Testing Tweaks

planemo/commands/cmd_shed_serve.py

@@ -15,6 +15,7 @@
 @options.galaxy_run_options()
 @options.galaxy_config_options()
 @options.pid_file_option()
+@options.daemon_option()
 @click.option(
     "--skip_dependencies",
     is_flag=True,

setup.cfg

@@ -3,7 +3,7 @@ universal = 1
 
 [nosetests]
 exclude=(planemo_ext|.*cwl2script.*)
-verbosity=1
+verbosity=6
 detailed-errors=1
 with-doctest=1
 with-coverage=1

tests/test_cmd_serve.py

@@ -46,13 +46,32 @@ def test_serve_workflow(self):
             "--extra_tools", cat,
         ]
         self._launch_thread_and_wait(self._run, extra_args)
-        time.sleep(40)
+        time.sleep(30)
         user_gi = self._user_gi
         assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
         user_gi.histories.create_history(TEST_HISTORY_NAME)
         assert user_gi.tools.get_tools(tool_id="random_lines1")
         assert len(user_gi.workflows.get_workflows()) == 1
 
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_shed_serve(self):
+        extra_args = ["--daemon", "--pid_file", self._pid_file, "--shed_target", "toolshed"]
+        fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
+        self._serve_artifact = fastqc_path
+        self._launch_thread_and_wait(self._run_shed, extra_args)
+        user_gi = self._user_gi
+        found = False
+        tool_ids = None
+        for i in range(30):
+            tool_ids = [t["id"] for t in user_gi.tools.get_tools()]
+            if "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71" in tool_ids:
+                found = True
+                break
+            time.sleep(5)
+
+        assert found, "Failed to find fastqc id in %s" % tool_ids
+        kill_pid_file(self._pid_file)
+
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_serve_profile(self):
         self._test_serve_profile()
@@ -105,9 +124,12 @@ def _launch_thread_and_wait(self, func, args=[]):
         time.sleep(1)
         assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
 
-    def _run(self, serve_args=[]):
+    def _run_shed(self, serve_args=[]):
+        return self._run(serve_args=serve_args, serve_cmd="shed_serve")
+
+    def _run(self, serve_args=[], serve_cmd="serve"):
         test_cmd = [
-            "serve",
+            serve_cmd,
             "--install_galaxy",
             "--no_dependency_resolution",
             "--port",

tests/test_cmd_test_conda.py

@@ -40,21 +40,6 @@ def test_conda_dependencies_implicit_resolution(self):
             ]
             self._check_exit_code(test_command, exit_code=0)
 
-    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    def test_conda_dependencies_verify_branch_testing_properly(self):
-        # This tries to test Conda dependency resolution with a pre-Conda Galaxy and
-        # expects a failure. This verifies the other test cases are in fact testing
-        # different versions of Galaxy as expected.
-        with self._isolate():
-            bwa_test = os.path.join(PROJECT_TEMPLATES_DIR, "conda_testing", "bwa.xml")
-            test_command = [
-                "--verbose",
-                "test",
-                "--galaxy_branch", "release_15.10",
-                bwa_test,
-            ]
-            self._check_exit_code(test_command, exit_code=self.non_zero_exit_code)
-
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_conda_dependencies_version(self):
         """Test tool with wrong version and ensure it fails."""
@@ -90,7 +75,7 @@ def test_local_conda_dependencies_version(self):
             self._check_exit_code(conda_install_command)
             test_command = [
                 "test",
-                "--galaxy_branch", "release_17.01",
+                "--galaxy_branch", "release_17.09",
                 fleeqtk_tool,
             ]
             self._check_exit_code(test_command)

tox.ini

@@ -1,7 +1,6 @@
-# TODO: py34 to envlist
 # TODO: implement doc linting
 [tox]
-envlist = py{27,34}-lint, py{27,34}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}
+envlist = py{27,34}-lint, py{27,34,35}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}
 source_dir = planemo
 test_dir = tests