Merge branch 'hotfix/1.1.1'

Author: denis-yuen

pom.xml

@@ -82,7 +82,7 @@
     <artifactId>seqware</artifactId>
     <packaging>pom</packaging>
     <groupId>com.github.seqware</groupId>
-    <version>1.1.0</version>
+    <version>1.1.1</version>
 
     <repositories>
         <repository>

seqware-admin-webservice/pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

seqware-archetypes/seqware-archetype-decider/pom.xml

@@ -9,7 +9,7 @@
     <description>SeqWare Java Decider archetype</description>
 
     <parent> 
-        <version>1.1.0</version> 
+        <version>1.1.1</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
 	<relativePath>../../pom.xml</relativePath>

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</seqware-version>
+        <seqware-version>1.1.1</seqware-version>
         <workflow-version>1.0</workflow-version>
         <workflow-name>${workflow-name}</workflow-name>
     </properties>

seqware-archetypes/seqware-archetype-java-workflow/pom.xml

@@ -9,7 +9,7 @@
     <description>SeqWare Java workflow archetype</description>
 
     <parent> 
-        <version>1.1.0</version> 
+        <version>1.1.1</version> 
         <groupId>com.github.seqware</groupId> 
         <artifactId>seqware</artifactId> 
         <relativePath>../../pom.xml</relativePath>

seqware-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</seqware-version>
+        <seqware-version>1.1.1</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>

seqware-archetypes/seqware-archetype-module/pom.xml

@@ -9,7 +9,7 @@
     <description>SeqWare module archetype</description>
 
     <parent>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
 	<relativePath>../../pom.xml</relativePath>

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</seqware-version>
+    <seqware-version>1.1.1</seqware-version>
   </properties>
 
   <build>

seqware-common/pom.xml

@@ -11,7 +11,7 @@
     <packaging>jar</packaging>
 
     <parent>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
         <groupId>com.github.seqware</groupId>
         <artifactId>seqware</artifactId>
         <relativePath>../pom.xml</relativePath>

seqware-common/src/main/java/io/seqware/Engines.java

@@ -36,7 +36,7 @@ public String toString() {
 
     /**
      * Check whether the workflow engine is Oozie-based.
-     * 
+     *
      * @param engine
      * @return
      */
@@ -46,7 +46,7 @@ public static boolean isOozie(final String engine) {
 
     /**
      * Check whether the workflow engine is whitestar-based.
-     * 
+     *
      * @param engine
      * @return
      */
@@ -56,7 +56,7 @@ public static boolean isWhiteStar(final String engine) {
 
     /**
      * Check whether the workflow engine supports parallel operation.
-     * 
+     *
      * @param engine
      * @return
      */
@@ -66,7 +66,7 @@ public static boolean isWhiteStarParallel(final String engine) {
 
     /**
      * Check whether the workflow engine supports cancel.
-     * 
+     *
      * @param engine
      * @return
      */
@@ -75,8 +75,8 @@ public static boolean supportsCancel(final String engine) {
     }
 
     /**
-     * Check whether the workflow engine supports retry.
-     * 
+     * Check whether the workflow engine supports retry. Here we mean asynchronous retry.
+     *
      * @param engine
      * @return
      */

seqware-common/src/main/java/io/seqware/pipeline/SqwKeys.java

@@ -55,11 +55,12 @@ public enum SqwKeys {
     OOZIE_QUEUENAME(null, Categories.LAUNCH, true, "Hadoop queue onto which to schedule jobs", "default"),
     OOZIE_WORK_DIR(null, Categories.LAUNCH, true,
             "Working directory where your workflow steps execute and where we store generated scripts and logs", "/usr/tmp/seqware-oozie"),
-    OOZIE_RETRY_MAX(null, Categories.LAUNCH, false, "Number of times that Oozie will retry user steps in workflows", "5"),
+    OOZIE_RETRY_MAX(null, Categories.LAUNCH, false, "Number of times that Oozie and Whitestar will retry user steps in workflows", "5"),
     OOZIE_RETRY_INTERVAL(null, Categories.LAUNCH, false, "Minutes to wait before retry for user steps in workflows", "5"),
     OOZIE_BATCH_THRESHOLD(null, Categories.LAUNCH, false,
             "Above this threshold, provision file events on the same job/workflow will be batched together", "10"),
     OOZIE_BATCH_SIZE(null, Categories.LAUNCH, false, "Number of provision file events that should be batched together", "100"),
+    WHITESTAR_MEMORY_LIMIT(null, Categories.WHITESTAR, false, "Restrict the number of parallel jobs invoked in WhiteStar to this amount of memory",String.valueOf(Integer.MAX_VALUE)),
     FS_HDFS_IMPL("FS.HDFS.IMPL", Categories.LAUNCH, true, "HDFS implementation class", "org.apache.hadoop.hdfs.DistributedFileSystem"),
     OOZIE_SGE_THREADS_PARAM_FORMAT(null, Categories.LAUNCH, false,
             "Only used for 'oozie-sge' engine. Format of qsub flag for specifying number of threads. "
@@ -171,6 +172,7 @@ public enum Categories {
                 "Settings used to configure the installation of workflow bundles"),
         LAUNCH(
                 "Oozie engine settings. Only used for both 'oozie' and 'oozie-sge' engines."),
+        WHITESTAR("WhiteStar engine settings. Only used for the 'whitestar' series of engines."),
         OOZIE_SGE(
                 "Oozie-SGE engine settings. Only used for 'oozie-sge' engine."),
         ADMIN("Settings used for administrators"),

seqware-common/src/main/java/net/sourceforge/seqware/common/metadata/MetadataInMemory.java

@@ -22,6 +22,7 @@
 import io.seqware.common.model.ProcessingStatus;
 import io.seqware.common.model.SequencerRunStatus;
 import io.seqware.common.model.WorkflowRunStatus;
+import io.seqware.pipeline.SqwKeys;
 import java.io.Writer;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -43,6 +44,7 @@
 import net.sourceforge.seqware.common.model.File;
 import net.sourceforge.seqware.common.model.FileAttribute;
 import net.sourceforge.seqware.common.model.FileProvenanceParam;
+import net.sourceforge.seqware.common.model.FirstTierModel;
 import net.sourceforge.seqware.common.model.IUS;
 import net.sourceforge.seqware.common.model.IUSAttribute;
 import net.sourceforge.seqware.common.model.Lane;
@@ -69,6 +71,7 @@
 import net.sourceforge.seqware.common.model.WorkflowRunAttribute;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.common.util.Log;
+import net.sourceforge.seqware.common.util.configtools.ConfigTools;
 
 /**
  * This stores some metadata in memory as an exploration of running workflows without a running database or web service.
@@ -82,14 +85,14 @@ public class MetadataInMemory implements Metadata {
     /**
      * Stores SWID/id -> Model object. Unlike the postgres database, we re-use the sw accession as the id
      */
-    private static final Table<Integer, Class, Object> STORE = HashBasedTable.create();
+    private static final Table<Integer, Class<?>, Object> STORE = HashBasedTable.create();
 
     /**
      * Not really thread-safe, why does Guava not have a synchronized wrapper?
      *
      * @return the store
      */
-    private static synchronized Table<Integer, Class, Object> getStore() {
+    private static synchronized Table<Integer, Class<?>, Object> getStore() {
         return STORE;
     }
 
@@ -230,6 +233,7 @@ public int add_workflow_run(int workflowAccession) {
         wr.setWorkflowRunId(wr.getSwAccession());
         wr.setCreateTimestamp(new Date());
         wr.setUpdateTimestamp(new Date());
+        wr.setOwnerUserName(ConfigTools.getSettings().get(SqwKeys.SW_REST_USER.getSettingKey()));
         Workflow workflow = (Workflow) MetadataInMemory.getStore().get(workflowAccession, Workflow.class);
         wr.setWorkflow(workflow);
         MetadataInMemory.getStore().put(wr.getSwAccession(), WorkflowRun.class, wr);
@@ -334,11 +338,27 @@ public ReturnValue addWorkflow(String name, String version, String description,
         return returnValue;
     }
 
+    private synchronized int getCurrentSwAccession() {
+        int currKey = MetadataInMemory.getStore().rowKeySet().size();
+        return currKey;
+    }
+
     private synchronized int getNextSwAccession() {
         int nextKey = MetadataInMemory.getStore().rowKeySet().size() + 1;
         return nextKey;
     }
 
+    public void loadEntity(FirstTierModel model) {
+        // populate store up to the desiredkey
+        int currSWID = getCurrentSwAccession();
+        while (currSWID < model.getSwAccession()) {
+            int swid = getNextSwAccession();
+            MetadataInMemory.getStore().put(swid, Integer.class, swid);
+            currSWID = getCurrentSwAccession();
+        }
+        MetadataInMemory.getStore().put(model.getSwAccession(), model.getClass(), model);
+    }
+
     @Override
     public ReturnValue updateWorkflow(int workflowId, String permanentBundleLocation) {
         throw new UnsupportedOperationException("Not supported yet.");
@@ -520,12 +540,14 @@ public String getWorkflowRunReport(int workflowRunSWID) {
 
     @Override
     public String getWorkflowRunReportStdErr(int workflowRunSWID) {
-        throw new UnsupportedOperationException("Not supported yet.");
+        WorkflowRun wr = (WorkflowRun) MetadataInMemory.getStore().get(workflowRunSWID, WorkflowRun.class);
+        return wr.getStdErr() == null ? "" : wr.getStdErr();
     }
 
     @Override
     public String getWorkflowRunReportStdOut(int workflowRunSWID) {
-        throw new UnsupportedOperationException("Not supported yet.");
+        WorkflowRun wr = (WorkflowRun) MetadataInMemory.getStore().get(workflowRunSWID, WorkflowRun.class);
+        return wr.getStdOut() == null ? "" : wr.getStdOut();
     }
 
     @Override

seqware-common/src/main/java/net/sourceforge/seqware/common/model/Experiment.java

@@ -27,7 +27,7 @@
  * @version $Id: $Id
  */
 public class Experiment extends PermissionsAware implements Serializable, Comparable<Experiment>, ParentAccessionModel,
-        Annotatable<ExperimentAttribute> {
+        Annotatable<ExperimentAttribute>, FirstTierModel {
 
     private static final long serialVersionUID = 2L;
     private Integer experimentId;
@@ -150,19 +150,19 @@ public int hashCode() {
 
     /*
      * public int compareTo(Experiment that) { if(that == null) return -1;
-     *
+     * 
      * if(that.getName() == this.getName()) // when both names are null return 0;
-     *
+     * 
      * if(that.getName() == null) return -1; // when only the other name is null
-     *
+     * 
      * return(that.getName().compareTo(this.getName())); }
-     *
+     * 
      * public String toString() { return new ToStringBuilder(this) .append("experimentId", getExperimentId()) .append("name", getName())
      * .toString(); }
-     *
+     * 
      * public boolean equals(Object other) { if ( (this == other ) ) return true; if ( !(other instanceof Experiment) ) return false;
      * Experiment castOther = (Experiment) other; return new EqualsBuilder() .append(this.getName(), castOther.getName()) .isEquals(); }
-     *
+     * 
      * public int hashCode() { return new HashCodeBuilder() .append(getName()) .toHashCode(); }
      */
     /**
@@ -425,6 +425,7 @@ public void setExperimentId(Integer experimentId) {
      *
      * @return a {@link java.lang.Integer} object.
      */
+    @Override
     public Integer getSwAccession() {
         return swAccession;
     }

seqware-common/src/main/java/net/sourceforge/seqware/common/model/File.java

@@ -19,7 +19,7 @@
  * @author boconnor
  * @version $Id: $Id
  */
-public class File extends PermissionsAware implements Serializable, Comparable<File>, Annotatable<FileAttribute> {
+public class File extends PermissionsAware implements Serializable, Comparable<File>, Annotatable<FileAttribute>, FirstTierModel {
 
     private static final long serialVersionUID = 3681322115923390568L;
     private Integer fileId;
@@ -268,6 +268,7 @@ public void setDescription(String description) {
      *
      * @return a {@link java.lang.Integer} object.
      */
+    @Override
     public Integer getSwAccession() {
         return swAccession;
     }

seqware-common/src/main/java/net/sourceforge/seqware/common/model/FirstTierModel.java

@@ -0,0 +1,32 @@
+/*
+ * Copyright (C) 2014 SeqWare
+ *
+ * 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 License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package net.sourceforge.seqware.common.model;
+
+/**
+ * This links together all models that have a FirstTierModel.
+ *
+ * @author dyuen
+ */
+public interface FirstTierModel {
+
+    /**
+     * A unique identifier for entities that are unique within the SeqWare database.
+     * 
+     * @return
+     */
+    public Integer getSwAccession();
+}

seqware-common/src/main/java/net/sourceforge/seqware/common/model/IUS.java

@@ -23,7 +23,7 @@
  * @author boconnor
  * @version $Id: $Id
  */
-public class IUS extends PermissionsAware implements Serializable, Comparable<IUS>, ParentAccessionModel, Annotatable<IUSAttribute> {
+public class IUS extends PermissionsAware implements Serializable, Comparable<IUS>, ParentAccessionModel, Annotatable<IUSAttribute>, FirstTierModel {
 
     private static final long serialVersionUID = 3472028115923390568L;
     private Integer iusId;

seqware-common/src/main/java/net/sourceforge/seqware/common/model/Invoice.java

@@ -19,7 +19,7 @@
  * @author boconnor
  * @version $Id: $Id
  */
-public class Invoice extends PermissionsAware implements Serializable, Comparable<Invoice> {
+public class Invoice extends PermissionsAware implements Serializable, Comparable<Invoice>, FirstTierModel {
     /**
      * LEFT OFF WITH: this needs to be finished
      */

seqware-common/src/main/java/net/sourceforge/seqware/common/model/Lane.java

@@ -25,7 +25,8 @@
  * @author boconnor
  * @version $Id: $Id
  */
-public class Lane extends PermissionsAware implements Serializable, Comparable<Lane>, ParentAccessionModel, Annotatable<LaneAttribute> {
+public class Lane extends PermissionsAware implements Serializable, Comparable<Lane>, ParentAccessionModel, Annotatable<LaneAttribute>,
+        FirstTierModel {
 
     private static final long serialVersionUID = 5681328115923390568L;
     private Integer laneId;
@@ -125,18 +126,18 @@ public int hashCode() {
 
     /*
      * public int compareTo(Lane that) { if(that == null || getSwAccession() == null) return -1;
-     *
+     * 
      * if(that.getSwAccession() == this.getSwAccession()) // when both names are null return 0;
-     *
+     * 
      * if(that.getSwAccession() == null) return -1; // when only the other name is null
-     *
+     * 
      * return(that.getSwAccession().compareTo(this.getSwAccession())); }
-     *
+     * 
      * public String toString() { return new ToStringBuilder(this) .append("laneId", getLaneId()) .toString(); }
-     *
+     * 
      * public boolean equals(Object other) { if ( (this == other ) ) return true; if ( !(other instanceof Lane) ) return false; Lane
      * castOther = (Lane) other; return new EqualsBuilder() .append(this.getSwAccession(), castOther.getSwAccession()) .isEquals(); }
-     *
+     * 
      * public int hashCode() { return new HashCodeBuilder() .append(getSwAccession()) .toHashCode(); }
      */
     /**
@@ -687,7 +688,7 @@ public void setSampleType(String sampleType) {
 
     /*
      * public String getSampleName() { return sampleName; }
-     *
+     * 
      * public void setSampleName(String sampleName) { this.sampleName = sampleName; }
      */
     /**