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 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']
# 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
