Merge branch 'release_20.05' into release_20.09

lib/galaxy/tool_util/parser/xml.py

@@ -179,13 +179,6 @@ class XmlToolSource(ToolSource):
         # break or modify any configurations by default.
         return "job_tmp_if_explicit"
 
-    def parse_docker_env_pass_through(self):
-        if self.parse_profile() < "18.01":
-            return ["GALAXY_SLOTS"]
-        else:
-            # Pass home, etc...
-            return super().parse_docker_env_pass_through()
-
     def parse_interpreter(self):
         interpreter = None
         command_el = self._command_el

test/functional/tools/job_environment_explicit_isolated_home.xml

@@ -0,0 +1,25 @@
+<tool id="job_environment_explicit_isolated_home" name="job_environment_explicit_isolated_home" version="0.1.0">
+    <requirements>
+        <container type="docker">busybox:ubuntu-14.04</container>
+    </requirements>
+    <command use_shared_home="false"><![CDATA[
+echo `id -u` > '$user_id';
+echo `id -g` > '$group_id';
+echo `pwd` > '$pwd';
+echo "\$HOME" > '$home';
+echo "\$TMP"  > '$tmp';
+echo "\$SOME_ENV_VAR" > '$some_env_var';
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="user_id" format="txt" label="user_id" />
+        <data name="group_id" format="txt" label="group_id" />
+        <data name="pwd" format="txt" label="pwd" />
+        <data name="home" format="txt" label="home" />
+        <data name="tmp" format="txt" label="tmp" />
+        <data name="some_env_var" format="txt" label="env_var" />
+    </outputs>
+    <help>
+    </help>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -77,6 +77,7 @@
   <tool file="job_environment_default.xml" />
   <tool file="job_environment_default_legacy.xml" />
   <tool file="job_environment_explicit_shared_home.xml" />
+  <tool file="job_environment_explicit_isolated_home.xml" />
   <tool file="galaxy_slots_and_memory.xml" />
   <tool file="version_command_plain.xml" />
   <tool file="version_command_interpreter.xml" />

test/integration/test_containerized_jobs.py

@@ -109,10 +109,22 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
         assert job_env.group_id == str(egid), job_env.group_id
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
-        # Should we change env_pass_through to just always include TMP and HOME for docker?
-        # I'm not sure, if yes this would change.
         assert not job_env.home.endswith('/home')
 
+    def test_container_job_environment_explicit_shared_home(self):
+        job_env = self._run_and_get_environment_properties("job_environment_explicit_shared_home")
+
+        assert job_env.pwd.startswith(self.jobs_directory)
+        assert job_env.pwd.endswith("/working")
+        assert not job_env.home.endswith('/home')
+
+    def test_container_job_environment_explicit_isolated_home(self):
+        job_env = self._run_and_get_environment_properties("job_environment_explicit_isolated_home")
+
+        assert job_env.pwd.startswith(self.jobs_directory)
+        assert job_env.pwd.endswith("/working")
+        assert job_env.home.endswith('/home')
+
     def test_build_mulled(self):
         if not which('docker'):
             raise unittest.SkipTest("Docker not found on PATH, required for building images via involucro")

test/integration/test_job_environments.py

@@ -77,7 +77,7 @@ class DefaultJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTest
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
 
-        # Newer tools have isolated home directories in job_directory/home
+        # Newer tools get isolated home directories in job_directory/home
         job_directory = os.path.dirname(job_env.pwd)
         assert job_env.home == os.path.join(job_directory, "home"), job_env.home
 
@@ -98,12 +98,22 @@ class DefaultJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTest
 
     @skip_without_tool("job_environment_explicit_shared_home")
     def test_default_environment_force_legacy_home(self):
-        # Home should not overridden because we haven't set legacy_home_dir in job_conf
-        # or app, so it should just HOME.
+        # Home should not be overridden because we haven't set legacy_home_dir in job_conf
+        # or app, so it should just be HOME.
         job_env = self._run_and_get_environment_properties("job_environment_explicit_shared_home")
         home = os.getenv("HOME")
         assert job_env.home == home, job_env.home
 
+    @skip_without_tool("job_environment_explicit_isolated_home")
+    def test_default_environment_explicit_isolated_home(self):
+        # A tool with no profile but setting `use_shared_home="false"` must get
+        # an isolated home directory in job_directory/home
+        job_env = self._run_and_get_environment_properties("job_environment_explicit_isolated_home")
+        assert job_env.pwd.startswith(self.jobs_directory)
+        assert job_env.pwd.endswith("/working")
+        job_directory = os.path.dirname(job_env.pwd)
+        assert job_env.home == os.path.join(job_directory, "home"), job_env.home
+
 
 class TmpDirToTrueJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
 
@@ -170,6 +180,13 @@ class SharedHomeJobEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationT
         job_env = self._run_and_get_environment_properties("job_environment_explicit_shared_home")
         assert job_env.home == self.shared_home_directory, job_env.home
 
+    @skip_without_tool("job_environment_explicit_isolated_home")
+    def test_default_environment_explicit_isolated_home(self):
+        # shared_home_dir ignored for tools setting `use_shared_home="false"`
+        job_env = self._run_and_get_environment_properties("job_environment_explicit_isolated_home")
+        job_directory = os.path.dirname(job_env.pwd)
+        assert job_env.home == os.path.join(job_directory, "home"), job_env.home
+
 
 class JobIOEnvironmentIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):