def populate_institute_form(form, institute_obj):
"""Populate institute settings form
Args:
form(scout.server.blueprints.institutes.models.InstituteForm)
institute_obj(dict) An institute object
"""
# get all other institutes to populate the select of the possible collaborators
institutes_tuples = []
for inst in store.institutes():
if not inst["_id"] == institute_obj["_id"]:
institutes_tuples.append(((inst["_id"], inst["display_name"])))
form.display_name.default = institute_obj.get("display_name")
form.institutes.choices = institutes_tuples
form.coverage_cutoff.default = institute_obj.get("coverage_cutoff")
form.frequency_cutoff.default = institute_obj.get("frequency_cutoff")
# collect all available default HPO terms and populate the pheno_groups form select with these values
default_phenotypes = [
choice[0].split(" ")[0] for choice in form.pheno_groups.choices
]
if institute_obj.get("phenotype_groups"):
for key, value in institute_obj["phenotype_groups"].items():
if not key in default_phenotypes:
custom_group = " ".join([
key, ",",
value.get("name"), "( {} )".format(value.get("abbr"))
])
form.pheno_groups.choices.append((custom_group, custom_group))
# populate gene panels multiselect with panels from institute
available_panels = list(store.latest_panels(institute_obj["_id"]))
# And from institute's collaborators
for collaborator in institute_obj.get("collaborators", []):
available_panels += list(store.latest_panels(collaborator))
panel_set = set()
for panel in available_panels:
panel_set.add((panel["panel_name"], panel["display_name"]))
form.gene_panels.choices = sorted(panel_set, key=lambda tup: tup[1])
return default_phenotypes
def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# update an existing panel
csv_file = request.files['csv_file']
content = csv_file.stream.read()
if b'\n' in content:
lines = content.decode().split('\n')
else:
lines = content.decode('windows-1252').split('\r')
new_panel_name = request.form.get('new_panel_name')
if new_panel_name:
panel_obj = controllers.new_panel(
store=store,
institute_id=request.form['institute'],
panel_name=new_panel_name,
display_name=request.form['display_name'],
csv_lines=lines,
)
if panel_obj is None:
return redirect(request.referrer)
flash("new gene panel added: {}!".format(panel_obj['panel_name']))
else:
panel_obj = controllers.update_panel(store,
request.form['panel_name'],
lines)
if panel_obj is None:
return abort(
404, "gene panel not found: {}".format(
request.form['panel_name']))
return redirect(url_for('panels.panel', panel_id=panel_obj['_id']))
institutes = list(user_institutes(store, current_user))
panel_names = [
name for institute in institutes for name in store.gene_panels(
institute_id=institute['_id']).distinct('panel_name')
]
panel_versions = {}
for name in panel_names:
panel_versions[name] = store.gene_panels(panel_id=name)
panel_groups = []
for institute_obj in institutes:
institute_panels = store.latest_panels(institute_obj['_id'])
panel_groups.append((institute_obj, institute_panels))
return dict(panel_groups=panel_groups,
panel_names=panel_names,
panel_versions=panel_versions,
institutes=institutes)
def panels():
"""Show all panels for a user"""
if request.method == "POST": # Edit/create a new panel and redirect to its page
redirect_panel_id = controllers.panel_create_or_update(store, request)
if redirect_panel_id:
return redirect(url_for("panels.panel",
panel_id=redirect_panel_id))
return redirect(url_for("panels.panels"))
institutes = list(user_institutes(store, current_user))
panel_names = [
name for institute in institutes for name
in store.gene_panels(institute_id=institute["_id"],
include_hidden=True).distinct("panel_name")
]
panel_versions = {}
for name in panel_names:
panels = store.gene_panels(panel_id=name, include_hidden=True)
panel_versions[name] = [
panel_obj for panel_obj in panels
if controllers.shall_display_panel(panel_obj, current_user)
]
panel_groups = []
for institute_obj in institutes:
institute_panels = (
panel_obj
for panel_obj in store.latest_panels(institute_obj["_id"],
include_hidden=True)
if controllers.shall_display_panel(panel_obj, current_user))
panel_groups.append((institute_obj, institute_panels))
return dict(
panel_groups=panel_groups,
panel_names=panel_names,
panel_versions=panel_versions,
institutes=institutes,
)
def panels():
"""Show all panels for a case."""
if request.method == "POST":
# update an existing panel
csv_file = request.files["csv_file"]
content = csv_file.stream.read()
lines = None
try:
if b"\n" in content:
lines = content.decode("utf-8-sig", "ignore").split("\n")
else:
lines = content.decode("windows-1252").split("\r")
except Exception as err:
flash(
"Something went wrong while parsing the panel CSV file! ({})".
format(err),
"danger",
)
return redirect(request.referrer)
new_panel_name = request.form.get("new_panel_name")
if new_panel_name: # create a new panel
new_panel_id = controllers.new_panel(
store=store,
institute_id=request.form["institute"],
panel_name=new_panel_name,
display_name=request.form["display_name"],
description=request.form["description"],
csv_lines=lines,
)
if new_panel_id is None:
flash(
"Something went wrong and the panel list was not updated!",
"warning",
)
return redirect(request.referrer)
else:
flash("new gene panel added, {}!".format(new_panel_name),
"success")
return redirect(url_for("panels.panel", panel_id=new_panel_id))
else: # modify an existing panel
update_option = request.form["modify_option"]
panel_obj = controllers.update_panel(
store=store,
panel_name=request.form["panel_name"],
csv_lines=lines,
option=update_option,
)
if panel_obj is None:
return abort(
404, "gene panel not found: {}".format(
request.form["panel_name"]))
else:
return redirect(
url_for("panels.panel", panel_id=panel_obj["_id"]))
institutes = list(user_institutes(store, current_user))
panel_names = [
name for institute in institutes for name in store.gene_panels(
institute_id=institute["_id"]).distinct("panel_name")
]
panel_versions = {}
for name in panel_names:
panel_versions[name] = store.gene_panels(panel_id=name)
panel_groups = []
for institute_obj in institutes:
institute_panels = store.latest_panels(institute_obj["_id"])
panel_groups.append((institute_obj, institute_panels))
return dict(
panel_groups=panel_groups,
panel_names=panel_names,
panel_versions=panel_versions,
institutes=institutes,
)
def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# update an existing panel
csv_file = request.files['csv_file']
content = csv_file.stream.read()
lines = None
try:
if b'\n' in content:
lines = content.decode('utf-8', 'ignore').split('\n')
else:
lines = content.decode('windows-1252').split('\r')
except Exception as err:
flash('Something went wrong while parsing the panel CSV file! ({})'.format(err), 'danger')
return redirect(request.referrer)
new_panel_name = request.form.get('new_panel_name')
if new_panel_name: #create a new panel
new_panel_id = controllers.new_panel(
store=store,
institute_id=request.form['institute'],
panel_name=new_panel_name,
display_name=request.form['display_name'],
description=request.form['description'],
csv_lines=lines,
)
if new_panel_id is None:
flash('Something went wrong and the panel list was not updated!','warning')
return redirect(request.referrer)
else:
flash("new gene panel added, {}!".format(new_panel_name),'success')
return redirect(url_for('panels.panel', panel_id=new_panel_id))
else: # modify an existing panel
update_option = request.form['modify_option']
panel_obj= controllers.update_panel(
store=store,
panel_name=request.form['panel_name'],
csv_lines=lines,
option=update_option
)
if panel_obj is None:
return abort(404, "gene panel not found: {}".format(request.form['panel_name']))
else:
return redirect(url_for('panels.panel', panel_id=panel_obj['_id']))
institutes = list(user_institutes(store, current_user))
panel_names = [name
for institute in institutes
for name in
store.gene_panels(institute_id=institute['_id']).distinct('panel_name')]
panel_versions = {}
for name in panel_names:
panel_versions[name]=store.gene_panels(panel_id=name)
panel_groups = []
for institute_obj in institutes:
institute_panels = store.latest_panels(institute_obj['_id'])
panel_groups.append((institute_obj, institute_panels))
return dict(panel_groups=panel_groups, panel_names=panel_names,
panel_versions=panel_versions, institutes=institutes)
def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# update an existing panel
csv_file = request.files['csv_file']
content = csv_file.stream.read()
lines = None
try:
if b'\n' in content:
lines = content.decode('utf-8', 'ignore').split('\n')
else:
lines = content.decode('windows-1252').split('\r')
except Exception as err:
flash('Something went wrong while parsing the panel CSV file! ({})'.format(err), 'danger')
return redirect(request.referrer)
new_panel_name = request.form.get('new_panel_name')
if new_panel_name: #create a new panel
new_panel_id = controllers.new_panel(
store=store,
institute_id=request.form['institute'],
panel_name=new_panel_name,
display_name=request.form['display_name'],
csv_lines=lines,
)
if new_panel_id is None:
flash('Something went wrong and the panel list was not updated!','warning')
return redirect(request.referrer)
else:
flash("new gene panel added, {}!".format(new_panel_name),'success')
return redirect(url_for('panels.panel', panel_id=new_panel_id))
else: # modify an existing panel
update_option = request.form['modify_option']
panel_obj= controllers.update_panel(
store=store,
panel_name=request.form['panel_name'],
csv_lines=lines,
option=update_option
)
if panel_obj is None:
return abort(404, "gene panel not found: {}".format(request.form['panel_name']))
else:
return redirect(url_for('panels.panel', panel_id=panel_obj['_id']))
institutes = list(user_institutes(store, current_user))
panel_names = [name
for institute in institutes
for name in
store.gene_panels(institute_id=institute['_id']).distinct('panel_name')]
panel_versions = {}
for name in panel_names:
panel_versions[name]=store.gene_panels(panel_id=name)
panel_groups = []
for institute_obj in institutes:
institute_panels = store.latest_panels(institute_obj['_id'])
panel_groups.append((institute_obj, institute_panels))
return dict(panel_groups=panel_groups, panel_names=panel_names,
panel_versions=panel_versions, institutes=institutes)
