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Many more upload tests. #4746

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merged 3 commits into from
Oct 4, 2017
Merged

Many more upload tests. #4746

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78d1dda
Refactor API upload tests into their own test class.
jmchilton Oct 2, 2017
8eac80a
More upload API tests.
jmchilton Oct 2, 2017
108e94c
FTP upload integration tests.
jmchilton Oct 3, 2017
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207 changes: 0 additions & 207 deletions test/api/test_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,8 @@
DatasetCollectionPopulator,
DatasetPopulator,
LibraryPopulator,
skip_without_datatype,
skip_without_tool,
)
from galaxy.tools.verify.test_data import TestDataResolver


class ToolsTestCase(api.ApiTestCase):
Expand Down Expand Up @@ -87,197 +85,6 @@ def _show_valid_tool(self, tool_id):
self._assert_has_keys(tool_info, "inputs", "outputs", "panel_section_id")
return tool_info

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_upload_posix_newline_fixes(self):
windows_content = "1\t2\t3\r4\t5\t6\r"
posix_content = windows_content.replace("\r", "\n")
result_content = self._upload_and_get_content(windows_content)
self.assertEquals(result_content, posix_content)

def test_upload_disable_posix_fix(self):
windows_content = "1\t2\t3\r4\t5\t6\r"
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 = "1 2 3\n4 5 6\n"
result_content = self._upload_and_get_content(table, space_to_tab="Yes")
self.assertEquals(result_content, "1\t2\t3\n4\t5\t6\n")

def test_upload_tab_to_space_off_by_default(self):
table = "1 2 3\n4 5 6\n"
result_content = self._upload_and_get_content(table)
self.assertEquals(result_content, table)

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 _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 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_unzip_collection(self):
with self.dataset_populator.test_history() as history_id:
hdca_id = self.__build_pair(history_id, ["123", "456"])
Expand Down Expand Up @@ -1470,20 +1277,6 @@ def _run(self, tool_id, history_id, inputs, assert_ok=False, tool_version=None):
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()
Expand Down
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