def put(self, dataset_uuid, study_id=None, user=None):
""" Update a dataset for a given study """
prop_id_to_name = get_property_map(key="id", value="name")
prop_name_to_id = reverse_map(prop_id_to_name)
# Used for helper route using only dataset_uuid
if study_id is None:
study_id = find_study_id_from_lvl1_uuid("dataset", dataset_uuid,
prop_name_to_id)
if study_id is None:
raise Exception(
f"Dataset not found in any study (uuid = {dataset_uuid})")
payload = api.payload
# 1. Split payload
form_name = payload["form_name"]
entries = payload["entries"]
entry_format = payload.get("entry_format", "api")
# 2. Get study data
study = Study.objects().get(id=study_id)
study_json = marshal(study, study_model)
study_converter = FormatConverter(mapper=prop_id_to_name)
study_converter.add_api_format(study_json["entries"])
# 3. Get current dataset data
datasets_entry = study_converter.get_entry_by_name("datasets")
dataset_nested_entry = datasets_entry.value.find_nested_entry(
"uuid", dataset_uuid)[0]
dataset_converter = FormatConverter(mapper=prop_id_to_name)
dataset_converter.entries = dataset_nested_entry.value
# 4. Get new dataset data and get entries to remove
new_dataset_converter, entries_to_remove = get_entity_converter(
entries, entry_format, prop_id_to_name, prop_name_to_id)
# 5. Update current dataset by adding, updating and deleting entries
# Nested entries not present in the original form are ignored (example: dataset["samples"])
# won't be deleted if not present in the new data), it needs to be None or "" to be deleted
dataset_converter.add_or_update_entries(new_dataset_converter.entries)
dataset_converter.remove_entries(entries=entries_to_remove)
dataset_nested_entry.value = dataset_converter.entries
# 6. Validate dataset data against form
validate_form_format_against_form(form_name,
dataset_converter.get_form_format())
# 7. Update study state, data and ulpoad on DB
message = "Updated dataset"
update_study(study, study_converter, payload, message, user)
return {"message": message}
def get(self, user=None):
""" Fetch a list with all entries """
# Convert query parameters
args = self._get_parser.parse_args()
include_deprecate = args["deprecated"]
res = Study.objects()
if not include_deprecate:
res = res.filter(meta_information__deprecated=False)
study_ids = [
u.strip()
for u in re.split(r",|;", args["study_ids"])
if u.strip().lower() not in ["", "0", "none", "false"]
]
if len(study_ids) > 0:
res = res.filter(id__in=study_ids)
if res.count() < len(study_ids):
found_ids = [str(s.id) for s in res.only("id")]
return {
"message": f"Some study ids were not found",
"missing_study_ids": list(set(study_ids) - set(found_ids)),
}, 404
# Limits and Skipping applied after main filters
res = res.all().skip(args["skip"])
# Issue with limit(0) that returns 0 items instead of all of them
if args["limit"] != 0:
res = res.limit(args["limit"])
if args["properties_id_only"] or args["entry_format"] == "form":
marchal_model = study_model_prop_id
else:
marchal_model = study_model
# Marshal studies
study_json_list = marshal(list(res.select_related()), marchal_model)
if args["entry_format"] == "api":
return study_json_list
elif args["entry_format"] == "form":
prop_map = get_property_map(key="id", value="name")
for study_json in study_json_list:
study_converter = FormatConverter(prop_map).add_api_format(
study_json["entries"]
)
study_json["entries"] = study_converter.get_form_format()
return study_json_list
def test_clean_data(self):
"Remove empty values and perform other cleaning (like stripping strings)"
mapper = {
"TO_KEEP": "0",
"TO_KEEP_1": "1",
"TO_KEEP_2": "2",
"TO_KEEP_3": "3",
"TO_KEEP_4": "4",
"TO_REMOVE": "5",
"TO_REMOVE_2": "6",
}
form_format = {
"TO_KEEP_1":
1,
"TO_REMOVE":
"",
"TO_KEEP_2": [1, 2, ""],
"TO_KEEP_3": {
"TO_KEEP": 31,
"TO_REMOVE": ""
},
"TO_KEEP_4": [
{
"TO_KEEP": 441,
"TO_REMOVE": ""
},
{
"TO_REMOVE": "",
"TO_REMOVE_2": ""
},
],
}
c = FormatConverter(mapper=mapper).add_form_format(form_format)
c.clean_data()
actual_output = c.get_form_format()
expected_output = {
"TO_KEEP_1": 1,
"TO_KEEP_2": [1, 2],
"TO_KEEP_3": {
"TO_KEEP": 31
},
"TO_KEEP_4": [{
"TO_KEEP": 441
}, {}],
}
self.assertEqual(actual_output, expected_output)
def get(self, id, user=None):
"""Fetch an entry given its unique identifier"""
args = self._get_parser.parse_args()
if args["properties_id_only"] or args["entry_format"] == "form":
marchal_model = study_model_prop_id
else:
marchal_model = study_model
study_json = marshal(Study.objects(id=id).get(), marchal_model)
if args["entry_format"] == "api":
return study_json
elif args["entry_format"] == "form":
prop_map = get_property_map(key="id", value="name")
study_converter = FormatConverter(prop_map).add_api_format(
study_json["entries"]
)
study_json["entries"] = study_converter.get_form_format()
return study_json
def put(self, sample_uuid, study_id=None, user=None):
""" Update a sample for a given study """
prop_id_to_name = get_property_map(key="id", value="name")
prop_name_to_id = reverse_map(prop_id_to_name)
# Used for helper route using only sample_uuid
if study_id is None:
study_id = find_study_id_from_lvl1_uuid("sample", sample_uuid,
prop_name_to_id)
if study_id is None:
raise Exception(
f"Sample not found in any study (uuid = {sample_uuid})")
payload = api.payload
# 1. Split payload
validate_dict = payload.get("validate", None)
form_names = payload.get("form_names", None)
entries = payload["entries"]
entry_format = payload.get("entry_format", "api")
# 2. Get forms for validation
forms = {}
for key, validate in validate_dict.items():
if validate:
forms[key] = app.form_manager.get_form_by_name(
form_name=form_names[key])
# 3. Get study data
study = Study.objects().get(id=study_id)
study_json = marshal(study, study_model)
study_converter = FormatConverter(mapper=prop_id_to_name)
study_converter.add_api_format(study_json["entries"])
# 3. Get current sample data
samples_entry = study_converter.get_entry_by_name("samples")
sample_nested_entry = samples_entry.value.find_nested_entry(
"uuid", sample_uuid)[0]
sample_converter = FormatConverter(mapper=prop_id_to_name)
sample_converter.entries = sample_nested_entry.value
# 4. Unify UUIDs with existing entities (including nested ones)
# Format and clean entity
new_sample_converter, _ = get_entity_converter(entries, entry_format,
prop_id_to_name,
prop_name_to_id)
new_sample_form_format = new_sample_converter.get_form_format()
[new_sample_form_format] = unify_sample_entities_uuids(
existing_samples=study_converter.get_form_format().get(
"samples", []),
new_samples=[new_sample_form_format],
)
# 5. Clean new data and get entries to remove
# Format and clean entity
new_sample_converter, entries_to_remove = get_entity_converter(
entries=new_sample_form_format,
entry_format="form",
prop_id_to_name=None,
prop_name_to_id=prop_name_to_id,
)
# 6. Update current sample by adding, updating and deleting entries
# Nested entries not present in the original form are ignored
# won't be deleted if not present in the new data), it needs to be None or "" to be deleted
sample_converter.add_or_update_entries(new_sample_converter.entries)
sample_converter.remove_entries(entries=entries_to_remove)
sample_nested_entry.value = sample_converter.entries
# 7. Validate data against form
validate_sample_against_form(sample_converter.get_form_format(),
validate_dict, forms)
# 8. Update study state, data and ulpoad on DB
message = "Updated sample"
update_study(study, study_converter, payload, message, user)
return {"message": message}
def post(self, study_id, user=None):
""" Add a new sample for a given study """
payload = api.payload
prop_id_to_name = get_property_map(key="id", value="name")
prop_name_to_id = reverse_map(prop_id_to_name)
# 1. Split payload
validate_dict = payload.get("validate", None)
form_names = payload.get("form_names", None)
entries = payload["entries"]
entry_format = payload.get("entry_format", "api")
# 2. Get forms for validation
forms = {}
for key, validate in validate_dict.items():
if validate:
forms[key] = app.form_manager.get_form_by_name(
form_name=form_names[key])
# 3. Get study data
study = Study.objects().get(id=study_id)
study_json = marshal(study, study_model)
study_converter = FormatConverter(mapper=prop_id_to_name)
study_converter.add_api_format(study_json["entries"])
# 4. Unify UUIDs with existing entities (including nested ones)
# Format and clean entity
sample_converter, _ = get_entity_converter(entries, entry_format,
prop_id_to_name,
prop_name_to_id)
new_sample_form_format = sample_converter.get_form_format()
[new_sample_form_format] = unify_sample_entities_uuids(
existing_samples=study_converter.get_form_format().get(
"samples", []),
new_samples=[new_sample_form_format],
)
# 5. Append new samples to "samples" in study
# Format and clean entity
sample_converter, _ = get_entity_converter(
entries=new_sample_form_format,
entry_format="form",
prop_id_to_name=None,
prop_name_to_id=prop_name_to_id,
)
# Generate UUID (redundant, UUIDs already generated by unify_sample_entities_uuids)
sample_converter, sample_uuid = add_uuid_entry_if_missing(
sample_converter, prop_name_to_id)
study_converter = add_entity_to_study_nested_list(
study_converter=study_converter,
entity_converter=sample_converter,
prop_name_to_id=prop_name_to_id,
study_list_prop="samples",
)
# 6. Validate data against form
validate_sample_against_form(sample_converter.get_form_format(),
validate_dict, forms)
# 7. Update study state, data and ulpoad on DB
message = "Added sample"
update_study(study, study_converter, payload, message, user)
return {"message": message, "uuid": sample_uuid}, 201