponse ex) { - return error(Response.Status.NOT_FOUND, "No such dataset"); + return ex.getResponse(); } dataset.setCurationLabelSetName(SystemConfig.DEFAULTCURATIONLABELSET); @@ -2681,6 +2721,31 @@ public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, return ok("Curation Label Set reset to default: " + SystemConfig.DEFAULTCURATIONLABELSET); } + @GET + @Path("{identifier}/allowedCurationLabels") + public Response getAllowedCurationLabels(@PathParam("identifier") String dvIdtf, + @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { + + try { + AuthenticatedUser user = findAuthenticatedUserOrDie(); + if (!user.isSuperuser()) { + return error(Response.Status.FORBIDDEN, "Superusers only."); + } + } catch (WrappedResponse wr) { + return wr.getResponse(); + } + + Dataset dataset; + + try { + dataset = findDatasetOrDie(dvIdtf); + } catch (WrappedResponse ex) { + return ex.getResponse(); + } + String[] labelArray = systemConfig.getCurationLabels().get(dataset.getEffectiveCurationLabelSetName()); + return response(req -> ok(Strings.concat(",", labelArray))); + } + @GET @Path("{identifier}/timestamps") @Produces(MediaType.APPLICATION_JSON) @@ -2869,7 +2934,7 @@ public Response getCurationStates() throws WrappedResponse { assignees.get(ra.getRole().getAlias()).add(ra.getAssigneeIdentifier()); } } - String name = dataset.getCurrentName().replace("\"", "\"\""); + String name = "\"" + dataset.getCurrentName().replace("\"", "\"\"") + "\""; String status = dataset.getLatestVersion().getExternalStatusLabel(); String url = systemConfig.getDataverseSiteUrl() + dataset.getTargetUrl() + dataset.getGlobalId().asString(); String date = new SimpleDateFormat("yyyy-MM-dd").format(dataset.getCreateDate()); diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetCurationStatusCommand.java similarity index 91% rename from src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java rename to src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetCurationStatusCommand.java index 97bbfae91f4..4a7b8ee1d34 100644 --- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetExternalStatusCommand.java +++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/SetCurationStatusCommand.java @@ -33,13 +33,13 @@ import com.google.api.LabelDescriptor; @RequiredPermissions(Permission.PublishDataset) -public class SetExternalStatusCommand extends AbstractDatasetCommand { +public class SetCurationStatusCommand extends AbstractDatasetCommand { - private static final Logger logger = Logger.getLogger(SetExternalStatusCommand.class.getName()); + private static final Logger logger = Logger.getLogger(SetCurationStatusCommand.class.getName()); String label; - public SetExternalStatusCommand(DataverseRequest aRequest, Dataset dataset, String label) { + public SetCurationStatusCommand(DataverseRequest aRequest, Dataset dataset, String label) { super(aRequest, dataset); this.label=label; } @@ -55,9 +55,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException { } else { String setName = getDataset().getEffectiveCurationLabelSetName(); if(setName.equals(SystemConfig.CURATIONLABELSDISABLED)) { - logger.info("External status labeling disbaled for dataset id: " + getDataset().getId()); throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.disabled"), this); - } String[] labelArray = ctxt.systemConfig().getCurationLabels().get(setName); boolean found = false; @@ -69,7 +67,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException { } } if(!found) { - logger.info("Label not found: " + label + " in set " + setName); + logger.fine("Label not found: " + label + " in set " + setName); throw new IllegalCommandException(BundleUtil.getStringFromBundle("dataset.status.failure.notallowed"), this); } } diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java index 1d811751494..7959e6b69b2 100644 --- a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java +++ b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java @@ -468,14 +468,17 @@ Whether Harvesting (OAI) service is enabled */ SendNotificationOnDatasetCreation, /** - * A comma separated list of allowed labels (up to 32 characters, spaces - * allowed) that can be set, via API or UI by users with the permission to - * publish a dataset. These should correspond to the states in an organizations - * curation process and are intended to help users/curators track the progress - * of a dataset through an externally defined curation process. A dataset may - * only have one label at a time and if a label is set, it will be removed at - * publication time. This functionality is disabled when this setting is - * empty/not set. + * A JSON Object containing named comma separated sets(s) of allowed labels (up + * to 32 characters, spaces allowed) that can be set on draft datasets, via API + * or UI by users with the permission to publish a dataset. (Set names are + * string keys, labels are a JSON array of strings). These should correspond to + * the states in an organizations curation process(es) and are intended to help + * users/curators track the progress of a dataset through an externally defined + * curation process. Only one set of labels are allowed per dataset (defined via + * API by a superuser per collection (UI or API) or per dataset (API only)). A + * dataset may only have one label at a time and if a label is set, it will be + * removed at publication time. This functionality is disabled when this setting + * is empty/not set. */ AllowedCurationLabels ; diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties index 98e7111520c..5dff90a209b 100644 --- a/src/main/java/propertyFiles/Bundle.properties +++ b/src/main/java/propertyFiles/Bundle.properties @@ -743,7 +743,8 @@ dataverse.identifier.title=Short name used for the URL of this dataverse. dataverse.affiliation.title=The organization with which this dataverse is affiliated. dataverse.storage.title=A storage service to be used for datasets in this dataverse. dataverse.metadatalanguage.title=Metadata entered for datasets in this dataverse will be assumed to be in the selected language. -dataverse.curationLabels.title=A set of curation labels that can be used for datasets in this collection. +dataverse.curationLabels.title=A set of curation status labels that are used to indicate the curation status of draft datasets. +dataverse.curationLabels.disabled=Disabled dataverse.category=Category dataverse.category.title=The type that most closely reflects this dataverse. dataverse.type.selectTab.top=Select one... diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java index c78cb4ceb85..948e4213dfa 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java @@ -7,6 +7,7 @@ import java.util.logging.Logger; import org.junit.BeforeClass; import org.junit.Test; +import org.mockito.Mockito; import org.skyscreamer.jsonassert.JSONAssert; import org.junit.Ignore; import com.jayway.restassured.path.json.JsonPath; @@ -22,6 +23,8 @@ import static javax.ws.rs.core.Response.Status.BAD_REQUEST; import static javax.ws.rs.core.Response.Status.METHOD_NOT_ALLOWED; import edu.harvard.iq.dataverse.DataFile; +import edu.harvard.iq.dataverse.DataverseServiceBean; + import static edu.harvard.iq.dataverse.api.UtilIT.API_TOKEN_HTTP_HEADER; import edu.harvard.iq.dataverse.authorization.DataverseRole; import edu.harvard.iq.dataverse.authorization.users.PrivateUrlUser; @@ -2299,7 +2302,7 @@ public void testSemanticMetadataAPIs() { assertEquals(200, deleteUserResponse.getStatusCode()); } - + @Test public void testReCreateDataset() { @@ -2368,6 +2371,59 @@ public void testReCreateDataset() { assertEquals(200, deleteUserResponse.getStatusCode()); } + @Test + public void testCurationLabelAPIs() { + Response createUser = UtilIT.createRandomUser(); + createUser.prettyPrint(); + String username = UtilIT.getUsernameFromResponse(createUser); + String apiToken = UtilIT.getApiTokenFromResponse(createUser); + + Response createDataverseResponse = UtilIT.createRandomDataverse(apiToken); + createDataverseResponse.prettyPrint(); + String dataverseAlias = UtilIT.getAliasFromResponse(createDataverseResponse); + + SystemConfig systemConfig = Mockito.mock(SystemConfig.class); + Map labelSets = new HashMap(); + labelSets.put("StandardProcess", new String[] { "Author contacted", "Privacy Review", "Awaiting paper publication", "Final Approval"}); + labelSets.put("AlternateProcess", new String[] {"State 1","State 2","State 3"}); + Mockito.when(systemConfig.getCurationLabels()).thenReturn(labelSets); + + //Set curation label set on dataverse + //Valid option, bad user + Response setDataverseCurationLabelSetResponse = UtilIT.setDataverseCurationLabelSet(dataverseAlias, apiToken, "AlternateProcess"); + setDataverseCurationLabelSetResponse.then().assertThat().statusCode(FORBIDDEN.getStatusCode()); + + Response makeSuperUser = UtilIT.makeSuperUser(username); + assertEquals(200, makeSuperUser.getStatusCode()); + + //Non-existent option + setDataverseCurationLabelSetResponse = UtilIT.setDataverseCurationLabelSet(dataverseAlias, apiToken, "OddProcess"); + setDataverseCurationLabelSetResponse.then().assertThat().statusCode(BAD_REQUEST.getStatusCode()); + //Valid option, bad user + setDataverseCurationLabelSetResponse = UtilIT.setDataverseCurationLabelSet(dataverseAlias, apiToken, "AlternateProcess"); + setDataverseCurationLabelSetResponse.then().assertThat().statusCode(OK.getStatusCode()); + + + // Create a dataset using native api + Response createDatasetResponse = UtilIT.createRandomDatasetViaNativeApi(dataverseAlias, apiToken); + createDatasetResponse.prettyPrint(); + Integer datasetId = UtilIT.getDatasetIdFromResponse(createDatasetResponse); + // Get the curation label set in use + Response response = UtilIT.getDatasetCurationLabelSet(datasetId, apiToken); + response.then().assertThat().statusCode(OK.getStatusCode()); + //Verify that the set name is what was set on the dataverse + String labelSetName = getData(response.getBody().asString()); + assertEquals("AlternateProcess", labelSetName); + + // Now set a label + //Option from the wrong set + response = UtilIT.setDatasetCurationLabel(datasetId, apiToken, "Author contacted"); + response.then().assertThat().statusCode(BAD_REQUEST.getStatusCode()); + // Valid option + response = UtilIT.setDatasetCurationLabel(datasetId, apiToken, "State 1"); + response.then().assertThat().statusCode(OK.getStatusCode()); + } + private String getData(String body) { try (StringReader rdr = new StringReader(body)) { return Json.createReader(rdr).readObject().getJsonObject("data").toString(); diff --git a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java index 4070f153a8e..0af67588a6e 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java @@ -2672,6 +2672,27 @@ public static Response recreateDatasetJsonLD(String apiToken, String dataverseAl .post("/api/dataverses/" + dataverseAlias +"/datasets"); return response; } + + static Response setDataverseCurationLabelSet(String alias, String apiToken, String labelSetName) { + Response response = given() + .header(API_TOKEN_HTTP_HEADER, apiToken) + .put("/api/dataverses/" + alias + "/curationLabelSet?name=" + labelSetName); + return response; + } + + static Response getDatasetCurationLabelSet(Integer datasetId, String apiToken) { + Response response = given() + .header(API_TOKEN_HTTP_HEADER, apiToken) + .get("/api/datasets/" + datasetId + "/curationLabelSet"); + return response; + } + + static Response setDatasetCurationLabel(Integer datasetId, String apiToken, String label) { + Response response = given() + .header(API_TOKEN_HTTP_HEADER, apiToken) + .put("/api/datasets/" + datasetId + "/curationLabelSet?label=" + label); + return response; + } private static DatasetField constructPrimitive(String fieldName, String value) { DatasetField field = new DatasetField(); From 24d4a57b8321f86e5a43959fe18317ac64cd5aa9 Mon Sep 17 00:00:00 2001 From: qqmyers Date: Wed, 29 Sep 2021 15:30:03 -0400 Subject: [PATCH 56/78] Apply suggestions from code review Co-authored-by: Philip Durbin --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index 560de3445c9..29043ec1368 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -61,7 +61,7 @@ The available drivers can be listed with:: (Individual datasets can be configured to use specific file stores as well. See the "Datasets" section below.) -Configure a Dataverse Collection to allow use of a given Curation Label Set +Configure a Dataverse Collection to Allow Use of a Given Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: @@ -180,7 +180,7 @@ The available drivers can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/storageDrivers -Configure a Dataset to allow use of a Curation Label Set +Configure a Dataset to Allow Use of a Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Configure a dataset to allow use of labels from a given Curation Label Set (as defined with the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting) This API can only be used by a superuser. :: From 1ce968042374b83935bc8cecd6e3becbc3948783 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 29 Sep 2021 15:31:09 -0400 Subject: [PATCH 57/78] add doc to index --- doc/sphinx-guides/source/developers/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/sphinx-guides/source/developers/index.rst b/doc/sphinx-guides/source/developers/index.rst index 405e2e64a59..b158f9798f4 100755 --- a/doc/sphinx-guides/source/developers/index.rst +++ b/doc/sphinx-guides/source/developers/index.rst @@ -39,3 +39,4 @@ Developer Guide dataset-migration-api workflows fontcustom + curation-label-api From b888b4163a8b7410fa9edea9aa89076af2562463 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 29 Sep 2021 15:36:20 -0400 Subject: [PATCH 58/78] Update dataverse example to match dataset one --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index 29043ec1368..0f777f3f2d2 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -68,7 +68,7 @@ Datasets within a given Dataverse collection can be annotated with a Curation La The curationLabelSet to use within a given collection can be set by specifying its name using:: - curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSet http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSetName http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet The reserved word "DISABLED" can be used to disable this feature within a given Dataverse collection. From 86fee632b46717a21d644258fae43ab82ba072f2 Mon Sep 17 00:00:00 2001 From: Danny Brooke Date: Thu, 30 Sep 2021 10:41:52 -0400 Subject: [PATCH 59/78] removing external --- doc/release-notes/7967-curation-labels.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index fddca33d0cd..d5470a5680a 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -1,8 +1,7 @@ -### External Curation Status Labels +### Curation Status Labels -A new :AllowedCurationLabels setting allows a site administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to an externally defined curation process. +A new :AllowedCurationLabels setting allows a site administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to a defined curation process. Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Site admins can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. - The solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. From 8a8f51e5ff69d9d2be1f96e0f4b5e162bb7f8a22 Mon Sep 17 00:00:00 2001 From: Danny Brooke Date: Thu, 30 Sep 2021 14:31:28 -0400 Subject: [PATCH 60/78] adding solr schema update notes --- doc/release-notes/7967-curation-labels.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index d5470a5680a..25d0bf85efc 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -5,3 +5,16 @@ A new :AllowedCurationLabels setting allows a site administrator to define one o Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Site admins can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. The solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. + +## Additional Release Steps + +1\. Run the script updateSchemaMDB.sh to generate updated solr schema files and preserve any other custom fields in your Solr configuration. + +For example: (modify the path names as needed) + +cd /usr/local/solr-8.8.1/server/solr/collection1/conf +wget https://github.com/IQSS/dataverse/releases/download/v5.7/updateSchemaMDB.sh +chmod +x updateSchemaMDB.sh +./updateSchemaMDB.sh -t . + +See for more information. \ No newline at end of file From cc5823732f5637f1fd31192522eb57eab73d2634 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 30 Sep 2021 14:57:32 -0400 Subject: [PATCH 61/78] Test fix --- src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java index 0af67588a6e..aab7ea76bfb 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java @@ -2676,7 +2676,7 @@ public static Response recreateDatasetJsonLD(String apiToken, String dataverseAl static Response setDataverseCurationLabelSet(String alias, String apiToken, String labelSetName) { Response response = given() .header(API_TOKEN_HTTP_HEADER, apiToken) - .put("/api/dataverses/" + alias + "/curationLabelSet?name=" + labelSetName); + .put("/api/admin/dataverse/" + alias + "/curationLabelSet?name=" + labelSetName); return response; } From d83c92ae57ada3b2774c2b85bb96619998d26b4f Mon Sep 17 00:00:00 2001 From: qqmyers Date: Thu, 30 Sep 2021 14:59:37 -0400 Subject: [PATCH 62/78] Apply suggestions from code review Co-authored-by: Philip Durbin --- doc/release-notes/7967-curation-labels.md | 4 ++-- doc/sphinx-guides/source/developers/curation-label-api.rst | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index 25d0bf85efc..de8f7e7d3c9 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -1,8 +1,8 @@ ### Curation Status Labels -A new :AllowedCurationLabels setting allows a site administrator to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to a defined curation process. +A new :AllowedCurationLabels setting allows a sysadmins to define one or more sets of labels that can be applied to a draft Dataset version via the user interface or API to indicate the status of the dataset with respect to a defined curation process. -Labels are arbitrary (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Site admins can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. +Labels are completely customizable (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Superusers can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. The solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. diff --git a/doc/sphinx-guides/source/developers/curation-label-api.rst b/doc/sphinx-guides/source/developers/curation-label-api.rst index cb68a8fadef..7b9875699fd 100644 --- a/doc/sphinx-guides/source/developers/curation-label-api.rst +++ b/doc/sphinx-guides/source/developers/curation-label-api.rst @@ -57,7 +57,7 @@ You should expect a 200 ("OK") response indicating that the label has been set. Delete a Draft Dataset's Curation Label --------------------------------------- -To delete the curation label on a draft Datasetspecify the Dataset ID (DATASET_ID) or Persistent identifier (DATASET_PID). +To delete the curation label on a draft Dataset, specify the Dataset ID (DATASET_ID) or Persistent identifier (DATASET_PID). .. code-block:: bash From 5e0a43e55092baa83711461a864aea9724d6b12c Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 30 Sep 2021 15:09:39 -0400 Subject: [PATCH 63/78] doc text/structure updates --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 4 ++-- .../curation-label-api.rst => api/curation-labels.rst} | 2 +- doc/sphinx-guides/source/api/index.rst | 1 + doc/sphinx-guides/source/developers/index.rst | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) rename doc/sphinx-guides/source/{developers/curation-label-api.rst => api/curation-labels.rst} (98%) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index 0f777f3f2d2..b255cbd3666 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -64,7 +64,7 @@ The available drivers can be listed with:: Configure a Dataverse Collection to Allow Use of a Given Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. :: +Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. The curationLabelSet to use within a given collection can be set by specifying its name using:: @@ -185,7 +185,7 @@ Configure a Dataset to Allow Use of a Curation Label Set Configure a dataset to allow use of labels from a given Curation Label Set (as defined with the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting) This API can only be used by a superuser. :: - The curationLabelSet to use within a given dataset can be set by specifying its name using:: +The curationLabelSet to use within a given dataset can be set by specifying its name using:: curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSetName http://$SERVER/api/datasets/$dataset-id/curationLabelSet diff --git a/doc/sphinx-guides/source/developers/curation-label-api.rst b/doc/sphinx-guides/source/api/curation-labels.rst similarity index 98% rename from doc/sphinx-guides/source/developers/curation-label-api.rst rename to doc/sphinx-guides/source/api/curation-labels.rst index 7b9875699fd..36950a37eb3 100644 --- a/doc/sphinx-guides/source/developers/curation-label-api.rst +++ b/doc/sphinx-guides/source/api/curation-labels.rst @@ -2,7 +2,7 @@ Dataset Curation Label API ========================== When the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting has been used to define Curation Labels, this API can be used to set these labels on draft datasets. -Superusers can define which set of labels are allowed for a given datasets in a collection/an individual dataset using the api described in the :doc:`dataverses-datasets` section. +Superusers can define which set of labels are allowed for a given datasets in a collection/an individual dataset using the api described in the :doc:`/admin/dataverses-datasets` section. The API here can be used by curators/those who have permission to publish the dataset to get/set/change/delete the label currently assigned to a draft dataset. This functionality is intended as a mechanism to integrate the Dataverse software with an external curation process/application: it is a way to make the state of a draft dataset, diff --git a/doc/sphinx-guides/source/api/index.rst b/doc/sphinx-guides/source/api/index.rst index 45cdb1918fe..9fc58ef4e5a 100755 --- a/doc/sphinx-guides/source/api/index.rst +++ b/doc/sphinx-guides/source/api/index.rst @@ -20,5 +20,6 @@ API Guide sword client-libraries external-tools + curation-labels apps faq diff --git a/doc/sphinx-guides/source/developers/index.rst b/doc/sphinx-guides/source/developers/index.rst index b158f9798f4..bf525422c84 100755 --- a/doc/sphinx-guides/source/developers/index.rst +++ b/doc/sphinx-guides/source/developers/index.rst @@ -39,4 +39,4 @@ Developer Guide dataset-migration-api workflows fontcustom - curation-label-api + From 5402636910ca19ea02a0132f02ef32ab45caa4d1 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 30 Sep 2021 15:17:18 -0400 Subject: [PATCH 64/78] remove word --- doc/sphinx-guides/source/installation/config.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst index 56207a3cf6f..50c856085a1 100644 --- a/doc/sphinx-guides/source/installation/config.rst +++ b/doc/sphinx-guides/source/installation/config.rst @@ -2392,7 +2392,7 @@ Scripts that implement this association for specific service protocols are maint A JSON Object containing lists of allowed labels (up to 32 characters, spaces allowed) that can be set, via API or UI by users with the permission to publish a dataset. The set of labels allowed for datasets can be selected by a superuser - via the Dataverse collection page (Edit/General Info) or set via API call. -The labels in a set should correspond to the states in an organization's curation process and are intended to help users/curators track the progress of a dataset through an externally defined curation process. +The labels in a set should correspond to the states in an organization's curation process and are intended to help users/curators track the progress of a dataset through a defined curation process. A dataset may only have one label at a time and if a label is set, it will be removed at publication time. This functionality is disabled when this setting is empty/not set. Each set of labels is identified by a curationLabelSet name and a JSON Array of the labels allowed in that set. From ae61cbeb53b1239978f487be34ecde69b24def23 Mon Sep 17 00:00:00 2001 From: Danny Brooke Date: Fri, 1 Oct 2021 13:08:42 -0400 Subject: [PATCH 65/78] adding more information about what labels do --- .../source/admin/dataverses-datasets.rst | 21 +++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index b255cbd3666..c3dd31c4b07 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -64,7 +64,11 @@ The available drivers can be listed with:: Configure a Dataverse Collection to Allow Use of a Given Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Datasets within a given Dataverse collection can be annotated with a Curation Label from one of the label sets defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. The allowed set can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. +Datasets within a given Dataverse collection can be annotated with a Curation Label to indicate the status of the dataset with respect to a defined curation process. Labels are completely customizable (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). + +The label is applied to a draft Dataset version via the user interface or API and the available label sets are defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. + +The label set used for a collection can be specified via the API as shown below, or by editing the 'General Information' for a Dataverse collection on the Dataverse collection page. Only accessible to superusers. The curationLabelSet to use within a given collection can be set by specifying its name using:: @@ -84,10 +88,9 @@ The available curation label sets can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSet -If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset +If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a given collection/dataset. -(Individual datasets can be configured to use specific curationLabelSets as well. See the "Datasets" section below.) - +Individual datasets can be configured to use specific curationLabelSets as well. See the "Datasets" section below. Datasets -------- @@ -183,7 +186,11 @@ The available drivers can be listed with:: Configure a Dataset to Allow Use of a Curation Label Set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Configure a dataset to allow use of labels from a given Curation Label Set (as defined with the :ref:`:AllowedCurationLabels <:AllowedCurationLabels>` setting) This API can only be used by a superuser. :: +A dataset can be annotated with a Curation Label to indicate the status of the dataset with respect to a defined curation process. Labels are completely customizable (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). + +The label is applied to a draft Dataset version via the user interface or API and the available label sets are defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. + +The label set used for a dataset can be specified via the API as shown below. Only accessible to superusers. :: The curationLabelSet to use within a given dataset can be set by specifying its name using:: @@ -203,4 +210,6 @@ The available curationLabelSets can be listed with:: curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSets -If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a give collection/dataset +If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a given collection/dataset. + +Collections can be configured to use specific curationLabelSets as well. See the "Dataverse Collections" section above. From a23d506c793430928df74e9555d236de0e5c1250 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Fri, 1 Oct 2021 14:45:49 -0400 Subject: [PATCH 66/78] get guides to build (`make html` was failing) #6886 The error was this: admin/dataverses-datasets.rst:195:Literal block expected; none found. --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index c3dd31c4b07..c3d7ff9d1dc 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -190,7 +190,7 @@ A dataset can be annotated with a Curation Label to indicate the status of the d The label is applied to a draft Dataset version via the user interface or API and the available label sets are defined by :ref:`:AllowedCurationLabels <:AllowedCurationLabels>`. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. -The label set used for a dataset can be specified via the API as shown below. Only accessible to superusers. :: +The label set used for a dataset can be specified via the API as shown below. Only accessible to superusers. The curationLabelSet to use within a given dataset can be set by specifying its name using:: From fa4f8cc735417ad3948736caa7ee015a22bbd942 Mon Sep 17 00:00:00 2001 From: Danny Brooke Date: Fri, 1 Oct 2021 16:07:20 -0400 Subject: [PATCH 67/78] updating release note --- doc/release-notes/7967-curation-labels.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index de8f7e7d3c9..452788382bd 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -4,17 +4,16 @@ A new :AllowedCurationLabels setting allows a sysadmins to define one or more se Labels are completely customizable (alphanumeric or spaces, up to 32 characters, e.g. "Author contacted", "Privacy Review", "Awaiting paper publication"). Superusers can select a specific set of labels, or disable this functionality per collection. Anyone who can publish a draft dataset (e.g. curators) can set/change/remove labels (from the set specified for the collection containing the dataset) via the user interface or via an API. The API also would allow external tools to search for, read and set labels on Datasets, providing an integration mechanism. Labels are visible on the Dataset page and in Dataverse collection listings/search results. Internally, the labels have no effect, and at publication, any existing label will be removed. A reporting API call allows admins to get a list of datasets and their curation statuses. -The solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. +The Solr schema must be updated as part of installing the release of Dataverse containing this feature for it to work. ## Additional Release Steps -1\. Run the script updateSchemaMDB.sh to generate updated solr schema files and preserve any other custom fields in your Solr configuration. +1\. Replace Solr schema.xml to allow Curation Labels to be used -For example: (modify the path names as needed) +-stop solr instance (usually service solr stop, depending on solr installation/OS, see the [Installation Guide](https://guides.dataverse.org/en/5.7/installation/prerequisites.html#solr-init-script) -cd /usr/local/solr-8.8.1/server/solr/collection1/conf -wget https://github.com/IQSS/dataverse/releases/download/v5.7/updateSchemaMDB.sh -chmod +x updateSchemaMDB.sh -./updateSchemaMDB.sh -t . +-replace schema.xml -See for more information. \ No newline at end of file +cp /tmp/dvinstall/schema.xml /usr/local/solr/solr-8.8.1/server/solr/collection1/conf + +-start solr instance (usually service solr start, depending on solr/OS) \ No newline at end of file From a79ce03e58b5110b28f7b4981b50568e01499177 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Mon, 4 Oct 2021 12:50:30 -0400 Subject: [PATCH 68/78] Fix PUT curationSetLabel and test --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 4 ++-- src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 8ef1fcefa11..de6bbe316aa 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2656,7 +2656,7 @@ public Response getCurationLabelSet(@PathParam("identifier") String dvIdtf, @PUT @Path("{identifier}/curationLabelSet") public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, - String curationLabelSet, + @QueryParam("name") String curationLabelSet, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { // Superuser-only: @@ -2664,7 +2664,7 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, try { user = findAuthenticatedUserOrDie(); } catch (WrappedResponse ex) { - return error(Response.Status.BAD_REQUEST, "Authentication is required."); + return error(Response.Status.UNAUTHORIZED, "Authentication is required."); } if (!user.isSuperuser()) { return error(Response.Status.FORBIDDEN, "Superusers only."); diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java index 948e4213dfa..b86b10af2a3 100644 --- a/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java +++ b/src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java @@ -2399,7 +2399,7 @@ public void testCurationLabelAPIs() { //Non-existent option setDataverseCurationLabelSetResponse = UtilIT.setDataverseCurationLabelSet(dataverseAlias, apiToken, "OddProcess"); setDataverseCurationLabelSetResponse.then().assertThat().statusCode(BAD_REQUEST.getStatusCode()); - //Valid option, bad user + //Valid option, superuser setDataverseCurationLabelSetResponse = UtilIT.setDataverseCurationLabelSet(dataverseAlias, apiToken, "AlternateProcess"); setDataverseCurationLabelSetResponse.then().assertThat().statusCode(OK.getStatusCode()); From 589cf64d120fda7e806b9f15dd87614f8942e565 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 6 Oct 2021 12:12:57 -0400 Subject: [PATCH 69/78] refactor issue --- src/main/webapp/dataset.xhtml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/webapp/dataset.xhtml b/src/main/webapp/dataset.xhtml index b0aec04b22c..dffe8256eb8 100644 --- a/src/main/webapp/dataset.xhtml +++ b/src/main/webapp/dataset.xhtml @@ -327,7 +327,7 @@
      • #{bundle['dataset.changestatus']}
          - +
        • #{status} From 6d5c2e00e5a07d09efd824c99d30edcdd046b4e7 Mon Sep 17 00:00:00 2001 From: Danny Brooke Date: Wed, 6 Oct 2021 12:45:59 -0400 Subject: [PATCH 70/78] updating release notes with instructions for custom metadata blocks --- doc/release-notes/7967-curation-labels.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/doc/release-notes/7967-curation-labels.md b/doc/release-notes/7967-curation-labels.md index 452788382bd..2742519329c 100644 --- a/doc/release-notes/7967-curation-labels.md +++ b/doc/release-notes/7967-curation-labels.md @@ -8,7 +8,23 @@ The Solr schema must be updated as part of installing the release of Dataverse c ## Additional Release Steps -1\. Replace Solr schema.xml to allow Curation Labels to be used +1\. Replace Solr schema.xml to allow Curation Labels to be used. See specific instructions below for those installations with custom metadata blocks (1a) and those without (1b). + +1a\. + +For installations with Custom Metadata Blocks: + +-stop solr instance (usually service solr stop, depending on solr installation/OS, see the [Installation Guide](https://guides.dataverse.org/en/5.7/installation/prerequisites.html#solr-init-script) + +- add the following line to your schema.xml: + + + +- restart solr instance (usually service solr start, depending on solr/OS) + +1b\. + +For installations without Custom Metadata Blocks: -stop solr instance (usually service solr stop, depending on solr installation/OS, see the [Installation Guide](https://guides.dataverse.org/en/5.7/installation/prerequisites.html#solr-init-script) From b4e24889dbd8a978dce951af07f611082d557e64 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 6 Oct 2021 13:25:48 -0400 Subject: [PATCH 71/78] missing 's' --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index c3d7ff9d1dc..3b7ce888511 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -86,7 +86,7 @@ and can be reset to the default (inherited from the parent collection or DISABLE The available curation label sets can be listed with:: - curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSet + curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/admin/dataverse/curationLabelSets If the :AllowedCurationLabels setting has a value, one of the available choices will always be "DISABLED" which allows curation labels to be turned off for a given collection/dataset. From fe7707270a292d182b6825a2165345e46da47594 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 6 Oct 2021 13:48:53 -0400 Subject: [PATCH 72/78] add api key for getting the current set --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index 3b7ce888511..c244d9ddadd 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -200,7 +200,7 @@ The reserved word "DISABLED" can be used to disable this feature within a given The name of the current curationLabelSet can be seen using:: - curl http://$SERVER/api/datasets/$dataset-id/curationLabelSet + curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/datasets/$dataset-id/curationLabelSet and can be reset to the default (inherited from the parent collection) with (only a superuser can do this) :: From cca90e55d57fc12698f8913913d7f4bb501a8a97 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 6 Oct 2021 13:57:26 -0400 Subject: [PATCH 73/78] fix api docs name param --- doc/sphinx-guides/source/admin/dataverses-datasets.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/sphinx-guides/source/admin/dataverses-datasets.rst b/doc/sphinx-guides/source/admin/dataverses-datasets.rst index c244d9ddadd..842dbc02b74 100644 --- a/doc/sphinx-guides/source/admin/dataverses-datasets.rst +++ b/doc/sphinx-guides/source/admin/dataverses-datasets.rst @@ -72,7 +72,7 @@ The label set used for a collection can be specified via the API as shown below, The curationLabelSet to use within a given collection can be set by specifying its name using:: - curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSetName http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT http://$SERVER/api/admin/dataverse/$dataverse-alias/curationLabelSet?name=$curationLabelSetName The reserved word "DISABLED" can be used to disable this feature within a given Dataverse collection. @@ -194,7 +194,7 @@ The label set used for a dataset can be specified via the API as shown below. On The curationLabelSet to use within a given dataset can be set by specifying its name using:: - curl -H "X-Dataverse-key: $API_TOKEN" -X PUT -d $curationLabelSetName http://$SERVER/api/datasets/$dataset-id/curationLabelSet + curl -H "X-Dataverse-key: $API_TOKEN" -X PUT http://$SERVER/api/datasets/$dataset-id/curationLabelSet?name=$curationLabelSetName The reserved word "DISABLED" can be used to disable this feature within a given Dataverse collection. From c72c57ac2b225b614824d4a5ffc4bed467d73a8b Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Wed, 6 Oct 2021 17:16:20 -0400 Subject: [PATCH 74/78] merge needed for put/delete --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index de6bbe316aa..ee4c5ffa125 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2679,11 +2679,13 @@ public Response setCurationLabelSet(@PathParam("identifier") String dvIdtf, } if (SystemConfig.CURATIONLABELSDISABLED.equals(curationLabelSet) || SystemConfig.DEFAULTCURATIONLABELSET.equals(curationLabelSet)) { dataset.setCurationLabelSetName(curationLabelSet); + datasetService.merge(dataset); return ok("Curation Label Set Name set to: " + curationLabelSet); } else { for (String setName : systemConfig.getCurationLabels().keySet()) { if (setName.equals(curationLabelSet)) { dataset.setCurationLabelSetName(curationLabelSet); + datasetService.merge(dataset); return ok("Curation Label Set Name set to: " + setName); } } From cc8e14604636b856e514bc80cc22002d8322b35f Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 7 Oct 2021 13:47:45 -0400 Subject: [PATCH 75/78] don't need to be super to get allowed curation labels in set --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index ee4c5ffa125..208d6f22455 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2730,9 +2730,6 @@ public Response getAllowedCurationLabels(@PathParam("identifier") String dvIdtf, try { AuthenticatedUser user = findAuthenticatedUserOrDie(); - if (!user.isSuperuser()) { - return error(Response.Status.FORBIDDEN, "Superusers only."); - } } catch (WrappedResponse wr) { return wr.getResponse(); } From 0b617f64ce3a90acc5565be92a2f533aa0bdb305 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 7 Oct 2021 13:56:05 -0400 Subject: [PATCH 76/78] add permission check --- .../java/edu/harvard/iq/dataverse/api/Datasets.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 208d6f22455..14d88ace657 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2727,9 +2727,9 @@ public Response resetCurationLabelSet(@PathParam("identifier") String dvIdtf, @Path("{identifier}/allowedCurationLabels") public Response getAllowedCurationLabels(@PathParam("identifier") String dvIdtf, @Context UriInfo uriInfo, @Context HttpHeaders headers) throws WrappedResponse { - + AuthenticatedUser user = null; try { - AuthenticatedUser user = findAuthenticatedUserOrDie(); + user = findAuthenticatedUserOrDie(); } catch (WrappedResponse wr) { return wr.getResponse(); } @@ -2741,8 +2741,12 @@ public Response getAllowedCurationLabels(@PathParam("identifier") String dvIdtf, } catch (WrappedResponse ex) { return ex.getResponse(); } - String[] labelArray = systemConfig.getCurationLabels().get(dataset.getEffectiveCurationLabelSetName()); - return response(req -> ok(Strings.concat(",", labelArray))); + if (permissionSvc.requestOn(createDataverseRequest(user), dataset).has(Permission.PublishDataset)) { + String[] labelArray = systemConfig.getCurationLabels().get(dataset.getEffectiveCurationLabelSetName()); + return response(req -> ok(Strings.concat(",", labelArray))); + } else { + return error(Response.Status.FORBIDDEN, "You are not permitted to view the allowed curation labels for this dataset."); + } } @GET From 10e8bc457d7a03e87a3ed047473dd1f42f2b9044 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 7 Oct 2021 14:13:06 -0400 Subject: [PATCH 77/78] fix concatenation --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index 14d88ace657..cdef18fedf3 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -2743,7 +2743,7 @@ public Response getAllowedCurationLabels(@PathParam("identifier") String dvIdtf, } if (permissionSvc.requestOn(createDataverseRequest(user), dataset).has(Permission.PublishDataset)) { String[] labelArray = systemConfig.getCurationLabels().get(dataset.getEffectiveCurationLabelSetName()); - return response(req -> ok(Strings.concat(",", labelArray))); + return response(req -> ok(String.join(",", labelArray))); } else { return error(Response.Status.FORBIDDEN, "You are not permitted to view the allowed curation labels for this dataset."); } From 0b681218a4fde3fc59a9d3874ccf4ea15f8a9ec5 Mon Sep 17 00:00:00 2001 From: Jim Myers Date: Thu, 7 Oct 2021 14:14:57 -0400 Subject: [PATCH 78/78] fix null for no label --- src/main/java/edu/harvard/iq/dataverse/api/Datasets.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java index cdef18fedf3..1cca0157844 100644 --- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java +++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java @@ -1767,7 +1767,7 @@ public Response getCurationStatus(@PathParam("id") String idSupplied) { Dataset ds = findDatasetOrDie(idSupplied); DatasetVersion dsv = ds.getLatestVersion(); if (dsv.isDraft() && permissionSvc.requestOn(createDataverseRequest(findUserOrDie()), ds).has(Permission.PublishDataset)) { - return response(req -> ok(dsv.getExternalStatusLabel())); + return response(req -> ok(dsv.getExternalStatusLabel()==null ? "":dsv.getExternalStatusLabel())); } else { return error(Response.Status.FORBIDDEN, "You are not permitted to view the curation status of this dataset."); }