def check_case(institute_id, case_name):
"""Mark a case that is has been checked.
This means to set case['needs_check'] to False
"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
store.case_collection.find_one_and_update({'_id':case_obj['_id']}, {'$set': {'needs_check': False}})
return redirect(request.referrer)
def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
phenotype_id, is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
phenotype_term = request.form['hpo_term']
if phenotype_term.startswith('HP:') or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(' | ', 1)[0]
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_term=hpo_term, is_group=is_group)
else:
# assume omim id
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype: {}".format(phenotype_term)))
return redirect(case_url)
def research(institute_id, case_name):
"""Open the research list 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('.case', institute_id=institute_id, case_name=case_name)
store.open_research(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def mt_report(institute_id, case_name):
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# create a temp folder to write excel files into
temp_excel_dir = os.path.join(cases_bp.static_folder, '_'.join([case_name, 'mt_reports']))
os.makedirs(temp_excel_dir, exist_ok=True)
# create mt excel files, one for each sample
n_files = controllers.mt_excel_files(store, case_obj, temp_excel_dir)
if n_files:
today = datetime.datetime.now().strftime('%Y-%m-%d')
# zip the files on the fly and serve the archive to the user
data = io.BytesIO()
with zipfile.ZipFile(data, mode='w') as z:
for f_name in pathlib.Path(temp_excel_dir).iterdir():
zipfile.ZipFile
z.write(f_name, os.path.basename(f_name))
data.seek(0)
# remove temp folder with excel files in it
shutil.rmtree(temp_excel_dir)
return send_file(
data,
mimetype='application/zip',
as_attachment=True,
attachment_filename='_'.join(['scout', case_name, 'MT_report', today])+'.zip'
)
else:
flash('No MT report excel file could be exported for this sample', 'warning')
return redirect(request.referrer)
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 multiqc(store, institute_id, case_name):
"""Find MultiQC report for the case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
return dict(
institute=institute_obj,
case=case_obj,
)
def matchmaker_delete(institute_id, case_name):
"""Remove a case from MatchMaker"""
# check that only authorized users can delete patients from MME
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# Required params for sending a delete request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_token:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
delete_result = controllers.mme_delete(case_obj, mme_base_url, mme_token)
n_deleted = 0
category = 'warning'
for resp in delete_result:
if resp['status_code'] == 200:
n_deleted += 1
else:
flash(resp['message'], category)
if n_deleted:
category = 'success'
# update case by removing mme submission
# and create events for patients deletion from MME
user_obj = store.user(current_user.email)
store.case_mme_delete(case_obj=case_obj, user_obj=user_obj)
flash('Number of patients deleted from Matchmaker: {} out of {}'.format(n_deleted, len(delete_result)), category)
return redirect(request.referrer)
def case_synopsis(institute_id, case_name):
"""Update (PUT) synopsis of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
new_synopsis = request.form.get('synopsis')
controllers.update_synopsis(store, institute_obj, case_obj, user_obj, new_synopsis)
return redirect(request.referrer)
def matchmaker_match(institute_id, case_name, target):
"""Starts an internal match or a match against one or all MME external nodes"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
# check that only authorized users can run matches
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
# Required params for sending an add request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_accepts = current_app.config.get('MME_ACCEPTS')
mme_token = current_app.config.get('MME_TOKEN')
nodes = current_app.mme_nodes
if not mme_base_url or not mme_token or not mme_accepts:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
match_results = controllers.mme_match(case_obj, target, mme_base_url, mme_token, nodes, mme_accepts)
ok_responses = 0
for match_results in match_results:
match_results['status_code'] == 200
ok_responses +=1
if ok_responses:
flash("Match request sent. Look for eventual matches in 'Matches' page.", 'info')
else:
flash('An error occurred while sending match request.', 'danger')
return redirect(request.referrer)
def vcf2cytosure(store, institute_id, case_name, individual_id):
"""vcf2cytosure CGH file for inidividual."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
for individual in case_obj['individuals']:
if individual['individual_id'] == individual_id:
individual_obj = individual
return (individual_obj['display_name'], individual_obj['vcf2cytosure'])
def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
action = request.form["action"]
hpo_ids = request.form.getlist("hpo_id")
user_obj = store.user(current_user.email)
if action == "PHENOMIZER":
if len(hpo_ids) == 0:
hpo_ids = [
term["phenotype_id"]
for term in case_obj.get("phenotype_terms", [])
]
username = current_app.config["PHENOMIZER_USERNAME"]
password = current_app.config["PHENOMIZER_PASSWORD"]
diseases = controllers.hpo_diseases(username, password, hpo_ids)
return render_template("cases/diseases.html",
diseases=diseases,
institute=institute_obj,
case=case_obj)
if action == "DELETE":
for hpo_id in hpo_ids:
# DELETE a phenotype from the list
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_id)
if action == "ADDGENE":
hgnc_ids = parse_raw_gene_ids(request.form.getlist("genes"))
store.update_dynamic_gene_list(case_obj,
hgnc_ids=list(hgnc_ids),
add_only=True)
if action == "GENES":
hgnc_symbols = parse_raw_gene_symbols(request.form.getlist("genes"))
store.update_dynamic_gene_list(case_obj,
hgnc_symbols=list(hgnc_symbols))
if action == "GENERATE":
if len(hpo_ids) == 0:
hpo_ids = [
term["phenotype_id"]
for term in case_obj.get("phenotype_terms", [])
]
results = store.generate_hpo_gene_list(*hpo_ids)
# determine how many HPO terms each gene must match
hpo_count = int(request.form.get("min_match") or 1)
hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
store.update_dynamic_gene_list(case_obj,
hgnc_ids=hgnc_ids,
phenotype_ids=hpo_ids)
return redirect(case_url)
def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def vcf2cytosure(store, institute_id, case_name, individual_id):
"""vcf2cytosure CGH file for inidividual."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
for individual in case_obj["individuals"]:
if individual["individual_id"] == individual_id:
individual_obj = individual
return (individual_obj["display_name"], individual_obj["vcf2cytosure"])
def vcf2cytosure(store, institute_id, case_name, individual_id):
"""vcf2cytosure CGH file for inidividual."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
for individual in case_obj['individuals']:
if individual['individual_id'] == individual_id:
individual_obj = individual
return (individual_obj['display_name'], individual_obj['vcf2cytosure'])
def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def variant_acmg(store, institute_id, case_name, variant_id):
"""Collect data relevant for rendering ACMG classification form."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
return dict(institute=institute_obj,
case=case_obj,
variant=variant_obj,
CRITERIA=ACMG_CRITERIA,
ACMG_OPTIONS=ACMG_OPTIONS)
def sv_variants(institute_id, case_name):
"""Display a list of structural variants."""
page = int(request.form.get("page", 1))
variant_type = request.args.get("variant_type", "clinical")
category = "sv"
# Define case and institute objects
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
if request.form.get("hpo_clinical_filter"):
case_obj["hpo_clinical_filter"] = True
if request.form.getlist("dismiss"): # dismiss a list of variants
controllers.dismiss_variant_list(
store,
institute_obj,
case_obj,
"variant.sv_variant",
request.form.getlist("dismiss"),
request.form.getlist("dismiss_choices"),
)
# update status of case if visited for the first time
controllers.activate_case(store, institute_obj, case_obj, current_user)
form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request)
cytobands = store.cytoband_by_chrom(case_obj.get("genome_build"))
variants_query = store.variants(case_obj["_id"], category=category, query=form.data)
# Setup variant count session with variant count by category
controllers.variant_count_session(store, institute_id, case_obj["_id"], variant_type, category)
result_size = store.count_variants(case_obj["_id"], form.data, None, category)
session["filtered_variants"] = result_size
# if variants should be exported
if request.form.get("export"):
return controllers.download_variants(store, case_obj, variants_query)
data = controllers.sv_variants(
store, institute_obj, case_obj, variants_query, result_size, page
)
return dict(
institute=institute_obj,
case=case_obj,
dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
variant_type=variant_type,
form=form,
cytobands=cytobands,
severe_so_terms=SEVERE_SO_TERMS,
manual_rank_options=MANUAL_RANK_OPTIONS,
page=page,
expand_search=str(request.method == "POST"),
**data,
)
def cohorts(institute_id, case_name):
"""Add/remove institute tags."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
cohort_tag = request.form['cohort_tag']
if request.args.get('remove') == 'yes':
store.remove_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
else:
store.add_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis 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('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' if 'phenotype' in request.form else 'gene'
omim_id = request.form['omim_id']
remove = True if request.args.get('remove') == 'yes' else False
store.diagnose(institute_obj, case_obj, user_obj, link, level=level,
omim_id=omim_id, remove=remove)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis 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('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' if 'phenotype' in request.form else 'gene'
omim_id = request.form['omim_id']
remove = True if request.args.get('remove') == 'yes' else False
store.diagnose(institute_obj, case_obj, user_obj, link, level=level,
omim_id=omim_id, remove=remove)
return redirect(request.referrer)
def cohorts(institute_id, case_name):
"""Add/remove institute tags."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
cohort_tag = request.form['cohort_tag']
if request.args.get('remove') == 'yes':
store.remove_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
else:
store.add_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
return redirect(request.referrer)
def manual_rank(institute_id, case_name, variant_id):
"""Update the manual variant rank for a variant."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
new_manual_rank = int(request.form['manual_rank'])
link = request.referrer
store.update_manual_rank(institute_obj, case_obj, user_obj, link,
variant_obj, new_manual_rank)
return redirect(request.referrer)
def case(institute_id, case_name):
"""Display one case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
if not case_obj:
flash("Case {} does not exist in database!".format(case_name))
return redirect(request.referrer)
data = controllers.case(store, institute_obj, case_obj)
return dict(**data, )
def update_clinical_filter_hpo(store, current_user, institute_id, case_name,
hpo_clinical_filter):
"""Update HPO clinical filter use 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)
store.update_clinical_filter_hpo(institute_obj, case_obj, user_obj, link,
hpo_clinical_filter)
def variant(institute_id, case_name, variant_id):
"""Display a specific SNV variant."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
data = controllers.variant(store, institute_obj, case_obj, variant_id)
if data is None:
return abort(404)
if current_app.config.get('LOQUSDB_SETTINGS'):
data['observations'] = controllers.observations(
store, loqusdb, case_obj, data['variant'])
return dict(institute=institute_obj, case=case_obj, **data)
def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
action = request.form['action']
hpo_ids = request.form.getlist('hpo_id')
user_obj = store.user(current_user.email)
if action == 'DELETE':
for hpo_id in hpo_ids:
# DELETE a phenotype from the list
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_id)
elif action == 'PHENOMIZER':
if len(hpo_ids) == 0:
hpo_ids = [
term['phenotype_id']
for term in case_obj.get('phenotype_terms', [])
]
username = current_app.config['PHENOMIZER_USERNAME']
password = current_app.config['PHENOMIZER_PASSWORD']
diseases = controllers.hpo_diseases(username, password, hpo_ids)
return render_template('cases/diseases.html',
diseases=diseases,
institute=institute_obj,
case=case_obj)
elif action == 'GENES':
hgnc_symbols = set()
for raw_symbols in request.form.getlist('genes'):
# avoid empty lists
if raw_symbols:
hgnc_symbols.update(
raw_symbol.split(' ', 1)[0]
for raw_symbol in raw_symbols.split('|'))
store.update_dynamic_gene_list(case_obj, hgnc_symbols=hgnc_symbols)
elif action == 'GENERATE':
if len(hpo_ids) == 0:
hpo_ids = [
term['phenotype_id']
for term in case_obj.get('phenotype_terms', [])
]
results = store.generate_hpo_gene_list(*hpo_ids)
# determine how many HPO terms each gene must match
hpo_count = int(request.form.get('min_match') or 1)
hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
store.update_dynamic_gene_list(case_obj,
hgnc_ids=hgnc_ids,
phenotype_ids=hpo_ids)
return redirect(case_url)
def check_case(institute_id, case_name):
"""Mark a case that is has been checked.
This means to set case['needs_check'] to False
"""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
store.case_collection.find_one_and_update({"_id": case_obj["_id"]},
{"$set": {
"needs_check": False
}})
return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj,
new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
new_dismiss = request.form.getlist('dismiss_variant')
if request.form.getlist('dismiss_variant'):
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
if new_dismiss:
flash("Dismissed variant: {}".format(new_dismiss), 'info')
if variant_obj.get('dismiss_variant') and not new_dismiss:
if 'dismiss' in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
else:
log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
mosaic_tags = request.form.getlist('mosaic_tags')
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
if new_dismiss:
flash("Added mosaic tags: {}".format(mosaic_tags), 'info')
if variant_obj.get('mosaic_tags') and not mosaic_tags:
if 'mosaic' in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info')
return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj,
new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
new_dismiss = request.form.getlist('dismiss_variant')
if request.form.getlist('dismiss_variant'):
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
if new_dismiss:
flash("Dismissed variant: {}".format(new_dismiss), 'info')
if variant_obj.get('dismiss_variant') and not new_dismiss:
if 'dismiss' in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
else:
log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
mosaic_tags = request.form.getlist('mosaic_tags')
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
if new_dismiss:
flash("Added mosaic tags: {}".format(mosaic_tags), 'info')
if variant_obj.get('mosaic_tags') and not mosaic_tags:
if 'mosaic' in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info')
return redirect(request.referrer)
def gene_variants(institute_id):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj = institute_and_case(store, institute_id)
# populate form, conditional on request method
if(request.method == "POST"):
form = GeneVariantFiltersForm(request.form)
else:
form = GeneVariantFiltersForm(request.args)
variant_type = form.data.get('variant_type', 'clinical')
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
data = {}
if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0:
is_clinical = form.data.get('variant_type', 'clinical') == 'clinical'
clinical_symbols = store.clinical_symbols(case_obj) if is_clinical else None
for hgnc_symbol in form.hgnc_symbols.data:
if hgnc_symbol.isdigit():
hgnc_gene = store.hgnc_gene(int(hgnc_symbol))
if hgnc_gene is None:
not_found_ids.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
not_found_symbols.append(hgnc_symbol)
elif is_clinical and (hgnc_symbol not in clinical_symbols):
non_clinical_symbols.append(hgnc_symbol)
else:
hgnc_symbols.append(hgnc_symbol)
if (not_found_ids):
flash("HGNC id not found: {}".format(", ".join(not_found_ids)), 'warning')
if (not_found_symbols):
flash("HGNC symbol not found: {}".format(", ".join(not_found_symbols)), 'warning')
if (non_clinical_symbols):
flash("Gene not included in clinical list: {}".format(", ".join(non_clinical_symbols)), 'warning')
form.hgnc_symbols.data = hgnc_symbols
log.debug("query {}".format(form.data))
variants_query = store.gene_variants(query=form.data, category='snv',
variant_type=variant_type)
data = controllers.gene_variants(store, variants_query, page)
return dict(institute=institute_obj, form=form, page=page, **data)
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 pin_variant(institute_id, case_name, variant_id):
"""Pin and unpin variants to/from the list of suspects."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.pin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unpin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
return redirect(request.referrer or link)
def sanger(institute_id, case_name, variant_id):
"""Send Sanger email for confirming a variant."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
try:
controllers.sanger(store, mail, institute_obj, case_obj, user_obj,
variant_obj, current_app.config['MAIL_USERNAME'])
except controllers.MissingSangerRecipientError:
flash('No sanger recipients added to institute.', 'danger')
return redirect(request.referrer)
def cases(institute_id):
"""Display a list of cases for an institute."""
institute_obj = institute_and_case(store, institute_id)
query = request.args.get("query")
limit = 100
if request.args.get("limit"):
limit = int(request.args.get("limit"))
skip_assigned = request.args.get("skip_assigned")
is_research = request.args.get("is_research")
all_cases = store.cases(
collaborator=institute_id,
name_query=query,
skip_assigned=skip_assigned,
is_research=is_research,
)
sort_by = request.args.get("sort")
sort_order = request.args.get("order") or "asc"
if sort_by:
pymongo_sort = pymongo.ASCENDING
if sort_order == "desc":
pymongo_sort = pymongo.DESCENDING
if sort_by == "analysis_date":
all_cases.sort("analysis_date", pymongo_sort)
elif sort_by == "track":
all_cases.sort("track", pymongo_sort)
elif sort_by == "status":
all_cases.sort("status", pymongo_sort)
LOG.debug("Prepare all cases")
prioritized_cases = store.prioritized_cases(institute_id=institute_id)
data = controllers.cases(store, all_cases, prioritized_cases, limit)
data["sort_order"] = sort_order
data["sort_by"] = sort_by
data["nr_cases"] = store.nr_cases(institute_id=institute_id)
sanger_unevaluated = controllers.get_sanger_unevaluated(
store, institute_id, current_user.email)
if len(sanger_unevaluated) > 0:
data["sanger_unevaluated"] = sanger_unevaluated
return dict(
institute=institute_obj,
skip_assigned=skip_assigned,
is_research=is_research,
query=query,
**data,
)
def pin_variant(institute_id, case_name, variant_id):
"""Pin and unpin variants to/from the list of suspects."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.pin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unpin_variant(institute_obj, case_obj, user_obj, link, variant_obj)
return redirect(request.referrer or link)
def clinvar_submissions(institute_id):
"""Handle clinVar submission objects and files"""
institute_obj = institute_and_case(store, institute_id)
data = {
"submissions": controllers.clinvar_submissions(store, institute_id),
"institute": institute_obj,
"variant_header_fields": CLINVAR_HEADER,
"casedata_header_fields": CASEDATA_HEADER,
}
return data
def assign(institute_id, case_name, user_id=None):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get('action') == 'DELETE':
store.unassign(institute_obj, case_obj, user_obj, link)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def assign(institute_id, case_name, user_id=None):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get('action') == 'DELETE':
store.unassign(institute_obj, case_obj, user_obj, link)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def rerun_monitor(institute_id, case_name):
"""Request a case to be monitored for future reruns."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
if request.form.get("rerun_monitoring") == "monitor":
store.monitor(institute_obj, case_obj, user_obj, link)
else:
store.unmonitor(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
try:
controllers.variant_verification(store=store, mail=mail, institute_obj=institute_obj, case_obj=case_obj, user_obj=user_obj,
variant_obj=variant_obj, sender=current_app.config['MAIL_USERNAME'], variant_url=request.referrer, order=order, url_builder=url_for)
except controllers.MissingVerificationRecipientError:
flash('No verification recipients added to institute.', 'danger')
return redirect(request.referrer)
def upload_panel(store, institute_id, case_name, stream):
"""Parse out HGNC symbols from a stream."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
raw_symbols = [line.strip().split('\t')[0] for line in stream if
line and not line.startswith('#')]
# check if supplied gene symbols exist
hgnc_symbols = []
for raw_symbol in raw_symbols:
if store.hgnc_genes(raw_symbol).count() == 0:
flash("HGNC symbol not found: {}".format(raw_symbol), 'warning')
else:
hgnc_symbols.append(raw_symbol)
return hgnc_symbols
def cohorts(institute_id, case_name):
"""Add/remove institute tags."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
cohort_tag = request.form["cohort_tag"]
if request.args.get("remove") == "yes":
store.remove_cohort(institute_obj, case_obj, user_obj, link,
cohort_tag)
else:
store.add_cohort(institute_obj, case_obj, user_obj, link, cohort_tag)
return redirect("#".join([request.referrer, "cohorts"]))
def cases(institute_id):
"""Display a list of cases for an institute."""
institute_obj = institute_and_case(store, institute_id)
query = request.args.get('query')
skip_assigned = request.args.get('skip_assigned')
all_cases = store.cases(institute_id,
name_query=query,
skip_assigned=skip_assigned)
data = controllers.cases(store, all_cases)
return dict(institute=institute_obj,
skip_assigned=skip_assigned,
query=query,
**data)
def delivery_report(institute_id, case_name):
"""Display delivery report."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
if case_obj.get("delivery_report") is None:
return abort(404)
date_str = request.args.get("date")
if date_str is not None:
delivery_report = None
for analysis_data in case_obj.get("analyses", []):
if str(analysis_data["date"].date()) == date_str:
delivery_report = analysis_data["delivery_report"]
if delivery_report is None:
return abort(404)
else:
delivery_report = case_obj["delivery_report"]
out_dir = os.path.abspath(os.path.dirname(delivery_report))
filename = os.path.basename(delivery_report)
report_format = request.args.get("format", "html")
if report_format == "pdf":
try: # file could not be available
html_file = open(delivery_report, "r")
source_code = html_file.read()
bytes_file = html_to_pdf_file(source_code, "portrait", 300)
file_name = "_".join([
case_obj["display_name"],
datetime.datetime.now().strftime("%Y-%m-%d"),
"scout_delivery.pdf",
])
return send_file(
bytes_file,
download_name=file_name,
mimetype="application/pdf",
as_attachment=True,
)
except Exception as ex:
flash(
"An error occurred while downloading delivery report {} -- {}".
format(delivery_report, ex),
"warning",
)
LOG.error(
f"An error occurred while downloading delivery report {delivery_report} -- {ex}"
)
return send_from_directory(out_dir, filename)
def assign(institute_id, case_name, user_id=None, inactivate=False):
"""Assign and unassign a user from a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
if user_id:
user_obj = store.user(user_id)
else:
user_obj = store.user(current_user.email)
if request.form.get("action") == "DELETE":
store.unassign(institute_obj, case_obj, user_obj, link, inactivate)
else:
store.assign(institute_obj, case_obj, user_obj, link)
return redirect(request.referrer)
def status(institute_id, case_name):
"""Update status of a specific case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
status = request.form.get('status', case_obj['status'])
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if status == 'archive':
store.archive_case(institute_obj, case_obj, user_obj, status, link)
else:
store.update_status(institute_obj, case_obj, user_obj, status, link)
return redirect(request.referrer)
def case(institute_id, case_name):
"""Display one case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
if not case_obj:
flash("Case {} does not exist in database!".format(case_name))
return redirect(request.referrer)
data = controllers.case(store, institute_obj, case_obj)
return dict(institute=institute_obj,
case=case_obj,
mme_nodes=current_app.mme_nodes,
tissue_types=SAMPLE_SOURCE,
**data)
def cancer_variants(store, request_args, institute_id, case_name):
"""Fetch data related to cancer variants for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = CancerFiltersForm(request_args)
variants_query = store.variants(case_obj['_id'], category='cancer', query=form.data).limit(50)
data = dict(
institute=institute_obj,
case=case_obj,
variants=(parse_variant(store, institute_obj, case_obj, variant, update=True) for
variant in variants_query),
form=form,
variant_type=request_args.get('variant_type', 'clinical'),
)
return data
def share(institute_id, case_name):
"""Share a case with a different institute."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
collaborator_id = request.form['collaborator']
revoke_access = 'revoke' in request.form
link = url_for('.case', institute_id=institute_id, case_name=case_name)
if revoke_access:
store.unshare(institute_obj, case_obj, collaborator_id, user_obj, link)
else:
store.share(institute_obj, case_obj, collaborator_id, user_obj, link)
return redirect(request.referrer)
def mark_causative(institute_id, case_name, variant_id):
"""Mark a variant as confirmed causative."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
if request.form['action'] == 'ADD':
store.mark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
elif request.form['action'] == 'DELETE':
store.unmark_causative(institute_obj, case_obj, user_obj, link, variant_obj)
# send the user back to the case that was marked as solved
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
return redirect(case_url)
def variant(institute_id, case_name, variant_id):
"""Display a specific SNV variant."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
log.debug("Variants view requesting data for variant {}".format(variant_id))
data = controllers.variant(store, institute_obj, case_obj, variant_id=variant_id)
if data is None:
log.warning("An error occurred: variants view requesting data for variant {}".format(variant_id))
flash('An error occurred while retrieving variant object', 'danger')
return redirect(request.referrer)
if current_app.config.get('LOQUSDB_SETTINGS'):
data['observations'] = controllers.observations(store, loqusdb,
case_obj, data['variant'])
data['cancer'] = request.args.get('cancer') == 'yes'
return dict(institute=institute_obj, case=case_obj, **data)
def verify(institute_id, case_name, variant_id, variant_category, order):
"""Start procedure to validate variant using other techniques."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
comment = request.form.get('verification_comment')
try:
controllers.variant_verification(store=store, mail=mail, institute_obj=institute_obj, case_obj=case_obj, user_obj=user_obj, comment=comment,
variant_obj=variant_obj, sender=current_app.config['MAIL_USERNAME'], variant_url=request.referrer, order=order, url_builder=url_for)
except controllers.MissingVerificationRecipientError:
flash('No verification recipients added to institute.', 'danger')
return redirect(request.referrer)
def pdf_case_report(institute_id, case_name):
"""Download a pdf report for a case"""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = controllers.case_report_content(store, institute_obj, case_obj)
# add coverage report on the bottom of this report
if current_app.config.get('SQLALCHEMY_DATABASE_URI'):
data['coverage_report'] = controllers.coverage_report_contents(store, institute_obj, case_obj, request.url_root)
# workaround to be able to print the case pedigree to pdf
if case_obj.get('madeline_info') is not None:
with open(os.path.join(cases_bp.static_folder, 'madeline.svg'), 'w') as temp_madeline:
temp_madeline.write(case_obj['madeline_info'])
html_report = render_template('cases/case_report.html', institute=institute_obj, case=case_obj, format='pdf', **data)
return render_pdf(HTML(string=html_report), download_filename=case_obj['display_name']+'_'+datetime.datetime.now().strftime("%Y-%m-%d")+'_scout.pdf')
def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
variants = store.check_causatives(institute_obj=institute_obj)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj['case_id'] not in all_cases:
case_obj = store.case(variant_obj['case_id'])
all_cases[variant_obj['case_id']] = case_obj
else:
case_obj = all_cases[variant_obj['case_id']]
if variant_obj['variant_id'] not in all_variants:
all_variants[variant_obj['variant_id']] = []
all_variants[variant_obj['variant_id']].append((case_obj, variant_obj))
return dict(institute=institute_obj, variant_groups=all_variants)
def str_variants(institute_id, case_name):
"""Display a list of STR variants."""
page = int(request.args.get('page', 1))
variant_type = request.args.get('variant_type', 'clinical')
form = StrFiltersForm(request.args)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
query = form.data
query['variant_type'] = variant_type
variants_query = store.variants(case_obj['_id'], category='str',
query=query)
data = controllers.str_variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj, case=case_obj,
variant_type = variant_type, form=form, page=page, **data)
def phenotypes_actions(institute_id, case_name):
"""Perform actions on multiple phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
action = request.form['action']
hpo_ids = request.form.getlist('hpo_id')
user_obj = store.user(current_user.email)
if action == 'DELETE':
for hpo_id in hpo_ids:
# DELETE a phenotype from the list
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url, hpo_id)
elif action == 'PHENOMIZER':
if len(hpo_ids) == 0:
hpo_ids = [term['phenotype_id'] for term in case_obj.get('phenotype_terms', [])]
username = current_app.config['PHENOMIZER_USERNAME']
password = current_app.config['PHENOMIZER_PASSWORD']
diseases = controllers.hpo_diseases(username, password, hpo_ids)
return render_template('cases/diseases.html', diseases=diseases,
institute=institute_obj, case=case_obj)
elif action == 'GENES':
hgnc_symbols = set()
for raw_symbols in request.form.getlist('genes'):
# avoid empty lists
if raw_symbols:
hgnc_symbols.update(raw_symbol.split(' ', 1)[0] for raw_symbol in
raw_symbols.split('|'))
store.update_dynamic_gene_list(case_obj, hgnc_symbols=hgnc_symbols)
elif action == 'GENERATE':
if len(hpo_ids) == 0:
hpo_ids = [term['phenotype_id'] for term in case_obj.get('phenotype_terms', [])]
results = store.generate_hpo_gene_list(*hpo_ids)
# determine how many HPO terms each gene must match
hpo_count = int(request.form.get('min_match') or 1)
hgnc_ids = [result[0] for result in results if result[1] >= hpo_count]
store.update_dynamic_gene_list(case_obj, hgnc_ids=hgnc_ids, phenotype_ids=hpo_ids)
return redirect(case_url)
def delivery_report(institute_id, case_name):
"""Display delivery report."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
if case_obj.get('delivery_report') is None:
return abort(404)
date_str = request.args.get('date')
if date_str:
delivery_report = None
analysis_date = parse_date(date_str)
for analysis_data in case_obj['analyses']:
if analysis_data['date'] == analysis_date:
delivery_report = analysis_data['delivery_report']
if delivery_report is None:
return abort(404)
else:
delivery_report = case_obj['delivery_report']
out_dir = os.path.dirname(delivery_report)
filename = os.path.basename(delivery_report)
return send_from_directory(out_dir, filename)
def cases(institute_id):
"""Display a list of cases for an institute."""
institute_obj = institute_and_case(store, institute_id)
query = request.args.get('query')
limit = 100
if request.args.get('limit'):
limit = int(request.args.get('limit'))
skip_assigned = request.args.get('skip_assigned')
is_research = request.args.get('is_research')
all_cases = store.cases(collaborator=institute_id, name_query=query,
skip_assigned=skip_assigned, is_research=is_research)
data = controllers.cases(store, all_cases, limit)
sanger_unevaluated = controllers.get_sanger_unevaluated(store, institute_id, current_user.email)
if len(sanger_unevaluated)> 0:
data['sanger_unevaluated'] = sanger_unevaluated
return dict(institute=institute_obj, skip_assigned=skip_assigned,
is_research=is_research, query=query, **data)
def rerun(store, mail, current_user, institute_id, case_name, sender, recipient):
"""Request a rerun by email."""
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)
store.request_rerun(institute_obj, case_obj, user_obj, link)
# this should send a JSON document to the SuSy API in the future
html = """
<p>{institute}: {case} ({case_id})</p>
<p>Re-run requested by: {name}</p>
""".format(institute=institute_obj['display_name'],
case=case_obj['display_name'], case_id=case_obj['_id'],
name=user_obj['name'].encode())
# compose and send the email message
msg = Message(subject=("SCOUT: request RERUN for {}"
.format(case_obj['display_name'])),
html=html, sender=sender, recipients=[recipient],
# cc the sender of the email for confirmation
cc=[user_obj['email']])
mail.send(msg)
def events(institute_id, case_name, event_id=None):
"""Handle events."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
link = request.form.get('link')
content = request.form.get('content')
variant_id = request.args.get('variant_id')
user_obj = store.user(current_user.email)
if event_id:
# delete the event
store.delete_event(event_id)
else:
if variant_id:
# create a variant comment
variant_obj = store.variant(variant_id)
level = request.form.get('level', 'specific')
store.comment(institute_obj, case_obj, user_obj, link,
variant=variant_obj, content=content, comment_level=level)
else:
# create a case comment
store.comment(institute_obj, case_obj, user_obj, link, content=content)
return redirect(request.referrer)
