def add_ena_sample(self, ena_collection_id, study_type_list, auto_fields):
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.studySamples.fields
auto_fields = ast.literal_eval(auto_fields)
sample_id = uuid.uuid4().hex
a = {'id': sample_id}
characteristics = []
for f in ena_d:
key_split = f.id.split(".")
a[key_split[len(key_split) - 1]] = "" # accommodates fields not displayed on form
if f.id in auto_fields.keys():
a[key_split[len(key_split) - 1]] = auto_fields[f.id]
if key_split[len(key_split) - 1] == "organism":
characteristics.append({
"categoryTerm": "organism",
"characteristics": auto_fields[f.id],
"termSourceREF": auto_fields["termSourceREF_organism"],
"termAccessionNumber": auto_fields["termAccessionNumber_organism"]
})
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.studySamples.sampleCollection.fields
for f in ena_d:
key_split = f.id.split(".")
a[key_split[len(key_split) - 1]] = ""
if f.id in auto_fields.keys():
a[key_split[len(key_split) - 1]] = auto_fields[f.id]
# get characteristics, we have already begun with the organism,
# retrieve and sort to maintain order as displayed form
categories = [key for key, value in auto_fields.items() if key.startswith('categoryTerm_')]
categories.sort()
for category in categories:
index_part = category.split("categoryTerm_")[1]
if auto_fields['categoryTerm_' + index_part]:
ch = {
"categoryTerm": auto_fields['categoryTerm_' + index_part],
"characteristics": auto_fields['characteristics_' + index_part],
"termSourceREF": auto_fields['termSourceREF_' + index_part],
"termAccessionNumber": auto_fields['termAccessionNumber_' + index_part],
"unit": auto_fields['unit_' + index_part]
}
characteristics.append(ch)
a["characteristics"] = characteristics
EnaCollections.update({"_id": ObjectId(ena_collection_id)},
{"$push": {"collectionCOPOMetadata.samples": a}})
# assign sample to studies
for study_id in study_type_list:
a = {'id': sample_id, 'deleted': '0'}
self.add_sample_to_ena_study(study_id, ena_collection_id, a)
return sample_id
def update_study_details(self, ena_collection_id, study_id, auto_fields):
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.fields
auto_fields = ast.literal_eval(auto_fields)
auto_dict = {}
for f in ena_d:
key_split = f.id.split(".")
if f.id in auto_fields.keys():
auto_dict["studies.$.study." + key_split[len(key_split) - 1]] = auto_fields[f.id]
EnaCollections.update({"_id": ObjectId(ena_collection_id), "studies.studyCOPOMetadata.id": study_id}, {
'$set': auto_dict})
def add_study_publication(self, study_id, ena_collection_id, auto_fields):
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.studyPublications.fields
auto_fields = ast.literal_eval(auto_fields)
# get target study
study = self.get_ena_study(study_id, ena_collection_id)
# each study should have an empty publication document for creating others
publication_dict = study["study"]["studyPublications"][0]
if publication_dict:
publication_dict["id"] = uuid.uuid4().hex
publication_dict["deleted"] = "0"
for f in ena_d:
key_split = f.id.split(".")
if f.id in auto_fields.keys():
publication_dict[key_split[len(key_split) - 1]] = auto_fields[f.id]
EnaCollections.update(
{"_id": ObjectId(ena_collection_id), "studies.studyCOPOMetadata.id": study_id},
{'$push': {"studies.$.study.studyPublications": publication_dict}})
def clone_ena_study(self, ena_collection_id, cloned_elements):
# get study template from the ENA db template
study_template = d_utils.get_db_template("ENA")['studies'][0]
if study_template:
study_dict = study_template
study_dict["studyCOPOMetadata"]["id"] = uuid.uuid4().hex
study_dict["studyCOPOMetadata"]["deleted"] = "0"
if cloned_elements["studyType"]:
study_dict["studyCOPOMetadata"]["studyType"] = cloned_elements["studyType"]
study_dict["studyCOPOMetadata"]["studyReference"] = ''.join(
random.choice(string.ascii_uppercase) for i in range(4)) + "_CLONE"
if cloned_elements["studyReference"]:
study_dict["studyCOPOMetadata"]["studyReference"] = cloned_elements["studyReference"]
# check for samples and other composite types
new_samples = []
for k, v in cloned_elements.items():
if k[:-2] == "sample":
new_samples.append({'id': v, 'deleted': '0'})
if new_samples:
study_dict["studyCOPOMetadata"]['samples'] = new_samples
# get study fields
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.fields
for f in ena_d:
key_split = f.id.split(".")
target_key = key_split[len(key_split) - 1]
if target_key in cloned_elements.keys():
study_dict["study"][target_key] = cloned_elements[target_key]
EnaCollections.update({"_id": ObjectId(ena_collection_id)},
{"$push": {"studies": study_dict}})
def edit_ena_sample(self, ena_collection_id, sample_id, study_type_list, auto_fields):
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.studySamples.fields
auto_fields = ast.literal_eval(auto_fields)
characteristics = []
for f in ena_d:
key_split = f.id.split(".")
if f.id in auto_fields.keys():
EnaCollections.update(
{"_id": ObjectId(ena_collection_id), "collectionCOPOMetadata.samples.id": sample_id},
{'$set': {"collectionCOPOMetadata.samples.$." + key_split[len(key_split) - 1]: auto_fields[f.id]}})
if key_split[len(key_split) - 1] == "organism":
characteristics.append({
"categoryTerm": "organism",
"characteristics": auto_fields[f.id],
"termSourceREF": auto_fields["termSourceREF_organism"],
"termAccessionNumber": auto_fields["termAccessionNumber_organism"]
})
ena_d = d_utils.get_ui_template_as_obj("ENA").studies.study.studySamples.sampleCollection.fields
for f in ena_d:
key_split = f.id.split(".")
if f.id in auto_fields.keys():
EnaCollections.update(
{"_id": ObjectId(ena_collection_id), "collectionCOPOMetadata.samples.id": sample_id},
{'$set': {"collectionCOPOMetadata.samples.$." + key_split[len(key_split) - 1]: auto_fields[f.id]}})
# get characteristics
#
categories = [key for key, value in auto_fields.items() if key.startswith('categoryTerm_')]
categories.sort()
for category in categories:
index_part = category.split("categoryTerm_")[1]
if auto_fields['categoryTerm_' + index_part]:
ch = {
"categoryTerm": auto_fields['categoryTerm_' + index_part],
"characteristics": auto_fields['characteristics_' + index_part],
"termSourceREF": auto_fields['termSourceREF_' + index_part],
"termAccessionNumber": auto_fields['termAccessionNumber_' + index_part],
"unit": auto_fields['unit_' + index_part]
}
characteristics.append(ch)
EnaCollections.update(
{"_id": ObjectId(ena_collection_id), "collectionCOPOMetadata.samples.id": sample_id},
{'$set': {"collectionCOPOMetadata.samples.$.characteristics": characteristics}})
# update studies: add sample to study if study in the selected list,
# delete from study not selected
studies = EnaCollection().get_ena_studies(ena_collection_id)
for st in studies:
study_id = st["studyCOPOMetadata"]["id"]
a = {'id': sample_id, 'deleted': '1'}
if study_id in study_type_list:
a = {'id': sample_id, 'deleted': '0'}
self.hard_delete_sample_from_study(sample_id, study_id, ena_collection_id)
self.add_sample_to_ena_study(study_id, ena_collection_id, a)
