def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = int(raw_hgnc_id)
action = request.form['action']
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(
url_for('.gene_edit', panel_id=panel_id, hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
store.add_pending(panel_obj, hgnc_id, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data['report_created_at'] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template('panels/panel_pdf_simple.html', **data)
return render_pdf(HTML(string=html_report), download_filename=data['panel']['panel_name']+'_'+str(data['panel']['version'])+'_'+datetime.datetime.now().strftime("%Y-%m-%d")+'_scout.pdf')
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 gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene(hgnc_id)
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
transcript_choices = []
for transcript in hgnc_gene['transcripts']:
if transcript.get('refseq_id'):
refseq_id = transcript.get('refseq_id')
transcript_choices.append((refseq_id, refseq_id))
form.disease_associated_transcripts.choices = transcript_choices
if form.validate_on_submit():
action = 'edit' if panel_gene else 'add'
info_data = form.data.copy()
if 'csrf_token' in info_data:
del info_data['csrf_token']
store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
return redirect(url_for('.panel', panel_id=panel_id))
if panel_gene:
for field_key in ['disease_associated_transcripts', 'reduced_penetrance',
'mosaicism', 'inheritance_models', 'database_entry_version', 'comment']:
form_field = getattr(form, field_key)
if not form_field.data:
panel_value = panel_gene.get(field_key)
if panel_value is not None:
form_field.process_data(panel_value)
return dict(panel=panel_obj, form=form, gene=hgnc_gene, panel_gene=panel_gene)
def gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene(hgnc_id)
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
transcript_choices = []
for transcript in hgnc_gene['transcripts']:
if transcript.get('refseq_id'):
refseq_id = transcript.get('refseq_id')
transcript_choices.append((refseq_id, refseq_id))
form.disease_associated_transcripts.choices = transcript_choices
if form.validate_on_submit():
action = 'edit' if panel_gene else 'add'
info_data = form.data.copy()
if 'csrf_token' in info_data:
del info_data['csrf_token']
store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
return redirect(url_for('.panel', panel_id=panel_id))
if panel_gene:
for field_key in ['disease_associated_transcripts', 'reduced_penetrance',
'mosaicism', 'inheritance_models', 'database_entry_version', 'comment']:
form_field = getattr(form, field_key)
if not form_field.data:
panel_value = panel_gene.get(field_key)
if panel_value is not None:
form_field.process_data(panel_value)
return dict(panel=panel_obj, form=form, gene=hgnc_gene, panel_gene=panel_gene)
def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data['report_created_at'] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template('panels/panel_pdf_simple.html', **data)
return render_pdf(HTML(string=html_report), download_filename=data['panel']['panel_name']+'_'+str(data['panel']['version'])+'_'+datetime.datetime.now().strftime("%Y-%m-%d")+'_scout.pdf')
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if not panel_obj:
flash("Panel with id {} not found.".format(panel_id), "warning")
return redirect(url_for("panels.panels"))
if request.method == "POST":
if request.form.get("update_description"):
panel_obj["description"] = request.form["panel_description"]
if controllers.panel_write_granted(panel_obj, current_user):
store.update_panel(panel_obj=panel_obj)
else:
flash(
"Permission denied: please ask a panel maintainer or admin for help.",
"danger",
)
return redirect(url_for("panels.panel", panel_id=panel_obj["_id"]))
raw_hgnc_id = request.form["hgnc_id"]
if "|" in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(" | ", 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except ValueError:
flash("Provided HGNC is not valid : '{}'".format(raw_hgnc_id),
"danger")
return redirect(request.referrer)
action = request.form["action"]
gene_obj = store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="37") or store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="38")
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), "warning")
return redirect(request.referrer)
if action == "add":
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene["symbol"]),
"warning")
else:
# ask user to fill-in more information about the gene
return redirect(
url_for(".gene_edit", panel_id=panel_id, hgnc_id=hgnc_id))
elif action == "delete":
LOG.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action="delete")
data = controllers.panel(store, panel_obj)
if request.args.get("case_id"):
data["case"] = store.case(request.args["case_id"])
if request.args.get("institute_id"):
data["institute"] = store.institute(request.args["institute_id"])
return data
def gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene(hgnc_id)
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
transcript_choices = []
for transcript in hgnc_gene["transcripts"]:
if transcript.get("refseq_id"):
refseq_id = transcript.get("refseq_id")
transcript_choices.append((refseq_id, refseq_id))
# collect even refseq version provided by user for this transcript (might have a version)
if panel_obj.get("genes"):
genes_dict = {gene_obj["symbol"]: gene_obj for gene_obj in panel_obj["genes"]}
gene_obj = genes_dict.get(hgnc_gene["hgnc_symbol"])
if gene_obj:
for transcript in gene_obj.get("disease_associated_transcripts", []):
if (transcript, transcript) not in transcript_choices:
transcript_choices.append((transcript, transcript))
form.disease_associated_transcripts.choices = transcript_choices
if form.validate_on_submit():
action = "edit" if panel_gene else "add"
info_data = form.data.copy()
if "csrf_token" in info_data:
del info_data["csrf_token"]
if info_data["custom_inheritance_models"] != "":
info_data["custom_inheritance_models"] = info_data[
"custom_inheritance_models"
].split(",")
store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
return redirect(url_for(".panel", panel_id=panel_id))
if panel_gene:
form.custom_inheritance_models.data = ", ".join(
panel_gene.get("custom_inheritance_models", [])
)
for field_key in [
"disease_associated_transcripts",
"reduced_penetrance",
"mosaicism",
"inheritance_models",
"custom_inheritance_models",
"database_entry_version",
"comment",
]:
form_field = getattr(form, field_key)
if not form_field.data:
panel_value = panel_gene.get(field_key)
if panel_value is not None:
form_field.process_data(panel_value)
return dict(panel=panel_obj, form=form, gene=hgnc_gene, panel_gene=panel_gene)
def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template("panels/panel_pdf_simple.html", **data)
return render_pdf(
HTML(string=html_report),
download_filename=data["panel"]["panel_name"] + "_" +
str(data["panel"]["version"]) + "_" +
datetime.datetime.now().strftime("%Y-%m-%d") + "_scout.pdf",
)
def panel_restore(panel_id):
"""Remove an existing panel."""
panel_obj = store.panel(panel_id)
# abort when trying to hide an already hidden panel
if controllers.panel_write_granted(panel_obj, current_user):
panel_obj["hidden"] = False
store.update_panel(panel_obj=panel_obj)
flash("Restored gene panel: %s" % panel_obj["display_name"], "success")
else:
flash(
"Permission denied: please ask a panel maintainer or admin for help.",
"danger",
)
return redirect(url_for("panels.panels", panel_id=panel_obj["_id"]))
def gene_edit(panel_id, hgnc_id):
"""Edit additional information about a panel gene."""
panel_obj = store.panel(panel_id)
hgnc_gene = store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="37") or store.hgnc_gene_caption(
hgnc_identifier=hgnc_id, build="38")
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
form = PanelGeneForm()
form.disease_associated_transcripts.choices = tx_choices(
hgnc_id, panel_obj)
if form.validate_on_submit():
action = "edit" if panel_gene else "add"
info_data = form.data.copy()
if "csrf_token" in info_data:
del info_data["csrf_token"]
if info_data["custom_inheritance_models"] != "":
info_data["custom_inheritance_models"] = info_data[
"custom_inheritance_models"].split(",")
store.add_pending(panel_obj, hgnc_gene, action=action, info=info_data)
return redirect(url_for(".panel", panel_id=panel_id))
if panel_gene:
custom_models = [
model for model in panel_gene.get("custom_inheritance_models", [])
if model != ""
]
if custom_models:
form.custom_inheritance_models.data = ", ".join(
panel_gene.get("custom_inheritance_models"))
for field_key in [
"disease_associated_transcripts",
"reduced_penetrance",
"mosaicism",
"inheritance_models",
"custom_inheritance_models",
"database_entry_version",
"comment",
]:
form_field = getattr(form, field_key)
if not form_field.data:
panel_value = panel_gene.get(field_key)
if panel_value is not None:
form_field.process_data(panel_value)
return dict(panel=panel_obj,
form=form,
gene=hgnc_gene,
panel_gene=panel_gene)
def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
if request.form.get("cancel_pending"):
updated_panel = store.reset_pending(panel_obj)
if updated_panel is None:
flash("Couldn't find a panel with ID {}".format(panel_id),
"warning")
elif updated_panel.get("pending") is None:
flash("Pending actions were correctly canceled!", "success")
return redirect(request.referrer)
else:
update_version = request.form.get("version", None)
new_panel_id = store.apply_pending(panel_obj, update_version)
return redirect(url_for("panels.panel", panel_id=new_panel_id))
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
if request.form.get('update_description'):
panel_obj['description'] = request.form['panel_description']
store.update_panel(panel_obj=panel_obj)
return redirect( url_for('panels.panel', panel_id=panel_obj['_id']) )
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except:
flash("Provided HGNC is not valid : '{}'". format(raw_hgnc_id), 'danger')
return redirect(request.referrer)
action = request.form['action']
gene_obj = store.hgnc_gene(hgnc_id)
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), 'warning')
return redirect(request.referrer)
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(url_for('.gene_edit', panel_id=panel_id,
hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def panel_export(panel_id):
"""Export panel to PDF file"""
panel_obj = store.panel(panel_id)
data = controllers.panel_export(store, panel_obj)
data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d")
html_report = render_template("panels/panel_pdf_simple.html", **data)
bytes_file = html_to_pdf_file(html_report, "portrait", 300)
file_name = "_".join([
data["panel"]["panel_name"],
str(data["panel"]["version"]),
datetime.datetime.now().strftime("%Y-%m-%d"),
"scout.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
def panel_delete(panel_id):
"""Remove an existing panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if panel_obj is None:
flash(
f"Panel object with id '{panel_id}' was not found.",
"danger",
)
return redirect(request.referrer)
if controllers.panel_write_granted(panel_obj, current_user):
LOG.info("Mark gene panel: %s as deleted (hidden)" %
panel_obj["display_name"])
panel_obj["hidden"] = True
store.update_panel(panel_obj=panel_obj)
flash("Removed gene panel: %s" % panel_obj["display_name"], "success")
else:
flash(
"Permission denied: please ask a panel maintainer or admin for help.",
"danger",
)
return redirect(url_for("panels.panels", panel_id=panel_obj["_id"]))
def panel(panel_id):
"""Display (and add pending updates to) a specific gene panel."""
panel_obj = store.gene_panel(panel_id) or store.panel(panel_id)
if request.method == 'POST':
raw_hgnc_id = request.form['hgnc_id']
if '|' in raw_hgnc_id:
raw_hgnc_id = raw_hgnc_id.split(' | ', 1)[0]
hgnc_id = 0
try:
hgnc_id = int(raw_hgnc_id)
except:
flash("Provided HGNC is not valid : '{}'". format(raw_hgnc_id), 'danger')
return redirect(request.referrer)
action = request.form['action']
gene_obj = store.hgnc_gene(hgnc_id)
if gene_obj is None:
flash("HGNC id not found: {}".format(hgnc_id), 'warning')
return redirect(request.referrer)
if action == 'add':
panel_gene = controllers.existing_gene(store, panel_obj, hgnc_id)
if panel_gene:
flash("gene already in panel: {}".format(panel_gene['symbol']),
'warning')
else:
# ask user to fill-in more information about the gene
return redirect(url_for('.gene_edit', panel_id=panel_id,
hgnc_id=hgnc_id))
elif action == 'delete':
log.debug("marking gene to be deleted: %s", hgnc_id)
panel_obj = store.add_pending(panel_obj, gene_obj, action='delete')
data = controllers.panel(store, panel_obj)
if request.args.get('case_id'):
data['case'] = store.case(request.args['case_id'])
if request.args.get('institute_id'):
data['institute'] = store.institute(request.args['institute_id'])
return data
def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
if request.form.get("cancel_pending"):
updated_panel = store.reset_pending(panel_obj)
if updated_panel is None:
flash("Couldn't find a panel with ID {}".format(panel_id), "warning")
elif updated_panel.get("pending") is None:
flash("Pending actions were correctly canceled!", "success")
return redirect(request.referrer)
if panel_write_granted(panel_obj, current_user):
update_version = request.form.get("version", None)
new_panel_id = store.apply_pending(panel_obj, update_version)
panel_id = new_panel_id
else:
flash(
"Permission denied: please ask a panel maintainer or admin for help.",
"danger",
)
return redirect(url_for("panels.panel", panel_id=panel_id))
def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
update_version = request.form.get('version', None)
new_panel_id = store.apply_pending(panel_obj, update_version)
return redirect(url_for('panels.panel', panel_id=new_panel_id))
def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
store.apply_pending(panel_obj)
return redirect(url_for('.panels'))
def panel_update(panel_id):
"""Update panel to a new version."""
panel_obj = store.panel(panel_id)
update_version = request.form.get('version', None)
new_panel_id = store.apply_pending(panel_obj, update_version)
return redirect(url_for('panels.panel', panel_id=new_panel_id))
