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 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 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)
if diseases:
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("#".join([case_url, "phenotypes_panel"]))
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 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
hpo_term = None
omim_term = None
phenotype_term = request.form["hpo_term"]
phenotype_inds = request.form.getlist(
"phenotype_inds") # Individual-level phenotypes
if phenotype_term.startswith("HP:") or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(" | ", 1)[0]
else:
omim_term = phenotype_term
store.add_phenotype(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=case_url,
hpo_term=hpo_term,
omim_term=omim_term,
is_group=is_group,
phenotype_inds=phenotype_inds,
)
except ValueError:
flash(
f"Unable to add phenotype for the given terms:{phenotype_term}",
"warning",
)
return redirect(case_url)
return redirect("#".join([case_url, "phenotypes_panel"]))
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 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 == "ADDGENE":
hgnc_symbol = None
for raw_symbol in request.form.getlist("genes"):
LOG.debug("raw gene: {}".format(raw_symbol))
# avoid empty lists
if raw_symbol:
# take the first nubmer before |, and remove any space.
try:
hgnc_symbol_split = raw_symbol.split("|", 1)[0]
hgnc_symbol = int(hgnc_symbol_split.replace(" ", ""))
except ValueError:
flash(
"Provided gene info could not be parsed! "
"Please allow autocompletion to finish.",
"warning",
)
LOG.debug("Parsed HGNC symbol {}".format(hgnc_symbol))
store.update_dynamic_gene_list(case_obj,
hgnc_ids=[hgnc_symbol],
add_only=True)
elif action == "GENES":
hgnc_symbols = set()
for raw_symbols in request.form.getlist("genes"):
LOG.debug("raw gene list: {}".format(raw_symbols))
# avoid empty lists
if raw_symbols:
try:
hgnc_symbols.update(
raw_symbol.split(" ", 1)[0]
for raw_symbol in raw_symbols.split("|"))
except ValueError:
flash(
"Provided gene info could not be parsed! "
"Please allow autocompletion to finish.",
"warning",
)
LOG.debug("HGNC symbols {}".format(hgnc_symbols))
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)
