Merge branch 'releases/1.8.0'

# Conflicts: # build.gradle
NrgXnat · Feb 20, 2021 · 1db58b3 · 1db58b3
2 parents 9482df6 + 3b9ccdc
commit 1db58b3
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Showing 5 changed files with 70 additions and 29 deletions.
diff --git a/build.gradle b/build.gradle
@@ -17,7 +17,7 @@ plugins {
 }
 
 group "org.nrg.xnat"
-version = "1.7.7-INTERNAL"
+version = "1.8.0"
 
 def id = "xnat-pipeline-${version}"
 
@@ -30,8 +30,8 @@ repositories {
     maven { url "https://nrgxnat.jfrog.io/nrgxnat/libs-snapshot" }
 }
 
-sourceCompatibility = 1.7
-targetCompatibility = 1.7
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
 
 String propertyWithDefault(String name, Object value) {
     hasProperty(name) ? property(name) : value

diff --git a/templates/resources/catalog/images/resources/WebBasedQCImageCreator.xml b/templates/resources/catalog/images/resources/WebBasedQCImageCreator.xml
@@ -41,6 +41,10 @@
 			<pip:name>pwd</pip:name>
 			<pip:description>XNAT Password</pip:description>
 		</pip:argument>
+        <pip:argument id="workflowid">
+            <pip:name>workflowid</pip:name>
+            <pip:description>Workflow ID</pip:description>
+        </pip:argument>
 		<pip:argument id="raw">
 			<pip:name>raw</pip:name>
 			<pip:description>Create QC Images for RAW Files</pip:description>

diff --git a/templates/resources/catalog/xnat_tools/AutoRun.xml b/templates/resources/catalog/xnat_tools/AutoRun.xml
@@ -8,10 +8,10 @@
   ~ Released under the Simplified BSD.
   -->
 
-<Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:autorun="http://www.xnat.org/java/org.nrg.pipeline.client.webservices.WebserviceClient" xmlns:fileUtils="org.nrg.imagingtools.utils.FileUtils" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://nrg.wustl.edu/pipeline ..\..\schema\pipeline.xsd">
+<Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:fileUtils="org.nrg.imagingtools.utils.FileUtils" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://nrg.wustl.edu/pipeline ..\..\schema\pipeline.xsd">
     <name>AutoRun</name>
     <location>xnat_tools</location>
-    <description>Auto-Archive Pipeline for XNAT </description>
+    <description>Auto-Archive Pipeline for XNAT: launches any other pipelines configured as "auto-run" for the project</description>
     <outputFileNamePrefix>^concat(/Pipeline/parameters/parameter[name='cachepath']/values/unique/text(),/Pipeline/parameters/parameter[name='label']/values/unique/text(),'/',/Pipeline/name/text())^</outputFileNamePrefix>
     <parameters>
         <parameter>
@@ -30,29 +30,6 @@
         </parameter>
     </parameters>
     <steps>
-        <step continueOnFailure="true" description="Create Quality Control Images" id="SNAPSHOTS">
-            <resource location="images/resources" name="WebBasedQCImageCreator">
-                <argument id="session">
-                    <value>^/Pipeline/parameters/parameter[name='label']/values/unique/text()^</value>
-                </argument>
-                <argument id="xnatId">
-                    <value>^/Pipeline/parameters/parameter[name='id']/values/unique/text()^</value>
-                </argument>
-                <argument id="project">
-                    <value>^/Pipeline/parameters/parameter[name='project']/values/unique/text()^</value>
-                </argument>
-                <argument id="host">
-                    <value>^/Pipeline/parameters/parameter[name='resolvedHost']/values/unique/text()^</value>
-                </argument>
-                <argument id="user">
-                    <value>^/Pipeline/parameters/parameter[name='user']/values/unique/text()^</value>
-                </argument>
-                <argument id="pwd">
-                    <value>^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^</value>
-                </argument>
-                <argument id="raw"/>
-            </resource>
-        </step>
         <step description="Launch auto-run pipelines" id="LAUNCH_PIPELINES">
             <resource location="xnat_tools" name="XnatDataClient">
                 <argument id="user">

diff --git a/templates/resources/catalog/xnat_tools/QCImageCreator.xml b/templates/resources/catalog/xnat_tools/QCImageCreator.xml
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  ~ pipeline: QCImageCreator.xml
+  ~ XNAT http://www.xnat.org
+  ~ Copyright (c) 2020, Washington University School of Medicine
+  ~ All Rights Reserved
+  ~
+  ~ Released under the Simplified BSD.
+  -->
+
+<Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:fileUtils="org.nrg.imagingtools.utils.FileUtils" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://nrg.wustl.edu/pipeline ../../schema/pipeline.xsd">
+    <name>QCImageCreator</name>
+    <location>xnat_tools</location>
+    <description>QCImageCreator Pipeline for XNAT: previously the AutoRun pipeline, now preserved as QCImageCreator if needed</description>
+    <outputFileNamePrefix>^concat(/Pipeline/parameters/parameter[name='cachepath']/values/unique/text(),/Pipeline/parameters/parameter[name='label']/values/unique/text(),'/',/Pipeline/name/text())^</outputFileNamePrefix>
+    <parameters>
+        <parameter>
+            <name>resolvedHost</name>
+            <values>
+                <unique>^if (boolean(/Pipeline/parameters/parameter[name='aliasHost']/values/unique)) then /Pipeline/parameters/parameter[name='aliasHost']/values/unique/text() else /Pipeline/parameters/parameter[name='host']/values/unique/text()^</unique>
+            </values>
+            <description>Use aliasHost if it exists, or host if not</description>
+        </parameter>
+        <parameter>
+            <name>cachepath</name>
+            <values>
+                <unique>^fileUtils:GetCachePath(/Pipeline/parameters/parameter[name='resolvedHost']/values/unique/text(), /Pipeline/parameters/parameter[name='user']/values/unique/text(), /Pipeline/parameters/parameter[name='pwd']/values/unique/text(),/Pipeline/parameters/parameter[name='project']/values/unique/text())^</unique>
+            </values>
+            <description>Project specific cachepath</description>
+        </parameter>
+    </parameters>
+    <steps>
+        <step continueOnFailure="true" description="Create Quality Control Images" id="SNAPSHOTS">
+            <resource location="images/resources" name="WebBasedQCImageCreator">
+                <argument id="session">
+                    <value>^/Pipeline/parameters/parameter[name='label']/values/unique/text()^</value>
+                </argument>
+                <argument id="xnatId">
+                    <value>^/Pipeline/parameters/parameter[name='id']/values/unique/text()^</value>
+                </argument>
+                <argument id="project">
+                    <value>^/Pipeline/parameters/parameter[name='project']/values/unique/text()^</value>
+                </argument>
+                <argument id="host">
+                    <value>^/Pipeline/parameters/parameter[name='resolvedHost']/values/unique/text()^</value>
+                </argument>
+                <argument id="user">
+                    <value>^/Pipeline/parameters/parameter[name='user']/values/unique/text()^</value>
+                </argument>
+                <argument id="pwd">
+                    <value>^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^</value>
+                </argument>
+                <argument id="workflowid">
+                    <value>^/Pipeline/parameters/parameter[name='workflowid']/values/unique/text()^</value>
+                </argument>
+                <argument id="raw"/>
+            </resource>
+        </step>
+    </steps>
+</Pipeline>
diff --git a/templates/scripts/xnat-tools/XnatDataClient b/templates/scripts/xnat-tools/XnatDataClient
@@ -1,2 +1,2 @@
 @SHELL_LINE@ 
-java -classpath "@PIPELINE_DIR_PATH@"/lib/commons-beanutils-@commons-beanutils:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-codec-@commons-codec:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-collections-@commons-collections:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-io-@commons-io:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-logging-@commons-logging:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/log4j-@log4j:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected] org.nrg.xnat.client.data.XnatDataClient @OS_ARG_SYM@
+java -classpath "@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-beanutils-@commons-beanutils:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-codec-@commons-codec:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-collections-@commons-collections:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-io-@commons-io:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/commons-logging-@commons-logging:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/log4j-@log4j:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected]@CP_SEP@"@PIPELINE_DIR_PATH@"/lib/[email protected]:[email protected] org.nrg.xnat.client.data.XnatDataClient @OS_ARG_SYM@