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Merge pull request #306 from SeqWare/hotfix/workflow_run_input_files
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Hotfix/workflow run input files
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@denis-yuen
denis-yuen committed Feb 27, 2015
2 parents 1c66ef0 + 60cb0f7 commit 165e6e7
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Showing 20 changed files with 74 additions and 45 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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<artifactId>seqware</artifactId>
<packaging>pom</packaging>
<groupId>com.github.seqware</groupId>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>

<repositories>
<repository>
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2 changes: 1 addition & 1 deletion seqware-admin-webservice/pom.xml
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Expand Up @@ -14,7 +14,7 @@
<parent>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion seqware-archetypes/seqware-archetype-decider/pom.xml
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Expand Up @@ -9,7 +9,7 @@
<description>SeqWare Java Decider archetype</description>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-archetypes/seqware-archetype-decider/src/main/resources/archetype-resources/pom.xml
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<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<seqware-version>1.1.0-rc.0</seqware-version>
<seqware-version>1.1.0-rc.1</seqware-version>
<workflow-version>1.0</workflow-version>
<workflow-name>${workflow-name}</workflow-name>
</properties>
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2 changes: 1 addition & 1 deletion seqware-archetypes/seqware-archetype-java-workflow/pom.xml
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<description>SeqWare Java workflow archetype</description>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion ...archetypes/seqware-archetype-java-workflow/src/main/resources/archetype-resources/pom.xml
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<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<seqware-version>1.1.0-rc.0</seqware-version>
<seqware-version>1.1.0-rc.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>
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2 changes: 1 addition & 1 deletion seqware-archetypes/seqware-archetype-module/pom.xml
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<description>SeqWare module archetype</description>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-archetypes/seqware-archetype-module/src/main/resources/archetype-resources/pom.xml
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<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<seqware-version>1.1.0-rc.0</seqware-version>
<seqware-version>1.1.0-rc.1</seqware-version>
</properties>

<build>
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2 changes: 1 addition & 1 deletion seqware-common/pom.xml
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<packaging>jar</packaging>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-distribution/pom.xml
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<modelVersion>4.0.0</modelVersion>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-ext-admin-testing/pom.xml
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<modelVersion>4.0.0</modelVersion>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-ext-testing/pom.xml
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<modelVersion>4.0.0</modelVersion>

<parent>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<relativePath>../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion seqware-meta-db/pom.xml
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Expand Up @@ -10,7 +10,7 @@
<parent>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<relativePath>../pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion seqware-pipeline/pom.xml
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Expand Up @@ -11,7 +11,7 @@
<parent>
<groupId>com.github.seqware</groupId>
<artifactId>seqware</artifactId>
<version>1.1.0-rc.0</version>
<version>1.1.0-rc.1</version>
<relativePath>../pom.xml</relativePath>
</parent>

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18 changes: 17 additions & 1 deletion seqware-pipeline/src/main/java/io/seqware/cli/Main.java
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Expand Up @@ -764,6 +764,13 @@ private static void runCreateTable(List<String> args, String table, String... co
runnerArgs.add("--file");
runnerArgs.add(file);
}
List<String> inputFiles = optVals(args, "--input-file");
for (String file : inputFiles) {
runnerArgs.add("--input-file");
// validate
int swid = swid(file);
runnerArgs.add(String.valueOf(swid));
}

// workflow runs should also have parent accessions in order to be visible to deciders
List<String> parentAccessions = optVals(args, "--parent-accession");
Expand Down Expand Up @@ -931,7 +938,9 @@ private static void createWorkflowRun(List<String> args) {
out(" --parent-accession <swid> The SWID of a parent to the workflow run");
out(" Repeat this parameter to provide multiple parents");
out("Optional fields:");
out(" --file <type::meta-type::path> Add files as a part of the workflow run.");
out(" --file <type::meta-type::path> Add (output) files as a part of the workflow run.");
out(" Repeat this parameter to add multiple files");
out(" --input-file <swid> Add (input) files as a part of the workflow run.");
out(" Repeat this parameter to add multiple files");
out("");
} else {
Expand Down Expand Up @@ -1300,11 +1309,14 @@ private static void workflowSchedule(List<String> args) {
out(" --override <key=value> Override specific parameters from the workflow.ini");
out(" --ini <ini-file> An ini file to configure the workflow run ");
out(" Repeat this parameter to provide multiple files");
out(" --input-file <input-file> Track input files to workflow runs");
out(" Repeat this parameter to provide multiple files");
out("");
} else {
String wfId = reqVal(args, "--accession");
String host = reqVal(args, "--host");
List<String> iniFiles = optVals(args, "--ini");
List<String> inputFiles = optVals(args, "--input-file");
String engine = optVal(args, "--engine", null);
List<String> parentIds = optVals(args, "--parent-accession");
List<String> override = optVals(args, "--override");
Expand All @@ -1329,6 +1341,10 @@ private static void workflowSchedule(List<String> args) {
runnerArgs.add("--parent-accessions");
runnerArgs.add(cdl(parentIds));
}
if (!inputFiles.isEmpty()) {
runnerArgs.add("--input-files");
runnerArgs.add(cdl(inputFiles));
}
if (host != null) {
runnerArgs.add("--host");
runnerArgs.add(host);
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1 change: 1 addition & 0 deletions seqware-pipeline/src/main/java/io/seqware/pipeline/plugins/WorkflowLifecycle.java
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Expand Up @@ -212,6 +212,7 @@ private void runWorkflowSchedulerPlugin(File outFile, File tempSchedulerFile) th
totalParams.add("--" + this.metadataWriteBackOffSpec.options().iterator().next());
}
if (options.has(this.nonOptionSpec)) {
totalParams.add("--");
for (String val : options.valuesOf(this.nonOptionSpec)) {
totalParams.add(val);
}
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