def test_step2_sbml_export(self):
"Second step selects an SBML Template."
with factory.load_test_file("ExportData_FBA_step2.post") as fp:
POST = QueryDict(fp.read())
response = self.client.post(reverse("export:sbml"), data=POST)
self.assertEqual(response.status_code, codes.ok)
self.assertEqual(len(response.context["sbml_warnings"]), 5)
def _build_import_context(self, base, import_id):
# load post data broken up across multiple files
filename = f"{base}.post.context.json"
with factory.load_test_file(filename, "rt") as context_file:
context = json.load(context_file)
# make sure import_id is a string if a raw UUID is passed
context.update(importId=str(import_id))
return context
def test_post_DescribeView_writer_xlsx(self):
self.client.force_login(self.user)
url = reverse("main:describe:describe", kwargs=self.study_kwargs)
filename = "ExperimentDescription_simple.xlsx"
with factory.load_test_file(filename) as fp:
file = io.BytesIO(fp.read())
file.name = filename
file.content_type = XLSX_CONTENT_TYPE
payload = {"file": file}
response = self.client.post(url, payload)
self.assertEqual(response.status_code, codes.ok)
self.assertEqual(self.study.line_set.count(), 2)
def _populateTestStrains(cls, registry):
with factory.load_test_file("ice_entries.csv") as entries_file:
registry.bulk_upload(entries_file)
# fetch the part IDs
it = registry.iter_entries(sort="created", asc="false", limit=10)
entries = list(itertools.islice(it, 10))
# set read permissions on some of the created strains
for entry in entries[:5]:
entry.set_permission(cls.read_ice_user._ice_id)
# stash the part IDs for use in tests
cls.entry_ids = [entry.part_id for entry in entries]
return entries
def _run_parse_view(self, filename, filetype, mode):
with factory.load_test_file(filename) as fp:
upload = BytesIO(fp.read())
upload.name = filename
response = self.client.post(
reverse("load_flat:parse"),
data={
"file": upload,
"X_EDD_FILE_TYPE": filetype,
"X_EDD_IMPORT_MODE": mode,
},
)
self.assertEqual(response.status_code, codes.ok)
with factory.load_test_file(filename + ".json") as fp:
reader = codecs.getreader("utf-8")
target = json.load(reader(fp))
# check that objects are the same when re-serialized with sorted keys
self.assertEqual(
json.dumps(target, sort_keys=True),
json.dumps(response.json(), sort_keys=True),
)
return response
def test_post_DescribeView_writer_xlsx_bad_headers(self):
self.client.force_login(self.user)
url = reverse("main:describe:describe", kwargs=self.study_kwargs)
filename = "ExperimentDescription_bad_headers.xlsx"
with factory.load_test_file(filename) as fp:
file = io.BytesIO(fp.read())
file.name = filename
file.content_type = XLSX_CONTENT_TYPE
payload = {"file": file}
response = self.client.post(url, payload)
self.assertEqual(response.status_code, codes.ok)
self.assertEqual(self.study.line_set.count(), 2)
messages = response.json()
self.assertNotIn("errors", messages)
self.assertIn("warnings", messages)
self.assertEqual(messages["warnings"][0]["category"],
"User input ignored")
def _populateTestStrains(cls, ice):
# create a BulkUpload object
response = ice.session.put(ice_url("/uploads"),
json={"type": "strain"})
upload_id = response.json()["id"]
# add file data to the BulkUpload
with factory.load_test_file("ice_entries.csv") as entries:
response = ice.session.post(
ice_url(f"/uploads/{upload_id}/file"),
files={
"type": "strain",
"file": entries
},
)
# set upload to approved to create (click "submit" button)
response = ice.session.put(
ice_url(f"/uploads/{upload_id}/status"),
json={
"id": upload_id,
"status": "APPROVED"
},
)
# fetch the part IDs
response = ice.session.get(
ice_url("/collections/available/entries"),
params={
"sort": "created",
"asc": "false"
},
)
entries = response.json()["data"][:10]
cls.part_ids = [p["partId"] for p in reversed(entries)]
cls.db_ids = [p["id"] for p in reversed(entries)]
# set read permissions on some of the created strains
for idx in range(5):
response = ice.session.post(
ice_url(f"/parts/{cls.part_ids[idx]}/permissions"),
json={
"article": "ACCOUNT",
"articleId": cls.read_ice_user._ice_id,
"type": "READ_ENTRY",
"typeId": cls.db_ids[idx],
},
)
def test_post_DescribeView_writer_xlsx_double_import(self):
# run test_post_DescribeView_writer_xlsx
self.test_post_DescribeView_writer_xlsx()
# then do its insides again, checking for errors
url = reverse("main:describe:describe", kwargs=self.study_kwargs)
filename = "ExperimentDescription_simple.xlsx"
with factory.load_test_file(filename) as fp:
file = io.BytesIO(fp.read())
file.name = filename
file.content_type = XLSX_CONTENT_TYPE
payload = {"file": file}
response = self.client.post(url, payload)
self.assertEqual(response.status_code, codes.bad_request)
self.assertEqual(self.study.line_set.count(), 2)
messages = response.json()
self.assertIn("errors", messages)
self.assertEqual(len(messages["errors"]), 1)
self.assertEqual(messages["errors"][0]["category"],
"Non-unique line names")
def test_upload_experiment_description_xlsx_adds_entry(self):
study = self._writable_study()
filename = "ExperimentDescription_simple.xlsx"
with factory.load_test_file(filename) as fp:
file = io.BytesIO(fp.read())
file.name = filename
file.content_type = (
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
)
self.client.post(
reverse("main:describe:describe", kwargs={"slug": study.slug}),
{"file": file},
)
qs = self._find_log(event=StudyLog.Event.DESCRIBED, study=study)
assert qs.count() == 1
sl = qs.get()
assert sl.detail == {"count": 2}
def test_post_DescribeView_writer_xlsx_bad_values(self):
self.client.force_login(self.user)
url = reverse("main:describe:describe", kwargs=self.study_kwargs)
filename = "ExperimentDescription_bad_values.xlsx"
with factory.load_test_file(filename) as fp:
file = io.BytesIO(fp.read())
file.name = filename
file.content_type = XLSX_CONTENT_TYPE
payload = {"file": file}
response = self.client.post(url, payload)
self.assertEqual(response.status_code, codes.bad_request)
self.assertEqual(self.study.line_set.count(), 0)
messages = response.json()
self.assertIn("errors", messages)
self.assertIn("warnings", messages)
self.assertEqual(len(messages["errors"]), 2)
self.assertEqual(
{"Incorrect file format", "Invalid values"},
{err["category"]
for err in messages["errors"]},
)
def _build_import_pages(self, base):
# load series data, slicing it up into pages if requested
filename = f"{base}.post.series.json"
with factory.load_test_file(filename, "rt") as series_file:
yield from self._slice_series_pages(series_file)
def test_step3_sbml_export(self):
"Third step maps metabolites to species/reactions, and selects an export timepoint."
with factory.load_test_file("ExportData_FBA_step3.post") as fp:
POST = QueryDict(fp.read())
response = self.client.post(reverse("export:sbml"), data=POST)
self.assertEqual(response.status_code, codes.ok)
