class FailJobWhenToolUnavailableTestCase(integration_util.IntegrationTestCase): require_admin_user = True def setUp(self): super(FailJobWhenToolUnavailableTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.workflow_populator = WorkflowPopulator(self.galaxy_interactor) self.history_id = self.dataset_populator.new_history() @classmethod def handle_galaxy_config_kwds( cls, config, ): # config["jobs_directory"] = cls.jobs_directory # Disable tool dependency resolution. config["tool_dependency_dir"] = "none" def test_fail_job_when_tool_unavailable(self): self.workflow_populator.run_workflow(""" class: GalaxyWorkflow steps: - label: sleep run: class: GalaxyTool command: sleep 20s && echo 'hello world 2' > '$output1' outputs: output1: format: txt - tool_id: cat1 state: input1: $link: sleep#output1 queries: input2: $link: sleep#output1 """, history_id=self.history_id, assert_ok=False, wait=False) # Wait until workflow is fully scheduled, otherwise can't test effect of removing tool from queued job time.sleep(10) self._app.toolbox.remove_tool_by_id('cat1') self.dataset_populator.wait_for_history(self.history_id, assert_ok=False) state_details = self.galaxy_interactor.get( 'histories/%s' % self.history_id).json()['state_details'] assert state_details['running'] == 0 assert state_details['ok'] == 1 assert state_details['error'] == 1 failed_hda = self.dataset_populator.get_history_dataset_details( history_id=self.history_id, assert_ok=False, details=True) assert failed_hda['state'] == 'error' job = self.galaxy_interactor.get("jobs/%s" % failed_hda['creating_job']).json() assert job['state'] == 'error'
class ToolsUploadTestCase(api.ApiTestCase): def setUp(self): super(ToolsUploadTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) def test_upload1_paste(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, 'Hello World') create_response = self._post("tools", data=payload) self._assert_has_keys(create_response.json(), 'outputs') def test_upload1_paste_bad_datatype(self): # Check that you get a nice message if you upload an incorrect datatype with self.dataset_populator.test_history() as history_id: file_type = "johnsawesomebutfakedatatype" payload = self.dataset_populator.upload_payload( history_id, 'Hello World', file_type=file_type) create = self._post("tools", data=payload).json() self._assert_has_keys(create, 'err_msg') assert file_type in create['err_msg'] def test_upload_posix_newline_fixes(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_disable_posix_fix(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, to_posix_lines=None) self.assertEquals(result_content, windows_content) def test_upload_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, space_to_tab="Yes") self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table) self.assertEquals(result_content, table) @skip_without_datatype("rdata") def test_rdata_not_decompressed(self): # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 rdata_path = TestDataResolver().get_filename("1.RData") rdata_metadata = self._upload_and_get_details(open(rdata_path, "rb"), file_type="auto") self.assertEquals(rdata_metadata["file_ext"], "rdata") @skip_without_datatype("velvet") def test_composite_datatype(self): with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps content", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_space_to_tab(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps\tcontent", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_posix_lines(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps\rcontent", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log\rcontent", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps\ncontent", roadmaps_content def test_upload_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19") run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert datasets[0].get("genome_build") == "hg19", datasets[0] def test_upload_multiple_files_1(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "tabular", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt" assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "tabular" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_2(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "tabular", datasets assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_3(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|dbkey": "hg18", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "hg18", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_no_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey=None, extra_inputs={ "files_0|file_type": "txt", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "?", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "?", datasets def test_upload_multiple_files_space_to_tab(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, content=ONE_TO_SIX_WITH_SPACES, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|space_to_tab": "Yes", "files_1|url_paste": ONE_TO_SIX_WITH_SPACES, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_2|url_paste": ONE_TO_SIX_WITH_SPACES, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "files_2|space_to_tab": "Yes", "file_count": "3", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_WITH_SPACES content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_multiple_files_posix_lines(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, content=ONE_TO_SIX_ON_WINDOWS, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|to_posix_lines": "Yes", "files_1|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|to_posix_lines": None, "files_2|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "file_count": "3", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_ON_WINDOWS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def _velvet_upload(self, history_id, extra_inputs): payload = self.dataset_populator.upload_payload( history_id, "sequences content", file_type="velvet", extra_inputs=extra_inputs, ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 1 dataset = datasets[0] return dataset def _get_roadmaps_content(self, history_id, dataset): roadmaps_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=dataset, filename="Roadmaps") return roadmaps_content def _upload_and_get_content(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_content( history_id, dataset=new_dataset) def _upload_and_get_details(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_details( history_id, dataset=new_dataset) def _upload(self, content, **upload_kwds): history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset(history_id, content=content, **upload_kwds) self.dataset_populator.wait_for_history(history_id, assert_ok=True) return history_id, new_dataset
class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets): def setUp(self): super(HistoryContentsApiTestCase, self).setUp() self.history_id = self._new_history() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor) self.library_populator = LibraryPopulator(self.galaxy_interactor) def test_index_hda_summary(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents" % self.history_id) hda_summary = self.__check_for_hda(contents_response, hda1) assert "display_types" not in hda_summary # Quick summary, not full details def test_make_private_and_public(self): hda1 = self._wait_for_new_hda() update_url = "histories/%s/contents/%s/permissions" % (self.history_id, hda1["id"]) role_id = self.dataset_populator.user_private_role_id() # Give manage permission to the user. payload = { "access": [], "manage": [role_id], } update_response = self._update_permissions(update_url, payload, admin=True) self._assert_status_code_is(update_response, 200) self._assert_other_user_can_access(hda1["id"]) # Then we restrict access. payload = { "action": "make_private", } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_cannot_access(hda1["id"]) # Then we restrict access. payload = { "action": "remove_restrictions", } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_can_access(hda1["id"]) def test_set_permissions_add_admin_history_contents(self): self._verify_dataset_permissions("history_contents") def test_set_permissions_add_admin_datasets(self): self._verify_dataset_permissions("dataset") def _verify_dataset_permissions(self, api_endpoint): hda1 = self._wait_for_new_hda() hda_id = hda1["id"] if api_endpoint == "history_contents": update_url = "histories/%s/contents/%s/permissions" % (self.history_id, hda_id) else: update_url = "datasets/%s/permissions" % hda_id role_id = self.dataset_populator.user_private_role_id() payload = { "access": [role_id], "manage": [role_id], } # Other users cannot modify permissions. with self._different_user(): update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 403) # First the details render for another user. self._assert_other_user_can_access(hda_id) # Then we restrict access. update_response = self._update_permissions(update_url, payload, admin=True) self._assert_status_code_is(update_response, 200) # Finally the details don't render. self._assert_other_user_cannot_access(hda_id) # But they do for the original user. contents_response = self._get("histories/%s/contents/%s" % (self.history_id, hda_id)).json() assert "name" in contents_response update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) payload = { "access": [role_id], "manage": [role_id], } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_cannot_access(hda_id) user_id = self.dataset_populator.user_id() with self._different_user(): different_user_id = self.dataset_populator.user_id() combined_user_role = self.dataset_populator.create_role([user_id, different_user_id], description="role for testing permissions") payload = { "access": [combined_user_role["id"]], "manage": [role_id], } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) # Now other user can see dataset again with access permission. self._assert_other_user_can_access(hda_id) # access doesn't imply management though... with self._different_user(): update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 403) def _assert_other_user_cannot_access(self, history_content_id): with self._different_user(): contents_response = self._get("histories/%s/contents/%s" % (self.history_id, history_content_id)).json() assert "name" not in contents_response def _assert_other_user_can_access(self, history_content_id): with self._different_user(): contents_response = self._get("histories/%s/contents/%s" % (self.history_id, history_content_id)).json() assert "name" in contents_response def test_index_hda_all_details(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents?details=all" % self.history_id) hda_details = self.__check_for_hda(contents_response, hda1) self.__assert_hda_has_full_details(hda_details) def test_index_hda_detail_by_id(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents?details=%s" % (self.history_id, hda1["id"])) hda_details = self.__check_for_hda(contents_response, hda1) self.__assert_hda_has_full_details(hda_details) def test_show_hda(self): hda1 = self._new_dataset(self.history_id) show_response = self.__show(hda1) self._assert_status_code_is(show_response, 200) self.__assert_matches_hda(hda1, show_response.json()) def test_hda_copy(self): hda1 = self._new_dataset(self.history_id) create_data = dict( source='hda', content=hda1["id"], ) second_history_id = self._new_history() assert self.__count_contents(second_history_id) == 0 create_response = self._post("histories/%s/contents" % second_history_id, create_data) self._assert_status_code_is(create_response, 200) assert self.__count_contents(second_history_id) == 1 def test_library_copy(self): ld = self.library_populator.new_library_dataset("lda_test_library") create_data = dict( source='library', content=ld["id"], ) assert self.__count_contents(self.history_id) == 0 create_response = self._post("histories/%s/contents" % self.history_id, create_data) self._assert_status_code_is(create_response, 200) assert self.__count_contents(self.history_id) == 1 def test_update(self): hda1 = self._wait_for_new_hda() assert str(hda1["deleted"]).lower() == "false" update_response = self._raw_update(hda1["id"], dict(deleted=True)) self._assert_status_code_is(update_response, 200) show_response = self.__show(hda1) assert str(show_response.json()["deleted"]).lower() == "true" update_response = self._raw_update(hda1["id"], dict(name="Updated Name")) assert self.__show(hda1).json()["name"] == "Updated Name" update_response = self._raw_update(hda1["id"], dict(name="Updated Name")) assert self.__show(hda1).json()["name"] == "Updated Name" unicode_name = u'ржевский сапоги' update_response = self._raw_update(hda1["id"], dict(name=unicode_name)) updated_hda = self.__show(hda1).json() assert updated_hda["name"] == unicode_name, updated_hda quoted_name = '"Mooo"' update_response = self._raw_update(hda1["id"], dict(name=quoted_name)) updated_hda = self.__show(hda1).json() assert updated_hda["name"] == quoted_name, quoted_name def test_update_type_failures(self): hda1 = self._wait_for_new_hda() update_response = self._raw_update(hda1["id"], dict(deleted='not valid')) self._assert_status_code_is(update_response, 400) def _wait_for_new_hda(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) return hda1 def _raw_update(self, item_id, data, admin=False, history_id=None): history_id = history_id or self.history_id key_param = "use_admin_key" if admin else "use_key" update_url = self._api_url("histories/%s/contents/%s" % (history_id, item_id), **{key_param: True}) update_response = put(update_url, json=data) return update_response def _update_permissions(self, url, data, admin=False): key_param = "use_admin_key" if admin else "use_key" update_url = self._api_url(url, **{key_param: True}) update_response = put(update_url, json=data) return update_response def test_delete(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) assert str(self.__show(hda1).json()["deleted"]).lower() == "false" delete_response = self._delete("histories/%s/contents/%s" % (self.history_id, hda1["id"])) assert delete_response.status_code < 300 # Something in the 200s :). assert str(self.__show(hda1).json()["deleted"]).lower() == "true" def test_purge(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) assert str(self.__show(hda1).json()["deleted"]).lower() == "false" assert str(self.__show(hda1).json()["purged"]).lower() == "false" data = {'purge': True} delete_response = self._delete("histories/%s/contents/%s" % (self.history_id, hda1["id"]), data=data) assert delete_response.status_code < 300 # Something in the 200s :). assert str(self.__show(hda1).json()["deleted"]).lower() == "true" assert str(self.__show(hda1).json()["purged"]).lower() == "true" def test_dataset_collection_creation_on_contents(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection" ) endpoint = "histories/%s/contents" % self.history_id self._check_pair_creation(endpoint, payload) def test_dataset_collection_creation_on_typed_contents(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, ) endpoint = "histories/%s/contents/dataset_collections" % self.history_id self._check_pair_creation(endpoint, payload) def test_dataset_collection_create_from_exisiting_datasets_with_new_tags(self): with self.dataset_populator.test_history() as history_id: hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] hda2_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] update_response = self._raw_update(hda2_id, dict(tags=['existing:tag']), history_id=history_id).json() assert update_response['tags'] == ['existing:tag'] creation_payload = {'collection_type': 'list', 'history_id': history_id, 'element_identifiers': json.dumps([{'id': hda_id, 'src': 'hda', 'name': 'element_id1', 'tags': ['my_new_tag']}, {'id': hda2_id, 'src': 'hda', 'name': 'element_id2', 'tags': ['another_new_tag']} ]), 'type': 'dataset_collection', 'copy_elements': True} r = self._post("histories/%s/contents" % self.history_id, creation_payload).json() assert r['elements'][0]['object']['id'] != hda_id, "HDA has not been copied" assert len(r['elements'][0]['object']['tags']) == 1 assert r['elements'][0]['object']['tags'][0] == 'my_new_tag' assert len(r['elements'][1]['object']['tags']) == 2, r['elements'][1]['object']['tags'] original_hda = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset_id=hda_id) assert len(original_hda['tags']) == 0, original_hda['tags'] def _check_pair_creation(self, endpoint, payload): pre_collection_count = self.__count_contents(type="dataset_collection") pre_dataset_count = self.__count_contents(type="dataset") pre_combined_count = self.__count_contents(type="dataset,dataset_collection") dataset_collection_response = self._post(endpoint, payload) dataset_collection = self.__check_create_collection_response(dataset_collection_response) post_collection_count = self.__count_contents(type="dataset_collection") post_dataset_count = self.__count_contents(type="dataset") post_combined_count = self.__count_contents(type="dataset,dataset_collection") # Test filtering types with index. assert pre_collection_count == 0 assert post_collection_count == 1 assert post_combined_count == pre_dataset_count + 1 assert post_combined_count == pre_combined_count + 1 assert pre_dataset_count == post_dataset_count # Test show dataset colleciton. collection_url = "histories/%s/contents/dataset_collections/%s" % (self.history_id, dataset_collection["id"]) show_response = self._get(collection_url) self._assert_status_code_is(show_response, 200) dataset_collection = show_response.json() self._assert_has_keys(dataset_collection, "url", "name", "deleted") assert not dataset_collection["deleted"] delete_response = delete(self._api_url(collection_url, use_key=True)) self._assert_status_code_is(delete_response, 200) show_response = self._get(collection_url) dataset_collection = show_response.json() assert dataset_collection["deleted"] @skip_without_tool("collection_creates_list") def test_jobs_summary_simple_hdca(self): create_response = self.dataset_collection_populator.create_list_in_history(self.history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]) hdca_id = create_response.json()["id"] run = self.dataset_populator.run_collection_creates_list(self.history_id, hdca_id) collections = run['output_collections'] collection = collections[0] jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % (self.history_id, collection["id"]) jobs_summary_response = self._get(jobs_summary_url) self._assert_status_code_is(jobs_summary_response, 200) jobs_summary = jobs_summary_response.json() self._assert_has_keys(jobs_summary, "populated_state", "states") @skip_without_tool("cat1") def test_jobs_summary_implicit_hdca(self): create_response = self.dataset_collection_populator.create_pair_in_history(self.history_id, contents=["123", "456"]) hdca_id = create_response.json()["id"] inputs = { "input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]}, } run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=self.history_id) self.dataset_populator.wait_for_history_jobs(self.history_id) collections = run['implicit_collections'] collection = collections[0] jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % (self.history_id, collection["id"]) jobs_summary_response = self._get(jobs_summary_url) self._assert_status_code_is(jobs_summary_response, 200) jobs_summary = jobs_summary_response.json() self._assert_has_keys(jobs_summary, "populated_state", "states") states = jobs_summary["states"] assert states.get("ok") == 2, states def test_dataset_collection_hide_originals(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection" ) payload["hide_source_items"] = True dataset_collection_response = self._post("histories/%s/contents" % self.history_id, payload) self.__check_create_collection_response(dataset_collection_response) contents_response = self._get("histories/%s/contents" % self.history_id) datasets = [d for d in contents_response.json() if d["history_content_type"] == "dataset" and d["hid"] in [1, 2]] # Assert two datasets in source were hidden. assert len(datasets) == 2 assert not datasets[0]["visible"] assert not datasets[1]["visible"] def test_update_dataset_collection(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection" ) dataset_collection_response = self._post("histories/%s/contents" % self.history_id, payload) self._assert_status_code_is(dataset_collection_response, 200) hdca = dataset_collection_response.json() update_url = self._api_url("histories/%s/contents/dataset_collections/%s" % (self.history_id, hdca["id"]), use_key=True) # Awkward json.dumps required here because of https://trello.com/c/CQwmCeG6 body = json.dumps(dict(name="newnameforpair")) update_response = put(update_url, data=body) self._assert_status_code_is(update_response, 200) show_response = self.__show(hdca) assert str(show_response.json()["name"]) == "newnameforpair" def test_hdca_copy(self): hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json() hdca_id = hdca["id"] second_history_id = self._new_history() create_data = dict( source='hdca', content=hdca_id, ) assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0 create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data) self.__check_create_collection_response(create_response) contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json() assert len(contents) == 1 new_forward, _ = self.__get_paired_response_elements(contents[0]) self._assert_has_keys(new_forward, "history_id") assert new_forward["history_id"] == self.history_id def test_hdca_copy_and_elements(self): hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json() hdca_id = hdca["id"] second_history_id = self._new_history() create_data = dict( source='hdca', content=hdca_id, copy_elements=True, ) assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0 create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data) self.__check_create_collection_response(create_response) contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json() assert len(contents) == 1 new_forward, _ = self.__get_paired_response_elements(contents[0]) self._assert_has_keys(new_forward, "history_id") assert new_forward["history_id"] == second_history_id def __get_paired_response_elements(self, contents): hdca = self.__show(contents).json() self._assert_has_keys(hdca, "name", "deleted", "visible", "elements") elements = hdca["elements"] assert len(elements) == 2 element0 = elements[0] element1 = elements[1] self._assert_has_keys(element0, "object") self._assert_has_keys(element1, "object") return element0["object"], element1["object"] def test_hdca_from_library_datasets(self): ld = self.library_populator.new_library_dataset("el1") ldda_id = ld["ldda_id"] element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}] create_data = dict( history_id=self.history_id, type="dataset_collection", name="Test From Library", element_identifiers=json.dumps(element_identifiers), collection_type="list", ) create_response = self._post("histories/%s/contents/dataset_collections" % self.history_id, create_data) hdca = self.__check_create_collection_response(create_response) elements = hdca["elements"] assert len(elements) == 1 hda = elements[0]["object"] assert hda["hda_ldda"] == "hda" assert hda["history_content_type"] == "dataset" assert hda["copied_from_ldda_id"] == ldda_id def test_hdca_from_inaccessible_library_datasets(self): library, library_dataset = self.library_populator.new_library_dataset_in_private_library("HDCACreateInaccesibleLibrary") ldda_id = library_dataset["id"] element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}] create_data = dict( history_id=self.history_id, type="dataset_collection", name="Test From Library", element_identifiers=json.dumps(element_identifiers), collection_type="list", ) with self._different_user(): second_history_id = self._new_history() create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data) self._assert_status_code_is(create_response, 403) def __check_create_collection_response(self, response): self._assert_status_code_is(response, 200) dataset_collection = response.json() self._assert_has_keys(dataset_collection, "url", "name", "deleted", "visible", "elements") return dataset_collection def __show(self, contents): show_response = self._get("histories/%s/contents/%ss/%s" % (self.history_id, contents["history_content_type"], contents["id"])) return show_response def __count_contents(self, history_id=None, **kwds): if history_id is None: history_id = self.history_id contents_response = self._get("histories/%s/contents" % history_id, kwds) return len(contents_response.json()) def __assert_hda_has_full_details(self, hda_details): self._assert_has_keys(hda_details, "display_types", "display_apps") def __check_for_hda(self, contents_response, hda): self._assert_status_code_is(contents_response, 200) contents = contents_response.json() assert len(contents) == 1 hda_summary = contents[0] self.__assert_matches_hda(hda, hda_summary) return hda_summary def __assert_matches_hda(self, input_hda, query_hda): self._assert_has_keys(query_hda, "id", "name") assert input_hda["name"] == query_hda["name"] assert input_hda["id"] == query_hda["id"]
class ToolsUploadTestCase(api.ApiTestCase): def setUp(self): super(ToolsUploadTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) def test_upload1_paste(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, 'Hello World') create_response = self._post("tools", data=payload) self._assert_has_keys(create_response.json(), 'outputs') def test_upload1_paste_bad_datatype(self): # Check that you get a nice message if you upload an incorrect datatype with self.dataset_populator.test_history() as history_id: file_type = "johnsawesomebutfakedatatype" payload = self.dataset_populator.upload_payload( history_id, 'Hello World', file_type=file_type) create = self._post("tools", data=payload).json() self._assert_has_keys(create, 'err_msg') assert file_type in create['err_msg'] # upload1 rewrites content with posix lines by default but this can be disabled by setting # to_posix_lines=None in the request. Newer fetch API does not do this by default prefering # to keep content unaltered if possible but it can be enabled with a simple JSON boolean switch # of the same name (to_posix_lines). def test_upload_posix_newline_fixes_by_default(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_posix_unaltered(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch") self.assertEquals(result_content, ONE_TO_SIX_ON_WINDOWS) def test_upload_disable_posix_fix(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, to_posix_lines=None) self.assertEquals(result_content, windows_content) def test_fetch_post_lines_option(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch", to_posix_lines=True) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table) self.assertEquals(result_content, table) def test_fetch_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api='fetch') self.assertEquals(result_content, table) def test_upload_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, space_to_tab="Yes") self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api="fetch", space_to_tab=True) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_compressed_with_explicit_type(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", ext="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz" def test_fetch_compressed_default(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details @uses_test_history(require_new=True) def test_fetch_compressed_auto_decompress_target(self, history_id): # TODO: this should definitely be fixed to allow auto decompression via that API. fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False, auto_decompress=True) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details def test_upload_decompress_off_with_auto_by_default(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bed", details def test_upload_decompresses_if_uncompressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="fastqsanger") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger", details assert details["file_size"] == 178, details def test_upload_decompress_off_if_compressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details assert details["file_size"] == 161, details def test_upload_auto_decompress_off(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto", assert_ok=False, auto_decompress=False) assert details["file_ext"] == "binary", details @uses_test_history(require_new=True) def test_fetch_compressed_with_auto(self, history_id): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. # TODO: this should definitely be fixed to allow auto decompression via that API. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, auto_decompress=True, assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bed" @skip_without_datatype("rdata") def test_rdata_not_decompressed(self): # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 rdata_path = TestDataResolver().get_filename("1.RData") with open(rdata_path, "rb") as fh: rdata_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(rdata_metadata["file_ext"], "rdata") @skip_without_datatype("csv") def test_csv_upload(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="csv") self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_upload_auto(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="csv", to_posix_lines=True) self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_sniff_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="auto", to_posix_lines=True) self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("tiff") def test_image_upload_auto(self): tiff_path = TestDataResolver().get_filename("1.tiff") with open(tiff_path, "rb") as fh: tiff_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(tiff_metadata["file_ext"], "tiff") @skip_without_datatype("velvet") def test_composite_datatype(self): with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps content", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_space_to_tab(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps\tcontent", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_posix_lines(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps\rcontent", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log\rcontent", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip( ) == "roadmaps\ncontent", roadmaps_content def test_upload_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19") run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert datasets[0].get("genome_build") == "hg19", datasets[0] @uses_test_history(require_new=False) def test_fetch_bam_file(self, history_id): bam_path = TestDataResolver().get_filename("1.bam") with open(bam_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bam", details def test_upload_bam_file(self): bam_path = TestDataResolver().get_filename("1.bam") with open(bam_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bam", details def test_fetch_metadata(self): table = ONE_TO_SIX_WITH_SPACES details = self._upload_and_get_details( table, api='fetch', dbkey="hg19", info="cool upload", tags=["name:data", "group:type:paired-end"]) assert details.get("genome_build") == "hg19" assert details.get("misc_info") == "cool upload", details tags = details.get("tags") assert len(tags) == 2, details assert "group:type:paired-end" in tags assert "name:data" in tags def test_upload_multiple_files_1(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "tabular", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt" assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "tabular" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_2(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "tabular", datasets assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_3(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|dbkey": "hg18", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "hg18", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_no_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, "Test123", file_type="tabular", dbkey=None, extra_inputs={ "files_0|file_type": "txt", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "file_count": "2", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "?", datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "?", datasets def test_upload_multiple_files_space_to_tab(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, content=ONE_TO_SIX_WITH_SPACES, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|space_to_tab": "Yes", "files_1|url_paste": ONE_TO_SIX_WITH_SPACES, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_2|url_paste": ONE_TO_SIX_WITH_SPACES, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "files_2|space_to_tab": "Yes", "file_count": "3", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_WITH_SPACES content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_multiple_files_posix_lines(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload( history_id, content=ONE_TO_SIX_ON_WINDOWS, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|to_posix_lines": "Yes", "files_1|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|to_posix_lines": None, "files_2|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "file_count": "3", }) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_ON_WINDOWS content = self.dataset_populator.get_history_dataset_content( history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_upload_from_invalid_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/bla123', assert_ok=False) dataset_details = self.dataset_populator.get_history_dataset_details( history_id, dataset_id=new_dataset["id"], assert_ok=False) assert dataset_details[ 'state'] == 'error', "expected dataset state to be 'error', but got '%s'" % dataset_details[ 'state'] def test_upload_from_valid_url(self): history_id, new_dataset = self._upload( 'https://usegalaxy.org/api/version') self.dataset_populator.get_history_dataset_details( history_id, dataset_id=new_dataset["id"], assert_ok=True) def _velvet_upload(self, history_id, extra_inputs): payload = self.dataset_populator.upload_payload( history_id, "sequences content", file_type="velvet", extra_inputs=extra_inputs, ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 1 dataset = datasets[0] return dataset def _get_roadmaps_content(self, history_id, dataset): roadmaps_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=dataset, filename="Roadmaps") return roadmaps_content def _upload_and_get_content(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_content( history_id, dataset=new_dataset) def _upload_and_get_details(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) assert_ok = upload_kwds.get("assert_ok", True) return self.dataset_populator.get_history_dataset_details( history_id, dataset=new_dataset, assert_ok=assert_ok) def _upload(self, content, api="upload1", history_id=None, **upload_kwds): assert_ok = upload_kwds.get("assert_ok", True) history_id = history_id or self.dataset_populator.new_history() if api == "upload1": new_dataset = self.dataset_populator.new_dataset(history_id, content=content, **upload_kwds) else: assert api == "fetch" element = dict(src="files", **upload_kwds) target = { "destination": { "type": "hdas" }, "elements": [element], } targets = json.dumps([target]) payload = { "history_id": history_id, "targets": targets, "__files": { "files_0|file_data": content } } new_dataset = self.dataset_populator.fetch( payload, assert_ok=assert_ok).json()["outputs"][0] self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok) return history_id, new_dataset
class HistoriesApiTestCase(api.ApiTestCase): def setUp(self): super(HistoriesApiTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor) def test_create_history(self): # Create a history. create_response = self._create_history("TestHistory1") created_id = create_response["id"] # Make sure new history appears in index of user's histories. index_response = self._get("histories").json() indexed_history = [h for h in index_response if h["id"] == created_id][0] self.assertEqual(indexed_history["name"], "TestHistory1") def test_show_history(self): history_id = self._create_history("TestHistoryForShow")["id"] show_response = self._show(history_id) self._assert_has_key( show_response, 'id', 'name', 'annotation', 'size', 'contents_url', 'state', 'state_details', 'state_ids' ) state_details = show_response["state_details"] state_ids = show_response["state_ids"] states = [ 'discarded', 'empty', 'error', 'failed_metadata', 'new', 'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload' ] assert isinstance(state_details, dict) assert isinstance(state_ids, dict) self._assert_has_keys(state_details, *states) self._assert_has_keys(state_ids, *states) def test_show_most_recently_used(self): history_id = self._create_history("TestHistoryRecent")["id"] show_response = self._get("histories/most_recently_used").json() assert show_response["id"] == history_id def test_index_order(self): slightly_older_history_id = self._create_history("TestHistorySlightlyOlder")["id"] newer_history_id = self._create_history("TestHistoryNewer")["id"] index_response = self._get("histories").json() assert index_response[0]["id"] == newer_history_id assert index_response[1]["id"] == slightly_older_history_id def test_delete(self): # Setup a history and ensure it is in the index history_id = self._create_history("TestHistoryForDelete")["id"] index_response = self._get("histories").json() assert index_response[0]["id"] == history_id show_response = self._show(history_id) assert not show_response["deleted"] # Delete the history self._delete("histories/%s" % history_id) # Check can view it - but it is deleted show_response = self._show(history_id) assert show_response["deleted"] # Verify it is dropped from history index index_response = self._get("histories").json() assert len(index_response) == 0 or index_response[0]["id"] != history_id # Add deleted filter to index to view it index_response = self._get("histories", {"deleted": "true"}).json() assert index_response[0]["id"] == history_id def test_purge(self): history_id = self._create_history("TestHistoryForPurge")["id"] data = {'purge': True} self._delete("histories/%s" % history_id, data=data) show_response = self._show(history_id) assert show_response["deleted"] assert show_response["purged"] def test_undelete(self): history_id = self._create_history("TestHistoryForDeleteAndUndelete")["id"] self._delete("histories/%s" % history_id) self._post("histories/deleted/%s/undelete" % history_id) show_response = self._show(history_id) assert not show_response["deleted"] def test_update(self): history_id = self._create_history("TestHistoryForUpdating")["id"] self._update(history_id, {"name": "New Name"}) show_response = self._show(history_id) assert show_response["name"] == "New Name" unicode_name = u'桜ゲノム' self._update(history_id, {"name": unicode_name}) show_response = self._show(history_id) assert show_response["name"] == unicode_name, show_response quoted_name = "'MooCow'" self._update(history_id, {"name": quoted_name}) show_response = self._show(history_id) assert show_response["name"] == quoted_name self._update(history_id, {"deleted": True}) show_response = self._show(history_id) assert show_response["deleted"], show_response self._update(history_id, {"deleted": False}) show_response = self._show(history_id) assert not show_response["deleted"] self._update(history_id, {"published": True}) show_response = self._show(history_id) assert show_response["published"] self._update(history_id, {"genome_build": "hg18"}) show_response = self._show(history_id) assert show_response["genome_build"] == "hg18" self._update(history_id, {"annotation": "The annotation is cool"}) show_response = self._show(history_id) assert show_response["annotation"] == "The annotation is cool" self._update(history_id, {"annotation": unicode_name}) show_response = self._show(history_id) assert show_response["annotation"] == unicode_name, show_response self._update(history_id, {"annotation": quoted_name}) show_response = self._show(history_id) assert show_response["annotation"] == quoted_name def test_update_invalid_attribute(self): history_id = self._create_history("TestHistoryForInvalidUpdating")["id"] put_response = self._update(history_id, {"invalidkey": "moo"}) assert "invalidkey" not in put_response.json() def test_update_invalid_types(self): history_id = self._create_history("TestHistoryForUpdatingInvalidTypes")["id"] for str_key in ["name", "annotation"]: assert self._update(history_id, {str_key: False}).status_code == 400 for bool_key in ['deleted', 'importable', 'published']: assert self._update(history_id, {bool_key: "a string"}).status_code == 400 assert self._update(history_id, {"tags": "a simple string"}).status_code == 400 assert self._update(history_id, {"tags": [True]}).status_code == 400 def test_invalid_keys(self): invalid_history_id = "1234123412341234" assert self._get("histories/%s" % invalid_history_id).status_code == 400 assert self._update(invalid_history_id, {"name": "new name"}).status_code == 400 assert self._delete("histories/%s" % invalid_history_id).status_code == 400 assert self._post("histories/deleted/%s/undelete" % invalid_history_id).status_code == 400 def test_create_anonymous_fails(self): post_data = dict(name="CannotCreate") # Using lower-level _api_url will cause key to not be injected. histories_url = self._api_url("histories") create_response = post(url=histories_url, data=post_data) self._assert_status_code_is(create_response, 403) def test_import_export(self): history_name = "for_export_default" history_id = self.dataset_populator.new_history(name=history_name) self.dataset_populator.new_dataset(history_id, content="1 2 3") deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3") self.dataset_populator.delete_dataset(history_id, deleted_hda["id"]) deleted_details = self.dataset_populator.get_history_dataset_details(history_id, id=deleted_hda["id"]) assert deleted_details["deleted"] imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2) def upload_job_check(job): assert job["tool_id"] == "upload1" def check_discarded(hda): assert hda["deleted"] assert hda["state"] == "discarded", hda assert hda["purged"] is True self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check) self._check_imported_dataset(history_id=imported_history_id, hid=2, has_job=False, hda_checker=check_discarded, job_checker=upload_job_check) imported_content = self.dataset_populator.get_history_dataset_content( history_id=imported_history_id, hid=1, ) assert imported_content == "1 2 3\n" def test_import_1901_histories(self): f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), 'rb') import_data = dict(archive_source='', archive_file=f) self._import_history_and_wait(import_data, "API Test History", wait_on_history_length=2) def test_import_export_include_deleted(self): history_name = "for_export_include_deleted" history_id = self.dataset_populator.new_history(name=history_name) self.dataset_populator.new_dataset(history_id, content="1 2 3") deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3") self.dataset_populator.delete_dataset(history_id, deleted_hda["id"]) imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2, export_kwds={"include_deleted": "True"}) self._assert_history_length(imported_history_id, 2) def upload_job_check(job): assert job["tool_id"] == "upload1" def check_ok(hda): assert hda["state"] == "ok", hda assert hda["deleted"] is True, hda self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check) self._check_imported_dataset(history_id=imported_history_id, hid=2, hda_checker=check_ok, job_checker=upload_job_check) imported_content = self.dataset_populator.get_history_dataset_content( history_id=imported_history_id, hid=1, ) assert imported_content == "1 2 3\n" def test_import_metadata_regeneration(self): history_name = "for_import_metadata_regeneration" history_id = self.dataset_populator.new_history(name=history_name) self.dataset_populator.new_dataset(history_id, content=open(self.test_data_resolver.get_filename("1.bam"), 'rb'), file_type='bam', wait=True) imported_history_id = self._reimport_history(history_id, history_name) self._assert_history_length(imported_history_id, 1) self._check_imported_dataset(history_id=imported_history_id, hid=1) import_bam_metadata = self.dataset_populator.get_history_dataset_details( history_id=imported_history_id, hid=1, ) # The cleanup() method of the __IMPORT_HISTORY__ job (which is executed # after the job has entered its final state): # - creates a new dataset with 'ok' state and adds it to the history # - starts a __SET_METADATA__ job to regenerate the dataset metadata, if # needed # We need to wait a bit for the creation of the __SET_METADATA__ job. time.sleep(1) self.dataset_populator.wait_for_history_jobs(imported_history_id, assert_ok=True) bai_metadata = import_bam_metadata["meta_files"][0] assert bai_metadata["file_type"] == "bam_index" api_url = bai_metadata["download_url"].split("api/", 1)[1] bai_response = self._get(api_url) self._assert_status_code_is(bai_response, 200) assert len(bai_response.content) > 4 def test_import_export_collection(self): history_name = "for_export_with_collections" history_id = self.dataset_populator.new_history(name=history_name) self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"], direct_upload=True) imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=3) self._assert_history_length(imported_history_id, 3) def check_elements(elements): assert len(elements) == 2 element0 = elements[0]["object"] element1 = elements[1]["object"] for element in [element0, element1]: assert not element["visible"] assert not element["deleted"] assert element["state"] == "ok" assert element0["hid"] == 2 assert element1["hid"] == 3 self._check_imported_collection(imported_history_id, hid=1, collection_type="list", elements_checker=check_elements) def test_import_export_nested_collection(self): history_name = "for_export_with_nested_collections" history_id = self.dataset_populator.new_history(name=history_name) self.dataset_collection_populator.create_list_of_pairs_in_history(history_id) imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=3) self._assert_history_length(imported_history_id, 3) def check_elements(elements): assert len(elements) == 1 element0 = elements[0]["object"] self._assert_has_keys(element0, "elements", "collection_type") child_elements = element0["elements"] assert len(child_elements) == 2 assert element0["collection_type"] == "paired" self._check_imported_collection(imported_history_id, hid=1, collection_type="list:paired", elements_checker=check_elements) def _reimport_history(self, history_id, history_name, wait_on_history_length=None, export_kwds={}): # Ensure the history is ready to go... self.dataset_populator.wait_for_history(history_id, assert_ok=True) return self.dataset_populator.reimport_history( history_id, history_name, wait_on_history_length=wait_on_history_length, export_kwds=export_kwds, url=self.url, api_key=self.galaxy_interactor.api_key ) def _import_history_and_wait(self, import_data, history_name, wait_on_history_length=None): imported_history_id = self.dataset_populator.import_history_and_wait_for_name(import_data, history_name) if wait_on_history_length: self.dataset_populator.wait_on_history_length(imported_history_id, wait_on_history_length) return imported_history_id def _assert_history_length(self, history_id, n): contents_response = self._get("histories/%s/contents" % history_id) self._assert_status_code_is(contents_response, 200) contents = contents_response.json() assert len(contents) == n, contents def _check_imported_dataset(self, history_id, hid, has_job=True, hda_checker=None, job_checker=None): imported_dataset_metadata = self.dataset_populator.get_history_dataset_details( history_id=history_id, hid=hid, ) assert imported_dataset_metadata["history_content_type"] == "dataset" assert imported_dataset_metadata["history_id"] == history_id if hda_checker is not None: hda_checker(imported_dataset_metadata) assert "creating_job" in imported_dataset_metadata job_id = imported_dataset_metadata["creating_job"] if has_job: assert job_id job_details = self.dataset_populator.get_job_details(job_id, full=True) assert job_details.status_code == 200, job_details.content job = job_details.json() assert 'history_id' in job, job assert job['history_id'] == history_id, job if job_checker is not None: job_checker(job) def _check_imported_collection(self, history_id, hid, collection_type=None, elements_checker=None): imported_collection_metadata = self.dataset_populator.get_history_collection_details( history_id=history_id, hid=hid, ) assert imported_collection_metadata["history_content_type"] == "dataset_collection" assert imported_collection_metadata["history_id"] == history_id assert "collection_type" in imported_collection_metadata assert "elements" in imported_collection_metadata if collection_type is not None: assert imported_collection_metadata["collection_type"] == collection_type, imported_collection_metadata if elements_checker is not None: elements_checker(imported_collection_metadata["elements"]) def test_create_tag(self): post_data = dict(name="TestHistoryForTag") history_id = self._post("histories", data=post_data).json()["id"] tag_data = dict(value="awesometagvalue") tag_url = "histories/%s/tags/awesometagname" % history_id tag_create_response = self._post(tag_url, data=tag_data) self._assert_status_code_is(tag_create_response, 200) def _show(self, history_id): return self._get("histories/%s" % history_id).json() def _update(self, history_id, data): update_url = self._api_url("histories/%s" % history_id, use_key=True) put_response = put(update_url, json=data) return put_response def _create_history(self, name): post_data = dict(name=name) create_response = self._post("histories", data=post_data).json() self._assert_has_keys(create_response, "name", "id") self.assertEqual(create_response["name"], name) return create_response
class ToolsUploadTestCase(api.ApiTestCase): def setUp(self): super(ToolsUploadTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) def test_upload1_paste(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, 'Hello World') create_response = self._post("tools", data=payload) self._assert_has_keys(create_response.json(), 'outputs') def test_upload1_paste_bad_datatype(self): # Check that you get a nice message if you upload an incorrect datatype with self.dataset_populator.test_history() as history_id: file_type = "johnsawesomebutfakedatatype" payload = self.dataset_populator.upload_payload(history_id, 'Hello World', file_type=file_type) create = self._post("tools", data=payload).json() self._assert_has_keys(create, 'err_msg') assert file_type in create['err_msg'] # upload1 rewrites content with posix lines by default but this can be disabled by setting # to_posix_lines=None in the request. Newer fetch API does not do this by default prefering # to keep content unaltered if possible but it can be enabled with a simple JSON boolean switch # of the same name (to_posix_lines). def test_upload_posix_newline_fixes_by_default(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_posix_unaltered(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch") self.assertEquals(result_content, ONE_TO_SIX_ON_WINDOWS) def test_upload_disable_posix_fix(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, to_posix_lines=None) self.assertEquals(result_content, windows_content) def test_fetch_post_lines_option(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch", to_posix_lines=True) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table) self.assertEquals(result_content, table) def test_fetch_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api='fetch') self.assertEquals(result_content, table) def test_upload_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, space_to_tab="Yes") self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api="fetch", space_to_tab=True) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_fetch_compressed_with_explicit_type(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", ext="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz" def test_fetch_compressed_default(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details @uses_test_history(require_new=True) def test_fetch_compressed_auto_decompress_target(self, history_id): # TODO: this should definitely be fixed to allow auto decompression via that API. fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False, auto_decompress=True) assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details def test_upload_decompress_off_with_auto_by_default(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bed", details def test_upload_decompresses_if_uncompressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="fastqsanger") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger", details assert details["file_size"] == 178, details def test_upload_decompress_off_if_compressed_type_selected(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="fastqsanger.gz") assert details["state"] == "ok" assert details["file_ext"] == "fastqsanger.gz", details assert details["file_size"] == 161, details def test_upload_auto_decompress_off(self): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto", assert_ok=False, auto_decompress=False) assert details["file_ext"] == "binary", details @uses_test_history(require_new=True) def test_fetch_compressed_with_auto(self, history_id): # UNSTABLE_FLAG: This might default to a bed.gz datatype in the future. # TODO: this should definitely be fixed to allow auto decompression via that API. bedgz_path = TestDataResolver().get_filename("4.bed.gz") with open(bedgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, auto_decompress=True, assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bed" @skip_without_datatype("rdata") def test_rdata_not_decompressed(self): # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 rdata_path = TestDataResolver().get_filename("1.RData") with open(rdata_path, "rb") as fh: rdata_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(rdata_metadata["file_ext"], "rdata") @skip_without_datatype("csv") def test_csv_upload(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="csv") self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_upload_auto(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="csv", to_posix_lines=True) self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("csv") def test_csv_sniff_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="auto", to_posix_lines=True) self.assertEquals(csv_metadata["file_ext"], "csv") @skip_without_datatype("tiff") def test_image_upload_auto(self): tiff_path = TestDataResolver().get_filename("1.tiff") with open(tiff_path, "rb") as fh: tiff_metadata = self._upload_and_get_details(fh, file_type="auto") self.assertEquals(tiff_metadata["file_ext"], "tiff") @skip_without_datatype("velvet") def test_composite_datatype(self): with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps content", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_space_to_tab(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps\tcontent", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_posix_lines(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps\rcontent", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log\rcontent", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps\ncontent", roadmaps_content def test_upload_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19") run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert datasets[0].get("genome_build") == "hg19", datasets[0] @uses_test_history(require_new=False) def test_fetch_bam_file(self, history_id): bam_path = TestDataResolver().get_filename("1.bam") with open(bam_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False) assert details["state"] == "ok" assert details["file_ext"] == "bam", details def test_upload_bam_file(self): bam_path = TestDataResolver().get_filename("1.bam") with open(bam_path, "rb") as fh: details = self._upload_and_get_details(fh, file_type="auto") assert details["state"] == "ok" assert details["file_ext"] == "bam", details def test_fetch_metadata(self): table = ONE_TO_SIX_WITH_SPACES details = self._upload_and_get_details(table, api='fetch', dbkey="hg19", info="cool upload", tags=["name:data", "group:type:paired-end"]) assert details.get("genome_build") == "hg19" assert details.get("misc_info") == "cool upload", details tags = details.get("tags") assert len(tags) == 2, details assert "group:type:paired-end" in tags assert "name:data" in tags def test_upload_multiple_files_1(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "tabular", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt" assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "tabular" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_2(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "tabular", datasets assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_3(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|dbkey": "hg18", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "hg18", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_no_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey=None, extra_inputs={ "files_0|file_type": "txt", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "?", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "?", datasets def test_upload_multiple_files_space_to_tab(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, content=ONE_TO_SIX_WITH_SPACES, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|space_to_tab": "Yes", "files_1|url_paste": ONE_TO_SIX_WITH_SPACES, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_2|url_paste": ONE_TO_SIX_WITH_SPACES, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "files_2|space_to_tab": "Yes", "file_count": "3", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_WITH_SPACES content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_multiple_files_posix_lines(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, content=ONE_TO_SIX_ON_WINDOWS, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|to_posix_lines": "Yes", "files_1|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|to_posix_lines": None, "files_2|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "file_count": "3", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_ON_WINDOWS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_upload_from_invalid_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/bla123', assert_ok=False) dataset_details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=False) assert dataset_details['state'] == 'error', "expected dataset state to be 'error', but got '%s'" % dataset_details['state'] def test_upload_from_valid_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/api/version') self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=True) def _velvet_upload(self, history_id, extra_inputs): payload = self.dataset_populator.upload_payload( history_id, "sequences content", file_type="velvet", extra_inputs=extra_inputs, ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 1 dataset = datasets[0] return dataset def _get_roadmaps_content(self, history_id, dataset): roadmaps_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=dataset, filename="Roadmaps") return roadmaps_content def _upload_and_get_content(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset) def _upload_and_get_details(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) assert_ok = upload_kwds.get("assert_ok", True) return self.dataset_populator.get_history_dataset_details(history_id, dataset=new_dataset, assert_ok=assert_ok) def _upload(self, content, api="upload1", history_id=None, **upload_kwds): assert_ok = upload_kwds.get("assert_ok", True) history_id = history_id or self.dataset_populator.new_history() if api == "upload1": new_dataset = self.dataset_populator.new_dataset(history_id, content=content, **upload_kwds) else: assert api == "fetch" element = dict(src="files", **upload_kwds) target = { "destination": {"type": "hdas"}, "elements": [element], } targets = json.dumps([target]) payload = { "history_id": history_id, "targets": targets, "__files": {"files_0|file_data": content} } new_dataset = self.dataset_populator.fetch(payload, assert_ok=assert_ok).json()["outputs"][0] self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok) return history_id, new_dataset
class ToolsUploadTestCase(api.ApiTestCase): def setUp(self): super(ToolsUploadTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) def test_upload1_paste(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, 'Hello World') create_response = self._post("tools", data=payload) self._assert_has_keys(create_response.json(), 'outputs') def test_upload1_paste_bad_datatype(self): # Check that you get a nice message if you upload an incorrect datatype with self.dataset_populator.test_history() as history_id: file_type = "johnsawesomebutfakedatatype" payload = self.dataset_populator.upload_payload(history_id, 'Hello World', file_type=file_type) create = self._post("tools", data=payload).json() self._assert_has_keys(create, 'err_msg') assert file_type in create['err_msg'] def test_upload_posix_newline_fixes(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content) self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_disable_posix_fix(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, to_posix_lines=None) self.assertEquals(result_content, windows_content) def test_upload_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, space_to_tab="Yes") self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS) def test_upload_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table) self.assertEquals(result_content, table) @skip_without_datatype("rdata") def test_rdata_not_decompressed(self): # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753 rdata_path = TestDataResolver().get_filename("1.RData") rdata_metadata = self._upload_and_get_details(open(rdata_path, "rb"), file_type="auto") self.assertEquals(rdata_metadata["file_ext"], "rdata") @skip_without_datatype("velvet") def test_composite_datatype(self): with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps content", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_space_to_tab(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps content", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log content", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps\tcontent", roadmaps_content @skip_without_datatype("velvet") def test_composite_datatype_posix_lines(self): # Like previous test but set one upload with space_to_tab to True to # verify that works. with self.dataset_populator.test_history() as history_id: dataset = self._velvet_upload(history_id, extra_inputs={ "files_1|url_paste": "roadmaps\rcontent", "files_1|type": "upload_dataset", "files_1|space_to_tab": "Yes", "files_2|url_paste": "log\rcontent", "files_2|type": "upload_dataset", }) roadmaps_content = self._get_roadmaps_content(history_id, dataset) assert roadmaps_content.strip() == "roadmaps\ncontent", roadmaps_content def test_upload_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19") run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert datasets[0].get("genome_build") == "hg19", datasets[0] def test_upload_multiple_files_1(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "tabular", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt" assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "tabular" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_2(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "tabular", datasets assert datasets[0]["genome_build"] == "hg19", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_3(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|dbkey": "hg18", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|dbkey": "hg18", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "hg18", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "hg18", datasets def test_upload_multiple_files_no_dbkey(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, "Test123", file_type="tabular", dbkey=None, extra_inputs={ "files_0|file_type": "txt", "files_1|url_paste": "SecondOutputContent", "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "file_count": "2", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 2, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content.strip() == "Test123" assert datasets[0]["file_ext"] == "txt", datasets assert datasets[0]["genome_build"] == "?", datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content.strip() == "SecondOutputContent" assert datasets[1]["file_ext"] == "txt" assert datasets[1]["genome_build"] == "?", datasets def test_upload_multiple_files_space_to_tab(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, content=ONE_TO_SIX_WITH_SPACES, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|space_to_tab": "Yes", "files_1|url_paste": ONE_TO_SIX_WITH_SPACES, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_2|url_paste": ONE_TO_SIX_WITH_SPACES, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "files_2|space_to_tab": "Yes", "file_count": "3", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_WITH_SPACES content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_multiple_files_posix_lines(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.upload_payload(history_id, content=ONE_TO_SIX_ON_WINDOWS, file_type="tabular", dbkey="hg19", extra_inputs={ "files_0|file_type": "txt", "files_0|to_posix_lines": "Yes", "files_1|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_1|NAME": "SecondOutputName", "files_1|file_type": "txt", "files_1|to_posix_lines": None, "files_2|url_paste": ONE_TO_SIX_ON_WINDOWS, "files_2|NAME": "ThirdOutputName", "files_2|file_type": "txt", "file_count": "3", } ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 3, datasets content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0]) assert content == ONE_TO_SIX_WITH_TABS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1]) assert content == ONE_TO_SIX_ON_WINDOWS content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2]) assert content == ONE_TO_SIX_WITH_TABS def test_upload_from_invalid_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/bla123', assert_ok=False) dataset_details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=False) assert dataset_details['state'] == 'error', "expected dataset state to be 'error', but got '%s'" % dataset_details['state'] def test_upload_from_valid_url(self): history_id, new_dataset = self._upload('https://usegalaxy.org/api/version') self.dataset_populator.get_history_dataset_details(history_id, dataset_id=new_dataset["id"], assert_ok=True) def _velvet_upload(self, history_id, extra_inputs): payload = self.dataset_populator.upload_payload( history_id, "sequences content", file_type="velvet", extra_inputs=extra_inputs, ) run_response = self.dataset_populator.tools_post(payload) self.dataset_populator.wait_for_tool_run(history_id, run_response) datasets = run_response.json()["outputs"] assert len(datasets) == 1 dataset = datasets[0] return dataset def _get_roadmaps_content(self, history_id, dataset): roadmaps_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=dataset, filename="Roadmaps") return roadmaps_content def _upload_and_get_content(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset) def _upload_and_get_details(self, content, **upload_kwds): history_id, new_dataset = self._upload(content, **upload_kwds) return self.dataset_populator.get_history_dataset_details(history_id, dataset=new_dataset) def _upload(self, content, **upload_kwds): history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset(history_id, content=content, **upload_kwds) self.dataset_populator.wait_for_history(history_id, assert_ok=upload_kwds.get("assert_ok", True)) return history_id, new_dataset
class JobsApiTestCase(api.ApiTestCase): def setUp(self): super(JobsApiTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor) @uses_test_history(require_new=True) def test_index(self, history_id): # Create HDA to ensure at least one job exists... self.__history_with_new_dataset(history_id) jobs = self.__jobs_index() assert "upload1" in map(itemgetter("tool_id"), jobs) @uses_test_history(require_new=True) def test_system_details_admin_only(self, history_id): self.__history_with_new_dataset(history_id) jobs = self.__jobs_index(admin=False) job = jobs[0] self._assert_not_has_keys(job, "command_line", "external_id") jobs = self.__jobs_index(admin=True) job = jobs[0] self._assert_has_keys(job, "command_line", "external_id") @uses_test_history(require_new=True) def test_index_state_filter(self, history_id): # Initial number of ok jobs original_count = len(self.__uploads_with_state("ok")) # Run through dataset upload to ensure num uplaods at least greater # by 1. self.__history_with_ok_dataset(history_id) # Verify number of ok jobs is actually greater. count_increased = False for i in range(10): new_count = len(self.__uploads_with_state("ok")) if original_count < new_count: count_increased = True break time.sleep(.1) if not count_increased: template = "Jobs in ok state did not increase (was %d, now %d)" message = template % (original_count, new_count) raise AssertionError(message) @uses_test_history(require_new=True) def test_index_date_filter(self, history_id): self.__history_with_new_dataset(history_id) two_weeks_ago = (datetime.datetime.utcnow() - datetime.timedelta(7)).isoformat() last_week = (datetime.datetime.utcnow() - datetime.timedelta(7)).isoformat() next_week = (datetime.datetime.utcnow() + datetime.timedelta(7)).isoformat() today = datetime.datetime.utcnow().isoformat() tomorrow = (datetime.datetime.utcnow() + datetime.timedelta(1)).isoformat() jobs = self.__jobs_index(data={ "date_range_min": today[0:10], "date_range_max": tomorrow[0:10] }) assert len(jobs) > 0 today_job_id = jobs[0]["id"] jobs = self.__jobs_index(data={ "date_range_min": two_weeks_ago, "date_range_max": last_week }) assert today_job_id not in map(itemgetter("id"), jobs) jobs = self.__jobs_index(data={ "date_range_min": last_week, "date_range_max": next_week }) assert today_job_id in map(itemgetter("id"), jobs) @uses_test_history(require_new=True) def test_index_history(self, history_id): self.__history_with_new_dataset(history_id) jobs = self.__jobs_index(data={"history_id": history_id}) assert len(jobs) > 0 with self.dataset_populator.test_history() as other_history_id: jobs = self.__jobs_index(data={"history_id": other_history_id}) assert len(jobs) == 0 @uses_test_history(require_new=True) def test_index_multiple_states_filter(self, history_id): # Initial number of ok jobs original_count = len(self.__uploads_with_state("ok", "new")) # Run through dataset upload to ensure num uplaods at least greater # by 1. self.__history_with_ok_dataset(history_id) # Verify number of ok jobs is actually greater. new_count = len(self.__uploads_with_state("new", "ok")) assert original_count < new_count, new_count @uses_test_history(require_new=True) def test_show(self, history_id): # Create HDA to ensure at least one job exists... self.__history_with_new_dataset(history_id) jobs_response = self._get("jobs") first_job = jobs_response.json()[0] self._assert_has_key(first_job, 'id', 'state', 'exit_code', 'update_time', 'create_time') job_id = first_job["id"] show_jobs_response = self._get("jobs/%s" % job_id) self._assert_status_code_is(show_jobs_response, 200) job_details = show_jobs_response.json() self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time') show_jobs_response = self._get("jobs/%s" % job_id, {"full": True}) self._assert_status_code_is(show_jobs_response, 200) job_details = show_jobs_response.json() self._assert_has_key(job_details, 'id', 'state', 'exit_code', 'update_time', 'create_time', 'stdout', 'stderr', 'job_messages') @uses_test_history(require_new=True) def test_show_security(self, history_id): self.__history_with_new_dataset(history_id) jobs_response = self._get("jobs", data={"history_id": history_id}) job = jobs_response.json()[0] job_id = job["id"] show_jobs_response = self._get("jobs/%s" % job_id, admin=False) self._assert_not_has_keys(show_jobs_response.json(), "command_line", "external_id") # TODO: Re-activate test case when API accepts privacy settings # with self._different_user(): # show_jobs_response = self._get( "jobs/%s" % job_id, admin=False ) # self._assert_status_code_is( show_jobs_response, 200 ) show_jobs_response = self._get("jobs/%s" % job_id, admin=True) self._assert_has_keys(show_jobs_response.json(), "command_line", "external_id") def _run_detect_errors(self, history_id, inputs): payload = self.dataset_populator.run_tool_payload( tool_id='detect_errors_aggressive', inputs=inputs, history_id=history_id, ) return self._post("tools", data=payload).json() @skip_without_tool("detect_errors_aggressive") def test_unhide_on_error(self): with self.dataset_populator.test_history() as history_id: inputs = {'error_bool': 'true'} run_response = self._run_detect_errors(history_id=history_id, inputs=inputs) job_id = run_response['jobs'][0]["id"] self.dataset_populator.wait_for_job(job_id) job = self.dataset_populator.get_job_details(job_id).json() assert job['state'] == 'error' dataset = self.dataset_populator.get_history_dataset_details( history_id=history_id, dataset_id=run_response['outputs'][0]['id'], assert_ok=False) assert dataset['visible'] @skip_without_tool("detect_errors_aggressive") def test_no_unhide_on_error_if_mapped_over(self): with self.dataset_populator.test_history() as history_id: hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=[("sample1-1", "1 2 3")]).json() inputs = { 'error_bool': 'true', 'dataset': { 'batch': True, 'values': [{ 'src': 'hdca', 'id': hdca1['id'] }], } } run_response = self._run_detect_errors(history_id=history_id, inputs=inputs) job_id = run_response['jobs'][0]["id"] self.dataset_populator.wait_for_job(job_id) job = self.dataset_populator.get_job_details(job_id).json() assert job['state'] == 'error' dataset = self.dataset_populator.get_history_dataset_details( history_id=history_id, dataset_id=run_response['outputs'][0]['id'], assert_ok=False) assert not dataset['visible'] @skip_without_tool('empty_output') def test_common_problems(self): with self.dataset_populator.test_history() as history_id: empty_run_response = self.dataset_populator.run_tool( tool_id='empty_output', inputs={}, history_id=history_id, ) empty_hda = empty_run_response["outputs"][0] cat_empty_twice_run_response = self.dataset_populator.run_tool( tool_id='cat1', inputs={ 'input1': { 'src': 'hda', 'id': empty_hda['id'] }, 'queries_0|input2': { 'src': 'hda', 'id': empty_hda['id'] } }, history_id=history_id, ) empty_output_job = empty_run_response["jobs"][0] cat_empty_job = cat_empty_twice_run_response["jobs"][0] empty_output_common_problems_response = self._get( 'jobs/%s/common_problems' % empty_output_job["id"]).json() cat_empty_common_problems_response = self._get( 'jobs/%s/common_problems' % cat_empty_job["id"]).json() self._assert_has_keys(empty_output_common_problems_response, "has_empty_inputs", "has_duplicate_inputs") self._assert_has_keys(cat_empty_common_problems_response, "has_empty_inputs", "has_duplicate_inputs") assert not empty_output_common_problems_response["has_empty_inputs"] assert cat_empty_common_problems_response["has_empty_inputs"] assert not empty_output_common_problems_response[ "has_duplicate_inputs"] assert cat_empty_common_problems_response["has_duplicate_inputs"] @skip_without_tool('detect_errors_aggressive') def test_report_error(self): with self.dataset_populator.test_history() as history_id: payload = self.dataset_populator.run_tool_payload( tool_id='detect_errors_aggressive', inputs={'error_bool': 'true'}, history_id=history_id, ) run_response = self._post("tools", data=payload).json() job_id = run_response['jobs'][0]["id"] dataset_id = run_response['outputs'][0]['id'] response = self._post('jobs/%s/error' % job_id, data={'dataset_id': dataset_id}) assert response.status_code == 200 @skip_without_tool('detect_errors_aggressive') def test_report_error_anon(self): # Need to get a cookie and use that for anonymous tool runs cookies = requests.get(self.url).cookies payload = json.dumps({ "tool_id": "detect_errors_aggressive", "inputs": { "error_bool": "true" } }) run_response = requests.post("%s/tools" % self.galaxy_interactor.api_url, data=payload, cookies=cookies).json() job_id = run_response['jobs'][0]["id"] dataset_id = run_response['outputs'][0]['id'] response = requests.post('%s/jobs/%s/error' % (self.galaxy_interactor.api_url, job_id), params={ 'email': '*****@*****.**', 'dataset_id': dataset_id }, cookies=cookies) assert response.status_code == 200 @uses_test_history(require_new=True) def test_deleting_output_keep_running_until_all_deleted(self, history_id): job_state, outputs = self._setup_running_two_output_job( history_id, 120) self._hack_to_skip_test_if_state_ok(job_state) # Delete one of the two outputs and make sure the job is still running. self._raw_update_history_item(history_id, outputs[0]["id"], {"deleted": True}) self._hack_to_skip_test_if_state_ok(job_state) time.sleep(1) self._hack_to_skip_test_if_state_ok(job_state) state = job_state().json()["state"] assert state == "running", state # Delete the second output and make sure the job is cancelled. self._raw_update_history_item(history_id, outputs[1]["id"], {"deleted": True}) final_state = wait_on_state(job_state, assert_ok=False, timeout=15) assert final_state in ["deleted_new", "deleted"], final_state @uses_test_history(require_new=True) def test_purging_output_keep_running_until_all_purged(self, history_id): job_state, outputs = self._setup_running_two_output_job( history_id, 120) # Pretty much right away after the job is running, these paths should be populated - # if they are grab them and make sure they are deleted at the end of the job. dataset_1 = self._get_history_item_as_admin(history_id, outputs[0]["id"]) dataset_2 = self._get_history_item_as_admin(history_id, outputs[1]["id"]) if "file_name" in dataset_1: output_dataset_paths = [ dataset_1["file_name"], dataset_2["file_name"] ] # This may or may not exist depending on if the test is local or not. output_dataset_paths_exist = os.path.exists( output_dataset_paths[0]) else: output_dataset_paths = [] output_dataset_paths_exist = False self._hack_to_skip_test_if_state_ok(job_state) current_state = job_state().json()["state"] assert current_state == "running", current_state # Purge one of the two outputs and make sure the job is still running. self._raw_update_history_item(history_id, outputs[0]["id"], {"purged": True}) time.sleep(1) self._hack_to_skip_test_if_state_ok(job_state) current_state = job_state().json()["state"] assert current_state == "running", current_state # Purge the second output and make sure the job is cancelled. self._raw_update_history_item(history_id, outputs[1]["id"], {"purged": True}) final_state = wait_on_state(job_state, assert_ok=False, timeout=15) assert final_state in ["deleted_new", "deleted"], final_state def paths_deleted(): if not os.path.exists( output_dataset_paths[0]) and not os.path.exists( output_dataset_paths[1]): return True if output_dataset_paths_exist: wait_on(paths_deleted, "path deletion") @uses_test_history(require_new=True) def test_purging_output_cleaned_after_ok_run(self, history_id): job_state, outputs = self._setup_running_two_output_job(history_id, 10) # Pretty much right away after the job is running, these paths should be populated - # if they are grab them and make sure they are deleted at the end of the job. dataset_1 = self._get_history_item_as_admin(history_id, outputs[0]["id"]) dataset_2 = self._get_history_item_as_admin(history_id, outputs[1]["id"]) if "file_name" in dataset_1: output_dataset_paths = [ dataset_1["file_name"], dataset_2["file_name"] ] # This may or may not exist depending on if the test is local or not. output_dataset_paths_exist = os.path.exists( output_dataset_paths[0]) else: output_dataset_paths = [] output_dataset_paths_exist = False if not output_dataset_paths_exist: # Given this Galaxy configuration - there is nothing more to be tested here. # Consider throwing a skip instead. return # Purge one of the two outputs and wait for the job to complete. self._raw_update_history_item(history_id, outputs[0]["id"], {"purged": True}) wait_on_state(job_state, assert_ok=True) if output_dataset_paths_exist: time.sleep(.5) # Make sure the non-purged dataset is on disk and the purged one is not. assert os.path.exists(output_dataset_paths[1]) assert not os.path.exists(output_dataset_paths[0]) def _hack_to_skip_test_if_state_ok(self, job_state): from nose.plugins.skip import SkipTest if job_state().json()["state"] == "ok": message = "Job state switch from running to ok too quickly - the rest of the test requires the job to be in a running state. Skipping test." raise SkipTest(message) def _setup_running_two_output_job(self, history_id, sleep_time): payload = self.dataset_populator.run_tool_payload( tool_id='create_2', inputs=dict(sleep_time=sleep_time, ), history_id=history_id, ) run_response = self._post("tools", data=payload).json() outputs = run_response["outputs"] jobs = run_response["jobs"] assert len(outputs) == 2 assert len(jobs) == 1 def job_state(): jobs_response = self._get("jobs/%s" % jobs[0]["id"]) return jobs_response # Give job some time to get up and running. time.sleep(2) running_state = wait_on_state(job_state, skip_states=["queued", "new"], assert_ok=False, timeout=15) assert running_state == "running", running_state def job_state(): jobs_response = self._get("jobs/%s" % jobs[0]["id"]) return jobs_response return job_state, outputs def _raw_update_history_item(self, history_id, item_id, data): update_url = self._api_url("histories/%s/contents/%s" % (history_id, item_id), use_key=True) update_response = requests.put(update_url, json=data) assert_status_code_is_ok(update_response) return update_response @skip_without_tool("cat_data_and_sleep") @uses_test_history(require_new=True) def test_resume_job(self, history_id): hda1 = self.dataset_populator.new_dataset( history_id, content="samp1\t10.0\nsamp2\t20.0\n") hda2 = self.dataset_populator.new_dataset( history_id, content="samp1\t30.0\nsamp2\t40.0\n") # Submit first job payload = self.dataset_populator.run_tool_payload( tool_id='cat_data_and_sleep', inputs={ 'sleep_time': 15, 'input1': { 'src': 'hda', 'id': hda2['id'] }, 'queries_0|input2': { 'src': 'hda', 'id': hda2['id'] } }, history_id=history_id, ) run_response = self._post("tools", data=payload).json() output = run_response["outputs"][0] # Submit second job that waits on job1 payload = self.dataset_populator.run_tool_payload( tool_id='cat1', inputs={ 'input1': { 'src': 'hda', 'id': hda1['id'] }, 'queries_0|input2': { 'src': 'hda', 'id': output['id'] } }, history_id=history_id, ) run_response = self._post("tools", data=payload).json() job_id = run_response['jobs'][0]['id'] output = run_response["outputs"][0] # Delete second jobs input while second job is waiting for first job delete_response = self._delete("histories/%s/contents/%s" % (history_id, hda1['id'])) self._assert_status_code_is(delete_response, 200) self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=False) dataset_details = self._get("histories/%s/contents/%s" % (history_id, output['id'])).json() assert dataset_details['state'] == 'paused' # Undelete input dataset undelete_response = self._put("histories/%s/contents/%s" % (history_id, hda1['id']), data=json.dumps({'deleted': False})) self._assert_status_code_is(undelete_response, 200) resume_response = self._put("jobs/%s/resume" % job_id) self._assert_status_code_is(resume_response, 200) self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=True) dataset_details = self._get("histories/%s/contents/%s" % (history_id, output['id'])).json() assert dataset_details['state'] == 'ok' def _get_history_item_as_admin(self, history_id, item_id): response = self._get("histories/%s/contents/%s?view=detailed" % (history_id, item_id), admin=True) assert_status_code_is_ok(response) return response.json() @uses_test_history(require_new=True) def test_search(self, history_id): dataset_id = self.__history_with_ok_dataset(history_id) # We first copy the datasets, so that the update time is lower than the job creation time new_history_id = self.dataset_populator.new_history() copy_payload = { "content": dataset_id, "source": "hda", "type": "dataset" } copy_response = self._post("histories/%s/contents" % new_history_id, data=copy_payload) self._assert_status_code_is(copy_response, 200) inputs = json.dumps({'input1': {'src': 'hda', 'id': dataset_id}}) self._job_search(tool_id='cat1', history_id=history_id, inputs=inputs) # We test that a job can be found even if the dataset has been copied to another history new_dataset_id = copy_response.json()['id'] copied_inputs = json.dumps( {'input1': { 'src': 'hda', 'id': new_dataset_id }}) search_payload = self._search_payload(history_id=history_id, tool_id='cat1', inputs=copied_inputs) self._search(search_payload, expected_search_count=1) # Now we delete the original input HDA that was used -- we should still be able to find the job delete_respone = self._delete("histories/%s/contents/%s" % (history_id, dataset_id)) self._assert_status_code_is(delete_respone, 200) self._search(search_payload, expected_search_count=1) # Now we also delete the copy -- we shouldn't find a job delete_respone = self._delete("histories/%s/contents/%s" % (new_history_id, new_dataset_id)) self._assert_status_code_is(delete_respone, 200) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_handle_identifiers(self, history_id): # Test that input name and element identifier of a jobs' output must match for a job to be returned. dataset_id = self.__history_with_ok_dataset(history_id) inputs = json.dumps({'input1': {'src': 'hda', 'id': dataset_id}}) self._job_search(tool_id='identifier_single', history_id=history_id, inputs=inputs) dataset_details = self._get("histories/%s/contents/%s" % (history_id, dataset_id)).json() dataset_details['name'] = 'Renamed Test Dataset' dataset_update_response = self._put( "histories/%s/contents/%s" % (history_id, dataset_id), data=dict(name='Renamed Test Dataset')) self._assert_status_code_is(dataset_update_response, 200) assert dataset_update_response.json()['name'] == 'Renamed Test Dataset' search_payload = self._search_payload(history_id=history_id, tool_id='identifier_single', inputs=inputs) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_delete_outputs(self, history_id): dataset_id = self.__history_with_ok_dataset(history_id) inputs = json.dumps({'input1': {'src': 'hda', 'id': dataset_id}}) tool_response = self._job_search(tool_id='cat1', history_id=history_id, inputs=inputs) output_id = tool_response.json()['outputs'][0]['id'] delete_respone = self._delete("histories/%s/contents/%s" % (history_id, output_id)) self._assert_status_code_is(delete_respone, 200) search_payload = self._search_payload(history_id=history_id, tool_id='cat1', inputs=inputs) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_with_hdca_list_input(self, history_id): list_id_a = self.__history_with_ok_collection(collection_type='list', history_id=history_id) list_id_b = self.__history_with_ok_collection(collection_type='list', history_id=history_id) inputs = json.dumps({ 'f1': { 'src': 'hdca', 'id': list_id_a }, 'f2': { 'src': 'hdca', 'id': list_id_b }, }) tool_response = self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs) # We switch the inputs, this should not return a match inputs_switched = json.dumps({ 'f2': { 'src': 'hdca', 'id': list_id_a }, 'f1': { 'src': 'hdca', 'id': list_id_b }, }) search_payload = self._search_payload(history_id=history_id, tool_id='multi_data_param', inputs=inputs_switched) self._search(search_payload, expected_search_count=0) # We delete the ouput (this is a HDA, as multi_data_param reduces collections) # and use the correct input job definition, the job should not be found output_id = tool_response.json()['outputs'][0]['id'] delete_respone = self._delete("histories/%s/contents/%s" % (history_id, output_id)) self._assert_status_code_is(delete_respone, 200) search_payload = self._search_payload(history_id=history_id, tool_id='multi_data_param', inputs=inputs) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_delete_hdca_output(self, history_id): list_id_a = self.__history_with_ok_collection(collection_type='list', history_id=history_id) inputs = json.dumps({ 'input1': { 'src': 'hdca', 'id': list_id_a }, }) tool_response = self._job_search(tool_id='collection_creates_list', history_id=history_id, inputs=inputs) output_id = tool_response.json()['outputs'][0]['id'] # We delete a single tool output, no job should be returned delete_respone = self._delete("histories/%s/contents/%s" % (history_id, output_id)) self._assert_status_code_is(delete_respone, 200) search_payload = self._search_payload( history_id=history_id, tool_id='collection_creates_list', inputs=inputs) self._search(search_payload, expected_search_count=0) tool_response = self._job_search(tool_id='collection_creates_list', history_id=history_id, inputs=inputs) output_collection_id = tool_response.json( )['output_collections'][0]['id'] # We delete a collection output, no job should be returned delete_respone = self._delete( "histories/%s/contents/dataset_collections/%s" % (history_id, output_collection_id)) self._assert_status_code_is(delete_respone, 200) search_payload = self._search_payload( history_id=history_id, tool_id='collection_creates_list', inputs=inputs) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_with_hdca_pair_input(self, history_id): list_id_a = self.__history_with_ok_collection(collection_type='pair', history_id=history_id) inputs = json.dumps({ 'f1': { 'src': 'hdca', 'id': list_id_a }, 'f2': { 'src': 'hdca', 'id': list_id_a }, }) self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs) # We test that a job can be found even if the collection has been copied to another history new_history_id = self.dataset_populator.new_history() copy_payload = { "content": list_id_a, "source": "hdca", "type": "dataset_collection" } copy_response = self._post("histories/%s/contents" % new_history_id, data=copy_payload) self._assert_status_code_is(copy_response, 200) new_list_a = copy_response.json()['id'] copied_inputs = json.dumps({ 'f1': { 'src': 'hdca', 'id': new_list_a }, 'f2': { 'src': 'hdca', 'id': new_list_a }, }) search_payload = self._search_payload(history_id=new_history_id, tool_id='multi_data_param', inputs=copied_inputs) self._search(search_payload, expected_search_count=1) # Now we delete the original input HDCA that was used -- we should still be able to find the job delete_respone = self._delete( "histories/%s/contents/dataset_collections/%s" % (history_id, list_id_a)) self._assert_status_code_is(delete_respone, 200) self._search(search_payload, expected_search_count=1) # Now we also delete the copy -- we shouldn't find a job delete_respone = self._delete( "histories/%s/contents/dataset_collections/%s" % (history_id, new_list_a)) self._assert_status_code_is(delete_respone, 200) self._search(search_payload, expected_search_count=0) @uses_test_history(require_new=True) def test_search_with_hdca_list_pair_input(self, history_id): list_id_a = self.__history_with_ok_collection( collection_type='list:pair', history_id=history_id) inputs = json.dumps({ 'f1': { 'src': 'hdca', 'id': list_id_a }, 'f2': { 'src': 'hdca', 'id': list_id_a }, }) self._job_search(tool_id='multi_data_param', history_id=history_id, inputs=inputs) def _job_search(self, tool_id, history_id, inputs): search_payload = self._search_payload(history_id=history_id, tool_id=tool_id, inputs=inputs) empty_search_response = self._post("jobs/search", data=search_payload) self._assert_status_code_is(empty_search_response, 200) self.assertEqual(len(empty_search_response.json()), 0) tool_response = self._post("tools", data=search_payload) self.dataset_populator.wait_for_tool_run(history_id, run_response=tool_response) self._search(search_payload, expected_search_count=1) return tool_response def _search_payload(self, history_id, tool_id, inputs, state='ok'): search_payload = dict(tool_id=tool_id, inputs=inputs, history_id=history_id, state=state) return search_payload def _search(self, payload, expected_search_count=1): # in case job and history aren't updated at exactly the same # time give time to wait for i in range(5): search_count = self._search_count(payload) if search_count == expected_search_count: break time.sleep(1) assert search_count == expected_search_count, "expected to find %d jobs, got %d jobs" % ( expected_search_count, search_count) return search_count def _search_count(self, search_payload): search_response = self._post("jobs/search", data=search_payload) self._assert_status_code_is(search_response, 200) search_json = search_response.json() return len(search_json) def __uploads_with_state(self, *states): jobs_response = self._get("jobs", data=dict(state=states)) self._assert_status_code_is(jobs_response, 200) jobs = jobs_response.json() assert not [j for j in jobs if not j['state'] in states] return [j for j in jobs if j['tool_id'] == 'upload1'] def __history_with_new_dataset(self, history_id): dataset_id = self.dataset_populator.new_dataset(history_id)["id"] return dataset_id def __history_with_ok_dataset(self, history_id): dataset_id = self.dataset_populator.new_dataset(history_id, wait=True)["id"] return dataset_id def __history_with_ok_collection(self, collection_type='list', history_id=None): if not history_id: history_id = self.dataset_populator.new_history() if collection_type == 'list': fetch_response = self.dataset_collection_populator.create_list_in_history( history_id, direct_upload=True).json() elif collection_type == 'pair': fetch_response = self.dataset_collection_populator.create_pair_in_history( history_id, direct_upload=True).json() elif collection_type == 'list:pair': fetch_response = self.dataset_collection_populator.create_list_of_pairs_in_history( history_id).json() self.dataset_collection_populator.wait_for_fetched_collection( fetch_response) return fetch_response["outputs"][0]['id'] def __jobs_index(self, **kwds): jobs_response = self._get("jobs", **kwds) self._assert_status_code_is(jobs_response, 200) jobs = jobs_response.json() assert isinstance(jobs, list) return jobs
class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets): def setUp(self): super(HistoryContentsApiTestCase, self).setUp() self.history_id = self._new_history() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor) self.library_populator = LibraryPopulator(self.galaxy_interactor) def test_index_hda_summary(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents" % self.history_id) hda_summary = self.__check_for_hda(contents_response, hda1) assert "display_types" not in hda_summary # Quick summary, not full details def test_make_private_and_public(self): hda1 = self._wait_for_new_hda() update_url = "histories/%s/contents/%s/permissions" % (self.history_id, hda1["id"]) role_id = self.dataset_populator.user_private_role_id() # Give manage permission to the user. payload = { "access": [], "manage": [role_id], } update_response = self._update_permissions(update_url, payload, admin=True) self._assert_status_code_is(update_response, 200) self._assert_other_user_can_access(hda1["id"]) # Then we restrict access. payload = { "action": "make_private", } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_cannot_access(hda1["id"]) # Then we restrict access. payload = { "action": "remove_restrictions", } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_can_access(hda1["id"]) def test_set_permissions_add_admin_history_contents(self): self._verify_dataset_permissions("history_contents") def test_set_permissions_add_admin_datasets(self): self._verify_dataset_permissions("dataset") def _verify_dataset_permissions(self, api_endpoint): hda1 = self._wait_for_new_hda() hda_id = hda1["id"] if api_endpoint == "history_contents": update_url = "histories/%s/contents/%s/permissions" % ( self.history_id, hda_id) else: update_url = "datasets/%s/permissions" % hda_id role_id = self.dataset_populator.user_private_role_id() payload = { "access": [role_id], "manage": [role_id], } # Other users cannot modify permissions. with self._different_user(): update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 403) # First the details render for another user. self._assert_other_user_can_access(hda_id) # Then we restrict access. update_response = self._update_permissions(update_url, payload, admin=True) self._assert_status_code_is(update_response, 200) # Finally the details don't render. self._assert_other_user_cannot_access(hda_id) # But they do for the original user. contents_response = self._get("histories/%s/contents/%s" % (self.history_id, hda_id)).json() assert "name" in contents_response update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) payload = { "access": [role_id], "manage": [role_id], } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) self._assert_other_user_cannot_access(hda_id) user_id = self.dataset_populator.user_id() with self._different_user(): different_user_id = self.dataset_populator.user_id() combined_user_role = self.dataset_populator.create_role( [user_id, different_user_id], description="role for testing permissions") payload = { "access": [combined_user_role["id"]], "manage": [role_id], } update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 200) # Now other user can see dataset again with access permission. self._assert_other_user_can_access(hda_id) # access doesn't imply management though... with self._different_user(): update_response = self._update_permissions(update_url, payload) self._assert_status_code_is(update_response, 403) def _assert_other_user_cannot_access(self, history_content_id): with self._different_user(): contents_response = self._get( "histories/%s/contents/%s" % (self.history_id, history_content_id)).json() assert "name" not in contents_response def _assert_other_user_can_access(self, history_content_id): with self._different_user(): contents_response = self._get( "histories/%s/contents/%s" % (self.history_id, history_content_id)).json() assert "name" in contents_response def test_index_hda_all_details(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents?details=all" % self.history_id) hda_details = self.__check_for_hda(contents_response, hda1) self.__assert_hda_has_full_details(hda_details) def test_index_hda_detail_by_id(self): hda1 = self._new_dataset(self.history_id) contents_response = self._get("histories/%s/contents?details=%s" % (self.history_id, hda1["id"])) hda_details = self.__check_for_hda(contents_response, hda1) self.__assert_hda_has_full_details(hda_details) def test_show_hda(self): hda1 = self._new_dataset(self.history_id) show_response = self.__show(hda1) self._assert_status_code_is(show_response, 200) self.__assert_matches_hda(hda1, show_response.json()) def test_hda_copy(self): hda1 = self._new_dataset(self.history_id) create_data = dict( source='hda', content=hda1["id"], ) second_history_id = self._new_history() assert self.__count_contents(second_history_id) == 0 create_response = self._post( "histories/%s/contents" % second_history_id, create_data) self._assert_status_code_is(create_response, 200) assert self.__count_contents(second_history_id) == 1 def test_library_copy(self): ld = self.library_populator.new_library_dataset("lda_test_library") create_data = dict( source='library', content=ld["id"], ) assert self.__count_contents(self.history_id) == 0 create_response = self._post("histories/%s/contents" % self.history_id, create_data) self._assert_status_code_is(create_response, 200) assert self.__count_contents(self.history_id) == 1 def test_update(self): hda1 = self._wait_for_new_hda() assert str(hda1["deleted"]).lower() == "false" update_response = self._raw_update(hda1["id"], dict(deleted=True)) self._assert_status_code_is(update_response, 200) show_response = self.__show(hda1) assert str(show_response.json()["deleted"]).lower() == "true" update_response = self._raw_update(hda1["id"], dict(name="Updated Name")) assert self.__show(hda1).json()["name"] == "Updated Name" update_response = self._raw_update(hda1["id"], dict(name="Updated Name")) assert self.__show(hda1).json()["name"] == "Updated Name" unicode_name = u'ржевский сапоги' update_response = self._raw_update(hda1["id"], dict(name=unicode_name)) updated_hda = self.__show(hda1).json() assert updated_hda["name"] == unicode_name, updated_hda quoted_name = '"Mooo"' update_response = self._raw_update(hda1["id"], dict(name=quoted_name)) updated_hda = self.__show(hda1).json() assert updated_hda["name"] == quoted_name, quoted_name data = { "dataset_id": hda1["id"], "name": "moocow", "dbkey": "?", "annotation": None, "info": "my info is", "operation": "attributes" } update_response = self._set_edit_update(data) # No key or anything supplied, expect a permission problem. # A bit questionable but I think this is a 400 instead of a 403 so that # we don't distinguish between this is a valid ID you don't have access to # and this is an invalid ID. assert update_response.status_code == 400, update_response.content def test_update_batch(self): hda1 = self._wait_for_new_hda() assert str(hda1["deleted"]).lower() == "false" payload = dict(items=[{ "history_content_type": "dataset", "id": hda1["id"] }], deleted=True) update_response = self._raw_update_batch(payload) objects = update_response.json() assert objects[0]["deleted"] def test_update_type_failures(self): hda1 = self._wait_for_new_hda() update_response = self._raw_update(hda1["id"], dict(deleted='not valid')) self._assert_status_code_is(update_response, 400) def _wait_for_new_hda(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) return hda1 def _set_edit_update(self, json): set_edit_url = "%s/dataset/set_edit" % self.url update_response = put(set_edit_url, json=json) return update_response def _raw_update(self, item_id, data, admin=False, history_id=None): history_id = history_id or self.history_id key_param = "use_admin_key" if admin else "use_key" update_url = self._api_url( "histories/%s/contents/%s" % (history_id, item_id), **{key_param: True}) update_response = put(update_url, json=data) return update_response def _update_permissions(self, url, data, admin=False): key_param = "use_admin_key" if admin else "use_key" update_url = self._api_url(url, **{key_param: True}) update_response = put(update_url, json=data) return update_response def _raw_update_batch(self, data): update_url = self._api_url("histories/%s/contents" % (self.history_id), use_key=True) update_response = put(update_url, json=data) return update_response def test_delete(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) assert str(self.__show(hda1).json()["deleted"]).lower() == "false" delete_response = self._delete("histories/%s/contents/%s" % (self.history_id, hda1["id"])) assert delete_response.status_code < 300 # Something in the 200s :). assert str(self.__show(hda1).json()["deleted"]).lower() == "true" def test_purge(self): hda1 = self._new_dataset(self.history_id) self._wait_for_history(self.history_id) assert str(self.__show(hda1).json()["deleted"]).lower() == "false" assert str(self.__show(hda1).json()["purged"]).lower() == "false" data = {'purge': True} delete_response = self._delete("histories/%s/contents/%s" % (self.history_id, hda1["id"]), data=data) assert delete_response.status_code < 300 # Something in the 200s :). assert str(self.__show(hda1).json()["deleted"]).lower() == "true" assert str(self.__show(hda1).json()["purged"]).lower() == "true" def test_dataset_collection_creation_on_contents(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection") endpoint = "histories/%s/contents" % self.history_id self._check_pair_creation(endpoint, payload) def test_dataset_collection_creation_on_typed_contents(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, ) endpoint = "histories/%s/contents/dataset_collections" % self.history_id self._check_pair_creation(endpoint, payload) def test_dataset_collection_create_from_exisiting_datasets_with_new_tags( self): with self.dataset_populator.test_history() as history_id: hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] hda2_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] update_response = self._raw_update(hda2_id, dict(tags=['existing:tag']), history_id=history_id).json() assert update_response['tags'] == ['existing:tag'] creation_payload = { 'collection_type': 'list', 'history_id': history_id, 'element_identifiers': json.dumps([{ 'id': hda_id, 'src': 'hda', 'name': 'element_id1', 'tags': ['my_new_tag'] }, { 'id': hda2_id, 'src': 'hda', 'name': 'element_id2', 'tags': ['another_new_tag'] }]), 'type': 'dataset_collection', 'copy_elements': True } r = self._post("histories/%s/contents" % self.history_id, creation_payload).json() assert r['elements'][0]['object'][ 'id'] != hda_id, "HDA has not been copied" assert len(r['elements'][0]['object']['tags']) == 1 assert r['elements'][0]['object']['tags'][0] == 'my_new_tag' assert len(r['elements'][1]['object'] ['tags']) == 2, r['elements'][1]['object']['tags'] original_hda = self.dataset_populator.get_history_dataset_details( history_id=history_id, dataset_id=hda_id) assert len(original_hda['tags']) == 0, original_hda['tags'] def _check_pair_creation(self, endpoint, payload): pre_collection_count = self.__count_contents(type="dataset_collection") pre_dataset_count = self.__count_contents(type="dataset") pre_combined_count = self.__count_contents( type="dataset,dataset_collection") dataset_collection_response = self._post(endpoint, payload) dataset_collection = self.__check_create_collection_response( dataset_collection_response) post_collection_count = self.__count_contents( type="dataset_collection") post_dataset_count = self.__count_contents(type="dataset") post_combined_count = self.__count_contents( type="dataset,dataset_collection") # Test filtering types with index. assert pre_collection_count == 0 assert post_collection_count == 1 assert post_combined_count == pre_dataset_count + 1 assert post_combined_count == pre_combined_count + 1 assert pre_dataset_count == post_dataset_count # Test show dataset colleciton. collection_url = "histories/%s/contents/dataset_collections/%s" % ( self.history_id, dataset_collection["id"]) show_response = self._get(collection_url) self._assert_status_code_is(show_response, 200) dataset_collection = show_response.json() self._assert_has_keys(dataset_collection, "url", "name", "deleted") assert not dataset_collection["deleted"] delete_response = delete(self._api_url(collection_url, use_key=True)) self._assert_status_code_is(delete_response, 200) show_response = self._get(collection_url) dataset_collection = show_response.json() assert dataset_collection["deleted"] @skip_without_tool("collection_creates_list") def test_jobs_summary_simple_hdca(self): create_response = self.dataset_collection_populator.create_list_in_history( self.history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]) hdca_id = create_response.json()["id"] run = self.dataset_populator.run_collection_creates_list( self.history_id, hdca_id) collections = run['output_collections'] collection = collections[0] jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % ( self.history_id, collection["id"]) jobs_summary_response = self._get(jobs_summary_url) self._assert_status_code_is(jobs_summary_response, 200) jobs_summary = jobs_summary_response.json() self._assert_has_keys(jobs_summary, "populated_state", "states") @skip_without_tool("cat1") def test_jobs_summary_implicit_hdca(self): create_response = self.dataset_collection_populator.create_pair_in_history( self.history_id, contents=["123", "456"]) hdca_id = create_response.json()["id"] inputs = { "input1": { 'batch': True, 'values': [{ 'src': 'hdca', 'id': hdca_id }] }, } run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=self.history_id) self.dataset_populator.wait_for_history_jobs(self.history_id) collections = run['implicit_collections'] collection = collections[0] jobs_summary_url = "histories/%s/contents/dataset_collections/%s/jobs_summary" % ( self.history_id, collection["id"]) jobs_summary_response = self._get(jobs_summary_url) self._assert_status_code_is(jobs_summary_response, 200) jobs_summary = jobs_summary_response.json() self._assert_has_keys(jobs_summary, "populated_state", "states") states = jobs_summary["states"] assert states.get("ok") == 2, states def test_dataset_collection_hide_originals(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection") payload["hide_source_items"] = True dataset_collection_response = self._post( "histories/%s/contents" % self.history_id, payload) self.__check_create_collection_response(dataset_collection_response) contents_response = self._get("histories/%s/contents" % self.history_id) datasets = [ d for d in contents_response.json() if d["history_content_type"] == "dataset" and d["hid"] in [1, 2] ] # Assert two datasets in source were hidden. assert len(datasets) == 2 assert not datasets[0]["visible"] assert not datasets[1]["visible"] def test_update_dataset_collection(self): payload = self.dataset_collection_populator.create_pair_payload( self.history_id, type="dataset_collection") dataset_collection_response = self._post( "histories/%s/contents" % self.history_id, payload) self._assert_status_code_is(dataset_collection_response, 200) hdca = dataset_collection_response.json() update_url = self._api_url( "histories/%s/contents/dataset_collections/%s" % (self.history_id, hdca["id"]), use_key=True) # Awkward json.dumps required here because of https://trello.com/c/CQwmCeG6 body = json.dumps(dict(name="newnameforpair")) update_response = put(update_url, data=body) self._assert_status_code_is(update_response, 200) show_response = self.__show(hdca) assert str(show_response.json()["name"]) == "newnameforpair" def test_hdca_copy(self): hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id).json() hdca_id = hdca["id"] second_history_id = self._new_history() create_data = dict( source='hdca', content=hdca_id, ) assert len( self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0 create_response = self._post( "histories/%s/contents/dataset_collections" % second_history_id, create_data) self.__check_create_collection_response(create_response) contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json() assert len(contents) == 1 new_forward, _ = self.__get_paired_response_elements(contents[0]) self._assert_has_keys(new_forward, "history_id") assert new_forward["history_id"] == self.history_id def test_hdca_copy_and_elements(self): hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id).json() hdca_id = hdca["id"] second_history_id = self._new_history() create_data = dict( source='hdca', content=hdca_id, copy_elements=True, ) assert len( self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0 create_response = self._post( "histories/%s/contents/dataset_collections" % second_history_id, create_data) self.__check_create_collection_response(create_response) contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json() assert len(contents) == 1 new_forward, _ = self.__get_paired_response_elements(contents[0]) self._assert_has_keys(new_forward, "history_id") assert new_forward["history_id"] == second_history_id def __get_paired_response_elements(self, contents): hdca = self.__show(contents).json() self._assert_has_keys(hdca, "name", "deleted", "visible", "elements") elements = hdca["elements"] assert len(elements) == 2 element0 = elements[0] element1 = elements[1] self._assert_has_keys(element0, "object") self._assert_has_keys(element1, "object") return element0["object"], element1["object"] def test_hdca_from_library_datasets(self): ld = self.library_populator.new_library_dataset("el1") ldda_id = ld["ldda_id"] element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}] create_data = dict( history_id=self.history_id, type="dataset_collection", name="Test From Library", element_identifiers=json.dumps(element_identifiers), collection_type="list", ) create_response = self._post( "histories/%s/contents/dataset_collections" % self.history_id, create_data) hdca = self.__check_create_collection_response(create_response) elements = hdca["elements"] assert len(elements) == 1 hda = elements[0]["object"] assert hda["hda_ldda"] == "hda" assert hda["history_content_type"] == "dataset" assert hda["copied_from_ldda_id"] == ldda_id def test_hdca_from_inaccessible_library_datasets(self): library, library_dataset = self.library_populator.new_library_dataset_in_private_library( "HDCACreateInaccesibleLibrary") ldda_id = library_dataset["id"] element_identifiers = [{"name": "el1", "src": "ldda", "id": ldda_id}] create_data = dict( history_id=self.history_id, type="dataset_collection", name="Test From Library", element_identifiers=json.dumps(element_identifiers), collection_type="list", ) with self._different_user(): second_history_id = self._new_history() create_response = self._post( "histories/%s/contents/dataset_collections" % second_history_id, create_data) self._assert_status_code_is(create_response, 403) def __check_create_collection_response(self, response): self._assert_status_code_is(response, 200) dataset_collection = response.json() self._assert_has_keys(dataset_collection, "url", "name", "deleted", "visible", "elements") return dataset_collection def __show(self, contents): show_response = self._get( "histories/%s/contents/%ss/%s" % (self.history_id, contents["history_content_type"], contents["id"])) return show_response def __count_contents(self, history_id=None, **kwds): if history_id is None: history_id = self.history_id contents_response = self._get("histories/%s/contents" % history_id, kwds) return len(contents_response.json()) def __assert_hda_has_full_details(self, hda_details): self._assert_has_keys(hda_details, "display_types", "display_apps") def __check_for_hda(self, contents_response, hda): self._assert_status_code_is(contents_response, 200) contents = contents_response.json() assert len(contents) == 1 hda_summary = contents[0] self.__assert_matches_hda(hda, hda_summary) return hda_summary def __assert_matches_hda(self, input_hda, query_hda): self._assert_has_keys(query_hda, "id", "name") assert input_hda["name"] == query_hda["name"] assert input_hda["id"] == query_hda["id"]