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Merge pull request #7874 from jmchilton/cleanup_integration_tests

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Cleanup integration test configuration code.
This commit is contained in:
Martin Cech
2019-05-02 11:32:10 -04:00
committed by GitHub
parent 8b0bbba1a7 c6fcd051c8
commit 918db5537e
14 changed files with 34 additions and 66 deletions
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test/integration/chained_dyndest_job_conf.xml
+1 -5
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@@ -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>
test/integration/delay_job_conf.xml
+1 -5
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@@ -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">
test/integration/dockerized_job_conf.xml
+1 -5
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@@ -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>
test/integration/embedded_pulsar_job_conf.xml
+1 -4
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@@ -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>
test/integration/embedded_pulsar_metadata_job_conf.xml
+20
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@@ -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>
test/integration/io_injection_job_conf.xml
+1 -6
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@@ -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>
test/integration/objectstore_selection_job_conf.xml
+1 -5
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@@ -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">
test/integration/resubmission_job_conf.xml
+1 -5
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@@ -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>
test/integration/resubmission_pulsar_job_conf.xml
+2 -6
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@@ -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 -->
test/integration/sets_tmp_dir_expression_job_conf.xml
+1 -5
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@@ -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>
test/integration/sets_tmp_dir_to_true_job_conf.xml
+1 -5
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@@ -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>
test/integration/simple_job_conf.xml
+1 -5
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@@ -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>
test/integration/singularity_job_conf.xml
+1 -5
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@@ -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>
test/integration/test_objectstore_jobs.py
+1 -5
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@@ -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>