def test_panel_update_description(app):
"""Test the endpoint that updates gene panel description"""
# GIVEN a panel in the database
panel_obj = store.gene_panels()[0]
assert panel_obj.get("description") is None
form_data = {
"update_description": True, # This is the submit button of the form
"panel_description": "Some description", # This is the text field
}
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
# WHEN posting an update description request to panel page
resp = client.post(
url_for("panels.panel", panel_id=panel_obj["_id"]),
data=form_data,
)
# THEN the panel object should be updated with the new description:
panel_obj = store.gene_panels()[0]
assert panel_obj["description"] == "Some description"
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 test_panel_modify_genes(app, real_panel_database):
"""Test the functionality to modify genes in a gene panel"""
# GIVEN a panel in the database
panel_obj = store.gene_panels()[0]
# WHEN posting a delete gene request to panel page
a_gene = panel_obj["genes"][0] # first gene of the panel
form_data = {"action": "delete", "hgnc_id": a_gene["hgnc_id"]}
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
resp = client.post(
url_for("panels.panel", panel_id=panel_obj["_id"]),
data=form_data,
)
# THEN the pending actions of panel should be updated:
panel_obj = store.gene_panels()[0]
assert panel_obj["pending"][0]["action"] == "delete"
assert panel_obj["pending"][0]["hgnc_id"] == a_gene["hgnc_id"]
# WHEN removing that gene using the client
new_version = panel_obj["version"] + 1
form_data = {"action": "submit", "version": new_version}
resp = client.post(
url_for("panels.panel_update", panel_id=panel_obj["_id"]),
data=form_data,
)
# THEN the new panel object should have the correct new version
new_panel_obj = store.gene_panel(panel_obj["panel_name"])
assert new_panel_obj["version"] == new_version
# remove gene from panel object using adapter:
panel_obj["genes"] = panel_obj["genes"][1:]
updated_panel = store.update_panel(panel_obj)
# WHEN posting an add gene request to panel page
form_data = {"action": "add", "hgnc_id": a_gene["hgnc_id"]}
resp = client.post(
url_for("panels.panel", panel_id=updated_panel["_id"]),
data=form_data,
)
# Then response should redirect to gene edit page
assert resp.status_code == 302
def panels():
"""Show all panels for a case."""
if request.method == 'POST':
# add new panel
csv_file = request.files['csv_file']
lines = csv_file.stream.read().decode().split('\r')
panel_genes = parse_panel(lines)
try:
panel_obj = build_panel(
adapter=store,
institute_id=request.form['institute_id'],
panel_name=request.form['panel_name'],
display_name=request.form['display_name'],
version=float(request.form['version'])
if request.form.get('version') else 1.0,
panel_genes=panel_genes,
)
except ValueError as error:
flash(error.args[0], 'warning')
return redirect(request.referrer)
store.add_gene_panel(panel_obj)
flash("new gene panel added: {}".format(panel_obj['panel_name']),
'info')
panel_groups = []
for institute_obj in user_institutes(store, current_user):
institute_panels = store.gene_panels(institute_id=institute_obj['_id'])
panel_groups.append((institute_obj, institute_panels))
return dict(panel_groups=panel_groups,
institutes=user_institutes(store, current_user))
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)
