Unverified Commit 5f373733 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #12308 from mvdbeek/more_fixes_ts_update 

[21.01] Fix test_repository_update
parents ba10688e cb8d157f

test/integration/test_repository_operations.py

+11 −8
Original line number Diff line number Diff line
@@ -26,10 +26,12 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC 


    def setUp(self):

        super().setUp()

        self.setup_shed_config()

        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)



    def tearDown(self):

        self.reset_shed_tools()

        return super().tearDown()



    def test_repository_installation(self):

        """
@@ -60,11 +62,12 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC 
    def test_repository_update(self):

        response = self._install_repository(revision=REVISION_4, version="0.0.3")[0]

        assert int(response['ctx_rev']) >= 4

        latest_revision = response['changeset_revision']

        repo_response = self._get("/api/tool_shed_repositories/%s" % response['id']).json()

        assert repo_response['tool_shed_status']['revision_update'] == 'False'  # that should really be a boolean

        # now checkout revision 3 and attempt an update

        path_components = [

            self._app.config.shed_tools_dir,

            os.path.dirname(self._app.config.shed_tool_config_file),

            'toolshed.g2.bx.psu.edu',

            'repos',

            REPO.owner,
@@ -73,25 +76,25 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC 
            REPO.name

        ]

        revision_3_path = os.path.join(*path_components[:6])

        revision_4_path = os.path.join(*path_components[:5] + [REVISION_4])

        latest_revision_path = os.path.join(*path_components[:5] + [latest_revision])

        repository_path = os.path.join(*path_components)

        # Move repo to location expected before minor update

        os.rename(revision_4_path, revision_3_path)

        os.rename(latest_revision_path, revision_3_path)

        # Checkout revision 3

        hg_util.update_repository(repository_path, ctx_rev='3')

        # change repo to revision 3 in database

        model = self._app.install_model

        tsr = model.context.query(model.ToolShedRepository).first()

        assert tsr.name == REPO.name

        assert tsr.changeset_revision == REVISION_4

        assert tsr.ctx_rev == '4'

        assert tsr.changeset_revision == latest_revision

        assert int(tsr.ctx_rev) >= 4

        tsr.ctx_rev = '3'

        tsr.installed_changeset_revision = REVISION_3

        tsr.changeset_revision = REVISION_3

        model.context.flush()

        # update shed_tool_conf.xml to look like revision 3 was the installed_changeset_revision

        with open(self._app.config.shed_tool_config_file) as shed_config:

            shed_text = shed_config.read().replace(REVISION_4, REVISION_3)

            shed_text = shed_config.read().replace(latest_revision, REVISION_3)

        with open(self._app.config.shed_tool_config_file, 'w') as shed_config:

            shed_config.write(shed_text)

        self._get(
@@ -104,9 +107,9 @@ class TestRepositoryInstallIntegrationTestCase(integration_util.IntegrationTestC 
        assert repo_response['tool_shed_status']['revision_update'] == 'True'

        assert repo_response['changeset_revision'] == REVISION_3

        assert repo_response['ctx_rev'] == '3'

        # now install revision 4 (a.k.a a minor update)

        # now install revision 4 (or newer) (a.k.a a minor update)

        response = self._install_repository(revision=REVISION_4, version="0.0.3", verify_tool_absent=False)[0]

        assert response['changeset_revision'] == REVISION_4

        assert response['changeset_revision'] == latest_revision

        assert response['installed_changeset_revision'] == REVISION_3

        # should be 4 or newer

        assert int(response['ctx_rev']) >= 4

test/integration/uses_shed.py

+5 −1
Original line number Diff line number Diff line
@@ -59,13 +59,17 @@ class UsesShed: 
        config["conda_auto_install"] = True

        config["conda_prefix"] = os.environ.get('GALAXY_TEST_CONDA_PREFIX') or os.path.join(cls.conda_tmp_prefix, 'conda')



    def reset_shed_tools(self):

    def setup_shed_config(self):

        shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True)

        os.makedirs(self._app.config.shed_tools_dir)

        self._app.config.shed_tools_dir = self.shed_tools_dir

        with open(self._app.config.shed_tool_config_file, "w") as tool_conf_file:

            tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=self._app.config.shed_tools_dir))

        # deleting the containing folder doesn't trigger a toolbox reload, so signal it now and wait until it's done

        self._app.queue_worker.send_control_task('reload_toolbox', get_response=True)



    def reset_shed_tools(self):

        self.setup_shed_config()

        model = self._app.install_model

        models_to_delete = [

            model.RepositoryRepositoryDependencyAssociation,