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 update_institute_settings(store, institute_obj, form):
"""Update institute settings with data collected from institute form
Args:
score(adapter.MongoAdapter)
institute_id(str)
form(dict)
Returns:
updated_institute(dict)
"""
sanger_recipients = []
sharing_institutes = []
phenotype_groups = []
gene_panels = {}
group_abbreviations = []
cohorts = []
for email in form.getlist("sanger_emails"):
sanger_recipients.append(email.strip())
for inst in form.getlist("institutes"):
sharing_institutes.append(inst)
for pheno_group in form.getlist("pheno_groups"):
phenotype_groups.append(pheno_group.split(" ,")[0])
group_abbreviations.append(pheno_group[pheno_group.find("( ") +
2:pheno_group.find(" )")])
if form.get("hpo_term") and form.get("pheno_abbrev"):
phenotype_groups.append(form["hpo_term"].split(" |")[0])
group_abbreviations.append(form["pheno_abbrev"])
for panel_name in form.getlist("gene_panels"):
panel_obj = store.gene_panel(panel_name)
if panel_obj is None:
continue
gene_panels[panel_name] = panel_obj["display_name"]
for cohort in form.getlist("cohorts"):
cohorts.append(cohort.strip())
updated_institute = store.update_institute(
internal_id=institute_obj["_id"],
sanger_recipients=sanger_recipients,
coverage_cutoff=int(form.get("coverage_cutoff")),
frequency_cutoff=float(form.get("frequency_cutoff")),
display_name=form.get("display_name"),
phenotype_groups=phenotype_groups,
gene_panels=gene_panels,
group_abbreviations=group_abbreviations,
add_groups=False,
sharing_institutes=sharing_institutes,
cohorts=cohorts,
loqusdb_ids=form.getlist("loqusdb_id"),
alamut_key=form.get("alamut_key"),
)
return updated_institute
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 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 coverage_report_contents(base_url, institute_obj, case_obj):
"""Capture the contents of a case coverage report (chanjo-report), to be displayed in the general case report
Args:
base_url(str): base url of this application
institute_obj(models.Institute)
case_obj(models.Case)
Returns:
html_body_content(str): A string corresponding to the text within the <body> of an HTML chanjo-report page
"""
request_data = {}
# extract sample ids from case_obj and add them to the post request object:
request_data["sample_id"] = [ind["individual_id"] for ind in case_obj["individuals"]]
# extract default panel names and default genes from case_obj and add them to the post request object
distinct_genes = set()
panel_names = []
for panel_info in case_obj.get("panels", []):
if panel_info.get("is_default") is False:
continue
panel_obj = store.gene_panel(panel_info["panel_name"], version=panel_info.get("version"))
distinct_genes.update([gene["hgnc_id"] for gene in panel_obj.get("genes", [])])
full_name = "{} ({})".format(panel_obj["display_name"], panel_obj["version"])
panel_names.append(full_name)
panel_names = " ,".join(panel_names)
request_data["gene_ids"] = ",".join([str(gene_id) for gene_id in list(distinct_genes)])
request_data["panel_name"] = panel_names
request_data["request_sent"] = datetime.datetime.now()
# add institute-specific cutoff level to the post request object
request_data["level"] = institute_obj.get("coverage_cutoff", 15)
# Collect the coverage report HTML string
try:
resp = requests.post(
base_url + "reports/report", timeout=COVERAGE_REPORT_TIMEOUT, data=request_data
)
except requests.Timeout:
html_body_content = "<span><b>Coverage report unavailable</b></span>"
return html_body_content
# Extract the contents between <body> and </body>
html_body_content = resp.text.split("<body>")[1].split("</body>")[0]
return html_body_content
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_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 case(store, institute_obj, case_obj):
"""Preprocess a single case.
Prepare the case to be displayed in the case view.
Args:
store(adapter.MongoAdapter)
institute_obj(models.Institute)
case_obj(models.Case)
Returns:
data(dict): includes the cases, how many there are and the limit.
"""
# Convert individual information to more readable format
case_obj["individual_ids"] = []
for individual in case_obj["individuals"]:
try:
sex = int(individual.get("sex", 0))
except ValueError as err:
sex = 0
individual["sex_human"] = SEX_MAP[sex]
pheno_map = PHENOTYPE_MAP
if case_obj.get("track", "rare") == "cancer":
pheno_map = CANCER_PHENOTYPE_MAP
individual["phenotype_human"] = pheno_map.get(individual["phenotype"])
case_obj["individual_ids"].append(individual["individual_id"])
case_obj["assignees"] = [store.user(user_email) for user_email in case_obj.get("assignees", [])]
# Provide basic info on alignment files availability for this case
case_has_alignments(case_obj)
case_has_mt_alignments(case_obj)
case_groups = {}
case_group_label = {}
_populate_case_groups(store, case_obj, case_groups, case_group_label)
# Fetch the variant objects for suspects and causatives
suspects = [
store.variant(variant_id) or variant_id for variant_id in case_obj.get("suspects", [])
]
_populate_assessments(suspects)
causatives = [
store.variant(variant_id) or variant_id for variant_id in case_obj.get("causatives", [])
]
_populate_assessments(causatives)
# get evaluated variants
evaluated_variants = store.evaluated_variants(case_obj["_id"], case_obj["owner"])
_populate_assessments(evaluated_variants)
# check for partial causatives and associated phenotypes
partial_causatives = []
if case_obj.get("partial_causatives"):
for var_id, values in case_obj["partial_causatives"].items():
causative_obj = {
"variant": store.variant(var_id) or var_id,
"omim_terms": values.get("diagnosis_phenotypes"),
"hpo_terms": values.get("phenotype_terms"),
}
partial_causatives.append(causative_obj)
_populate_assessments(partial_causatives)
# Set of all unique genes in the default gene panels
distinct_genes = set()
case_obj["panel_names"] = []
case_obj["outdated_panels"] = {}
for panel_info in case_obj.get("panels", []):
if not panel_info.get("is_default"):
continue
panel_name = panel_info["panel_name"]
panel_version = panel_info.get("version")
panel_obj = store.gene_panel(panel_name, version=panel_version)
latest_panel = store.gene_panel(panel_name)
panel_info["removed"] = False if latest_panel is None else latest_panel.get("hidden", False)
if not panel_obj:
panel_obj = latest_panel
if not panel_obj:
flash(f"Case default panel '{panel_name}' could not be found.", "warning")
continue
flash(
f"Case default panel '{panel_name}' version {panel_version} could not be found, using latest existing version",
"warning",
)
# Check if case-specific panel is up-to-date with latest version of the panel
if panel_obj["version"] < latest_panel["version"]:
extra_genes, missing_genes = _check_outdated_gene_panel(panel_obj, latest_panel)
if extra_genes or missing_genes:
case_obj["outdated_panels"][panel_name] = {
"missing_genes": missing_genes,
"extra_genes": extra_genes,
}
distinct_genes.update([gene["hgnc_id"] for gene in panel_obj.get("genes", [])])
full_name = "{} ({})".format(panel_obj["display_name"], panel_obj["version"])
case_obj["panel_names"].append(full_name)
case_obj["default_genes"] = list(distinct_genes)
for hpo_term in itertools.chain(
case_obj.get("phenotype_groups", []), case_obj.get("phenotype_terms", [])
):
hpo_term["hpo_link"] = "http://hpo.jax.org/app/browse/term/{}".format(
hpo_term["phenotype_id"]
)
if case_obj.get("rank_model_version"):
rank_model_link = "".join(
[
current_app.config.get("RANK_MODEL_LINK_PREFIX", ""),
str(case_obj["rank_model_version"]),
current_app.config.get("RANK_MODEL_LINK_POSTFIX", ""),
]
)
case_obj["rank_model_link"] = rank_model_link
if case_obj.get("sv_rank_model_version"):
case_obj["sv_rank_model_link"] = "".join(
[
current_app.config.get("SV_RANK_MODEL_LINK_PREFIX", ""),
str(case_obj["sv_rank_model_version"]),
current_app.config.get("SV_RANK_MODEL_LINK_POSTFIX", ""),
]
)
# other collaborators than the owner of the case
o_collaborators = []
for collab_id in case_obj.get("collaborators", []):
if collab_id != case_obj["owner"] and store.institute(collab_id):
o_collaborators.append(store.institute(collab_id))
case_obj["o_collaborators"] = [
(collab_obj["_id"], collab_obj["display_name"]) for collab_obj in o_collaborators
]
collab_ids = None
if institute_obj.get("collaborators"):
collab_ids = [
(collab["_id"], collab["display_name"])
for collab in store.institutes()
if institute_obj.get("collaborators")
and collab["_id"] in institute_obj.get("collaborators")
]
events = list(store.events(institute_obj, case=case_obj))
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"],
csv_lines=lines,
maintainer=[current_user._id],
description=request.form["description"],
)
if new_panel_id is None:
flash(
"Something went wrong and the panel list was not updated!",
"warning",
)
return redirect(request.referrer)
flash("new gene panel added, {}!".format(new_panel_name),
"success")
return redirect(url_for("panels.panel", panel_id=new_panel_id))
# modify an existing panel
update_option = request.form["modify_option"]
panel_obj = store.gene_panel(request.form["panel_name"])
if panel_obj is None:
return abort(
404,
"gene panel not found: {}".format(request.form["panel_name"]))
if panel_write_granted(panel_obj, current_user):
panel_obj = controllers.update_panel(
store=store,
panel_name=request.form["panel_name"],
csv_lines=lines,
option=update_option,
)
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"]))
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,
)