def update_clinvar_submission_status(store, request_obj, institute_id,
submission_id):
"""Update the status of a clinVar submission
Args:
store(adapter.MongoAdapter)
request_obj(flask.request) POST request sent by form submission
institute_id(str) institute id
submission_id(str) the database id of a clinvar submission
"""
update_status = request_obj.form.get("update_submission")
if update_status in ["open", "closed"]: # open or close a submission
store.update_clinvar_submission_status(institute_id, submission_id,
update_status)
if update_status == "register_id": # register an official clinvar submission ID
result = store.update_clinvar_id(
clinvar_id=request_obj.form.get("clinvar_id"),
submission_id=submission_id,
)
if update_status == "delete": # delete a submission
deleted_objects, deleted_submissions = store.delete_submission(
submission_id=submission_id)
flash(
f"Removed {deleted_objects} objects and {deleted_submissions} submission from database",
"info",
)
def clinvar_submissions(institute_id):
def generate_csv(header, lines):
yield header + '\n'
for line in lines: # lines have already quoted fields
yield line + '\n'
if request.method == 'POST':
submission_id = request.form.get('submission_id')
if request.form.get('update_submission'):
if request.form.get('update_submission') == 'close': # close a submission
store.update_clinvar_submission_status(current_user.email, submission_id, 'closed')
elif request.form.get('update_submission') == 'open':
store.update_clinvar_submission_status(current_user.email, submission_id, 'open') # open a submission
elif request.form.get('update_submission') == 'register_id' and request.form.get('clinvar_id'): # provide an official clinvar submission ID
result = store.update_clinvar_id(clinvar_id = request.form.get('clinvar_id'), submission_id = submission_id)
elif request.form.get('update_submission') == 'delete': # delete a submission
deleted_objects, deleted_submissions = store.delete_submission(submission_id = submission_id)
flash("Removed {} objects and {} submission from database".format(deleted_objects, deleted_submissions), 'info')
elif request.form.get('delete_variant'): # delete a variant from a submission
store.delete_clinvar_object(object_id = request.form.get('delete_variant'), object_type='variant_data', submission_id = submission_id) # remove variant and associated_casedata
elif request.form.get('delete_casedata'): # delete a case from a submission
store.delete_clinvar_object(object_id = request.form.get('delete_casedata'), object_type='case_data', submission_id = submission_id) # remove just the casedata associated to a variant
else: # Download submission CSV files (for variants or casedata)
clinvar_subm_id = request.form.get('clinvar_id')
if clinvar_subm_id =='':
flash('In order to download a submission CSV file you should register a Clinvar submission Name first!','warning')
return redirect(request.referrer)
csv_type = ''
csv_type = request.form.get('csv_type')
submission_objs = store.clinvar_objs(submission_id=submission_id, key_id=csv_type) # a list of clinvar submission objects (variants or casedata)
if submission_objs:
csv_header_obj = controllers.clinvar_header(submission_objs, csv_type) # custom csv header (dict as in constants CLINVAR_HEADER and CASEDATA_HEADER, but with required fields only)
csv_lines = controllers.clinvar_lines(submission_objs, csv_header_obj) # csv lines (one for each variant/casedata to be submitted)
csv_header = list(csv_header_obj.values())
csv_header = ['"'+str(x)+'"' for x in csv_header] # quote columns in header for csv rendering
headers = Headers()
headers.add('Content-Disposition','attachment', filename=clinvar_subm_id+'_'+str(datetime.datetime.now().strftime("%Y-%m-%d"))+'.csv')
return Response(generate_csv(','.join(csv_header), csv_lines), mimetype='text/csv', headers=headers)
else:
flash('There are no submission objects of type "{}" to include in the csv file!'.format(csv_type),'warning')
data = {
'submissions' : controllers.clinvar_submissions(store, current_user.email, institute_id),
'institute_id' : institute_id,
'variant_header_fields' : CLINVAR_HEADER ,
'casedata_header_fields' : CASEDATA_HEADER
}
return data
def clinvar_submissions(institute_id):
def generate_csv(header, lines):
yield header + "\n"
for line in lines: # lines have already quoted fields
yield line + "\n"
if request.method == "POST":
submission_id = request.form.get("submission_id")
if request.form.get("update_submission"):
if request.form.get(
"update_submission") == "close": # close a submission
store.update_clinvar_submission_status(institute_id,
submission_id, "closed")
elif request.form.get("update_submission") == "open":
store.update_clinvar_submission_status(
institute_id, submission_id, "open") # open a submission
elif request.form.get(
"update_submission") == "register_id" and request.form.get(
"clinvar_id"
): # provide an official clinvar submission ID
result = store.update_clinvar_id(
clinvar_id=request.form.get("clinvar_id"),
submission_id=submission_id,
)
elif (request.form.get("update_submission") == "delete"
): # delete a submission
deleted_objects, deleted_submissions = store.delete_submission(
submission_id=submission_id)
flash(
"Removed {} objects and {} submission from database".
format(deleted_objects, deleted_submissions),
"info",
)
elif request.form.get(
"delete_variant"): # delete a variant from a submission
store.delete_clinvar_object(
object_id=request.form.get("delete_variant"),
object_type="variant_data",
submission_id=submission_id,
) # remove variant and associated_casedata
elif request.form.get(
"delete_casedata"): # delete a case from a submission
store.delete_clinvar_object(
object_id=request.form.get("delete_casedata"),
object_type="case_data",
submission_id=submission_id,
) # remove just the casedata associated to a variant
else: # Download submission CSV files (for variants or casedata)
clinvar_subm_id = request.form.get("clinvar_id")
if clinvar_subm_id == "":
flash(
"In order to download a submission CSV file you should register a Clinvar submission Name first!",
"warning",
)
return redirect(request.referrer)
csv_type = request.form.get("csv_type", "")
submission_objs = store.clinvar_objs(
submission_id=submission_id, key_id=csv_type
) # a list of clinvar submission objects (variants or casedata)
if submission_objs:
csv_header_obj = controllers.clinvar_header(
submission_objs, csv_type
) # custom csv header (dict as in constants CLINVAR_HEADER and CASEDATA_HEADER, but with required fields only)
csv_lines = controllers.clinvar_lines(
submission_objs, csv_header_obj
) # csv lines (one for each variant/casedata to be submitted)
csv_header = list(csv_header_obj.values())
csv_header = ['"' + str(x) + '"' for x in csv_header
] # quote columns in header for csv rendering
download_day = str(
datetime.datetime.now().strftime("%Y-%m-%d"))
headers = Headers()
headers.add(
"Content-Disposition",
"attachment",
filename=f"{clinvar_subm_id}_{csv_type}_{download_day}.csv",
)
return Response(
generate_csv(",".join(csv_header), csv_lines),
mimetype="text/csv",
headers=headers,
)
else:
flash(
'There are no submission objects of type "{}" to include in the csv file!'
.format(csv_type),
"warning",
)
institute_obj = institute_and_case(store, institute_id)
data = {
"submissions": controllers.clinvar_submissions(store, institute_id),
"institute": institute_obj,
"variant_header_fields": CLINVAR_HEADER,
"casedata_header_fields": CASEDATA_HEADER,
}
return data
def clinvar_submissions(institute_id):
def generate_csv(header, lines):
yield header + '\n'
for line in lines: # lines have already quoted fields
yield line + '\n'
if request.method == 'POST':
submission_id = request.form.get('submission_id')
if request.form.get('update_submission'):
if request.form.get(
'update_submission') == 'close': # close a submission
store.update_clinvar_submission_status(current_user.email,
submission_id, 'closed')
elif request.form.get('update_submission') == 'open':
store.update_clinvar_submission_status(
current_user.email, submission_id,
'open') # open a submission
elif request.form.get(
'update_submission') == 'register_id' and request.form.get(
'clinvar_id'
): # provide an official clinvar submission ID
result = store.update_clinvar_id(
clinvar_id=request.form.get('clinvar_id'),
submission_id=submission_id)
elif request.form.get(
'update_submission') == 'delete': # delete a submission
deleted_objects, deleted_submissions = store.delete_submission(
submission_id=submission_id)
flash(
"Removed {} objects and {} submission from database".
format(deleted_objects, deleted_submissions), 'info')
elif request.form.get(
'delete_variant'): # delete a variant from a submission
store.delete_clinvar_object(
object_id=request.form.get('delete_variant'),
object_type='variant_data',
submission_id=submission_id
) # remove variant and associated_casedata
elif request.form.get(
'delete_casedata'): # delete a case from a submission
store.delete_clinvar_object(
object_id=request.form.get('delete_casedata'),
object_type='case_data',
submission_id=submission_id
) # remove just the casedata associated to a variant
else: # Download submission CSV files (for variants or casedata)
clinvar_subm_id = request.form.get('clinvar_id')
if clinvar_subm_id == '':
flash(
'In order to download a submission CSV file you should register a Clinvar submission Name first!',
'warning')
return redirect(request.referrer)
csv_type = ''
csv_type = request.form.get('csv_type')
submission_objs = store.clinvar_objs(
submission_id=submission_id, key_id=csv_type
) # a list of clinvar submission objects (variants or casedata)
if submission_objs:
csv_header_obj = controllers.clinvar_header(
submission_objs, csv_type
) # custom csv header (dict as in constants CLINVAR_HEADER and CASEDATA_HEADER, but with required fields only)
csv_lines = controllers.clinvar_lines(
submission_objs, csv_header_obj
) # csv lines (one for each variant/casedata to be submitted)
csv_header = list(csv_header_obj.values())
csv_header = ['"' + str(x) + '"' for x in csv_header
] # quote columns in header for csv rendering
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=clinvar_subm_id + '_' +
str(datetime.datetime.now().strftime("%Y-%m-%d")) +
'.csv')
return Response(generate_csv(','.join(csv_header), csv_lines),
mimetype='text/csv',
headers=headers)
else:
flash(
'There are no submission objects of type "{}" to include in the csv file!'
.format(csv_type), 'warning')
data = {
'submissions':
controllers.clinvar_submissions(store, current_user.email,
institute_id),
'institute_id':
institute_id,
'variant_header_fields':
CLINVAR_HEADER,
'casedata_header_fields':
CASEDATA_HEADER
}
return data