def index():
"""Display the Scout dashboard."""
accessible_institutes = None
if not 'admin' in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash(
'Not allowed to see information - please visit the dashboard later!'
)
return redirect(url_for('cases.index'))
institutes = [inst for inst in store.institutes(accessible_institutes)]
# Insert a entry that displays all institutes in the beginning of the array
institutes.insert(0, {'_id': None, 'display_name': 'All institutes'})
institute_id = None
if request.method == 'POST':
institute_id = request.form.get('institute')
LOG.info("Fetch all cases with institute: %s", institute_id)
data = get_dashboard_info(store, institute_id)
data['institutes'] = institutes
data['choice'] = institute_id
total_cases = data['total_cases']
LOG.info("Found %s cases", total_cases)
if total_cases == 0:
flash(
'no cases loaded for institute {} - please visit the dashboard later!'
.format(institute_id), 'info')
return redirect(url_for('cases.index'))
return render_template('dashboard/index.html', **data)
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
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 default_phenotypes
def download_verified():
"""Download all verified variants for user's cases"""
user_obj = store.user(current_user.email)
user_institutes = (
[inst["_id"] for inst in store.institutes()]
if current_user.is_admin
else user_obj.get("institutes")
)
temp_excel_dir = os.path.join(variants_bp.static_folder, "verified_folder")
os.makedirs(temp_excel_dir, exist_ok=True)
if controllers.verified_excel_file(store, user_institutes, temp_excel_dir):
data = zip_dir_to_obj(temp_excel_dir)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
today = datetime.datetime.now().strftime("%Y-%m-%d")
return send_file(
data,
mimetype="application/zip",
as_attachment=True,
download_name="_".join(["scout", "verified_variants", today]) + ".zip",
cache_timeout=0,
)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
flash("No verified variants could be exported for user's institutes", "warning")
return redirect(request.referrer)
def index():
"""Display the Scout dashboard."""
accessible_institutes = current_user.institutes
if not 'admin' in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash('Not allowed to see information - please visit the dashboard later!')
return redirect(url_for('cases.dahboard_general.html'))
LOG.debug('User accessible institutes: {}'.format(accessible_institutes))
institutes = [inst for inst in store.institutes(accessible_institutes)]
# Insert a entry that displays all institutes in the beginning of the array
institutes.insert(0, {'_id': None, 'display_name': 'All institutes'})
institute_id = None
slice_query = None
panel=1
if request.method=='POST':
institute_id = request.form.get('institute')
slice_query = request.form.get('query')
panel=request.form.get('pane_id')
elif request.method=='GET':
institute_id = request.args.get('institute')
slice_query = request.args.get('query')
# User should be restricted to their own institute if:
#1) Their default institute when the page is first loaded
#2) if they ask for an institute that they don't belong to
#3) if they want perform a query on all institutes
if not institute_id:
institute_id = accessible_institutes[0]
elif (not current_user.is_admin) and (slice_query and institute_id == 'None'):
institute_id = accessible_institutes[0]
elif (not institute_id in accessible_institutes) and not (institute_id == 'None'):
institute_id = accessible_institutes[0]
LOG.info("Fetch all cases with institute: %s", institute_id)
data = get_dashboard_info(store, institute_id, slice_query)
data['institutes'] = institutes
data['choice'] = institute_id
total_cases = data['total_cases']
LOG.info("Found %s cases", total_cases)
if total_cases == 0:
flash('no cases found for institute {} (with that query) - please visit the dashboard later!'.format(institute_id), 'info')
# return redirect(url_for('cases.index'))
return render_template(
'dashboard/dashboard_general.html', institute=institute_id, query=slice_query, panel=panel, **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 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 index():
"""Display the Scout dashboard."""
accessible_institutes = current_user.institutes
if not 'admin' in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash(
'Not allowed to see information - please visit the dashboard later!'
)
return redirect(url_for('cases.dahboard_general.html'))
LOG.debug('User accessible institutes: {}'.format(accessible_institutes))
institutes = [inst for inst in store.institutes(accessible_institutes)]
# Insert a entry that displays all institutes in the beginning of the array
institutes.insert(0, {'_id': None, 'display_name': 'All institutes'})
institute_id = None
slice_query = None
panel = 1
if request.method == 'POST':
institute_id = request.form.get('institute')
slice_query = request.form.get('query')
panel = request.form.get('pane_id')
elif request.method == 'GET':
institute_id = request.args.get('institute')
slice_query = request.args.get('query')
# User should be restricted to their own institute if:
#1) Their default institute when the page is first loaded
#2) if they ask for an institute that they don't belong to
#3) if they want perform a query on all institutes
if not institute_id:
institute_id = accessible_institutes[0]
elif (not current_user.is_admin) and (slice_query
and institute_id == 'None'):
institute_id = accessible_institutes[0]
elif (not institute_id in accessible_institutes) and not (institute_id
== 'None'):
institute_id = accessible_institutes[0]
LOG.info("Fetch all cases with institute: %s", institute_id)
data = get_dashboard_info(store, institute_id, slice_query)
data['institutes'] = institutes
data['choice'] = institute_id
total_cases = data['total_cases']
LOG.info("Found %s cases", total_cases)
if total_cases == 0:
flash(
'no cases found for institute {} (with that query) - please visit the dashboard later!'
.format(institute_id), 'info')
# return redirect(url_for('cases.index'))
return render_template('dashboard/dashboard_general.html',
institute=institute_id,
query=slice_query,
panel=panel,
**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 index():
"""Display the Scout dashboard."""
accessible_institutes = current_user.institutes
if not "admin" in current_user.roles:
accessible_institutes = current_user.institutes
if not accessible_institutes:
flash(
"Not allowed to see information - please visit the dashboard later!"
)
return redirect(url_for("cases.dahboard_general.html"))
LOG.debug("User accessible institutes: {}".format(accessible_institutes))
institutes = [inst for inst in store.institutes(accessible_institutes)]
# Insert a entry that displays all institutes in the beginning of the array
institutes.insert(0, {"_id": None, "display_name": "All institutes"})
institute_id = None
slice_query = None
panel = 1
if request.method == "POST":
institute_id = request.form.get("institute")
slice_query = request.form.get("query")
panel = request.form.get("pane_id")
elif request.method == "GET":
institute_id = request.args.get("institute")
slice_query = request.args.get("query")
# User should be restricted to their own institute if:
# 1) Their default institute when the page is first loaded
# 2) if they ask for an institute that they don't belong to
# 3) if they want perform a query on all institutes
if not institute_id:
institute_id = accessible_institutes[0]
elif (not current_user.is_admin) and (slice_query
and institute_id == "None"):
institute_id = accessible_institutes[0]
elif (not institute_id in accessible_institutes) and not (institute_id
== "None"):
institute_id = accessible_institutes[0]
LOG.info("Fetch all cases with institute: %s", institute_id)
data = get_dashboard_info(store, institute_id, slice_query)
data["institutes"] = institutes
data["choice"] = institute_id
total_cases = data["total_cases"]
LOG.info("Found %s cases", total_cases)
if total_cases == 0:
flash(
"no cases found for institute {} (with that query) - please visit the dashboard later!"
.format(institute_id),
"info",
)
# return redirect(url_for('cases.index'))
return render_template("dashboard/dashboard_general.html",
institute=institute_id,
query=slice_query,
panel=panel,
**data)