start to extend tests

for container env variable setting
galaxyproject · Jul 31, 2024 · 0cac78a · 0cac78a
1 parent 51e7291
commit 0cac78a
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Showing 5 changed files with 9 additions and 1 deletion.
diff --git a/test/functional/tools/job_environment_default.xml b/test/functional/tools/job_environment_default.xml
@@ -13,6 +13,7 @@ echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
 echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
+echo "\$CONTAINER_ENV_VAR" > '$container_env_var' &&
 touch "\$_GALAXY_JOB_TMP_DIR/tmp_test" &&
 touch "\$HOME/home_test" &&
 
@@ -30,6 +31,7 @@ touch "\${TMPDIR:-/tmp}/job_tmpdir"
         <data name="tmp" format="txt" label="tmp" />
         <data name="some_env_var" format="txt" label="env_var" />
         <data name="jobconf_env_var" format="txt" label="jobconf_env_var" />
+        <data name="container_env_var" format="txt" label="container_env_var" />
     </outputs>
     <tests>
     </tests>

diff --git a/test/functional/tools/job_environment_default_legacy.xml b/test/functional/tools/job_environment_default_legacy.xml
@@ -11,6 +11,7 @@ echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
 echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
+echo "\$CONTAINER_ENV_VAR" > '$container_env_var' &&
 
 touch "\${TMP:-/tmp}/job_tmp" &&
 touch "\${TEMP:-/tmp}/job_temp" &&
@@ -26,6 +27,7 @@ touch "\${TMPDIR:-/tmp}/job_tmpdir"
         <data name="tmp" format="txt" label="tmp" />
         <data name="some_env_var" format="txt" label="env_var" />
         <data name="jobconf_env_var" format="txt" label="jobconf_env_var" />
+        <data name="container_env_var" format="txt" label="container_env_var" />
     </outputs>
     <tests>
     </tests>

diff --git a/test/integration/dockerized_job_conf.yml b/test/integration/dockerized_job_conf.yml
@@ -14,6 +14,7 @@ execution:
           value: 'YEAH'
         - execute: 'true' # just check that this does not confuse env setup
       docker_enabled: true
+      docker_env_CONTAINER_VAR: "DOCKER_VAR_VALUE"
       require_container: true
       tmp_dir: '$(mktemp -d)'
     local_docker_inline_container_resolvers:

diff --git a/test/integration/singularity_job_conf.yml b/test/integration/singularity_job_conf.yml
@@ -13,6 +13,7 @@ execution:
         - name: 'JOBCONF_ENV_VAR'
           value: 'YEAH'
       singularity_enabled: true
+      singularity_env_CONTAINER_VAR: "SINGULARITY_VAR_VALUE"
       # Since tests run in /tmp/ , we apparently need to forbid the default mounting of /tmp
       singularity_run_extra_arguments: '--no-mount tmp'
       require_container: true

diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
@@ -27,6 +27,7 @@
         "tmp",
         "some_env",
         "jobconf_env_var",
+        "container_env_var",
     ],
 )
 
@@ -62,7 +63,8 @@ def _environment_properties(self, history_id):
         tmp = self.dataset_populator.get_history_dataset_content(history_id, hid=5).strip()
         some_env = self.dataset_populator.get_history_dataset_content(history_id, hid=6).strip()
         jobconf_env_var = self.dataset_populator.get_history_dataset_content(history_id, hid=7).strip()
-        return JobEnvironmentProperties(user_id, group_id, pwd, home, tmp, some_env, jobconf_env_var)
+        container_env_var = self.dataset_populator.get_history_dataset_content(history_id, hid=7).strip()
+        return JobEnvironmentProperties(user_id, group_id, pwd, home, tmp, some_env, jobconf_env_var, container_env_var)
 
     def _check_completed_history(self, history_id):
         """Extension point that lets subclasses investigate the completed job."""