Merge pull request #7874 from jmchilton/cleanup_integration_tests

Cleanup integration test configuration code.
galaxyproject · May 2, 2019 · 918db55 · 918db55
2 parents 8b0bbba + c6fcd05
commit 918db55
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Showing 14 changed files with 34 additions and 66 deletions.
diff --git a/test/integration/chained_dyndest_job_conf.xml b/test/integration/chained_dyndest_job_conf.xml
@@ -1,16 +1,12 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.chained_dyndest_rules.module1</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="dyn_dest1">
         <destination id="dyn_dest1" runner="dynamic">
             <param id="type">python</param>

diff --git a/test/integration/delay_job_conf.xml b/test/integration/delay_job_conf.xml
@@ -4,16 +4,12 @@
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.delay_rules</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_dest">
 
         <destination id="local_dest" runner="dynamic">

diff --git a/test/integration/dockerized_job_conf.xml b/test/integration/dockerized_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_docker">
         <destination id="local_docker" runner="local">
             <param id="docker_enabled">true</param>

diff --git a/test/integration/embedded_pulsar_job_conf.xml b/test/integration/embedded_pulsar_job_conf.xml
@@ -2,13 +2,10 @@
 <!-- A job config for testing the Pulsar embedded runner -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="pulsar_embed" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
         </plugin>
     </plugins>
-    <handlers>
-        <handler id="main"/>
-    </handlers>
     <destinations default="pulsar_embed">
         <destination id="local" runner="local">
         </destination>

diff --git a/test/integration/embedded_pulsar_metadata_job_conf.xml b/test/integration/embedded_pulsar_metadata_job_conf.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<!-- A job config for testing the Pulsar embedded runner -->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
+        <plugin id="pulsar_embed" type="runner" load="galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner">
+        </plugin>
+    </plugins>
+    <destinations default="pulsar_embed">
+        <destination id="local" runner="local">
+        </destination>
+        <destination id="pulsar_embed" runner="pulsar_embed">
+            <param id="remote_metadata">true</param>
+            <param id="default_file_action">copy</param>
+        </destination>
+    </destinations>
+    <tools>
+        <tool id="upload1" destination="local" />
+    </tools>
+</job_conf>
diff --git a/test/integration/io_injection_job_conf.xml b/test/integration/io_injection_job_conf.xml
@@ -1,18 +1,13 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
             <env exec="echo 'moo std cow'" />
             <env exec="(>&amp;2 echo 'moo err cow')" />
         </destination>
     </destinations>
-
 </job_conf>
diff --git a/test/integration/objectstore_selection_job_conf.xml b/test/integration/objectstore_selection_job_conf.xml
@@ -5,16 +5,12 @@
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="dynamic" type="runner">
             <param id="rules_module">integration.objectstore_selection_rules</param>
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local">
         <!-- Upload destination. -->
         <destination id="local" runner="local">

diff --git a/test/integration/resubmission_job_conf.xml b/test/integration/resubmission_job_conf.xml
@@ -5,7 +5,7 @@
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="failure_runner" type="runner" load="integration.resubmission_runners:FailsJobRunner" workers="2">
         </plugin>
         <plugin id="assertion_runner" type="runner" load="integration.resubmission_runners:AssertionJobRunner" workers="2">
@@ -15,10 +15,6 @@
         </plugin>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="initial_destination">
         <destination id="initial_destination" runner="dynamic">
             <param id="type">python</param>

diff --git a/test/integration/resubmission_pulsar_job_conf.xml b/test/integration/resubmission_pulsar_job_conf.xml
@@ -1,17 +1,13 @@
 <?xml version="1.0"?>
 <!-- 
-    Slimmed down resubmission_job_conf.xml for testing default resubmission rules.
+    Variant of resubmission_job_conf for testing Pulsar resubmission.
 -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
         <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="initial_pulsar">
         <destination id="initial_pulsar" runner="pulsar_rest">
             <!-- Use a reserved, unused ip to force a resubmission -->

diff --git a/test/integration/sets_tmp_dir_expression_job_conf.xml b/test/integration/sets_tmp_dir_expression_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
             <param id="tmp_dir">$(mktemp cooltmpXXXXXXXXXXXX)</param>

diff --git a/test/integration/sets_tmp_dir_to_true_job_conf.xml b/test/integration/sets_tmp_dir_to_true_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
             <param id="tmp_dir">True</param>

diff --git a/test/integration/simple_job_conf.xml b/test/integration/simple_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations>
         <destination id="local_dest" runner="local">
         </destination>

diff --git a/test/integration/singularity_job_conf.xml b/test/integration/singularity_job_conf.xml
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
     </plugins>
 
-    <handlers>
-        <handler id="main"/>
-    </handlers>
-
     <destinations default="local_singularity">
         <destination id="local_singularity" runner="local">
             <param id="singularity_enabled">true</param>

diff --git a/test/integration/test_objectstore_jobs.py b/test/integration/test_objectstore_jobs.py
@@ -1,4 +1,4 @@
-"""Integration tests for object stores."""
+"""Integration tests for job and object store interactions."""
 
 import os
 import string
@@ -8,10 +8,6 @@
     DatasetPopulator,
 )
 
-SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
-
-
 DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template("""<?xml version="1.0"?>
 <object_store type="hierarchical">
     <backends>