Merge branch 'hotfix/1.1.0-beta.1'

SeqWare · Jan 16, 2015 · 5e4ae85 · 5e4ae85
2 parents 3c0a669 + 3f3ddf5
commit 5e4ae85
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Showing 42 changed files with 189 additions and 113 deletions.
diff --git a/pom.xml b/pom.xml
@@ -82,7 +82,7 @@
     <artifactId>seqware</artifactId>
     <packaging>pom</packaging>
     <groupId>com.github.seqware</groupId>
-    <version>1.1.0-beta.0</version>
+    <version>1.1.0-beta.1-SNAPSHOT</version>
 
     <repositories>
         <repository>

diff --git a/seqware-admin-webservice/pom.xml b/seqware-admin-webservice/pom.xml
@@ -14,7 +14,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -112,7 +112,7 @@
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
-            <version>2.6</version>
+            <version>2.7</version>
         </dependency>
         <dependency>
             <groupId>com.google.guava</groupId>

diff --git a/seqware-archetypes/seqware-archetype-decider/pom.xml b/seqware-archetypes/seqware-archetype-decider/pom.xml
@@ -9,7 +9,7 @@
     <description>SeqWare Java Decider archetype</description>
 
     <parent> 
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
 	<relativePath>../../pom.xml</relativePath>

diff --git a/seqware-archetypes/seqware-archetype-decider/src/main/resources/archetype-resources/pom.xml b/seqware-archetypes/seqware-archetype-decider/src/main/resources/archetype-resources/pom.xml
@@ -15,7 +15,7 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <seqware-version>1.1.0-beta.0</seqware-version>
+        <seqware-version>1.1.0-beta.1-SNAPSHOT</seqware-version>
         <workflow-version>1.0</workflow-version>
         <workflow-name>${workflow-name}</workflow-name>
     </properties>

diff --git a/seqware-archetypes/seqware-archetype-java-workflow/pom.xml b/seqware-archetypes/seqware-archetype-java-workflow/pom.xml
@@ -9,7 +9,7 @@
     <description>SeqWare Java workflow archetype</description>
 
     <parent> 
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
         <relativePath>../../pom.xml</relativePath>

diff --git a/...archetypes/seqware-archetype-java-workflow/src/main/resources/archetype-resources/pom.xml b/...archetypes/seqware-archetype-java-workflow/src/main/resources/archetype-resources/pom.xml
@@ -19,7 +19,7 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <seqware-version>1.1.0-beta.0</seqware-version>
+        <seqware-version>1.1.0-beta.1-SNAPSHOT</seqware-version>
         <skipITs>true</skipITs>
         <workflow-full-name>Workflow_Bundle_${workflow-name}_${workflow-version}_SeqWare_${seqware-version}</workflow-full-name>
         <workflow-dir>${project.build.directory}/${workflow-full-name}/Workflow_Bundle_${workflow-name}/${workflow-version}</workflow-dir>

diff --git a/seqware-archetypes/seqware-archetype-module/pom.xml b/seqware-archetypes/seqware-archetype-module/pom.xml
@@ -9,7 +9,7 @@
     <description>SeqWare module archetype</description>
 
     <parent>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
 	<relativePath>../../pom.xml</relativePath>

diff --git a/seqware-archetypes/seqware-archetype-module/src/main/resources/archetype-resources/pom.xml b/seqware-archetypes/seqware-archetype-module/src/main/resources/archetype-resources/pom.xml
@@ -14,7 +14,7 @@
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-    <seqware-version>1.1.0-beta.0</seqware-version>
+    <seqware-version>1.1.0-beta.1-SNAPSHOT</seqware-version>
   </properties>
 
   <build>

diff --git a/seqware-common/pom.xml b/seqware-common/pom.xml
@@ -11,7 +11,7 @@
     <packaging>jar</packaging>
 
     <parent>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
         <relativePath>../pom.xml</relativePath>

diff --git a/seqware-distribution/pom.xml b/seqware-distribution/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <parent> 
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
         <relativePath>../pom.xml</relativePath> 

diff --git a/seqware-ext-admin-testing/pom.xml b/seqware-ext-admin-testing/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <parent> 
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
         <relativePath>../pom.xml</relativePath> 

diff --git a/seqware-ext-testing/pom.xml b/seqware-ext-testing/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
         <relativePath>../pom.xml</relativePath>

diff --git a/seqware-meta-db/pom.xml b/seqware-meta-db/pom.xml
@@ -10,7 +10,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/seqware-pipeline/pom.xml b/seqware-pipeline/pom.xml
@@ -11,7 +11,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java b/seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/deciders/BasicDecider.java
@@ -613,8 +613,11 @@ private void addFileToSets(ReturnValue file, FileMetadata fm, Collection<String>
             if (swid == null || swid.trim().isEmpty()) {
                 swid = file.getAttribute(Header.LANE_SWA.getTitle());
             }
+            // seqware-2002 it is possible that both are null if the path goes through sample_processing
+            if (swid == null || swid.trim().isEmpty()) {
+                return;
+            }
             workflowParentAccessionsToRun.add(swid);
-
         }
     }
 
@@ -1040,16 +1043,6 @@ private List<ReturnValue> convertFileProvenanceReport(List<Map<String, String>>
             handleAttributes(map, row, Header.SEQUENCER_RUN_ATTRIBUTES, Header.SEQUENCER_RUN_TAG_PREFIX);
             handleAttributes(map, row, Header.PROCESSING_ATTRIBUTES, Header.PROCESSING_TAG_PREFIX);
             handleAttributes(map, row, Header.FILE_ATTRIBUTES, Header.FILE_TAG_PREFIX);
-
-            // handle additional quirks that don't belong in the files report here FindAllTheFiles
-            // parent sample name and parent sample swid end with ':' for some reason and OicrDecider seems to have code relying on this
-            String parentSampleName = map.get(Header.PARENT_SAMPLE_NAME.getTitle());
-            parentSampleName += ":";
-            map.put(Header.PARENT_SAMPLE_NAME.getTitle(), parentSampleName);
-            String parentSampleSWID = map.get(Header.PARENT_SAMPLE_SWA.getTitle());
-            parentSampleSWID += ":";
-            map.put(Header.PARENT_SAMPLE_SWA.getTitle(), parentSampleSWID);
-
         }
         return list;
     }

diff --git a/.../main/java/net/sourceforge/seqware/pipeline/plugins/fileprovenance/ProvenanceUtility.java b/.../main/java/net/sourceforge/seqware/pipeline/plugins/fileprovenance/ProvenanceUtility.java
@@ -17,21 +17,25 @@
 package net.sourceforge.seqware.pipeline.plugins.fileprovenance;
 
 import com.google.common.collect.ImmutableList;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.EnumMap;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+
 import joptsimple.ArgumentAcceptingOptionSpec;
 import joptsimple.OptionParser;
 import joptsimple.OptionSet;
 import joptsimple.OptionSpec;
+import net.sourceforge.seqware.common.err.NotFoundException;
 import net.sourceforge.seqware.common.metadata.Metadata;
 import net.sourceforge.seqware.common.model.FileProvenanceParam;
 import net.sourceforge.seqware.common.model.Sample;
 import net.sourceforge.seqware.common.model.SequencerRun;
 import net.sourceforge.seqware.common.model.Study;
+import net.sourceforge.seqware.common.util.Log;
 
 /**
  * Convenience methods that can be shared by utilities that access the FileProvenance report
@@ -122,16 +126,30 @@ public static Map<FileProvenanceParam, List<String>> convertOptionsToMap(OptionS
                 } else if (filter == HumanProvenanceFilters.STUDY_NAME) {
                     for (String value : (List<String>) swaValues) {
                         List<Study> studiesByName = metadata.getStudyByName(value);
+                        // User must be notified if the sample name or root sample name was invalid (could not be found).
+                        if (studiesByName == null || studiesByName.size() == 0) {
+                            String errorText = "The study with the name \"" + value + "\" could not be found.";
+                            Log.error(errorText);
+                            throw new NotFoundException(errorText);
+                        }
                         for (Study study : studiesByName) {
                             swaStrings.add(String.valueOf(study.getSwAccession()));
                         }
+
                     }
                 } else if (filter == HumanProvenanceFilters.SAMPLE_NAME || filter == HumanProvenanceFilters.ROOT_SAMPLE_NAME) {
                     for (String value : (List<String>) swaValues) {
                         List<Sample> samplesByName = metadata.getSampleByName(value);
+                        // User must be notified if the sample name or root sample name was invalid (could not be found).
+                        if (samplesByName == null || samplesByName.size() == 0) {
+                            String errorText = "The sample with the name \"" + value + "\" could not be found.";
+                            Log.error(errorText);
+                            throw new NotFoundException(errorText);
+                        }
                         for (Sample sample : samplesByName) {
                             swaStrings.add(String.valueOf(sample.getSwAccession()));
                         }
+
                     }
                 } else if (filter == HumanProvenanceFilters.SEQUENCER_RUN_NAME) {
                     for (String value : (List<String>) swaValues) {

diff --git a/...ain/java/net/sourceforge/seqware/pipeline/workflowV2/engine/oozie/object/WorkflowApp.java b/...ain/java/net/sourceforge/seqware/pipeline/workflowV2/engine/oozie/object/WorkflowApp.java
@@ -34,7 +34,8 @@ public class WorkflowApp {
     public static final int THRESHOLD = Integer.valueOf(ConfigTools.getSettings()
             .containsKey(SqwKeys.OOZIE_BATCH_THRESHOLD.getSettingKey()) ? ConfigTools.getSettings().get(
             SqwKeys.OOZIE_BATCH_THRESHOLD.getSettingKey()) : "5");
-    public static final String JOB_PREFIX = "swa_";
+    // note: jobs must be prefixed with a valid character from the alphabet
+    public static final String JOB_PREFIX = "s";
 
     private final AbstractWorkflowDataModel wfdm;
     /**
@@ -486,7 +487,8 @@ private void handleUnattachedProvisionFileEvents(final AbstractWorkflowDataModel
         if (!wfdm.getFiles().isEmpty()) {
             Set<OozieJob> newParents = new LinkedHashSet<>();
             for (Map.Entry<String, SqwFile> entry : wfdm.getFiles().entrySet()) {
-                AbstractJob abstractProvisionXJob = new BashJob("provisionFile_" + entry.getKey().replaceAll("\\.", "_"));
+                AbstractJob abstractProvisionXJob = new BashJob("pf" + (entry.getValue().isInput() ? "i" : "o") + "_"
+                        + entry.getKey().replaceAll("\\.", "_"));
                 abstractProvisionXJob.getFiles().add(entry.getValue());
                 OozieProvisionFileJob oozieProvisionXJob = new OozieProvisionFileJob(abstractProvisionXJob, entry.getValue(), JOB_PREFIX
                         + workflowRunAccession + "_" + abstractProvisionXJob.getAlgo() + "_" + this.jobs.size(), this.uniqueWorkingDir,
@@ -581,7 +583,7 @@ private void handleAttachedProvisionFileEventsForJob(final AbstractJob job, fina
                 // create a provisionfile job
                 if (file.isInput()) {
                     // create a provisionFileJob;
-                    AbstractJob abstractProvisionInJob = new BashJob("provisionFile_in");
+                    AbstractJob abstractProvisionInJob = new BashJob("pfi");
                     abstractProvisionInJob.getFiles().add(file);
                     OozieProvisionFileJob oozieProvisionInJob = new OozieProvisionFileJob(abstractProvisionInJob, file, JOB_PREFIX
                             + workflowRunAccession + "_" + abstractProvisionInJob.getAlgo() + "_" + jobs.size(), this.uniqueWorkingDir,
@@ -615,7 +617,7 @@ private void handleAttachedProvisionFileEventsForJob(final AbstractJob job, fina
                     }
                 } else {
                     // create a provisionFileJob;
-                    AbstractJob abstractProvisionOutJob = new BashJob("provisionFile_out");
+                    AbstractJob abstractProvisionOutJob = new BashJob("pfo");
                     abstractProvisionOutJob.getFiles().add(file);
                     OozieProvisionFileJob oozieProvisionOutJob = new OozieProvisionFileJob(abstractProvisionOutJob, file, JOB_PREFIX
                             + workflowRunAccession + "_" + abstractProvisionOutJob.getAlgo() + "_" + jobs.size(), this.uniqueWorkingDir,
@@ -689,8 +691,7 @@ public BucketGenerator(boolean input, String uniqueName, String workflowRunAcces
          * @return
          */
         private BatchedOozieProvisionFileJob createBucket() {
-            String name = JOB_PREFIX + workflowRunAccession + "_provisionFile_" + (input ? "In" : "Out") + "_" + uniqueName + "_Batch_"
-                    + currentBucketCount;
+            String name = JOB_PREFIX + workflowRunAccession + "_pf" + (input ? "i" : "o") + "_" + uniqueName + "_b" + currentBucketCount;
             currentBucketCount += BUCKET_SIZE;
             AbstractJob abstractBucketJob = new BashJob(name);
             currentBucket = new BatchedOozieProvisionFileJob(abstractBucketJob, name, WorkflowApp.this.uniqueWorkingDir,

diff --git a/seqware-portal/pom.xml b/seqware-portal/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/seqware-sanity-check/pom.xml b/seqware-sanity-check/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <parent> 
-        <version>1.1.0-beta.0</version> 
+        <version>1.1.0-beta.1-SNAPSHOT</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
         <relativePath>../pom.xml</relativePath> 

diff --git a/seqware-webservice/pom.xml b/seqware-webservice/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0-beta.0</version>
+        <version>1.1.0-beta.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>