def institute_settings(institute_id):
"""Show institute settings page"""
if institute_id not in current_user.institutes and current_user.is_admin is False:
flash(
"Current user doesn't have the permission to modify this institute",
"warning",
)
return redirect(request.referrer)
institute_obj = store.institute(institute_id)
form = InstituteForm(request.form)
# if institute is to be updated
if request.method == "POST" and form.validate_on_submit():
institute_obj = controllers.update_institute_settings(
store, institute_obj, request.form)
if isinstance(institute_obj, dict):
flash("institute was updated ", "success")
else: # an error message was retuned
flash(institute_obj, "warning")
return redirect(request.referrer)
data = controllers.institute(store, institute_id)
default_phenotypes = controllers.populate_institute_form(
form, institute_obj)
return render_template(
"/overview/institute_settings.html",
form=form,
default_phenotypes=default_phenotypes,
panel=1,
**data,
)
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(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 institute(institute_id):
""" Edit institute data """
if institute_id not in current_user.institutes and current_user.is_admin is False:
flash(
"Current user doesn't have the permission to modify this institute",
"warning",
)
return redirect(request.referrer)
institute_obj = store.institute(institute_id)
form = InstituteForm(request.form)
# if institute is to be updated
if request.method == "POST" and form.validate_on_submit():
institute_obj = controllers.update_institute_settings(
store, institute_obj, request.form)
if isinstance(institute_obj, dict):
flash("institute was updated ", "success")
else: # an error message was retuned
flash(institute_obj, "warning")
return redirect(request.referrer)
data = controllers.institute(store, institute_id)
# get all other institutes to populate the select of the possible collaborators
institutes_tuples = []
for inst in store.institutes():
if not inst["_id"] == institute_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
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))
return render_template("/overview/institute.html",
form=form,
default_phenotypes=default_phenotypes,
**data)
def add_beacon_dataset(institute_id):
"""Add a dataset to Beacon for a given institute"""
if current_user.is_admin is False:
flash(
"Only an admin can create a new Beacon dataset",
"warning",
)
return redirect(request.referrer)
dataset_id = request.form.get("beacon_dataset")
institute_obj = store.institute(institute_id)
beacon.add_dataset(institute_obj, dataset_id)
return redirect(request.referrer)
def institute(store, institute_id):
"""Process institute data.
Args:
store(adapter.MongoAdapter)
institute_id(str)
Returns
data(dict): includes institute obj and specific settings
"""
institute_obj = store.institute(institute_id)
users = list(store.users(institute_id))
data = {"institute": institute_obj, "users": users}
return data
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(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))