def test_get_entry_by_name(self):
"""Get an entry based on its prop_name"""
mapper = {"1": "user", "2": "username", "3": "phone"}
input_format = [{
"prop":
"1",
"value": [
{
"prop": "2",
"value": "Edward"
},
{
"prop": "3",
"value": "+33(0)123456789"
},
],
}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
c.add_api_format(input_format)
user_entry = c.entries[0]
self.assertEqual(
user_entry.value.get_entry_by_name("username").value, "Edward")
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_form_to_api_format_case_3(self):
mapper = {"storage": "1", "location": "2", "number_of_files": "3"}
form_format = {
"storage": {
"location": "C:/Documents",
"number_of_files": 1000
}
}
expected_api_format = [{
"prop":
"1",
"value": [
{
"prop": "2",
"value": "C:/Documents"
},
{
"prop": "3",
"value": 1000
},
],
}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
actual_api_format = c.add_form_format(form_format).get_api_format()
self.assertEqual(expected_api_format, actual_api_format)
def test_api_to_form_format_case_3(self):
"""A nested form field. Only one form field is accepted"""
mapper = {"1": "storage", "2": "location", "3": "number_of_files"}
input_format = [{
"prop":
"1",
"value": [
{
"prop": "2",
"value": "C:/Documents"
},
{
"prop": "3",
"value": 1000
},
],
}]
expected_form_format = {
"storage": {
"location": "C:/Documents",
"number_of_files": 1000
}
}
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
actual_form_format = c.add_api_format(input_format).get_form_format()
self.assertEqual(expected_form_format, actual_form_format)
def test_remove_entries(self):
mapper = {
"KEEP": "0",
"REMOVE_1": "1",
"REMOVE_2": "2",
"REMOVE_3": "3"
}
form_format = {"KEEP": 1, "REMOVE_1": 2, "REMOVE_2": 3, "REMOVE_3": 4}
c = FormatConverter(mapper=mapper).add_form_format(form_format)
assert len(c.entries) == 4
form_format_to_remove = {"REMOVE_1": 2}
c_remove = FormatConverter(
mapper=mapper).add_form_format(form_format_to_remove)
c.remove_entries(entries=c_remove.entries)
assert len(c.entries) == 3
c.remove_entries(prop_names=["REMOVE_2"])
assert len(c.entries) == 2
c.remove_entries(prop_ids=["3"])
assert len(c.entries) == 1
assert c.entries[0].prop_name == "KEEP"
def test_api_to_api_format_case_2(self):
"""List of simple values"""
mapper = {"1": "username"}
input_format = [{"prop": "1", "value": ["Edward", "Annie"]}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
reconstructed_api_format = c.add_api_format(
input_format).get_api_format()
self.assertEqual(input_format, reconstructed_api_format)
def test_form_to_api_format_case_2(self):
mapper = {"username": "******"}
form_format = {"username": ["Edward", "Annie"]}
expected_api_format = [{"prop": "1", "value": ["Edward", "Annie"]}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
actual_api_format = c.add_form_format(form_format).get_api_format()
self.assertEqual(expected_api_format, actual_api_format)
def test_api_to_form_format_case_1(self):
"""Simple value"""
mapper = {"1": "username"}
input_format = [{"prop": "1", "value": "Edward"}]
expected_form_format = {"username": "******"}
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
actual_form_format = c.add_api_format(input_format).get_form_format()
self.assertEqual(expected_form_format, actual_form_format)
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 delete(self, pe_uuid, study_id=None, dataset_uuid=None, user=None):
""" Delete a processing event 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 pe_uuid
if dataset_uuid is None:
study_id, dataset_uuid = find_study_id_and_lvl1_entity_from_lvl2_uuid(
lvl1_prop="dataset",
lvl2_prop="process_event",
lvl2_uuid=pe_uuid,
prop_name_to_id=prop_name_to_id,
prop_id_to_name=prop_id_to_name,
)
if study_id is None or dataset_uuid is None:
raise Exception(
f"Processing event not found in any dataset (uuid = {pe_uuid})"
)
# 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. Get dataset data
datasets_entry = study_converter.get_entry_by_name("datasets")
dataset_nested_entry = datasets_entry.value.find_nested_entry(
"uuid", dataset_uuid)[0]
# 3. Delete specific processing event
pes_entry = dataset_nested_entry.get_entry_by_name("process_events")
pes_entry.value.delete_nested_entry("uuid", pe_uuid)
if len(pes_entry.value.value) == 0:
dataset_nested_entry.remove_entries(prop_names=["process_events"])
# 4. Update study state, data and ulpoad on DB
message = f"Deleted processing event"
update_study(study, study_converter, api.payload, message, user)
return {"message": message}
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 test_api_to_form_format_case_4(self):
"""List of nested form fields. Each form field is incorporated into a list"""
mapper = {"1": "contacts", "3": "name", "4": "phone"}
input_format = [{
"prop":
"1",
"value": [
[
{
"prop": "3",
"value": "Edward"
},
{
"prop": "4",
"value": "903 367 2072"
},
],
[
{
"prop": "3",
"value": "Annie"
},
{
"prop": "4",
"value": "731 222 8842"
},
],
],
}]
expected_form_format = {
"contacts": [
{
"name": "Edward",
"phone": "903 367 2072"
},
{
"name": "Annie",
"phone": "731 222 8842"
},
]
}
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
actual_form_format = c.add_api_format(input_format).get_form_format()
self.assertEqual(expected_form_format, actual_form_format)
def find_study_id_and_lvl1_entity_from_lvl2_uuid(lvl1_prop, lvl2_prop,
lvl2_uuid, prop_name_to_id,
prop_id_to_name):
""" Find parent study and lvl1 entity (ex: Dataset) given a lvl2 uuid (ex: Processing event) """
study_id = None
lvl1_uuid = None
aggregated_studies = get_aggregated_studies(
prop_map=prop_name_to_id,
level_1=lvl1_prop,
level_2=lvl2_prop,
)
for potential_study in aggregated_studies:
if lvl2_uuid in potential_study[f"{lvl2_prop}s_uuids"]:
study = potential_study
study_id = study["id"]
break
else:
return study_id, lvl1_uuid
lvl1_list_entry = NestedListEntry(
FormatConverter(prop_id_to_name)).add_api_format(study["datasets"])
for lvl1_nested_entry in lvl1_list_entry.value:
lvl1_uuid = lvl1_nested_entry.get_entry_by_name("uuid").value
lvl1_entry = lvl1_nested_entry.get_entry_by_name(f"{lvl2_prop}s")
try:
lvl1_entry.value.find_nested_entry("uuid", lvl2_uuid)
return study_id, lvl1_uuid
except:
pass # Lvl 2 entity not in this lvl 1 entity
return study_id, lvl1_uuid
def test_form_to_api_format_case_4(self):
mapper = {"contacts": "1", "name": "3", "phone": "4"}
form_format = {
"contacts": [
{
"name": "Edward",
"phone": "903 367 2072"
},
{
"name": "Annie",
"phone": "731 222 8842"
},
]
}
actual_api_format = [{
"prop":
"1",
"value": [
[
{
"prop": "3",
"value": "Edward"
},
{
"prop": "4",
"value": "903 367 2072"
},
],
[
{
"prop": "3",
"value": "Annie"
},
{
"prop": "4",
"value": "731 222 8842"
},
],
],
}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
expected_api_format = c.add_form_format(form_format).get_api_format()
self.assertEqual(expected_api_format, actual_api_format)
def delete(self, sample_uuid, study_id=None, user=None):
""" Delete a sample 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 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})")
# 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 entity
samples_entry = study_converter.get_entry_by_name("samples")
samples_entry.value.delete_nested_entry("uuid", sample_uuid)
if len(samples_entry.value.value) == 0:
study_converter.remove_entries(prop_names=["samples"])
# 3. Update study state, data and ulpoad on DB
message = f"Deleted sample"
update_study(study, study_converter, api.payload, message, user)
return {"message": message}
def test_add_or_update_entries(self):
mapper = {"username": "******", "first_name": "2", "last_name": "3"}
form_format_1 = {"username": "******", "first_name": "John"}
form_format_2 = {"username": "******", "last_name": "Doe"}
c_1 = FormatConverter(mapper=mapper).add_form_format(form_format_1)
c_2 = FormatConverter(mapper=mapper).add_form_format(form_format_2)
expected_output = {
"username": "******",
"first_name": "John",
"last_name": "Doe",
}
actual_output = c_1.add_or_update_entries(
c_2.entries).get_form_format()
self.assertEqual(actual_output, expected_output)
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 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 test_find_nested_entry(self):
"""Get a specific NestedEntry based on the value of a property"""
mapper = {"1": "users", "2": "username", "3": "phone"}
input_format = [{
"prop":
"1",
"value": [
[
{
"prop": "2",
"value": "Edward"
},
{
"prop": "3",
"value": "+33(0)123456789"
},
],
[
{
"prop": "2",
"value": "John"
},
{
"prop": "3",
"value": "+33(9)876543210"
},
],
],
}]
c = FormatConverter(key_name="prop", value_name="value", mapper=mapper)
c.add_api_format(input_format)
users_entry = c.entries[0]
nested_entry, position = users_entry.value.find_nested_entry(
"username", "John")
self.assertEqual(nested_entry.get_form_format()["phone"],
"+33(9)876543210")
self.assertEqual(position, 1)
def get(self, study_id, user=None):
""" Fetch a list of all datasets for a given study """
args = self._get_parser.parse_args()
study = Study.objects().get(id=study_id)
study_json = marshal(study, study_model)
prop_map = get_property_map(key="id", value="name")
# The converter is used for its get_entry_by_name() method
study_converter = FormatConverter(mapper=prop_map)
study_converter.add_api_format(study_json["entries"])
datasets_entry = study_converter.get_entry_by_name("datasets")
if datasets_entry is not None:
# The "datasets" entry is a NestedListEntry (return list of list)
if args["entry_format"] == "api":
return datasets_entry.get_api_format()
elif args["entry_format"] == "form":
return datasets_entry.get_form_format()
else:
return []
def validate_against_form(form_cls, form_name, entries):
prop_map = get_property_map(key="id", value="name")
form_data_json = FormatConverter(prop_map).add_api_format(entries).get_form_format()
# 3. Validate data against form
form_instance = form_cls()
form_instance.process(data=form_data_json)
if not form_instance.validate():
raise RequestBodyException(
f"Passed data did not validate with the form {form_name}: {form_instance.errors}"
)
return form_data_json
def delete(self, study_id, user=None):
""" Delete all samples from a study given its unique identifier """
prop_id_to_name = get_property_map(key="id", value="name")
# 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 samples
study_converter.remove_entries(prop_names=["samples"])
# 3. Update study state, data and ulpoad on DB
message = "Deleted samples"
update_study(study, study_converter, api.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
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 upload_study_related_entity(data, url, method, property_url, headers):
"""Send data to the API (study related entity) in form format"""
entry_format = data.pop("entry_format", "form")
# Format data (cleaning + conversion from "form format" to "api format")
if entry_format == "form":
prop_name_to_id = map_key_value(property_url, key="name", value="id")
converter = FormatConverter(mapper=prop_name_to_id)
converter.add_form_format(data["entries"])
elif entry_format == "api":
prop_id_to_name = map_key_value(property_url, key="id", value="name")
converter = FormatConverter(mapper=prop_id_to_name)
converter.add_api_format(data["entries"])
converter.clean_data()
data["entries"] = converter.get_api_format()
data["entry_format"] = "api"
# Send data to API
if method == "post":
res = requests.post(url=url, json=data, headers=headers)
if res.status_code != 201:
message = f"Failed to POST study related entity. {res.json()}"
success = False
else:
message = "Succeded to POST study related entity"
success = True
elif method == "put":
res = requests.put(url=url, json=data, headers=headers)
if res.status_code != 200:
message = f"Failed to PUT study related entity. {res.json()}"
success = False
else:
message = "Succeded to PUT study related entity"
success = True
return (res.json(), message, success)
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, pe_uuid, study_id=None, dataset_uuid=None, user=None):
""" Update a processing event for a given dataset """
payload = api.payload
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 pe_uuid
if dataset_uuid is None:
study_id, dataset_uuid = find_study_id_and_lvl1_entity_from_lvl2_uuid(
lvl1_prop="dataset",
lvl2_prop="process_event",
lvl2_uuid=pe_uuid,
prop_name_to_id=prop_name_to_id,
prop_id_to_name=prop_id_to_name,
)
if study_id is None or dataset_uuid is None:
raise Exception(
f"Processing event not found in any dataset (uuid = {pe_uuid})"
)
# 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. 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 dataset data
datasets_entry = study_converter.get_entry_by_name("datasets")
dataset_nested_entry = datasets_entry.value.find_nested_entry(
"uuid", dataset_uuid)[0]
# 4. Get current processing event data
pes_entry = dataset_nested_entry.get_entry_by_name("process_events")
pe_nested_entry = pes_entry.value.find_nested_entry("uuid", pe_uuid)[0]
pe_converter = FormatConverter(mapper=prop_id_to_name)
pe_converter.entries = pe_nested_entry.value
# 5. Get new processing event data
new_pe_converter, entries_to_remove = get_entity_converter(
entries, entry_format, prop_id_to_name, prop_name_to_id)
# 6. Update current processing event by adding, updating and deleting entries
# Nested entries not present in the original form are ignored (example: pe["results"])
# won't be deleted if not present in the new data), it needs to be None or "" to be deleted
pe_converter.add_or_update_entries(new_pe_converter.entries)
pe_converter.remove_entries(entries=entries_to_remove)
pe_nested_entry.value = pe_converter.entries
# 7. Validate processing event data against form
validate_form_format_against_form(form_name,
pe_converter.get_form_format())
# 8. Update study state, data and ulpoad on DB
message = "Updated processing event"
update_study(study, study_converter, payload, message, user)
return {"message": message}
def post(self, user=None):
""" Add a new entry """
payload = api.payload
# 1. Split payload
form_name = payload["form_name"]
initial_state = payload["initial_state"]
entries = payload["entries"]
entry_format = payload.get("entry_format", "api")
form_cls = app.form_manager.get_form_by_name(form_name=form_name)
if initial_state == "rna_sequencing_biokit":
initial_state = "BiokitUploadState"
app.study_state_machine.load_state(name=initial_state)
prop_map = get_property_map(key="name", value="id")
# 2. Make sure to have both API and form format
if entry_format == "api":
try:
if len(entries) != len({prop["property"] for prop in entries}):
raise IdenticalPropertyException(
"The entries cannot have several identical property values."
)
except TypeError as e:
raise RequestBodyException("Entries has wrong format.") from e
entries = {
"api_format": entries,
"form_format": validate_against_form(form_cls, form_name, entries),
}
else:
validate_form_format_against_form(form_name, entries)
entries = {
"api_format": FormatConverter(prop_map)
.add_form_format(entries)
.get_api_format(),
"form_format": entries,
}
# 3. Check unicity of pseudo alternate pk in entries
check_alternate_pk_unicity(
entries=entries["form_format"], pseudo_apks=["study_id"], prop_map=prop_map
)
# 4. Evaluate new state of study by passing form data
app.study_state_machine.create_study(**entries["form_format"])
state = app.study_state_machine.current_state
meta_info = MetaInformation(state=str(state))
log = ChangeLog(
user_id=user.id if user else None,
action="Created study",
timestamp=datetime.now(),
manual_user=payload.get("manual_meta_information", {}).get("user", None),
)
meta_info.add_log(log)
study_data = {
"entries": entries["api_format"],
"meta_information": meta_info.to_json(),
}
# 5. Insert data into database
study = Study(**study_data)
study.save()
# Index study on ES
index_study_if_es(study, entries["form_format"], "add")
return {"message": f"Study added", "id": str(study.id)}, 201
def put(self, id, user=None):
""" Update an entry given its unique identifier """
payload = api.payload
# 1. Split payload
study_id = id
form_name = payload["form_name"]
entries = payload["entries"]
entry_format = payload.get("entry_format", "api")
study = Study.objects(id=study_id).first()
prop_map = get_property_map(key="name", value="id")
# 1. Extract form name and create form from FormManager
form_cls = app.form_manager.get_form_by_name(form_name=form_name)
# 2. Make sure to have both API and form format
if entry_format == "api":
entries = {
"api_format": entries,
"form_format": validate_against_form(form_cls, form_name, entries),
}
else:
validate_form_format_against_form(form_name, entries)
entries = {
"api_format": FormatConverter(prop_map)
.add_form_format(entries)
.get_api_format(),
"form_format": entries,
}
# 3. Check unicity of pseudo alternate pk in entries
# check_alternate_pk_unicity(entries=entries["form_format"], pseudo_apks=["study_id"], prop_map=prop_map)
# 4. Determine current state and evaluate next state
state_name = str(study.meta_information.state)
if state_name == "rna_sequencing_biokit":
state_name = "BiokitUploadState"
app.study_state_machine.load_state(name=state_name)
app.study_state_machine.change_state(**entries["form_format"])
new_state = app.study_state_machine.current_state
# 5. Create and append meta information to the study
meta_info = MetaInformation(
state=state_name, change_log=study.meta_information.change_log
)
log = ChangeLog(
action="Updated study",
user_id=user.id if user else None,
timestamp=datetime.now(),
manual_user=payload.get("manual_meta_information", {}).get("user", None),
)
meta_info.state = str(new_state)
meta_info.add_log(log)
study_data = {
"entries": entries["api_format"],
"meta_information": meta_info.to_json(),
}
# 6. Update data in database
study.update(**study_data)
# Index study on ES
index_study_if_es(study, entries["form_format"], "update")
return {"message": f"Update study"}