def matchmaker_delete(institute_id, case_name):
"""Remove a case from MatchMaker"""
# check that only authorized users can delete patients from MME
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# Required params for sending a delete request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_token:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
delete_result = controllers.mme_delete(case_obj, mme_base_url, mme_token)
n_deleted = 0
category = 'warning'
for resp in delete_result:
if resp['status_code'] == 200:
n_deleted += 1
else:
flash(resp['message'], category)
if n_deleted:
category = 'success'
# update case by removing mme submission
# and create events for patients deletion from MME
user_obj = store.user(current_user.email)
store.case_mme_delete(case_obj=case_obj, user_obj=user_obj)
flash('Number of patients deleted from Matchmaker: {} out of {}'.format(n_deleted, len(delete_result)), category)
return redirect(request.referrer)
def assign(institute_id, case_name, user_id=None):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get('action') == 'DELETE':
store.unassign(institute_obj, case_obj, user_obj, link)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def assign(institute_id, case_name, user_id=None):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get('action') == 'DELETE':
store.unassign(institute_obj, case_obj, user_obj, link)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def assign(institute_id, case_name, user_id=None, inactivate=False):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get("action") == "DELETE":
store.unassign(institute_obj, case_obj, user_obj, link, inactivate)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def institutes():
"""Display a list of all user institutes."""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get("sanger_recipients", []):
user_obj = store.user(user_mail)
if not user_obj:
continue
sanger_recipients.append(user_obj["name"])
institutes.append({
"display_name":
ins_obj["display_name"],
"internal_id":
ins_obj["_id"],
"coverage_cutoff":
ins_obj.get("coverage_cutoff", "None"),
"sanger_recipients":
sanger_recipients,
"frequency_cutoff":
ins_obj.get("frequency_cutoff", "None"),
"phenotype_groups":
ins_obj.get("phenotype_groups", PHENOTYPE_GROUPS),
"case_count":
sum(1 for i in store.cases(collaborator=ins_obj["_id"])),
})
data = dict(institutes=institutes)
return render_template("overview/institutes.html", **data)
def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = (
[inst["_id"] for inst in store.institutes()]
if current_user.is_admin
else user_obj.get("institutes")
)
temp_excel_dir = os.path.join(variants_bp.static_folder, "verified_folder")
os.makedirs(temp_excel_dir, exist_ok=True)
if controllers.verified_excel_file(store, user_institutes, temp_excel_dir):
data = zip_dir_to_obj(temp_excel_dir)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
today = datetime.datetime.now().strftime("%Y-%m-%d")
return send_file(
data,
mimetype="application/zip",
as_attachment=True,
download_name="_".join(["scout", "verified_variants", today]) + ".zip",
cache_timeout=0,
)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
flash("No verified variants could be exported for user's institutes", "warning")
return redirect(request.referrer)
def institutes():
"""Display a list of all user institutes."""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get('sanger_recipients',[]):
user_obj = store.user(user_mail)
if not user_obj:
continue
sanger_recipients.append(user_obj['name'])
institutes.append(
{
'display_name': ins_obj['display_name'],
'internal_id': ins_obj['_id'],
'coverage_cutoff': ins_obj.get('coverage_cutoff', 'None'),
'sanger_recipients': sanger_recipients,
'frequency_cutoff': ins_obj.get('frequency_cutoff', 'None'),
'phenotype_groups': ins_obj.get('phenotype_groups', PHENOTYPE_GROUPS)
}
)
data = dict(institutes=institutes)
return render_template(
'overview/institutes.html', **data)
def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
comment = request.form.get('verification_comment')
try:
controllers.variant_verification(
store=store,
mail=mail,
institute_obj=institute_obj,
case_obj=case_obj,
user_obj=user_obj,
comment=comment,
variant_obj=variant_obj,
sender=current_app.config['MAIL_USERNAME'],
variant_url=request.referrer,
order=order,
url_builder=url_for)
except controllers.MissingVerificationRecipientError:
flash('No verification recipients added to institute.', 'danger')
return redirect(request.referrer)
def test_update_tracks_settings(app, user_obj, mocker, mock_redirect):
"""Test the endpoint that updates the IGV track preferences for a user"""
mocker.patch("scout.server.blueprints.variant.views.redirect", return_value=mock_redirect)
preferred_tracks = ["Genes", "ClinVar"]
# GIVEN an initialized app
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
# GIVEN that the user wants to see only Genes and ClinVar SNVs tracks
form_data = {
"user_tracks": preferred_tracks,
}
# WHEN sending a POST request to the update
resp = client.post(
url_for(
"variant.update_tracks_settings",
),
data=form_data,
)
# THEN the user object in the database should be updated with the right track info
user_obj = store.user(email=user_obj["email"])
for track in preferred_tracks:
assert track in preferred_tracks
def institutes():
"""Display a list of all user institutes."""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get('sanger_recipients', []):
user_obj = store.user(user_mail)
if not user_obj:
continue
sanger_recipients.append(user_obj['name'])
institutes.append({
'display_name':
ins_obj['display_name'],
'internal_id':
ins_obj['_id'],
'coverage_cutoff':
ins_obj.get('coverage_cutoff', 'None'),
'sanger_recipients':
sanger_recipients,
'frequency_cutoff':
ins_obj.get('frequency_cutoff', 'None'),
'phenotype_groups':
ins_obj.get('phenotype_groups', PHENOTYPE_GROUPS)
})
data = dict(institutes=institutes)
return render_template('overview/institutes.html', **data)
def matchmaker_matches(institute_id, case_name):
"""Show all MatchMaker matches for a given case"""
# check that only authorized users can access MME patients matches
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
# Required params for getting matches from MME server:
mme_base_url = current_app.config.get('MME_URL')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_token:
flash(
'An error occurred reading matchmaker connection parameters. Please check config file!',
'danger')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
data = controllers.mme_matches(case_obj, institute_obj, mme_base_url,
mme_token)
if data and data.get('server_errors'):
flash(
'MatchMaker server returned error:{}'.format(
data['server_errors']), 'danger')
return redirect(request.referrer)
elif not data:
data = {'institute': institute_obj, 'case': case_obj}
return data
def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
phenotype_id, is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
phenotype_term = request.form['hpo_term']
if phenotype_term.startswith('HP:') or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(' | ', 1)[0]
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_term=hpo_term, is_group=is_group)
else:
# assume omim id
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype: {}".format(phenotype_term)))
return redirect(case_url)
def case_synopsis(institute_id, case_name):
"""Update (PUT) synopsis of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
new_synopsis = request.form.get('synopsis')
controllers.update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis)
return redirect(request.referrer)
def institutes():
"""Returns institutes info available for a user
Returns:
data(list): a list of institute dictionaries
"""
institute_objs = user_institutes(store, current_user)
institutes = []
for ins_obj in institute_objs:
sanger_recipients = []
for user_mail in ins_obj.get("sanger_recipients", []):
user_obj = store.user(user_mail)
if not user_obj:
continue
sanger_recipients.append(user_obj["name"])
institutes.append({
"display_name":
ins_obj["display_name"],
"internal_id":
ins_obj["_id"],
"coverage_cutoff":
ins_obj.get("coverage_cutoff", "None"),
"sanger_recipients":
sanger_recipients,
"frequency_cutoff":
ins_obj.get("frequency_cutoff", "None"),
"phenotype_groups":
ins_obj.get("phenotype_groups", PHENOTYPE_GROUPS),
"case_count":
sum(1 for i in store.cases(collaborator=ins_obj["_id"])),
})
return institutes
def events(institute_id, case_name, event_id=None):
"""Handle events."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
link = request.form.get("link")
content = request.form.get("content")
variant_id = request.args.get("variant_id")
user_obj = store.user(current_user.email)
if event_id:
# delete the event
store.delete_event(event_id)
else:
if variant_id:
# create a variant comment
variant_obj = store.variant(variant_id)
level = request.form.get("level", "specific")
store.comment(
institute_obj,
case_obj,
user_obj,
link,
variant=variant_obj,
content=content,
comment_level=level,
)
else:
# create a case comment
store.comment(institute_obj,
case_obj,
user_obj,
link,
content=content)
return redirect(request.referrer)
def reset_research(institute_id, case_name):
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
store.reset_research(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def matchmaker_delete(request, institute_id, case_name):
"""Delete all affected samples for a case from MatchMaker
Args:
request(werkzeug.local.LocalProxy)
institute_id(str): _id of an institute
case_name(str): display name of a case
"""
# Check that general MME request requirements are fulfilled
matchmaker_check_requirements(request)
_, case_obj = institute_and_case(store, institute_id, case_name)
# Delete each patient submitted for this case
for patient in case_obj.get("mme_submission", {}).get("patients", []):
# Send delete request to server and capture server's response
patient_id = patient["id"]
resp = matchmaker.patient_delete(patient_id)
category = "warning"
if resp["status_code"] == 200:
category = "success"
# update case by removing mme submission
# and create events for patients deletion from MME
user_obj = store.user(current_user.email)
store.case_mme_delete(case_obj=case_obj, user_obj=user_obj)
flash(
f"Deleted patient '{patient_id}', case '{case_name}' from MatchMaker",
"success",
)
continue
flash(f"An error occurred while deleting patient from MatchMaker", "danger")
def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = user_obj.get('institutes')
temp_excel_dir = os.path.join(variants_bp.static_folder, 'verified_folder')
os.makedirs(temp_excel_dir, exist_ok=True)
written_files = controllers.verified_excel_file(store, user_institutes,
temp_excel_dir)
if written_files:
today = datetime.datetime.now().strftime('%Y-%m-%d')
# zip the files on the fly and serve the archive to the user
data = io.BytesIO()
with zipfile.ZipFile(data, mode='w') as z:
for f_name in pathlib.Path(temp_excel_dir).iterdir():
zipfile.ZipFile
z.write(f_name, os.path.basename(f_name))
data.seek(0)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
return send_file(data,
mimetype='application/zip',
as_attachment=True,
attachment_filename='_'.join(
['scout', 'verified_variants', today]) + '.zip')
else:
flash("No verified variants could be exported for user's institutes",
'warning')
return redirect(request.referrer)
def matchmaker_match(institute_id, case_name, target):
"""Starts an internal match or a match against one or all MME external nodes"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# check that only authorized users can run matches
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
# Required params for sending an add request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_accepts = current_app.config.get('MME_ACCEPTS')
mme_token = current_app.config.get('MME_TOKEN')
nodes = current_app.mme_nodes
if not mme_base_url or not mme_token or not mme_accepts:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
match_results = controllers.mme_match(case_obj, target, mme_base_url, mme_token, nodes, mme_accepts)
ok_responses = 0
for match_results in match_results:
match_results['status_code'] == 200
ok_responses +=1
if ok_responses:
flash("Match request sent. Look for eventual matches in 'Matches' page.", 'info')
else:
flash('An error occurred while sending match request.', 'danger')
return redirect(request.referrer)
def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = user_obj.get('institutes')
temp_excel_dir = os.path.join(variants_bp.static_folder, 'verified_folder')
os.makedirs(temp_excel_dir, exist_ok=True)
written_files = controllers.verified_excel_file(store, user_institutes, temp_excel_dir)
if written_files:
today = datetime.datetime.now().strftime('%Y-%m-%d')
# zip the files on the fly and serve the archive to the user
data = io.BytesIO()
with zipfile.ZipFile(data, mode='w') as z:
for f_name in pathlib.Path(temp_excel_dir).iterdir():
zipfile.ZipFile
z.write(f_name, os.path.basename(f_name))
data.seek(0)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
return send_file(
data,
mimetype='application/zip',
as_attachment=True,
attachment_filename='_'.join(['scout', 'verified_variants', today])+'.zip'
)
else:
flash("No verified variants could be exported for user's institutes", 'warning')
return redirect(request.referrer)
def case_synopsis(institute_id, case_name):
"""Update (PUT) synopsis of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
new_synopsis = request.form.get('synopsis')
controllers.update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis)
return redirect(request.referrer)
def mark_causative(institute_id,
case_name,
variant_id,
partial_causative=False):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for("variant.variant",
institute_id=institute_id,
case_name=case_name,
variant_id=variant_id)
if request.form["action"] == "ADD":
if "partial_causative" in request.form:
omim_terms = request.form.getlist("omim_select")
hpo_terms = request.form.getlist("hpo_select")
store.mark_partial_causative(institute_obj, case_obj, user_obj,
link, variant_obj, omim_terms,
hpo_terms)
else:
store.mark_causative(institute_obj, case_obj, user_obj, link,
variant_obj)
elif request.form["action"] == "DELETE":
if partial_causative == "True":
store.unmark_partial_causative(institute_obj, case_obj, user_obj,
link, variant_obj)
else:
store.unmark_causative(institute_obj, case_obj, user_obj, link,
variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
return redirect(request.referrer)
def matchmaker_matches(institute_id, case_name):
"""Show all MatchMaker matches for a given case"""
# check that only authorized users can access MME patients matches
panel = 1
if request.method == "POST":
panel = panel = request.form.get("pane_id")
user_obj = store.user(current_user.email)
if "mme_submitter" not in user_obj["roles"]:
flash("unauthorized request", "warning")
return redirect(request.referrer)
# Required params for getting matches from MME server:
mme_base_url = current_app.config.get("MME_URL")
mme_token = current_app.config.get("MME_TOKEN")
if not mme_base_url or not mme_token:
flash(
"An error occurred reading matchmaker connection parameters. Please check config file!",
"danger",
)
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
data = controllers.mme_matches(case_obj, institute_obj, mme_base_url,
mme_token)
data["panel"] = panel
if data and data.get("server_errors"):
flash(
"MatchMaker server returned error:{}".format(
data["server_errors"]),
"danger",
)
return redirect(request.referrer)
elif not data:
data = {"institute": institute_obj, "case": case_obj, "panel": panel}
return data
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
level = "phenotype" if "phenotype" in request.form else "gene"
omim_id = request.form["omim_term"].split("|")[0]
if not "OMIM:" in omim_id: # Could be an omim number provided by user
omim_id = ":".join(["OMIM", omim_id])
# Make sure omim term exists in database:
omim_obj = store.disease_term(omim_id.strip())
if not omim_obj:
flash("Couldn't find any disease term with id: {}".format(omim_id),
"warning")
remove = True if request.args.get("remove") == "yes" else False
store.diagnose(
institute_obj,
case_obj,
user_obj,
link,
level=level,
omim_id=omim_id,
remove=remove,
)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
omim_id = request.form["omim_term"].split("|")[0]
omim_inds = request.form.getlist(
"omim_inds") # Individual-level phenotypes
if not "OMIM:" in omim_id: # Could be an omim number provided by user
omim_id = ":".join(["OMIM", omim_id])
# Make sure omim term exists in database:
omim_obj = store.disease_term(omim_id.strip())
if omim_obj is None:
flash("Couldn't find any disease term with id: {}".format(omim_id),
"warning")
return redirect(request.referrer)
remove = True if request.args.get("remove") == "yes" else False
store.diagnose(institute_obj, case_obj, user_obj, link, omim_obj,
omim_inds, remove)
return redirect("#".join([link, "omim_assign"]))
def research(institute_id, case_name):
"""Open the research list for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
store.open_research(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def matchmaker_check_requirements(request):
"""Make sure requirements are fulfilled before submitting any request to MatchMaker Exchange
Args:
request(werkzeug.local.LocalProxy)
Returns:
None, if requirements are fulfilled, otherwise redirects to previous page with error message
"""
# Make sure all MME connection parameters are available in scout instance
if (
any(
[
hasattr(matchmaker, "host"),
hasattr(matchmaker, "accept"),
hasattr(matchmaker, "token"),
]
)
is None
):
flash(
"An error occurred reading matchmaker connection parameters. Please check config file!",
"danger",
)
return redirect(request.referrer)
# Check that request comes from an authorized user (mme_submitter role)
user_obj = store.user(current_user.email)
if "mme_submitter" not in user_obj.get("roles", []):
flash("unauthorized request", "warning")
return redirect(request.referrer)
def call_rerunner(store, institute_id, case_name, metadata):
"""Call rerunner with updated pedigree metadata."""
# define the data to be passed
payload = {"case_id": case_name, "sample_ids": [m["sample_id"] for m in metadata]}
cnf = rerunner.connection_settings
url = cnf.get("entrypoint")
if not url:
raise ValueError("Rerunner API entrypoint not configured")
auth = HTTPBasicAuth(current_user.email, cnf.get("api_key"))
LOG.info(f"Sending request -- {url}; params={payload}")
resp = requests.post(
url,
params=payload,
json=metadata,
timeout=rerunner.timeout,
headers={"Content-Type": "application/json"},
auth=auth,
)
if resp.status_code == 200:
LOG.info(f"Reanalysis was successfully started; case: {case_name}")
# get institute, case and user objects for adding a notification of the rerun to the database
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
store.request_rerun(institute_obj, case_obj, user_obj, link)
# notfiy the user of the rerun
flash(f"Reanalysis was successfully started; case: {case_name}", "info")
else:
raise RerunnerError(f"{resp.reason}, {resp.status_code}")
def authorized():
oauth_response = None
try:
oauth_response = google.authorized_response()
except OAuthException as error:
current_app.logger.warn(oauth_response.message)
flash("{} - try again!".format(oauth_response.message), 'warning')
return redirect(url_for('public.index'))
if oauth_response is None:
flash("Access denied: reason={} error={}"
.format(request.args.get['error_reason'],
request.args['error_description']), 'danger')
return abort(403)
# add token to session, do it before validation to be able to fetch
# additional data (like email) on the authenticated user
session['google_token'] = (oauth_response['access_token'], '')
# get additional user info with the access token
google_user = google.get('userinfo')
google_data = google_user.data
user_obj = store.user(google_data['email'])
if user_obj is None:
flash('your email is not whitelisted, contact admin.', 'warning')
return redirect(url_for('public.index'))
user_obj['name'] = google_data['name']
user_obj['location'] = google_data['locale']
user_obj['accessed_at'] = datetime.now()
store.update_user(user_obj)
return perform_login(user_obj)
def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
phenotype_id, is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
phenotype_term = request.form['hpo_term']
if phenotype_term.startswith('HP:') or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(' | ', 1)[0]
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_term=hpo_term, is_group=is_group)
else:
# assume omim id
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype: {}".format(phenotype_term)))
return redirect(case_url)
def update_default_panels(store, current_user, institute_id, case_name, panel_ids):
"""Update default panels for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
panel_objs = [store.panel(panel_id) for panel_id in panel_ids]
store.update_default_panels(institute_obj, case_obj, user_obj, link, panel_objs)
def add_case_group(store, current_user, institute_id, case_name, group=None):
"""Bind a case group in a selected a case, creating it in current institute if not given.
Args:
current_user (user)current user
institute_id (str)institute id
case_name (str)case display name
group (str)case group id - converts to ObjectId
Returns:
updated_case (InsertOneResult)
"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for("cases.case", institute_id=institute_id, case_name=case_name)
user_obj = store.user(current_user.email)
if not group:
group = store.init_case_group(institute_id)
current_group_ids = set(case_obj.get("group", []))
current_group_ids.add(ObjectId(group))
updated_case = store.update_case_group_ids(
institute_obj, case_obj, user_obj, link, list(current_group_ids)
)
return updated_case
def research(institute_id, case_name):
"""Open the research list for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
store.open_research(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link,
variant_obj, new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj['manual_rank']),
'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification,
int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj,
new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
return redirect(request.referrer)
def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
action = request.form["action"]
hpo_ids = request.form.getlist("hpo_id")
user_obj = store.user(current_user.email)
if action == "PHENOMIZER":
if len(hpo_ids) == 0:
hpo_ids = [
term["phenotype_id"]
for term in case_obj.get("phenotype_terms", [])
]
username = current_app.config["PHENOMIZER_USERNAME"]
password = current_app.config["PHENOMIZER_PASSWORD"]
diseases = controllers.hpo_diseases(username, password, hpo_ids)
if diseases:
return render_template(
"cases/diseases.html",
diseases=diseases,
institute=institute_obj,
case=case_obj,
)
if action == "DELETE":
for hpo_id in hpo_ids:
# DELETE a phenotype from the list
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_id)
if action == "ADDGENE":
hgnc_ids = parse_raw_gene_ids(request.form.getlist("genes"))
store.update_dynamic_gene_list(case_obj,
hgnc_ids=list(hgnc_ids),
add_only=True)
if action == "GENES":
hgnc_symbols = parse_raw_gene_symbols(request.form.getlist("genes"))
store.update_dynamic_gene_list(case_obj,
hgnc_symbols=list(hgnc_symbols))
if action == "GENERATE":
if len(hpo_ids) == 0:
hpo_ids = [
term["phenotype_id"]
for term in case_obj.get("phenotype_terms", [])
]
results = store.generate_hpo_gene_list(*hpo_ids)
# determine how many HPO terms each gene must match
hpo_count = int(request.form.get("min_match") or 1)
hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
store.update_dynamic_gene_list(case_obj,
hgnc_ids=hgnc_ids,
phenotype_ids=hpo_ids)
return redirect("#".join([case_url, "phenotypes_panel"]))
def update_tracks_settings():
"""Update custom track settings for a user according to form choices"""
user_obj = store.user(email=current_user.email)
selected_tracks = request.form.getlist("user_tracks") or []
# update user in database with custom tracks info
user_obj["igv_tracks"] = selected_tracks
store.update_user(user_obj)
return redirect(request.referrer)
def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def matchmaker_delete(institute_id, case_name):
"""Remove a case from MatchMaker"""
# check that only authorized users can delete patients from MME
user_obj = store.user(current_user.email)
if "mme_submitter" not in user_obj["roles"]:
flash("unauthorized request", "warning")
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
# Required params for sending a delete request to MME:
mme_base_url = current_app.config.get("MME_URL")
mme_token = current_app.config.get("MME_TOKEN")
if not mme_base_url or not mme_token:
flash(
"An error occurred reading matchmaker connection parameters. Please check config file!",
"danger",
)
return redirect(request.referrer)
delete_result = controllers.mme_delete(case_obj, mme_base_url, mme_token)
n_deleted = 0
category = "warning"
for resp in delete_result:
if resp["status_code"] == 200:
n_deleted += 1
else:
flash(resp["message"], category)
if n_deleted:
category = "success"
# update case by removing mme submission
# and create events for patients deletion from MME
user_obj = store.user(current_user.email)
store.case_mme_delete(case_obj=case_obj, user_obj=user_obj)
flash(
"Number of patients deleted from Matchmaker: {} out of {}".format(
n_deleted, len(delete_result)),
category,
)
return redirect(request.referrer)
def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' if 'phenotype' in request.form else 'gene'
omim_id = request.form['omim_id']
remove = True if request.args.get('remove') == 'yes' else False
store.diagnose(institute_obj, case_obj, user_obj, link, level=level,
omim_id=omim_id, remove=remove)
return redirect(request.referrer)
def cohorts(institute_id, case_name):
"""Add/remove institute tags."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
cohort_tag = request.form['cohort_tag']
if request.args.get('remove') == 'yes':
store.remove_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
else:
store.add_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
return redirect(request.referrer)
def pin_variant(institute_id, case_name, variant_id):
"""Pin and unpin variants to/from the list of suspects."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.pin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unpin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
return redirect(request.referrer or link)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj,
new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
new_dismiss = request.form.getlist('dismiss_variant')
if request.form.getlist('dismiss_variant'):
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
if new_dismiss:
flash("Dismissed variant: {}".format(new_dismiss), 'info')
if variant_obj.get('dismiss_variant') and not new_dismiss:
if 'dismiss' in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
else:
log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
mosaic_tags = request.form.getlist('mosaic_tags')
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
if new_dismiss:
flash("Added mosaic tags: {}".format(mosaic_tags), 'info')
if variant_obj.get('mosaic_tags') and not mosaic_tags:
if 'mosaic' in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info')
return redirect(request.referrer)
def authorized():
oauth_response = None
try:
oauth_response = google.authorized_response()
except OAuthException as error:
current_app.logger.warn(oauth_response.message)
flash("{} - try again!".format(oauth_response.message), 'warning')
return redirect(url_for('public.index'))
if oauth_response is None:
flash("Access denied: reason={} error={}"
.format(request.args.get['error_reason'],
request.args['error_description']), 'danger')
return abort(403)
# add token to session, do it before validation to be able to fetch
# additional data (like email) on the authenticated user
session['google_token'] = (oauth_response['access_token'], '')
# get additional user info with the access token
google_user = google.get('userinfo')
google_data = google_user.data
user_obj = store.user(google_data['email'])
# Try again with lower-cased email address if no match
if user_obj is None:
user_obj = store.user(google_data['email'].lower())
if user_obj is None:
flash("email not whitelisted: {}".format(google_data['email']), 'warning')
return redirect(url_for('public.index'))
user_obj['name'] = google_data['name']
user_obj['location'] = google_data['locale']
user_obj['accessed_at'] = datetime.now()
store.update_user(user_obj)
return perform_login(user_obj)
def status(institute_id, case_name):
"""Update status of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
status = request.form.get('status', case_obj['status'])
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if status == 'archive':
store.archive_case(institute_obj, case_obj, user_obj, status, link)
else:
store.update_status(institute_obj, case_obj, user_obj, status, link)
return redirect(request.referrer)
def share(institute_id, case_name):
"""Share a case with a different institute."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
collaborator_id = request.form['collaborator']
revoke_access = 'revoke' in request.form
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if revoke_access:
store.unshare(institute_obj, case_obj, collaborator_id, user_obj, link)
else:
store.share(institute_obj, case_obj, collaborator_id, user_obj, link)
return redirect(request.referrer)
def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
comment = request.form.get('verification_comment')
try:
controllers.variant_verification(store=store, mail=mail, institute_obj=institute_obj, case_obj=case_obj, user_obj=user_obj, comment=comment,
variant_obj=variant_obj, sender=current_app.config['MAIL_USERNAME'], variant_url=request.referrer, order=order, url_builder=url_for)
except controllers.MissingVerificationRecipientError:
flash('No verification recipients added to institute.', 'danger')
return redirect(request.referrer)
def mark_causative(institute_id, case_name, variant_id):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.mark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unmark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
return redirect(case_url)
def login():
"""Login a user if they have access."""
# store potential next param URL in the session
if 'next' in request.args:
session['next_url'] = request.args['next']
if current_app.config.get('GOOGLE'):
callback_url = url_for('.authorized', _external=True)
return google.authorize(callback=callback_url)
user_email = request.args.get('email')
user_obj = store.user(user_email)
if user_obj is None:
flash("email not whitelisted: {}".format(user_email), 'warning')
return redirect(url_for('public.index'))
return perform_login(user_obj)
def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
action = request.form['action']
hpo_ids = request.form.getlist('hpo_id')
user_obj = store.user(current_user.email)
if action == 'DELETE':
for hpo_id in hpo_ids:
# DELETE a phenotype from the list
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url, hpo_id)
elif action == 'PHENOMIZER':
if len(hpo_ids) == 0:
hpo_ids = [term['phenotype_id'] for term in case_obj.get('phenotype_terms', [])]
username = current_app.config['PHENOMIZER_USERNAME']
password = current_app.config['PHENOMIZER_PASSWORD']
diseases = controllers.hpo_diseases(username, password, hpo_ids)
return render_template('cases/diseases.html', diseases=diseases,
institute=institute_obj, case=case_obj)
elif action == 'GENES':
hgnc_symbols = set()
for raw_symbols in request.form.getlist('genes'):
# avoid empty lists
if raw_symbols:
hgnc_symbols.update(raw_symbol.split(' ', 1)[0] for raw_symbol in
raw_symbols.split('|'))
store.update_dynamic_gene_list(case_obj, hgnc_symbols=hgnc_symbols)
elif action == 'GENERATE':
if len(hpo_ids) == 0:
hpo_ids = [term['phenotype_id'] for term in case_obj.get('phenotype_terms', [])]
results = store.generate_hpo_gene_list(*hpo_ids)
# determine how many HPO terms each gene must match
hpo_count = int(request.form.get('min_match') or 1)
hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
store.update_dynamic_gene_list(case_obj, hgnc_ids=hgnc_ids, phenotype_ids=hpo_ids)
return redirect(case_url)
def events(institute_id, case_name, event_id=None):
"""Handle events."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = request.form.get('link')
content = request.form.get('content')
variant_id = request.args.get('variant_id')
user_obj = store.user(current_user.email)
if event_id:
# delete the event
store.delete_event(event_id)
else:
if variant_id:
# create a variant comment
variant_obj = store.variant(variant_id)
level = request.form.get('level', 'specific')
store.comment(institute_obj, case_obj, user_obj, link,
variant=variant_obj, content=content, comment_level=level)
else:
# create a case comment
store.comment(institute_obj, case_obj, user_obj, link, content=content)
return redirect(request.referrer)
def matchmaker_matches(institute_id, case_name):
"""Show all MatchMaker matches for a given case"""
# check that only authorized users can access MME patients matches
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
# Required params for getting matches from MME server:
mme_base_url = current_app.config.get('MME_URL')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_token:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = controllers.mme_matches(case_obj, institute_obj, mme_base_url, mme_token)
if data and data.get('server_errors'):
flash('MatchMaker server returned error:{}'.format(data['server_errors']), 'danger')
return redirect(request.referrer)
elif not data:
data = {
'institute' : institute_obj,
'case' : case_obj
}
return data
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_type = request.args.get('variant_type', 'clinical')
# Update filter settings if Clinical Filter was requested
default_panels = []
for panel in case_obj['panels']:
if panel.get('is_default'):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'clinsig': [4,5],
'clinsig_confident_always_returned': True,
'gnomad_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = FiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = FiltersForm(request.form)
else:
form = FiltersForm(request.args)
# populate available panel choices
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# upload gene panel if symbol file exists
if (request.files):
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != '':
log.debug("Upload file request files: {0}".format(request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode('utf-8'), newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", 'warning')
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ''
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get('variant_type', 'clinical') == 'clinical'
clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
not_found_symbols.append(hgnc_symbol)
elif is_clinical and (hgnc_symbol not in clinical_symbols):
non_clinical_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if (not_found_ids):
flash("HGNC id not found: {}".format(", ".join(not_found_ids)), 'warning')
if (not_found_symbols):
flash("HGNC symbol not found: {}".format(", ".join(not_found_symbols)), 'warning')
if (non_clinical_symbols):
flash("Gene not included in clinical list: {}".format(", ".join(non_clinical_symbols)), 'warning')
form.hgnc_symbols.data = hgnc_symbols
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_variants.csv')
# return a csv with the exported variants
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv',
headers=headers)
data = controllers.variants(store, institute_obj, case_obj, variants_query, page)
return dict(institute=institute_obj, case=case_obj, form=form,
severe_so_terms=SEVERE_SO_TERMS, page=page, **data)
def sv_variants(institute_id, case_name):
"""Display a list of structural variants."""
page = int(request.form.get('page', 1))
variant_type = request.args.get('variant_type', 'clinical')
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = SvFiltersForm(request.form)
default_panels = []
for panel in case_obj['panels']:
if panel['is_default']:
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'thousand_genomes_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'clingen_ngi': 10,
'swegen': 10,
'size': 100,
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = SvFiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = SvFiltersForm(request.form)
else:
form = SvFiltersForm(request.args)
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
variants_query = store.variants(case_obj['_id'], category='sv',
query=form.data)
data = {}
# if variants should be exported
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_sv-variants.csv')
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv', headers=headers) # return a csv with the exported variants
else:
data = controllers.sv_variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj, case=case_obj, variant_type=variant_type,
form=form, severe_so_terms=SEVERE_SO_TERMS, page=page, **data)
def matchmaker_add(institute_id, case_name):
"""Add or update a case in MatchMaker"""
# check that only authorized users can add patients to MME
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
causatives = False
features = False
if case_obj.get('suspects') and len(case_obj.get('suspects'))>3:
flash('At the moment it is not possible to save to MatchMaker more than 3 pinned variants', 'warning')
return redirect(request.referrer)
elif case_obj.get('suspects'):
causatives = True
if case_obj.get('phenotype_terms'):
features = True
mme_save_options = ['sex', 'features', 'disorders']
for index, item in enumerate(mme_save_options):
if item in request.form:
log.info('item {} is in request form'.format(item))
mme_save_options[index] = True
else:
mme_save_options[index] = False
genomic_features = request.form.get('genomicfeatures')
genes_only = True # upload to matchmaker only gene names
if genomic_features == 'variants':
genes_only = False # upload to matchmaker both variants and gene names
# If there are no genomic features nor HPO terms to share for this case, abort
if (not case_obj.get('suspects') and not mme_save_options[1]) or (causatives is False and features is False):
flash('In order to upload a case to MatchMaker you need to pin a variant or at least assign a phenotype (HPO term)', 'danger')
return redirect(request.referrer)
user_obj = store.user(current_user.email)
# Required params for sending an add request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_accepts = current_app.config.get('MME_ACCEPTS')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_accepts or not mme_token:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
add_result = controllers.mme_add(store=store, user_obj=user_obj, case_obj=case_obj,
add_gender=mme_save_options[0], add_features=mme_save_options[1],
add_disorders=mme_save_options[2], genes_only=genes_only,
mme_base_url = mme_base_url, mme_accepts=mme_accepts, mme_token=mme_token)
# flash MME responses (one for each patient posted)
n_succes_response = 0
n_inserted = 0
n_updated = 0
category = 'warning'
for resp in add_result['server_responses']:
message = resp.get('message')
if resp.get('status_code') == 200:
n_succes_response += 1
else:
flash('an error occurred while adding patient to matchmaker: {}'.format(message), 'warning')
if message == 'Patient was successfully updated.':
n_updated +=1
elif message == 'Patient was successfully inserted into database.':
n_inserted +=1
# if at least one patient was inserted or updated into matchmaker, save submission at the case level:
if n_inserted or n_updated:
category = 'success'
store.case_mme_update(case_obj=case_obj, user_obj=user_obj, mme_subm_obj=add_result)
flash('Number of new patients in matchmaker:{0}, number of updated records:{1}, number of failed requests:{2}'.format(
n_inserted, n_updated, len(add_result.get('server_responses')) - n_succes_response), category)
return redirect(request.referrer)
def load_user(user_email):
"""Returns the currently active user as an object."""
user_obj = store.user(user_email)
user_inst = LoginUser(user_obj) if user_obj else None
return user_inst
