Merge pull request #11 from qbicsoftware/development

Development
qbicsoftware-archive · Dec 19, 2017 · a33e5fb · a33e5fb
2 parents b2a2903 + 3ae9d66
commit a33e5fb
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diff --git a/QBiCMainPortlet/WebContent/WEB-INF/lib/LiferayAndVaadinHelpers_410f9ea.jar b/QBiCMainPortlet/WebContent/WEB-INF/lib/LiferayAndVaadinHelpers_410f9ea.jar
diff --git a/QBiCMainPortlet/WebContent/WEB-INF/lib/workflowapi_1087929.jar b/QBiCMainPortlet/WebContent/WEB-INF/lib/workflowapi_1087929.jar
diff --git a/QBiCMainPortlet/WebContent/WEB-INF/lib/workflowapi_8311939.jar b/QBiCMainPortlet/WebContent/WEB-INF/lib/workflowapi_8311939.jar
diff --git a/QBiCMainPortlet/ivy.xml b/QBiCMainPortlet/ivy.xml
@@ -61,12 +61,14 @@
   		<!--upload -->
   		<dependency org="com.github.lookfirst" name="sardine" rev="5.5" />
   		<dependency org="commons-io" name="commons-io" rev="2.4" />
-  		<dependency org="org.apache.httpcomponents" name="httpclient"  rev="4.3" />
+  		<dependency org="commons-httpclient" name="commons-httpclient" rev="3.1" />
+  		<!--<dependency org="org.apache.httpcomponents" name="httpclient"  rev="4.3" />-->
+
   		<!--QBiC -->
   		<dependency org="life.qbic.openbis" name="openbisclient" rev="1.1.3" />
+  		<dependency org="life.qbic.openbis" name="liferayandvaadinhelpers" rev="1.1.3-SNAPSHOT" />
   		<!--name conversion -->
   		<dependency org="org.apache.commons" name="commons-collections4" rev="4.0" />
-
   		<!--vaadin charts -->
   		<!--<dependency org="com.vaadin.addon" name="vaadin-charts" rev="3.2.0" />-->
 

diff --git a/QBiCMainPortlet/ivysettings.xml b/QBiCMainPortlet/ivysettings.xml
@@ -5,8 +5,9 @@
 		<chain name="default">
 			<!-- Public Maven repository -->
 			<ibiblio name="public" m2compatible="true" />
-			<!-- <ibiblio name="nexus-snapshots" m2compatible="true" usepoms="true" root="https://peltzer.com.de/nexus/content/repositories/snapshots" changingPattern="*-SNAPSHOT" />-->
-			<ibiblio name="nexus-releases" m2compatible="true" usepoms="true" root="https://peltzer.com.de/nexus/content/repositories/releases" />
+			<ibiblio name="QBiC Snapshots" m2compatible="true" usepoms="true" root="https://qbic-repo.am10.uni-tuebingen.de/repository/maven-snapshots" changingPattern=".+\\.-SNAPSHOT" checkmodified="true" changingMatcher="regexp" />
+			<ibiblio name="QBiC Releases" m2compatible="true" usepoms="true" root="https://qbic-repo.am10.uni-tuebingen.de/repository/maven-releases" />
+
 			<!-- Vaadin Add-on repository -->
 			<ibiblio name="vaadin-addons" usepoms="true" m2compatible="true"
 				root="http://maven.vaadin.com/vaadin-addons" />

diff --git a/QBiCMainPortlet/src/controllers/WorkflowViewController.java b/QBiCMainPortlet/src/controllers/WorkflowViewController.java
@@ -1,6 +1,6 @@
 /*******************************************************************************
- * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016”
- * Christopher Mohr, David Wojnar, Andreas Friedrich
+ * QBiC Project qNavigator enables users to manage their projects. Copyright (C) "2016” Christopher
+ * Mohr, David Wojnar, Andreas Friedrich
  * 
  * This program is free software: you can redistribute it and/or modify it under the terms of the
  * GNU General Public License as published by the Free Software Foundation, either version 3 of the
@@ -15,9 +15,6 @@
  *******************************************************************************/
 package controllers;
 
-import helpers.Utils;
-import life.qbic.openbis.openbisclient.OpenBisClient;
-
 import java.io.Serializable;
 import java.net.ConnectException;
 import java.nio.file.Paths;
@@ -31,31 +28,31 @@
 
 import javax.xml.bind.JAXBException;
 
-import logging.Log4j2Logger;
-
 import org.apache.commons.lang.NotImplementedException;
 
-import parser.XMLParser;
-import properties.Property;
-import submitter.SubmitFailedException;
-import submitter.Submitter;
-import submitter.Workflow;
+import com.vaadin.data.Container;
+import com.vaadin.data.util.BeanItemContainer;
+
 import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
 import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
 import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-import com.vaadin.data.Container;
-import com.vaadin.data.util.BeanItemContainer;
-
 import de.uni_tuebingen.qbic.beans.DatasetBean;
 import de.uni_tuebingen.qbic.qbicmainportlet.DataHandler;
 import de.uni_tuebingen.qbic.qbicmainportlet.DatasetView;
 import de.uni_tuebingen.qbic.qbicmainportlet.ExperimentView;
 import de.uni_tuebingen.qbic.qbicmainportlet.PatientView;
 import de.uni_tuebingen.qbic.qbicmainportlet.ProjectView;
 import de.uni_tuebingen.qbic.qbicmainportlet.SampleView;
+import helpers.Utils;
+import life.qbic.openbis.openbisclient.OpenBisClient;
+import logging.Log4j2Logger;
+import parser.XMLParser;
+import properties.Property;
+import submitter.SubmitFailedException;
+import submitter.Submitter;
+import submitter.Workflow;
 
 public class WorkflowViewController {
   private DataHandler datahandler;
@@ -69,7 +66,7 @@ public class WorkflowViewController {
   private final String wf_started = "Q_WF_STARTED_AT";
   private final String wf_status = "Q_WF_STATUS";
   private final String wf_name = "Q_WF_NAME";
-  private final String openbis_dss = "DSS1";
+  private final String openbis_dss = "DSS1"; // TODO this shouldn't be hardcoded
 
   // used by Microarray QC Workflow. See function mapExperimentalProperties
   private Map<String, String> expProps;
@@ -113,10 +110,9 @@ public Container fillTable(
     for (model.DatasetBean bean : datasetBeans) {
       fileNames.add(bean.getFileName());
 
-      DatasetBean newBean =
-          new DatasetBean(bean.getFileName(), dataMap.get(bean.getCode()).getDataSetTypeCode(),
-              bean.getCode(), bean.getDssPath(), dataMap.get(bean.getCode())
-                  .getSampleIdentifierOrNull());
+      DatasetBean newBean = new DatasetBean(bean.getFileName(),
+          dataMap.get(bean.getCode()).getDataSetTypeCode(), bean.getCode(), bean.getDssPath(),
+          dataMap.get(bean.getCode()).getSampleIdentifierOrNull());
 
       if (dataMap.get(bean.getCode()).getProperties() != null) {
         newBean.setProperties(dataMap.get(bean.getCode()).getProperties());
@@ -198,9 +194,8 @@ public List<String> getConnectedSamples(List<DatasetBean> datasetBeans) {
   public String registerWFSample(String space, String project, String experiment, String typecode,
       List<String> parents, List<DatasetBean> datasets) {
     int last = 0;
-    for (Sample s : datahandler.getOpenBisClient().getSamplesofExperiment(
-        (new StringBuilder("/")).append(space).append("/").append(project).append("/")
-            .append(experiment).toString())) {
+    for (Sample s : datahandler.getOpenBisClient().getSamplesofExperiment((new StringBuilder("/"))
+        .append(space).append("/").append(project).append("/").append(experiment).toString())) {
       String[] codeSplit = s.getCode().split("R");
       String number = codeSplit[codeSplit.length - 1];
       int num = 0;
@@ -413,25 +408,23 @@ public Submitter getSubmitter() {
   }
 
   public String submitAndRegisterWf(String type, String id, Workflow workflow,
-      List<DatasetBean> selectedDatasets) throws ConnectException, IllegalArgumentException,
-      SubmitFailedException {
+      List<DatasetBean> selectedDatasets)
+      throws ConnectException, IllegalArgumentException, SubmitFailedException {
 
     SpaceAndProjectCodes spaceandproject = getSpaceAndProjects(type, id);
 
     String spaceCode = spaceandproject.space;
     String projectCode = spaceandproject.project;
 
 
-    String experimentCode =
-        registerWFExperiment(spaceCode, projectCode, workflow.getExperimentType(),
-            workflow.getID(), workflow.getVersion(), user);
+    String experimentCode = registerWFExperiment(spaceCode, projectCode,
+        workflow.getExperimentType(), workflow.getID(), workflow.getVersion(), user);
 
     List<String> parents = getConnectedSamples(selectedDatasets);
     String sampleType = workflow.getSampleType();
 
-    String sampleCode =
-        registerWFSample(spaceCode, projectCode, experimentCode, sampleType, parents,
-            selectedDatasets);
+    String sampleCode = registerWFSample(spaceCode, projectCode, experimentCode, sampleType,
+        parents, selectedDatasets);
 
     String openbisId =
         String.format("%s-%s-%s-%s", spaceCode, projectCode, experimentCode, sampleCode);
@@ -458,10 +451,9 @@ private SpaceAndProjectCodes getSpaceAndProjects(String type, String id) {
       case "workflowExperimentType":
         return new SpaceAndProjectCodes(split[1], split[2]);
       case SampleView.navigateToLabel:
-        String expId =
-            datahandler.getOpenBisClient()
-                .getSampleByIdentifier(String.format("%s/%s", split[1], split[2]))
-                .getExperimentIdentifierOrNull();
+        String expId = datahandler.getOpenBisClient()
+            .getSampleByIdentifier(String.format("%s/%s", split[1], split[2]))
+            .getExperimentIdentifierOrNull();
         if (expId == null)
           return null;
         return getSpaceAndProjects(ExperimentView.navigateToLabel, expId);
@@ -508,6 +500,7 @@ public String getDatasetsNfsPath(DatasetBean bean) throws IllegalArgumentExcepti
       // TODO get rid of hardocded paths
       path = path.replaceFirst("/mnt/" + openbis_dss, "/mnt/nfs/qbic");
       path = path.replaceFirst("/mnt/DSS_icgc", "/mnt/glusterfs/DSS_icgc");
+      path = path.replaceFirst("/beegfs/bigbio", "/mnt/nfs/bigbio_temp");
       return path;
     } catch (Exception e) {
       e.printStackTrace();

diff --git a/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/AddPatientView.java b/QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/AddPatientView.java
@@ -51,8 +51,8 @@
 import com.vaadin.ui.themes.ValoTheme;
 
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import de.uni_tuebingen.qbic.main.LiferayAndVaadinUtils;
 import helpers.Utils;
+import life.qbic.portal.liferayandvaadinhelpers.main.LiferayAndVaadinUtils;
 import model.NewIvacSampleBean;
 
 

diff --git a/...nPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/ChangeExperimentMetadataComponent.java b/...nPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/ChangeExperimentMetadataComponent.java
@@ -15,8 +15,6 @@
  *******************************************************************************/
 package de.uni_tuebingen.qbic.qbicmainportlet;
 
-import helpers.Utils;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -25,13 +23,6 @@
 
 import javax.xml.bind.JAXBException;
 
-import model.PropertyBean;
-import parser.XMLParser;
-import properties.Property;
-import properties.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm;
-
 import com.vaadin.data.fieldgroup.FieldGroup;
 import com.vaadin.server.Page;
 import com.vaadin.shared.ui.MarginInfo;
@@ -47,7 +38,14 @@
 import com.vaadin.ui.VerticalLayout;
 import com.vaadin.ui.themes.ValoTheme;
 
-import de.uni_tuebingen.qbic.main.LiferayAndVaadinUtils;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm;
+import helpers.Utils;
+import life.qbic.portal.liferayandvaadinhelpers.main.LiferayAndVaadinUtils;
+import model.PropertyBean;
+import parser.XMLParser;
+import properties.Property;
+import properties.PropertyType;
 
 public class ChangeExperimentMetadataComponent extends CustomComponent {
   private DataHandler datahandler;
@@ -230,12 +228,12 @@ private void buildFormLayout() {
 
     for (Property f : xmlProps) {
       PropertyType type = f.getType();
-      
+
       String label = f.getLabel();
       if (f.hasUnit())
         label += " in " + f.getUnit();
       TextField tf = new TextField(label);
-      tf.setData(type);//save property type for later, when it is written back
+      tf.setData(type);// save property type for later, when it is written back
       fieldGroup.bind(tf, label);
       tf.setCaption(label);
       tf.setDescription("Q_PROPERTIES");