Fix container integration tests

test/functional/tools/job_environment_default.xml

@@ -2,7 +2,7 @@
     <requirements>
       <container type="docker">busybox:ubuntu-14.04</container>
     </requirements>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
       echo `id -u` > '$user_id';
       echo `id -g` > '$group_id';
       echo `pwd` > '$pwd';

test/functional/tools/job_environment_default_legacy.xml

@@ -2,7 +2,7 @@
     <requirements>
       <container type="docker">busybox:ubuntu-14.04</container>
     </requirements>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
       echo `id -u` > '$user_id';
       echo `id -g` > '$group_id';
       echo `pwd` > '$pwd';

test/integration/test_containerized_jobs.py

@@ -1,24 +1,29 @@
 """Integration tests for running tools in Docker containers."""
 
 import os
+import unittest
 
 from base import integration_util
 from base.populators import (
     DatasetPopulator,
 )
 
+from galaxy.tools.deps.commands import which
 from .test_job_environments import RunsEnvironmentJobs
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 DOCKERIZED_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "dockerized_job_conf.xml")
 SINGULARITY_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "singularity_job_conf.xml")
+EXTENDED_TIMEOUT = 120
 
 
-@integration_util.skip_unless_docker()
 class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, RunsEnvironmentJobs):
 
     framework_tool_and_types = True
     job_config_file = DOCKERIZED_JOB_CONFIG_FILE
+    build_mulled_resolver = 'build_mulled'
+    container_type = 'docker'
+    default_container_home_dir = '/'
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -31,6 +36,12 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
         config["conda_auto_install"] = False
         config["enable_beta_mulled_containers"] = "true"
 
+    @classmethod
+    def setUpClass(cls):
+        if not which(cls.container_type):
+            raise unittest.SkipTest("Executable '%s' not found on PATH" % cls.container_type)
+        super(DockerizedJobsIntegrationTestCase, cls).setUpClass()
+
     def setUp(self):
         super(DockerizedJobsIntegrationTestCase, self).setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
@@ -39,13 +50,13 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
     def test_explicit(self):
         self.dataset_populator.run_tool("mulled_example_explicit", {}, self.history_id)
         self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
-        output = self.dataset_populator.get_history_dataset_content(self.history_id)
+        output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
         assert "0.7.15-r1140" in output
 
     def test_mulled_simple(self):
         self.dataset_populator.run_tool("mulled_example_simple", {}, self.history_id)
         self.dataset_populator.wait_for_history(self.history_id, assert_ok=True)
-        output = self.dataset_populator.get_history_dataset_content(self.history_id)
+        output = self.dataset_populator.get_history_dataset_content(self.history_id, timeout=EXTENDED_TIMEOUT)
         assert "0.7.15-r1140" in output
 
     def test_container_job_enviornment(self):
@@ -73,10 +84,25 @@ class DockerizedJobsIntegrationTestCase(integration_util.IntegrationTestCase, Ru
         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 job_env.home == "/", job_env.home
+        assert job_env.home == self.default_container_home_dir, job_env.home
+
+    def test_build_mulled(self):
+        if not which('docker'):
+            raise unittest.SkipTest("Docker not found on PATH, required for building images via involucro")
+        resolver_type = self.build_mulled_resolver
+        tool_id = 'mulled_example_multi_1'
+        endpoint = "tools/%s/dependencies" % tool_id
+        data = {'id': tool_id, 'resolver_type': resolver_type}
+        create_response = self._post(endpoint, data=data, admin=True)
+        self._assert_status_code_is(create_response, 200)
+        response = create_response.json()
+        assert any([True for d in response if d['dependency_type'] == self.container_type])
 
 
-@integration_util.skip_unless_singularity()
 class SingularityJobsIntegrationTestCase(DockerizedJobsIntegrationTestCase):
 
     job_config_file = SINGULARITY_JOB_CONFIG_FILE
+    build_mulled_resolver = 'build_mulled_singularity'
+    container_type = 'singularity'
+    # singularity passes $HOME by default
+    default_container_home_dir = os.environ.get('HOME', '/')