def delete(self, dataset_uuid, study_id=None, user=None):
""" Delete a dataset from a study given its unique identifier """
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})")
# 1. 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"])
# 2. Delete specific dataset
datasets_entry = study_converter.get_entry_by_name("datasets")
datasets_entry.value.delete_nested_entry("uuid", dataset_uuid)
if len(datasets_entry.value.value) == 0:
study_converter.remove_entries(prop_names=["datasets"])
# 3. Update study state, data and ulpoad on DB
message = f"Deleted dataset"
update_study(study, study_converter, api.payload, message, user)
return {"message": message}
def get(self, dataset_uuid, study_id=None, user=None):
""" Fetch a specific dataset for a given study """
args = self._get_parser.parse_args()
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})")
study = Study.objects().get(id=study_id)
study_json = marshal(study, study_model)
# The converter is used for its get_entry_by_name() method
study_converter = FormatConverter(mapper=prop_id_to_name)
study_converter.add_api_format(study_json["entries"])
datasets_entry = study_converter.get_entry_by_name("datasets")
dataset_nested_entry = datasets_entry.value.find_nested_entry(
"uuid", dataset_uuid)[0]
# The "dataset_nested_entry" entry is a NestedEntry (return list of dict)
if args["entry_format"] == "api":
return dataset_nested_entry.get_api_format()
elif args["entry_format"] == "form":
return dataset_nested_entry.get_form_format()
def test_reverse_map(self):
input_data = {
"key_1": "value_1",
"key_2": "value_2",
"key_3": "value_3"
}
expected_output = {
"value_1": "key_1",
"value_2": "key_2",
"value_3": "key_3"
}
self.assertEqual(reverse_map(input_data), expected_output)
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 post(self, study_id, user=None):
""" Add a new dataset 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
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. Create dataset entry and append it to "datasets"
# Format and clean entity
dataset_converter, _ = get_entity_converter(entries, entry_format,
prop_id_to_name,
prop_name_to_id)
# Generate UUID
dataset_converter, dataset_uuid = add_uuid_entry_if_missing(
dataset_converter, prop_name_to_id)
study_converter = add_entity_to_study_nested_list(
study_converter=study_converter,
entity_converter=dataset_converter,
prop_name_to_id=prop_name_to_id,
study_list_prop="datasets",
)
# 4. Validate dataset data against form
validate_form_format_against_form(form_name,
dataset_converter.get_form_format())
# 5. Update study state, data and ulpoad on DB
message = "Added dataset"
update_study(study, study_converter, payload, message, user)
return {"message": message, "uuid": dataset_uuid}, 201
def post(self, dataset_uuid, study_id=None, user=None):
""" Add a new processing event for a given dataset """
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 and dataset 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"])
datasets_entry = study_converter.get_entry_by_name("datasets")
dataset_nested_entry, dataset_position = datasets_entry.value.find_nested_entry(
"uuid", dataset_uuid)
# 3. Format and clean processing event data
pe_converter, _ = get_entity_converter(entries, entry_format,
prop_id_to_name,
prop_name_to_id)
# 4. Generate UUID
pe_converter, pe_uuid = add_uuid_entry_if_missing(pe_converter,
prop_name_to_id,
replace=False)
pe_nested_entry = NestedEntry(pe_converter)
pe_nested_entry.value = pe_converter.entries
# 5. Check if "process_events"" entry already exist study, creates it if it doesn't
pes_entry = dataset_nested_entry.get_entry_by_name("process_events")
if pes_entry is not None:
pes_entry.value.value.append(pe_nested_entry)
else:
pes_entry = Entry(
FormatConverter(prop_name_to_id)).add_form_format(
"process_events", [pe_nested_entry.get_form_format()])
dataset_nested_entry.value.append(pes_entry)
datasets_entry.value.value[dataset_position] = dataset_nested_entry
# 6. Validate processing data against form
validate_form_format_against_form(form_name,
pe_converter.get_form_format())
# 7. Update study state, data and ulpoad on DB
message = "Added processing event"
update_study(study, study_converter, payload, message, user)
return {"message": message, "uuid": pe_uuid}, 201
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