mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
5a7a15d161
- Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter. - Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators. - The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec. - Slightly improve the documentation for these composite_data elements in the XSD.
1428 lines
68 KiB
Python
1428 lines
68 KiB
Python
# Test tools API.
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import json
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from base import api
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from base.populators import (
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DatasetCollectionPopulator,
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DatasetPopulator,
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LibraryPopulator,
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skip_without_tool,
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skip_without_datatype,
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)
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from galaxy.tools.verify.test_data import TestDataResolver
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class ToolsTestCase(api.ApiTestCase):
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def setUp(self):
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super(ToolsTestCase, self).setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
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def test_index(self):
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tool_ids = self.__tool_ids()
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assert "upload1" in tool_ids
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def test_no_panel_index(self):
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index = self._get("tools", data=dict(in_panel="false"))
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tools_index = index.json()
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# No need to flatten out sections, with in_panel=False, only tools are
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# returned.
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tool_ids = [_["id"] for _ in tools_index]
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assert "upload1" in tool_ids
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@skip_without_tool("cat1")
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def test_show_repeat(self):
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tool_info = self._show_valid_tool("cat1")
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parameters = tool_info["inputs"]
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assert len(parameters) == 2, "Expected two inputs - got [%s]" % parameters
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assert parameters[0]["name"] == "input1"
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assert parameters[1]["name"] == "queries"
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repeat_info = parameters[1]
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self._assert_has_keys(repeat_info, "min", "max", "title", "help")
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repeat_params = repeat_info["inputs"]
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assert len(repeat_params) == 1
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assert repeat_params[0]["name"] == "input2"
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@skip_without_tool("random_lines1")
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def test_show_conditional(self):
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tool_info = self._show_valid_tool("random_lines1")
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cond_info = tool_info["inputs"][2]
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self._assert_has_keys(cond_info, "cases", "test_param")
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self._assert_has_keys(cond_info["test_param"], 'name', 'type', 'label', 'help')
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cases = cond_info["cases"]
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assert len(cases) == 2
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case1 = cases[0]
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self._assert_has_keys(case1, "value", "inputs")
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assert case1["value"] == "no_seed"
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assert len(case1["inputs"]) == 0
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case2 = cases[1]
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self._assert_has_keys(case2, "value", "inputs")
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case2_inputs = case2["inputs"]
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assert len(case2_inputs) == 1
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self._assert_has_keys(case2_inputs[0], 'name', 'type', 'label', 'help', 'argument')
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assert case2_inputs[0]["name"] == "seed"
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@skip_without_tool("multi_data_param")
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def test_show_multi_data(self):
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tool_info = self._show_valid_tool("multi_data_param")
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f1_info, f2_info = tool_info["inputs"][0], tool_info["inputs"][1]
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self._assert_has_keys(f1_info, "min", "max")
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assert f1_info["min"] == 1
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assert f1_info["max"] == 1235
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self._assert_has_keys(f2_info, "min", "max")
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assert f2_info["min"] is None
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assert f2_info["max"] is None
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def _show_valid_tool(self, tool_id):
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tool_show_response = self._get("tools/%s" % tool_id, data=dict(io_details=True))
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self._assert_status_code_is(tool_show_response, 200)
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tool_info = tool_show_response.json()
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self._assert_has_keys(tool_info, "inputs", "outputs", "panel_section_id")
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return tool_info
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def test_upload1_paste(self):
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with self.dataset_populator.test_history() as history_id:
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payload = self.dataset_populator.upload_payload(history_id, 'Hello World')
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create_response = self._post("tools", data=payload)
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self._assert_has_keys(create_response.json(), 'outputs')
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def test_upload_posix_newline_fixes(self):
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windows_content = "1\t2\t3\r4\t5\t6\r"
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posix_content = windows_content.replace("\r", "\n")
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result_content = self._upload_and_get_content(windows_content)
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self.assertEquals(result_content, posix_content)
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def test_upload_disable_posix_fix(self):
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windows_content = "1\t2\t3\r4\t5\t6\r"
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result_content = self._upload_and_get_content(windows_content, to_posix_lines=None)
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self.assertEquals(result_content, windows_content)
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def test_upload_tab_to_space(self):
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table = "1 2 3\n4 5 6\n"
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result_content = self._upload_and_get_content(table, space_to_tab="Yes")
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self.assertEquals(result_content, "1\t2\t3\n4\t5\t6\n")
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def test_upload_tab_to_space_off_by_default(self):
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table = "1 2 3\n4 5 6\n"
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result_content = self._upload_and_get_content(table)
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self.assertEquals(result_content, table)
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def test_rdata_not_decompressed(self):
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# Prevent regression of https://github.com/galaxyproject/galaxy/issues/753
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rdata_path = TestDataResolver().get_filename("1.RData")
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rdata_metadata = self._upload_and_get_details(open(rdata_path, "rb"), file_type="auto")
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self.assertEquals(rdata_metadata["file_ext"], "rdata")
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@skip_without_datatype("velvet")
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def test_composite_datatype(self):
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with self.dataset_populator.test_history() as history_id:
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dataset = self._velvet_upload(history_id, extra_inputs={
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"files_1|url_paste": "roadmaps content",
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"files_1|type": "upload_dataset",
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"files_2|url_paste": "log content",
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"files_2|type": "upload_dataset",
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})
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roadmaps_content = self._get_roadmaps_content(history_id, dataset)
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assert roadmaps_content.strip() == "roadmaps content", roadmaps_content
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@skip_without_datatype("velvet")
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def test_composite_datatype_space_to_tab(self):
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# Like previous test but set one upload with space_to_tab to True to
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# verify that works.
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with self.dataset_populator.test_history() as history_id:
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dataset = self._velvet_upload(history_id, extra_inputs={
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"files_1|url_paste": "roadmaps content",
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"files_1|type": "upload_dataset",
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"files_1|space_to_tab": "Yes",
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"files_2|url_paste": "log content",
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"files_2|type": "upload_dataset",
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})
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roadmaps_content = self._get_roadmaps_content(history_id, dataset)
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assert roadmaps_content.strip() == "roadmaps\tcontent", roadmaps_content
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@skip_without_datatype("velvet")
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def test_composite_datatype_posix_lines(self):
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# Like previous test but set one upload with space_to_tab to True to
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# verify that works.
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with self.dataset_populator.test_history() as history_id:
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dataset = self._velvet_upload(history_id, extra_inputs={
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"files_1|url_paste": "roadmaps\rcontent",
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"files_1|type": "upload_dataset",
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"files_1|space_to_tab": "Yes",
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"files_2|url_paste": "log\rcontent",
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"files_2|type": "upload_dataset",
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})
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roadmaps_content = self._get_roadmaps_content(history_id, dataset)
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assert roadmaps_content.strip() == "roadmaps\ncontent", roadmaps_content
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def _velvet_upload(self, history_id, extra_inputs):
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payload = self.dataset_populator.upload_payload(
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history_id,
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"sequences content",
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file_type="velvet",
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extra_inputs=extra_inputs,
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)
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run_response = self.dataset_populator.tools_post(payload)
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self.dataset_populator.wait_for_tool_run(history_id, run_response)
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datasets = run_response.json()["outputs"]
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assert len(datasets) == 1
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dataset = datasets[0]
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return dataset
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def _get_roadmaps_content(self, history_id, dataset):
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roadmaps_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=dataset, filename="Roadmaps")
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return roadmaps_content
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def test_unzip_collection(self):
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with self.dataset_populator.test_history() as history_id:
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hdca_id = self.__build_pair(history_id, ["123", "456"])
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inputs = {
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"input": {"src": "hdca", "id": hdca_id},
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}
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
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outputs = response["outputs"]
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self.assertEquals(len(outputs), 2)
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output_forward = outputs[0]
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output_reverse = outputs[1]
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output_forward_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output_forward)
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output_reverse_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output_reverse)
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assert output_forward_content.strip() == "123"
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assert output_reverse_content.strip() == "456"
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output_forward = self.dataset_populator.get_history_dataset_details(history_id, dataset=output_forward)
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output_reverse = self.dataset_populator.get_history_dataset_details(history_id, dataset=output_reverse)
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assert output_forward["history_id"] == history_id
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assert output_reverse["history_id"] == history_id
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def test_unzip_nested(self):
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with self.dataset_populator.test_history() as history_id:
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hdca_list_id = self.__build_nested_list(history_id)
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inputs = {
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"input": {
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'batch': True,
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'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': hdca_list_id}],
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}
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}
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
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def test_zip_inputs(self):
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with self.dataset_populator.test_history() as history_id:
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hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='1\t2\t3'))
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hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='4\t5\t6'))
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inputs = {
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"input_forward": hda1,
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"input_reverse": hda2,
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}
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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response = self._run("__ZIP_COLLECTION__", history_id, inputs, assert_ok=True)
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output_collections = response["output_collections"]
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self.assertEquals(len(output_collections), 1)
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self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
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zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_collections[0]["hid"])
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assert zipped_hdca["collection_type"] == "paired"
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def test_zip_list_inputs(self):
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with self.dataset_populator.test_history() as history_id:
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hdca1_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"]).json()["id"]
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hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["1\n2\n3\n4", "5\n6\n7\n8"]).json()["id"]
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inputs = {
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"input_forward": {'batch': True, 'values': [{"src": "hdca", "id": hdca1_id}]},
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"input_reverse": {'batch': True, 'values': [{"src": "hdca", "id": hdca2_id}]},
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}
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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response = self._run("__ZIP_COLLECTION__", history_id, inputs, assert_ok=True)
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implicit_collections = response["implicit_collections"]
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self.assertEquals(len(implicit_collections), 1)
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self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
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zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
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assert zipped_hdca["collection_type"] == "list:paired"
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def test_filter_failed(self):
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with self.dataset_populator.test_history() as history_id:
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history_id = self.dataset_populator.new_history()
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ok_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["0", "1", "0", "1"]).json()["id"]
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exit_code_inputs = {
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"input": {'batch': True, 'values': [{"src": "hdca", "id": ok_hdca_id}]},
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}
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response = self._run("exit_code_from_file", history_id, exit_code_inputs, assert_ok=False).json()
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self.dataset_populator.wait_for_history(history_id, assert_ok=False)
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mixed_implicit_collections = response["implicit_collections"]
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self.assertEquals(len(mixed_implicit_collections), 1)
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mixed_hdca_hid = mixed_implicit_collections[0]["hid"]
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mixed_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=mixed_hdca_hid, wait=False)
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def get_state(dce):
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return dce["object"]["state"]
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mixed_states = [get_state(_) for _ in mixed_hdca["elements"]]
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assert mixed_states == [u"ok", u"error", u"ok", u"error"], mixed_states
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inputs = {
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"input": {"src": "hdca", "id": mixed_hdca["id"]},
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}
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response = self._run("__FILTER_FAILED_DATASETS__", history_id, inputs, assert_ok=False).json()
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self.dataset_populator.wait_for_history(history_id, assert_ok=False)
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filter_output_collections = response["output_collections"]
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self.assertEquals(len(filter_output_collections), 1)
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filtered_hid = filter_output_collections[0]["hid"]
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filtered_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=filtered_hid, wait=False)
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filtered_states = [get_state(_) for _ in filtered_hdca["elements"]]
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assert filtered_states == [u"ok", u"ok"], filtered_states
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@skip_without_tool("multi_select")
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def test_multi_select_as_list(self):
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with self.dataset_populator.test_history() as history_id:
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inputs = {
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"select_ex": ["--ex1", "ex2"],
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}
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response = self._run("multi_select", history_id, inputs, assert_ok=True)
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output = response["outputs"][0]
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output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
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assert output1_content == "--ex1,ex2"
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@skip_without_tool("multi_select")
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def test_multi_select_optional(self):
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with self.dataset_populator.test_history() as history_id:
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inputs = {
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"select_ex": ["--ex1"],
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"select_optional": None,
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}
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response = self._run("multi_select", history_id, inputs, assert_ok=True)
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output = response["outputs"]
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output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
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output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[1])
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assert output1_content.strip() == "--ex1"
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assert output2_content.strip() == "None", output2_content
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@skip_without_tool("library_data")
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def test_library_data_param(self):
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with self.dataset_populator.test_history() as history_id:
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ld = LibraryPopulator(self).new_library_dataset("lda_test_library")
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inputs = {
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"library_dataset": ld["ldda_id"],
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"library_dataset_multiple": [ld["ldda_id"], ld["ldda_id"]]
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}
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response = self._run("library_data", history_id, inputs, assert_ok=True)
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output = response["outputs"]
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output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[0])
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assert output_content == "TestData\n", output_content
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output_multiple_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output[1])
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assert output_multiple_content == "TestData\nTestData\n", output_multiple_content
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@skip_without_tool("multi_data_param")
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def test_multidata_param(self):
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with self.dataset_populator.test_history() as history_id:
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hda1 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='1\t2\t3'))
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hda2 = dataset_to_param(self.dataset_populator.new_dataset(history_id, content='4\t5\t6'))
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inputs = {
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"f1": {'batch': False, 'values': [hda1, hda2]},
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"f2": {'batch': False, 'values': [hda2, hda1]},
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}
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response = self._run("multi_data_param", history_id, inputs, assert_ok=True)
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output1 = response["outputs"][0]
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output2 = response["outputs"][1]
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output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
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output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
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assert output1_content == "1\t2\t3\n4\t5\t6\n", output1_content
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assert output2_content == "4\t5\t6\n1\t2\t3\n", output2_content
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@skip_without_tool("cat1")
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def test_run_cat1(self):
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with self.dataset_populator.test_history() as history_id:
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# Run simple non-upload tool with an input data parameter.
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history_id = self.dataset_populator.new_history()
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new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
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inputs = dict(
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input1=dataset_to_param(new_dataset),
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)
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outputs = self._cat1_outputs(history_id, inputs=inputs)
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self.assertEquals(len(outputs), 1)
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output1 = outputs[0]
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output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
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self.assertEqual(output1_content.strip(), "Cat1Test")
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@skip_without_tool("cat1")
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def test_run_cat1_listified_param(self):
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# Run simple non-upload tool with an input data parameter.
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history_id = self.dataset_populator.new_history()
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new_dataset = self.dataset_populator.new_dataset(history_id, content='Cat1Testlistified')
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inputs = dict(
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input1=[dataset_to_param(new_dataset)],
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)
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outputs = self._cat1_outputs(history_id, inputs=inputs)
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self.assertEquals(len(outputs), 1)
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output1 = outputs[0]
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output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
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self.assertEqual(output1_content.strip(), "Cat1Testlistified")
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@skip_without_tool("multiple_versions")
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def test_run_by_versions(self):
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for version in ["0.1", "0.2"]:
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# Run simple non-upload tool with an input data parameter.
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history_id = self.dataset_populator.new_history()
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inputs = dict()
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outputs = self._run_and_get_outputs(tool_id="multiple_versions", history_id=history_id, inputs=inputs, tool_version=version)
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self.assertEquals(len(outputs), 1)
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|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEqual(output1_content.strip(), "Version " + version)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_run_cat1_single_meta_wrapper(self):
|
|
# Wrap input in a no-op meta parameter wrapper like Sam is planning to
|
|
# use for all UI API submissions.
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset = self.dataset_populator.new_dataset(history_id, content='123')
|
|
inputs = dict(
|
|
input1={'batch': False, 'values': [dataset_to_param(new_dataset)]},
|
|
)
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
self.assertEquals(len(outputs), 1)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEqual(output1_content.strip(), "123")
|
|
|
|
@skip_without_tool("validation_default")
|
|
def test_validation(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
inputs = {
|
|
'select_param': "\" ; echo \"moo",
|
|
}
|
|
response = self._run("validation_default", history_id, inputs)
|
|
self._assert_status_code_is(response, 400)
|
|
|
|
@skip_without_tool("validation_empty_dataset")
|
|
def test_validation_empty_dataset(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
inputs = {
|
|
}
|
|
outputs = self._run_and_get_outputs('empty_output', history_id, inputs)
|
|
empty_dataset = outputs[0]
|
|
inputs = {
|
|
'input1': dataset_to_param(empty_dataset),
|
|
}
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
response = self._run("validation_empty_dataset", history_id, inputs)
|
|
self._assert_status_code_is(response, 400)
|
|
|
|
@skip_without_tool("validation_repeat")
|
|
def test_validation_in_repeat(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
inputs = {
|
|
'r1_0|text': "123",
|
|
'r2_0|text': "",
|
|
}
|
|
response = self._run("validation_repeat", history_id, inputs)
|
|
self._assert_status_code_is(response, 400)
|
|
|
|
@skip_without_tool("multi_select")
|
|
def test_select_legal_values(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
inputs = {
|
|
'select_ex': 'not_option',
|
|
}
|
|
response = self._run("multi_select", history_id, inputs)
|
|
self._assert_status_code_is(response, 400)
|
|
|
|
@skip_without_tool("column_param")
|
|
def test_column_legal_values(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='#col1\tcol2')
|
|
inputs = {
|
|
'input1': {"src": "hda", "id": new_dataset1["id"]},
|
|
'col': "' ; echo 'moo",
|
|
}
|
|
response = self._run("column_param", history_id, inputs)
|
|
assert response.status_code != 200
|
|
|
|
@skip_without_tool("collection_paired_test")
|
|
def test_collection_parameter(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"f1": {"src": "hdca", "id": hdca_id},
|
|
}
|
|
output = self._run("collection_paired_test", history_id, inputs, assert_ok=True)
|
|
assert len(output['jobs']) == 1
|
|
assert len(output['implicit_collections']) == 0
|
|
assert len(output['outputs']) == 1
|
|
contents = self.dataset_populator.get_history_dataset_content(history_id, hid=4)
|
|
assert contents.strip() == "123\n456", contents
|
|
|
|
@skip_without_tool("collection_creates_pair")
|
|
def test_paired_collection_output(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789\n0ab')
|
|
inputs = {
|
|
"input1": {"src": "hda", "id": new_dataset1["id"]},
|
|
}
|
|
# TODO: shouldn't need this wait
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("collection_creates_pair", history_id, inputs, assert_ok=True)
|
|
output_collection = self._assert_one_job_one_collection_run(create)
|
|
element0, element1 = self._assert_elements_are(output_collection, "forward", "reverse")
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
self._verify_element(history_id, element0, contents="123\n789\n", file_ext="txt", visible=False)
|
|
self._verify_element(history_id, element1, contents="456\n0ab\n", file_ext="txt", visible=False)
|
|
|
|
@skip_without_tool("collection_creates_list")
|
|
def test_list_collection_output(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
|
|
hdca_id = create_response.json()["id"]
|
|
inputs = {
|
|
"input1": {"src": "hdca", "id": hdca_id},
|
|
}
|
|
# TODO: real problem here - shouldn't have to have this wait.
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("collection_creates_list", history_id, inputs, assert_ok=True)
|
|
output_collection = self._assert_one_job_one_collection_run(create)
|
|
element0, element1 = self._assert_elements_are(output_collection, "data1", "data2")
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
self._verify_element(history_id, element0, contents="identifier is data1\n", file_ext="txt")
|
|
self._verify_element(history_id, element1, contents="identifier is data2\n", file_ext="txt")
|
|
|
|
@skip_without_tool("collection_creates_list_2")
|
|
def test_list_collection_output_format_source(self):
|
|
# test using format_source with a tool
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='#col1\tcol2')
|
|
create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\tb\nc\td", "e\tf\ng\th"])
|
|
hdca_id = create_response.json()["id"]
|
|
inputs = {
|
|
"header": {"src": "hda", "id": new_dataset1["id"]},
|
|
"input_collect": {"src": "hdca", "id": hdca_id},
|
|
}
|
|
# TODO: real problem here - shouldn't have to have this wait.
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("collection_creates_list_2", history_id, inputs, assert_ok=True)
|
|
output_collection = self._assert_one_job_one_collection_run(create)
|
|
element0, element1 = self._assert_elements_are(output_collection, "data1", "data2")
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
self._verify_element(history_id, element0, contents="#col1\tcol2\na\tb\nc\td\n", file_ext="txt")
|
|
self._verify_element(history_id, element1, contents="#col1\tcol2\ne\tf\ng\th\n", file_ext="txt")
|
|
|
|
@skip_without_tool("collection_split_on_column")
|
|
def test_dynamic_list_output(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='samp1\t1\nsamp1\t3\nsamp2\t2\nsamp2\t4\n')
|
|
inputs = {
|
|
'input1': dataset_to_param(new_dataset1),
|
|
}
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("collection_split_on_column", history_id, inputs, assert_ok=True)
|
|
|
|
output_collection = self._assert_one_job_one_collection_run(create)
|
|
self._assert_has_keys(output_collection, "id", "name", "elements", "populated")
|
|
assert not output_collection["populated"]
|
|
assert len(output_collection["elements"]) == 0
|
|
self.assertEquals(output_collection["name"], "Table split on first column")
|
|
self.dataset_populator.wait_for_job(create["jobs"][0]["id"], assert_ok=True)
|
|
|
|
get_collection_response = self._get("dataset_collections/%s" % output_collection["id"], data={"instance_type": "history"})
|
|
self._assert_status_code_is(get_collection_response, 200)
|
|
|
|
output_collection = get_collection_response.json()
|
|
self._assert_has_keys(output_collection, "id", "name", "elements", "populated")
|
|
assert output_collection["populated"]
|
|
self.assertEquals(output_collection["name"], "Table split on first column")
|
|
|
|
assert len(output_collection["elements"]) == 2
|
|
output_element_0 = output_collection["elements"][0]
|
|
assert output_element_0["element_index"] == 0
|
|
assert output_element_0["element_identifier"] == "samp1"
|
|
output_element_hda_0 = output_element_0["object"]
|
|
assert output_element_hda_0["metadata_column_types"] is not None
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_run_cat1_with_two_inputs(self):
|
|
# Run tool with an multiple data parameter and grouping (repeat)
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='Cat1Test')
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='Cat2Test')
|
|
inputs = {
|
|
'input1': dataset_to_param(new_dataset1),
|
|
'queries_0|input2': dataset_to_param(new_dataset2)
|
|
}
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
self.assertEquals(len(outputs), 1)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEqual(output1_content.strip(), "Cat1Test\nCat2Test")
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_multirun_cat1(self):
|
|
history_id, datasets = self._prepare_cat1_multirun()
|
|
inputs = {
|
|
"input1": {
|
|
'batch': True,
|
|
'values': datasets,
|
|
},
|
|
}
|
|
self._check_cat1_multirun(history_id, inputs)
|
|
|
|
def _prepare_cat1_multirun(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
|
|
return history_id, [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]
|
|
|
|
def _check_cat1_multirun(self, history_id, inputs):
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
self.assertEquals(len(outputs), 2)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "123")
|
|
self.assertEquals(output2_content.strip(), "456")
|
|
|
|
@skip_without_tool("random_lines1")
|
|
def test_multirun_non_data_parameter(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123\n456\n789')
|
|
inputs = {
|
|
'input': dataset_to_param(new_dataset1),
|
|
'num_lines': {'batch': True, 'values': [1, 2, 3]}
|
|
}
|
|
outputs = self._run_and_get_outputs('random_lines1', history_id, inputs)
|
|
# Assert we have three outputs with 1, 2, and 3 lines respectively.
|
|
assert len(outputs) == 3
|
|
outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
|
|
assert sorted(len(c.split("\n")) for c in outputs_contents) == [1, 2, 3]
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_multirun_in_repeat(self):
|
|
history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
|
|
inputs = {
|
|
"input1": common_dataset,
|
|
'queries_0|input2': {'batch': True, 'values': repeat_datasets},
|
|
}
|
|
self._check_repeat_multirun(history_id, inputs)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_multirun_in_repeat_mismatch(self):
|
|
history_id, common_dataset, repeat_datasets = self._setup_repeat_multirun()
|
|
inputs = {
|
|
"input1": {'batch': False, 'values': [common_dataset]},
|
|
'queries_0|input2': {'batch': True, 'values': repeat_datasets},
|
|
}
|
|
self._check_repeat_multirun(history_id, inputs)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_multirun_on_multiple_inputs(self):
|
|
history_id, first_two, second_two = self._setup_two_multiruns()
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': first_two},
|
|
'queries_0|input2': {'batch': True, 'values': second_two},
|
|
}
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
self.assertEquals(len(outputs), 2)
|
|
outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
|
|
assert "123\n789" in outputs_contents
|
|
assert "456\n0ab" in outputs_contents
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_multirun_on_multiple_inputs_unlinked(self):
|
|
history_id, first_two, second_two = self._setup_two_multiruns()
|
|
inputs = {
|
|
"input1": {'batch': True, 'linked': False, 'values': first_two},
|
|
'queries_0|input2': {'batch': True, 'linked': False, 'values': second_two},
|
|
}
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
outputs_contents = [self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs]
|
|
self.assertEquals(len(outputs), 4)
|
|
assert "123\n789" in outputs_contents
|
|
assert "456\n0ab" in outputs_contents
|
|
assert "123\n0ab" in outputs_contents
|
|
assert "456\n789" in outputs_contents
|
|
|
|
def _assert_one_job_one_collection_run(self, create):
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
collections = create['output_collections']
|
|
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
self.assertEquals(len(collections), 1)
|
|
|
|
output_collection = collections[0]
|
|
return output_collection
|
|
|
|
def _assert_elements_are(self, collection, *args):
|
|
elements = collection["elements"]
|
|
self.assertEquals(len(elements), len(args))
|
|
for index, element in enumerate(elements):
|
|
arg = args[index]
|
|
self.assertEquals(arg, element["element_identifier"])
|
|
return elements
|
|
|
|
def _verify_element(self, history_id, element, **props):
|
|
object_id = element["object"]["id"]
|
|
|
|
if "contents" in props:
|
|
expected_contents = props["contents"]
|
|
|
|
contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=object_id)
|
|
self.assertEquals(contents, expected_contents)
|
|
|
|
del props["contents"]
|
|
|
|
if props:
|
|
details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=object_id)
|
|
for key, value in props.items():
|
|
self.assertEquals(details[key], value)
|
|
|
|
def _setup_repeat_multirun(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
|
|
common_dataset = self.dataset_populator.new_dataset(history_id, content='Common')
|
|
return (
|
|
history_id,
|
|
dataset_to_param(common_dataset),
|
|
[dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]
|
|
)
|
|
|
|
def _check_repeat_multirun(self, history_id, inputs):
|
|
outputs = self._cat1_outputs(history_id, inputs=inputs)
|
|
self.assertEquals(len(outputs), 2)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "Common\n123")
|
|
self.assertEquals(output2_content.strip(), "Common\n456")
|
|
|
|
def _setup_two_multiruns(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123')
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456')
|
|
new_dataset3 = self.dataset_populator.new_dataset(history_id, content='789')
|
|
new_dataset4 = self.dataset_populator.new_dataset(history_id, content='0ab')
|
|
return (
|
|
history_id,
|
|
[dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)],
|
|
[dataset_to_param(new_dataset3), dataset_to_param(new_dataset4)]
|
|
)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_map_over_collection(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
|
|
}
|
|
self._run_and_check_simple_collection_mapping(history_id, inputs)
|
|
|
|
@skip_without_tool("output_action_change_format")
|
|
def test_map_over_with_output_format_actions(self):
|
|
for use_action in ["do", "dont"]:
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"input_cond|dispatch": use_action,
|
|
"input_cond|input": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
|
|
}
|
|
create = self._run('output_action_change_format', history_id, inputs).json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(outputs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1)
|
|
output2_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output2)
|
|
assert output1_details["file_ext"] == "txt" if (use_action == "do") else "data"
|
|
assert output2_details["file_ext"] == "txt" if (use_action == "do") else "data"
|
|
|
|
@skip_without_tool("Cut1")
|
|
def test_map_over_with_complex_output_actions(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self._bed_list(history_id)
|
|
inputs = {
|
|
"columnList": "c1,c2,c3,c4,c5",
|
|
"delimiter": "T",
|
|
"input": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
|
|
}
|
|
create = self._run('Cut1', history_id, inputs).json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(outputs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
assert output1_content.startswith("chr1")
|
|
assert output2_content.startswith("chr1")
|
|
|
|
def _bed_list(self, history_id):
|
|
bed1_contents = open(self.get_filename("1.bed"), "r").read()
|
|
bed2_contents = open(self.get_filename("2.bed"), "r").read()
|
|
contents = [bed1_contents, bed2_contents]
|
|
hdca = self.dataset_collection_populator.create_list_in_history(history_id, contents=contents).json()
|
|
return hdca["id"]
|
|
|
|
def _run_and_check_simple_collection_mapping(self, history_id, inputs):
|
|
create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(outputs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "123")
|
|
self.assertEquals(output2_content.strip(), "456")
|
|
|
|
@skip_without_tool("identifier_single")
|
|
def test_identifier_in_map(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca_id}]},
|
|
}
|
|
create_response = self._run("identifier_single", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(outputs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "forward")
|
|
self.assertEquals(output2_content.strip(), "reverse")
|
|
|
|
@skip_without_tool("identifier_single")
|
|
def test_identifier_outside_map(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Plain HDA")
|
|
inputs = {
|
|
"input1": {'src': 'hda', 'id': new_dataset1["id"]},
|
|
}
|
|
create_response = self._run("identifier_single", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "Plain HDA")
|
|
|
|
@skip_without_tool("identifier_multiple")
|
|
def test_identifier_in_multiple_reduce(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"input1": {'src': 'hdca', 'id': hdca_id},
|
|
}
|
|
create_response = self._run("identifier_multiple", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "forward\nreverse")
|
|
|
|
@skip_without_tool("identifier_multiple_in_conditional")
|
|
def test_identifier_multiple_reduce_in_conditional(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"outer_cond|inner_cond|input1": {'src': 'hdca', 'id': hdca_id},
|
|
}
|
|
create_response = self._run("identifier_multiple_in_conditional", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "forward\nreverse")
|
|
|
|
@skip_without_tool("identifier_multiple_in_repeat")
|
|
def test_identifier_multiple_reduce_in_repeat(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"the_repeat_0|the_data|input1": {'src': 'hdca', 'id': hdca_id},
|
|
}
|
|
create_response = self._run("identifier_multiple_in_repeat", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "forward\nreverse")
|
|
|
|
@skip_without_tool("identifier_multiple_in_conditional")
|
|
def test_identifier_multiple_in_conditional(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Normal HDA1")
|
|
inputs = {
|
|
"outer_cond|inner_cond|input1": {'src': 'hda', 'id': new_dataset1["id"]},
|
|
}
|
|
create_response = self._run("identifier_multiple_in_conditional", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "Normal HDA1")
|
|
|
|
@skip_without_tool("identifier_multiple")
|
|
def test_identifier_with_multiple_normal_datasets(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='123', name="Normal HDA1")
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='456', name="Normal HDA2")
|
|
inputs = {
|
|
"input1": [
|
|
{'src': 'hda', 'id': new_dataset1["id"]},
|
|
{'src': 'hda', 'id': new_dataset2["id"]}
|
|
]
|
|
}
|
|
create_response = self._run("identifier_multiple", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
self.assertEquals(len(implicit_collections), 0)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), "Normal HDA1\nNormal HDA2")
|
|
|
|
@skip_without_tool("identifier_collection")
|
|
def test_identifier_with_data_collection(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
|
|
element_identifiers = self.dataset_collection_populator.list_identifiers(history_id)
|
|
|
|
payload = dict(
|
|
instance_type="history",
|
|
history_id=history_id,
|
|
element_identifiers=json.dumps(element_identifiers),
|
|
collection_type="list",
|
|
)
|
|
|
|
create_response = self._post("dataset_collections", payload)
|
|
dataset_collection = create_response.json()
|
|
|
|
inputs = {
|
|
"input1": {'src': 'hdca', 'id': dataset_collection['id']},
|
|
}
|
|
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create_response = self._run("identifier_collection", history_id, inputs)
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
self.assertEquals(output1_content.strip(), '\n'.join([d['name'] for d in element_identifiers]))
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_map_over_nested_collections(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_nested_list(history_id)
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]},
|
|
}
|
|
self._check_simple_cat1_over_nested_collections(history_id, inputs)
|
|
|
|
@skip_without_tool("paired_collection_map_over_structured_like")
|
|
def test_paired_input_map_over_nested_collections(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_id = self.__build_nested_list(history_id)
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [dict(map_over_type='paired', src="hdca", id=hdca_id)]},
|
|
}
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("paired_collection_map_over_structured_like", history_id, inputs, assert_ok=True)
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
implicit_collection = implicit_collections[0]
|
|
assert implicit_collection["collection_type"] == "list:paired", implicit_collection
|
|
outer_elements = implicit_collection["elements"]
|
|
assert len(outer_elements) == 2
|
|
|
|
def _check_simple_cat1_over_nested_collections(self, history_id, inputs):
|
|
create = self._run_cat1(history_id, inputs=inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 4)
|
|
self.assertEquals(len(outputs), 4)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
implicit_collection = implicit_collections[0]
|
|
self._assert_has_keys(implicit_collection, "collection_type", "elements")
|
|
assert implicit_collection["collection_type"] == "list:paired"
|
|
assert len(implicit_collection["elements"]) == 2
|
|
first_element, second_element = implicit_collection["elements"]
|
|
assert first_element["element_identifier"] == "test0"
|
|
assert second_element["element_identifier"] == "test1"
|
|
|
|
first_object = first_element["object"]
|
|
assert first_object["collection_type"] == "paired"
|
|
assert len(first_object["elements"]) == 2
|
|
first_object_forward_element = first_object["elements"][0]
|
|
self.assertEquals(outputs[0]["id"], first_object_forward_element["object"]["id"])
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_map_over_two_collections(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.__build_pair(history_id, ["789", "0ab"])
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
|
|
"queries_0|input2": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca2_id}]},
|
|
}
|
|
self._check_map_cat1_over_two_collections(history_id, inputs)
|
|
|
|
def _check_map_cat1_over_two_collections(self, history_id, inputs):
|
|
response = self._run_cat1(history_id, inputs)
|
|
self._assert_status_code_is(response, 200)
|
|
response_object = response.json()
|
|
outputs = response_object['outputs']
|
|
self.assertEquals(len(outputs), 2)
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
self.dataset_populator.wait_for_history(history_id)
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "123\n789")
|
|
self.assertEquals(output2_content.strip(), "456\n0ab")
|
|
|
|
self.assertEquals(len(response_object['jobs']), 2)
|
|
self.assertEquals(len(response_object['implicit_collections']), 1)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_map_over_two_collections_unlinked(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.__build_pair(history_id, ["789", "0ab"])
|
|
inputs = {
|
|
"input1": {'batch': True, 'linked': False, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
|
|
"queries_0|input2": {'batch': True, 'linked': False, 'values': [{'src': 'hdca', 'id': hdca2_id}]},
|
|
}
|
|
response = self._run_cat1(history_id, inputs)
|
|
self._assert_status_code_is(response, 200)
|
|
response_object = response.json()
|
|
outputs = response_object['outputs']
|
|
self.assertEquals(len(outputs), 4)
|
|
|
|
self.assertEquals(len(response_object['jobs']), 4)
|
|
implicit_collections = response_object['implicit_collections']
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
implicit_collection = implicit_collections[0]
|
|
self.assertEquals(implicit_collection["collection_type"], "paired:paired")
|
|
|
|
outer_elements = implicit_collection["elements"]
|
|
assert len(outer_elements) == 2
|
|
element0, element1 = outer_elements
|
|
assert element0["element_identifier"] == "forward"
|
|
assert element1["element_identifier"] == "reverse"
|
|
|
|
elements0 = element0["object"]["elements"]
|
|
elements1 = element1["object"]["elements"]
|
|
|
|
assert len(elements0) == 2
|
|
assert len(elements1) == 2
|
|
|
|
element00, element01 = elements0
|
|
assert element00["element_identifier"] == "forward"
|
|
assert element01["element_identifier"] == "reverse"
|
|
|
|
element10, element11 = elements1
|
|
assert element10["element_identifier"] == "forward"
|
|
assert element11["element_identifier"] == "reverse"
|
|
|
|
expected_contents_list = [
|
|
(element00, "123\n789\n"),
|
|
(element01, "123\n0ab\n"),
|
|
(element10, "456\n789\n"),
|
|
(element11, "456\n0ab\n"),
|
|
]
|
|
for (element, expected_contents) in expected_contents_list:
|
|
dataset_id = element["object"]["id"]
|
|
contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id)
|
|
self.assertEquals(expected_contents, contents)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_map_over_collected_and_individual_datasets(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
new_dataset1 = self.dataset_populator.new_dataset(history_id, content='789')
|
|
new_dataset2 = self.dataset_populator.new_dataset(history_id, content='0ab')
|
|
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [{'src': 'hdca', 'id': hdca1_id}]},
|
|
"queries_0|input2": {'batch': True, 'values': [dataset_to_param(new_dataset1), dataset_to_param(new_dataset2)]},
|
|
}
|
|
response = self._run_cat1(history_id, inputs)
|
|
self._assert_status_code_is(response, 200)
|
|
response_object = response.json()
|
|
outputs = response_object['outputs']
|
|
self.assertEquals(len(outputs), 2)
|
|
|
|
self.assertEquals(len(response_object['jobs']), 2)
|
|
self.assertEquals(len(response_object['implicit_collections']), 1)
|
|
|
|
@skip_without_tool("identifier_source")
|
|
def test_default_identifier_source_map_over(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
input_a_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("A", "A content")]).json()['id']
|
|
input_b_hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=[("B", "B content")]).json()['id']
|
|
inputs = {
|
|
"inputA": {'batch': True, 'values': [dict(src="hdca", id=input_a_hdca_id)]},
|
|
"inputB": {'batch': True, 'values': [dict(src="hdca", id=input_b_hdca_id)]},
|
|
}
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("identifier_source", history_id, inputs, assert_ok=True)
|
|
assert create['implicit_collections'][0]['elements'][0]['element_identifier'] == 'B'
|
|
assert create['implicit_collections'][1]['elements'][0]['element_identifier'] == 'A'
|
|
|
|
@skip_without_tool("collection_creates_pair")
|
|
def test_map_over_collection_output(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["a\nb\nc\nd", "e\nf\ng\nh"])
|
|
hdca_id = create_response.json()["id"]
|
|
inputs = {
|
|
"input1": {'batch': True, 'values': [dict(src="hdca", id=hdca_id)]},
|
|
}
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
create = self._run("collection_creates_pair", history_id, inputs, assert_ok=True)
|
|
jobs = create['jobs']
|
|
implicit_collections = create['implicit_collections']
|
|
self.assertEquals(len(jobs), 2)
|
|
self.assertEquals(len(implicit_collections), 1)
|
|
implicit_collection = implicit_collections[0]
|
|
assert implicit_collection["collection_type"] == "list:paired", implicit_collection
|
|
outer_elements = implicit_collection["elements"]
|
|
assert len(outer_elements) == 2
|
|
element0, element1 = outer_elements
|
|
assert element0["element_identifier"] == "data1"
|
|
assert element1["element_identifier"] == "data2"
|
|
|
|
pair0, pair1 = element0["object"], element1["object"]
|
|
pair00, pair01 = pair0["elements"]
|
|
pair10, pair11 = pair1["elements"]
|
|
|
|
for pair in pair0, pair1:
|
|
assert "collection_type" in pair, pair
|
|
assert pair["collection_type"] == "paired", pair
|
|
|
|
pair_ids = []
|
|
for pair_element in pair00, pair01, pair10, pair11:
|
|
assert "object" in pair_element
|
|
pair_ids.append(pair_element["object"]["id"])
|
|
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
expected_contents = [
|
|
"a\nc\n",
|
|
"b\nd\n",
|
|
"e\ng\n",
|
|
"f\nh\n",
|
|
]
|
|
for i in range(4):
|
|
contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=pair_ids[i])
|
|
self.assertEquals(expected_contents[i], contents)
|
|
|
|
@skip_without_tool("cat1")
|
|
def test_cannot_map_over_incompatible_collections(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
|
|
inputs = {
|
|
"input1": {
|
|
'batch': True,
|
|
'values': [{'src': 'hdca', 'id': hdca1_id}],
|
|
},
|
|
"queries_0|input2": {
|
|
'batch': True,
|
|
'values': [{'src': 'hdca', 'id': hdca2_id}],
|
|
},
|
|
}
|
|
run_response = self._run_cat1(history_id, inputs)
|
|
# TODO: Fix this error checking once switch over to new API decorator
|
|
# on server.
|
|
assert run_response.status_code >= 400
|
|
|
|
@skip_without_tool("multi_data_param")
|
|
def test_reduce_collections_legacy(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
|
|
inputs = {
|
|
"f1": "__collection_reduce__|%s" % hdca1_id,
|
|
"f2": "__collection_reduce__|%s" % hdca2_id,
|
|
}
|
|
self._check_simple_reduce_job(history_id, inputs)
|
|
|
|
@skip_without_tool("multi_data_param")
|
|
def test_reduce_collections(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
|
|
inputs = {
|
|
"f1": {'src': 'hdca', 'id': hdca1_id},
|
|
"f2": {'src': 'hdca', 'id': hdca2_id},
|
|
}
|
|
self._check_simple_reduce_job(history_id, inputs)
|
|
|
|
@skip_without_tool("multi_data_repeat")
|
|
def test_reduce_collections_in_repeat(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"outer_repeat_0|f1": {'src': 'hdca', 'id': hdca1_id},
|
|
}
|
|
create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
assert output1_content.strip() == "123\n456", output1_content
|
|
|
|
@skip_without_tool("multi_data_repeat")
|
|
def test_reduce_collections_in_repeat_legacy(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
inputs = {
|
|
"outer_repeat_0|f1": "__collection_reduce__|%s" % hdca1_id,
|
|
}
|
|
create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 1)
|
|
output1 = outputs[0]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
assert output1_content.strip() == "123\n456", output1_content
|
|
|
|
@skip_without_tool("multi_data_param")
|
|
def test_reduce_multiple_lists_on_multi_data(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.dataset_collection_populator.create_list_in_history(history_id).json()["id"]
|
|
inputs = {
|
|
"f1": [{'src': 'hdca', 'id': hdca1_id}, {'src': 'hdca', 'id': hdca2_id}],
|
|
"f2": [{'src': 'hdca', 'id': hdca1_id}],
|
|
}
|
|
create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 2)
|
|
output1, output2 = outputs
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
self.assertEquals(output1_content.strip(), "123\n456\nTestData123\nTestData123\nTestData123")
|
|
self.assertEquals(output2_content.strip(), "123\n456")
|
|
|
|
def _check_simple_reduce_job(self, history_id, inputs):
|
|
create = self._run("multi_data_param", history_id, inputs, assert_ok=True)
|
|
outputs = create['outputs']
|
|
jobs = create['jobs']
|
|
self.assertEquals(len(jobs), 1)
|
|
self.assertEquals(len(outputs), 2)
|
|
output1, output2 = outputs
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
assert output1_content.strip() == "123\n456"
|
|
assert len(output2_content.strip().split("\n")) == 3, output2_content
|
|
|
|
@skip_without_tool("collection_paired_test")
|
|
def test_subcollection_mapping(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
hdca_list_id = self.__build_nested_list(history_id)
|
|
inputs = {
|
|
"f1": {
|
|
'batch': True,
|
|
'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': hdca_list_id}],
|
|
}
|
|
}
|
|
self._check_simple_subcollection_mapping(history_id, inputs)
|
|
|
|
def _check_simple_subcollection_mapping(self, history_id, inputs):
|
|
# Following wait not really needed - just getting so many database
|
|
# locked errors with sqlite.
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
outputs = self._run_and_get_outputs("collection_paired_test", history_id, inputs)
|
|
assert len(outputs), 2
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
assert output1_content.strip() == "123\n456", output1_content
|
|
assert output2_content.strip() == "789\n0ab", output2_content
|
|
|
|
@skip_without_tool("collection_mixed_param")
|
|
def test_combined_mapping_and_subcollection_mapping(self):
|
|
history_id = self.dataset_populator.new_history()
|
|
nested_list_id = self.__build_nested_list(history_id)
|
|
create_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx", "yyy"])
|
|
list_id = create_response.json()["id"]
|
|
inputs = {
|
|
"f1": {
|
|
'batch': True,
|
|
'values': [{'src': 'hdca', 'map_over_type': 'paired', 'id': nested_list_id}],
|
|
},
|
|
"f2": {
|
|
'batch': True,
|
|
'values': [{'src': 'hdca', 'id': list_id}],
|
|
},
|
|
}
|
|
self._check_combined_mapping_and_subcollection_mapping(history_id, inputs)
|
|
|
|
def _check_combined_mapping_and_subcollection_mapping(self, history_id, inputs):
|
|
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
|
|
outputs = self._run_and_get_outputs("collection_mixed_param", history_id, inputs)
|
|
assert len(outputs), 2
|
|
output1 = outputs[0]
|
|
output2 = outputs[1]
|
|
output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1)
|
|
output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2)
|
|
assert output1_content.strip() == "123\n456\nxxx", output1_content
|
|
assert output2_content.strip() == "789\n0ab\nyyy", output2_content
|
|
|
|
def _cat1_outputs(self, history_id, inputs):
|
|
return self._run_outputs(self._run_cat1(history_id, inputs))
|
|
|
|
def _run_and_get_outputs(self, tool_id, history_id, inputs, tool_version=None):
|
|
return self._run_outputs(self._run(tool_id, history_id, inputs, tool_version=tool_version))
|
|
|
|
def _run_outputs(self, create_response):
|
|
self._assert_status_code_is(create_response, 200)
|
|
return create_response.json()['outputs']
|
|
|
|
def _run_cat1(self, history_id, inputs, assert_ok=False):
|
|
return self._run('cat1', history_id, inputs, assert_ok=assert_ok)
|
|
|
|
def _run(self, tool_id, history_id, inputs, assert_ok=False, tool_version=None):
|
|
payload = self.dataset_populator.run_tool_payload(
|
|
tool_id=tool_id,
|
|
inputs=inputs,
|
|
history_id=history_id,
|
|
)
|
|
if tool_version is not None:
|
|
payload["tool_version"] = tool_version
|
|
create_response = self._post("tools", data=payload)
|
|
if assert_ok:
|
|
self._assert_status_code_is(create_response, 200)
|
|
create = create_response.json()
|
|
self._assert_has_keys(create, 'outputs')
|
|
return create
|
|
else:
|
|
return create_response
|
|
|
|
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
|
|
|
|
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 __tool_ids(self):
|
|
index = self._get("tools")
|
|
tools_index = index.json()
|
|
# In panels by default, so flatten out sections...
|
|
tools = []
|
|
for tool_or_section in tools_index:
|
|
if "elems" in tool_or_section:
|
|
tools.extend(tool_or_section["elems"])
|
|
else:
|
|
tools.append(tool_or_section)
|
|
|
|
tool_ids = [_["id"] for _ in tools]
|
|
return tool_ids
|
|
|
|
def __build_nested_list(self, history_id):
|
|
hdca1_id = self.__build_pair(history_id, ["123", "456"])
|
|
hdca2_id = self.__build_pair(history_id, ["789", "0ab"])
|
|
|
|
response = self.dataset_collection_populator.create_list_from_pairs(history_id, [hdca1_id, hdca2_id])
|
|
self._assert_status_code_is(response, 200)
|
|
hdca_list_id = response.json()["id"]
|
|
return hdca_list_id
|
|
|
|
def __build_pair(self, history_id, contents):
|
|
create_response = self.dataset_collection_populator.create_pair_in_history(history_id, contents=contents)
|
|
hdca_id = create_response.json()["id"]
|
|
return hdca_id
|
|
|
|
|
|
def dataset_to_param(dataset):
|
|
return dict(
|
|
src='hda',
|
|
id=dataset['id']
|
|
)
|