From faae919af121cfde61db5437eca7b73b63f2ba38 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 2 May 2019 08:27:04 -0400
Subject: [PATCH 1/2] Add file missing from #7694

---
 .../embedded_pulsar_metadata_job_conf.xml     | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 test/integration/embedded_pulsar_metadata_job_conf.xml

diff --git a/test/integration/embedded_pulsar_metadata_job_conf.xml b/test/integration/embedded_pulsar_metadata_job_conf.xml
new file mode 100644
index 00000000000..42e5573f6f0
--- /dev/null
+++ b/test/integration/embedded_pulsar_metadata_job_conf.xml
@@ -0,0 +1,23 @@
+<?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="4"/>
+        <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>
+        <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>

From c6fcd051c8e252cd2c6786b85cfed68150f129cd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 2 May 2019 08:43:19 -0400
Subject: [PATCH 2/2] Cleanup integration test configuration code.

Remove copy and paste problems, remote excess configuration unrelated to the what is being tested (handler configuration, multiple worker counts, etc..).
---
 test/integration/chained_dyndest_job_conf.xml          | 6 +-----
 test/integration/delay_job_conf.xml                    | 6 +-----
 test/integration/dockerized_job_conf.xml               | 6 +-----
 test/integration/embedded_pulsar_job_conf.xml          | 5 +----
 test/integration/embedded_pulsar_metadata_job_conf.xml | 5 +----
 test/integration/io_injection_job_conf.xml             | 7 +------
 test/integration/objectstore_selection_job_conf.xml    | 6 +-----
 test/integration/resubmission_job_conf.xml             | 6 +-----
 test/integration/resubmission_pulsar_job_conf.xml      | 8 ++------
 test/integration/sets_tmp_dir_expression_job_conf.xml  | 6 +-----
 test/integration/sets_tmp_dir_to_true_job_conf.xml     | 6 +-----
 test/integration/simple_job_conf.xml                   | 6 +-----
 test/integration/singularity_job_conf.xml              | 6 +-----
 test/integration/test_objectstore_jobs.py              | 6 +-----
 14 files changed, 15 insertions(+), 70 deletions(-)

diff --git a/test/integration/chained_dyndest_job_conf.xml b/test/integration/chained_dyndest_job_conf.xml
index 5fc420259ed..a8d8deee901 100644
--- 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
index 76c68373506..cb36d405079 100644
--- 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
index 44097003630..d4cdce9f651 100644
--- 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
index cabf0c79cd5..f7d08cb3347 100644
--- 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
index 42e5573f6f0..478f19787a0 100644
--- a/test/integration/embedded_pulsar_metadata_job_conf.xml
+++ b/test/integration/embedded_pulsar_metadata_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/io_injection_job_conf.xml b/test/integration/io_injection_job_conf.xml
index ebecf1652f9..4b8822777a6 100644
--- 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
index 9973e095dea..78628a2319f 100644
--- 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
index 0c43cc1935c..40f73acbc51 100644
--- 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
index e7b6a1eabc7..9ee1c867ae2 100644
--- 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
index ac7e5b1b233..b4be01bda77 100644
--- 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
index e976483f389..e5ac91ef453 100644
--- 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
index abcb0768234..568e60f79dd 100644
--- 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
index 8743b71ef7e..ccdc921727e 100644
--- 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
index 3aed7e2944c..c1db9c522e7 100644
--- 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 @@ from base.populators import (
     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>