Merge pull request #17061 from mvdbeek/no_conda_auto_init_pulsar

Disable conda_auto_init in embedded pulsar test cases
galaxyproject · Nov 21, 2023 · e8a288b · e8a288b
2 parents 788050d + a98f830
commit e8a288b
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Showing 5 changed files with 28 additions and 21 deletions.
diff --git a/test/integration/embedded_pulsar_job_conf.xml b/test/integration/embedded_pulsar_job_conf.xml
diff --git a/test/integration/embedded_pulsar_job_conf.yml b/test/integration/embedded_pulsar_job_conf.yml
@@ -0,0 +1,22 @@
+runners:
+  local:
+    load: galaxy.jobs.runners.local:LocalJobRunner
+  pulsar_embed:
+    load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+    pulsar_app_config:  # this doesn't start without disabling - filelock problem
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
+
+execution:
+  default: pulsar_embed
+  environments:
+    local:
+      runner: local
+    pulsar_embed:
+      runner: pulsar_embed
+      remote_metadata: true
+
+tools:
+- class: local
+  environment: local
diff --git a/test/integration/embedded_pulsar_metadata_extended_job_conf.yml b/test/integration/embedded_pulsar_metadata_extended_job_conf.yml
@@ -3,6 +3,10 @@ runners:
     load: galaxy.jobs.runners.local:LocalJobRunner
   pulsar_embed:
     load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
+    pulsar_app_config:
+      tool_dependency_dir: none
+      conda_auto_init: false
+      conda_auto_install: false
 
 execution:
   default: pulsar_embed

diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
@@ -15,7 +15,7 @@
 IO_INJECTION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "io_injection_job_conf.yml")
 SETS_TMP_DIR_TO_TRUE_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_to_true_job_conf.xml")
 SETS_TMP_DIR_AS_EXPRESSION_JOB_CONFIG = os.path.join(SCRIPT_DIRECTORY, "sets_tmp_dir_expression_job_conf.xml")
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
 
 JobEnvironmentProperties = collections.namedtuple(
     "JobEnvironmentProperties",

diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
@@ -5,7 +5,7 @@
 from galaxy_test.driver import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
-EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml")
+EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml")
 
 
 class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance):