Merge branch 'rollback-retro-sistr-updates'

CHANGELOG.md

@@ -1,6 +1,10 @@
 Changes
 =======
 
+0.20.0 to 0.21.0
+----------------
+* [Administration]: Disabled automated SISTR results from saving to sample metadata.  Also disabled retrospective results from being added during the database update.  Installations that have already performed the 0.20.0 update will have their retrospective automated SISTR results automatically added to sample metadata.  Installations that jump directly to 0.20.1 and above will not have this data added to sample metadata. (0.20.1)
+
 0.19.0 to 0.20.0
 ----------------
 * [Developer]: Fixed exception being thrown related to permission denied for updating samples when a normal user (collaborator on a project) runs the assembly pipeline (0.19.1).

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>ca.corefacility.bioinformatics</groupId>
 	<artifactId>irida</artifactId>
 	<packaging>war</packaging>
-	<version>0.20.0</version>
+	<version>0.20.1</version>
 	<name>irida</name>
 	<url>http://www.irida.ca</url>
 

src/main/java/ca/corefacility/bioinformatics/irida/model/project/Project.java

@@ -82,7 +82,8 @@ public class Project extends IridaResourceSupport
 
 	@NotNull
 	@Column(name="sistr_typing_uploads")
-	private boolean sistrTypingUploads;
+	@Enumerated(EnumType.STRING)
+	private AutomatedSISTRSetting sistrTypingUploads;
 
 	@OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.REMOVE, mappedBy = "project")
 	private List<ProjectUserJoin> users;
@@ -139,7 +140,7 @@ public class Project extends IridaResourceSupport
 
 	public Project() {
 		assembleUploads = false;
-		sistrTypingUploads = false;
+		sistrTypingUploads = AutomatedSISTRSetting.OFF;
 		createdDate = new Date();
 	}
 
@@ -168,7 +169,8 @@ public void setId(final Long id) {
 	public boolean equals(Object other) {
 		if (other instanceof Project) {
 			Project p = (Project) other;
-			return Objects.equals(createdDate, p.createdDate) && Objects.equals(name, p.name);
+			return Objects.equals(createdDate, p.createdDate) && Objects.equals(modifiedDate, modifiedDate) && Objects
+					.equals(name, p.name);
 		}
 
 		return false;
@@ -286,11 +288,23 @@ public void setMaximumCoverage(Integer maximumCoverage) {
 		this.maximumCoverage = maximumCoverage;
 	}
 
-	public boolean getSistrTypingUploads() {
+	public AutomatedSISTRSetting getSistrTypingUploads() {
 		return sistrTypingUploads;
 	}
 
-	public void setSistrTypingUploads(boolean sistrTypingUploads) {
+	public void setSistrTypingUploads(AutomatedSISTRSetting sistrTypingUploads) {
 		this.sistrTypingUploads = sistrTypingUploads;
 	}
+
+	/**
+	 * Setting for how to run automated SISTR analyses.
+	 * OFF - Do not run
+	 * AUTO - Run SISTR
+	 * AUTO_METADATA - Run and save results to metadata
+	 */
+	public enum AutomatedSISTRSetting {
+		OFF,
+		AUTO,
+		AUTO_METADATA
+	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/processing/impl/SistrTypingFileProcessor.java

@@ -1,7 +1,9 @@
 package ca.corefacility.bioinformatics.irida.processing.impl;
 
 import java.util.List;
+import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -65,12 +67,13 @@ public SistrTypingFileProcessor(SequencingObjectRepository objectRepository,
 	 * {@inheritDoc}
 	 */
 	@Override
-	@Transactional
 	public void process(SequencingObject sequencingObject) {
 		logger.debug("Setting up SISTR typing for sequence " + sequencingObject.getId());
 
 		User admin = userRepository.loadUserByUsername("admin");
 
+		Project.AutomatedSISTRSetting automatedSISTRSetting = shouldTypeWithSISTR(sequencingObject);
+
 		// Ensure it's a paired upload. Single end can't currently be
 		// assembled/typed.
 		if (sequencingObject instanceof SequenceFilePair) {
@@ -87,8 +90,16 @@ public void process(SequencingObject sequencingObject) {
 
 			// build an AnalysisSubmission
 			Builder builder = new AnalysisSubmission.Builder(pipelineUUID);
+
+			if(automatedSISTRSetting.equals(Project.AutomatedSISTRSetting.AUTO_METADATA)){
+				builder.updateSamples(true);
+			}
+			else if(automatedSISTRSetting.equals(Project.AutomatedSISTRSetting.AUTO)){
+				builder.updateSamples(false);
+			}
+
 			AnalysisSubmission submission = builder.inputFiles(Sets.newHashSet((SequenceFilePair) sequencingObject))
-					.priority(AnalysisSubmission.Priority.LOW).updateSamples(true)
+					.priority(AnalysisSubmission.Priority.LOW)
 					.name("Automated SISTR Typing " + sequencingObject.toString()).build();
 			submission.setSubmitter(admin);
 
@@ -123,19 +134,18 @@ public Boolean modifiesFile() {
 	public boolean shouldProcessFile(Long sequencingObjectId) {
 		SequencingObject sequencingObject = objectRepository.findOne(sequencingObjectId);
 
-		return shouldTypeWithSISTR(sequencingObject);
+		return !shouldTypeWithSISTR(sequencingObject).equals(Project.AutomatedSISTRSetting.OFF);
 	}
 
 	/**
 	 * Check whether any {@link Project} associated with the
 	 * {@link SequencingObject} is set to type with SISTR.
-	 * 
-	 * @param object
-	 *            {@link SequencingObject} to check to type with SISTR.
+	 *
+	 * @param object {@link SequencingObject} to check to type with SISTR.
 	 * @return true if it should type with SISTR, false otherwise
 	 */
-	private boolean shouldTypeWithSISTR(SequencingObject object) {
-		boolean type = false;
+	private Project.AutomatedSISTRSetting shouldTypeWithSISTR(SequencingObject object) {
+		Project.AutomatedSISTRSetting type = Project.AutomatedSISTRSetting.OFF;
 
 		SampleSequencingObjectJoin sampleForSequencingObject = ssoRepository.getSampleForSequencingObject(object);
 
@@ -147,7 +157,13 @@ private boolean shouldTypeWithSISTR(SequencingObject object) {
 			List<Join<Project, Sample>> projectForSample = psjRepository
 					.getProjectForSample(sampleForSequencingObject.getSubject());
 
-			type = projectForSample.stream().anyMatch(j -> j.getSubject().getSistrTypingUploads());
+			Set<Project.AutomatedSISTRSetting> sistrOptions = projectForSample.stream()
+					.map(j -> j.getSubject().getSistrTypingUploads()).collect(Collectors.toSet());
+
+			if (sistrOptions.contains(Project.AutomatedSISTRSetting.AUTO_METADATA)) {
+				return Project.AutomatedSISTRSetting.AUTO_METADATA;
+			} else if (sistrOptions.contains(Project.AutomatedSISTRSetting.AUTO))
+				return Project.AutomatedSISTRSetting.AUTO;
 		} else {
 			logger.warn("Cannot find sample for sequencing object.  Not typing with SISTR");
 		}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSettingsController.java

@@ -301,7 +301,8 @@ public Map<String, String> updateAssemblySetting(@PathVariable Long projectId, @
 	 */
 	@RequestMapping(value = "/sistr", method = RequestMethod.POST)
 	@ResponseBody
-	public Map<String, String> updateSistrSetting(@PathVariable Long projectId, @RequestParam boolean sistr,
+	public Map<String, String> updateSistrSetting(@PathVariable Long projectId, @RequestParam
+			Project.AutomatedSISTRSetting sistr,
 			final Model model, Locale locale) {
 		Project read = projectService.read(projectId);
 
@@ -311,7 +312,7 @@ public Map<String, String> updateSistrSetting(@PathVariable Long projectId, @Req
 		projectService.updateProjectSettings(read, updates);
 
 		String message = null;
-		if (sistr) {
+		if (sistr.equals(Project.AutomatedSISTRSetting.AUTO) || sistr.equals(Project.AutomatedSISTRSetting.AUTO_METADATA)) {
 			message = messageSource.getMessage("project.settings.notifications.sistr.enabled",
 					new Object[] { read.getLabel() }, locale);
 		} else {

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/0.20.0/all-changes.xml

@@ -11,4 +11,5 @@
     <include file="add-job-error-table.xml"
              relativeToChangelogFile="true"/>
     <include file="pipeline-metadata-entry.xml" relativeToChangelogFile="true"/>
+    <include file="post-update-fix.xml" relativeToChangelogFile="true"/>
 </databaseChangeLog>

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/0.20.0/pipeline-metadata-entry.xml

@@ -7,6 +7,9 @@
 
     <changeSet id="pipeline-metadata-entry" author="tom">
 
+        <validCheckSum>7:04d990c0430b5fd7bd63f5bfc462584b</validCheckSum>
+        <validCheckSum>7:fe424670afa75882a10c9178073eecc1</validCheckSum>
+
         <createTable tableName="pipeline_metadata_entry">
             <column name="id" type="bigint(20)">
                 <constraints nullable="false" primaryKey="true" foreignKeyName="FK_PIPELINE_METADATA_ENTRY"
@@ -38,9 +41,5 @@
         <modifyDataType columnName="value" newDataType="longtext" tableName="metadata_entry"/>
         <modifyDataType columnName="value" newDataType="longtext" tableName="metadata_entry_AUD"/>
 
-        <customChange
-                class="ca.corefacility.bioinformatics.irida.database.changesets.AutomatedSISTRUpdate"></customChange>
-
-
     </changeSet>
 </databaseChangeLog>

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/0.20.0/post-update-fix.xml

@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
+
+    <changeSet id="post-update-fix" author="tom">
+
+        <renameColumn
+                columnDataType="bit(1)"
+                newColumnName="sistr_tmp"
+                oldColumnName="sistr_typing_uploads"
+                tableName="project"/>
+
+        <addColumn tableName="project">
+            <column name="sistr_typing_uploads" type="varchar(255)"/>
+        </addColumn>
+
+        <sql>
+            UPDATE project SET sistr_typing_uploads="AUTO" WHERE sistr_tmp=1
+        </sql>
+
+        <sql>
+            UPDATE project SET sistr_typing_uploads="OFF" WHERE sistr_tmp=0
+        </sql>
+
+        <addNotNullConstraint
+                columnDataType="varchar(255)"
+                columnName="sistr_typing_uploads"
+                defaultNullValue="OFF"
+                tableName="project"/>
+
+        <dropColumn tableName="project" columnName="sistr_tmp"/>
+
+        <renameColumn
+                columnDataType="bit(1)"
+                newColumnName="sistr_tmp"
+                oldColumnName="sistr_typing_uploads"
+                tableName="project_AUD"/>
+
+        <addColumn tableName="project_AUD">
+            <column name="sistr_typing_uploads" type="varchar(255)"/>
+        </addColumn>
+
+        <sql>
+            UPDATE project_AUD SET sistr_typing_uploads="AUTO" WHERE sistr_tmp=1
+        </sql>
+
+        <sql>
+            UPDATE project_AUD SET sistr_typing_uploads="OFF" WHERE sistr_tmp=0
+        </sql>
+
+        <dropColumn tableName="project_AUD" columnName="sistr_tmp"/>
+
+    </changeSet>
+</databaseChangeLog>