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 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 variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.args.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = FiltersForm(request.args)
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in case_obj.get('panels', [])]
form.gene_panels.choices = panel_choices
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = controllers.variants(store, variants_query, page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_type = request.args.get('variant_type', 'clinical')
# Update filter settings if Clinical Filter was requested
default_panels = []
for panel in case_obj['panels']:
if panel.get('is_default'):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type':
'clinical',
'region_annotations': ['exonic', 'splicing'],
'functional_annotations':
SEVERE_SO_TERMS,
'clinsig': [4, 5],
'clinsig_confident_always_returned':
True,
'gnomad_frequency':
str(institute_obj['frequency_cutoff']),
'variant_type':
'clinical',
'gene_panels':
default_panels
})
if (request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = FiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = FiltersForm(request.form)
else:
form = FiltersForm(request.args)
# populate available panel choices
available_panels = case_obj.get('panels', []) + [{
'panel_name': 'hpo',
'display_name': 'HPO'
}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# upload gene panel if symbol file exists
if (request.files):
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != '':
log.debug("Upload file request files: {0}".format(
request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode('utf-8'),
newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", 'warning')
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(store, institute_id,
case_name, stream)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ''
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=str(case_obj['display_name']) +
'-filtered_variants.csv')
# return a csv with the exported variants
return Response(generate(",".join(document_header), export_lines),
mimetype='text/csv',
headers=headers)
data = controllers.variants(store, institute_obj, case_obj, variants_query,
page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
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')
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = SvFiltersForm(request.form)
default_panels = []
for panel in case_obj['panels']:
if panel['is_default']:
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type':
'clinical',
'region_annotations': ['exonic', 'splicing'],
'functional_annotations':
SEVERE_SO_TERMS,
'thousand_genomes_frequency':
str(institute_obj['frequency_cutoff']),
'variant_type':
'clinical',
'clingen_ngi':
10,
'swegen':
10,
'size':
100,
'gene_panels':
default_panels
})
if (request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = SvFiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = SvFiltersForm(request.form)
else:
form = SvFiltersForm(request.args)
available_panels = case_obj.get('panels', []) + [{
'panel_name': 'hpo',
'display_name': 'HPO'
}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
variants_query = store.variants(case_obj['_id'],
category='sv',
query=form.data)
data = {}
# if variants should be exported
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
# Return max 500 variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=str(case_obj['display_name']) +
'-filtered_sv-variants.csv')
return Response(
generate(",".join(document_header), export_lines),
mimetype='text/csv',
headers=headers) # return a csv with the exported variants
else:
data = controllers.sv_variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj,
case=case_obj,
variant_type=variant_type,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.args.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = FiltersForm(request.args)
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in case_obj.get('panels', [])]
form.gene_panels.choices = panel_choices
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
if 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:
flash("HGNC id not found: {}".format(hgnc_symbol),
'warning')
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
flash("HGNC symbol not found: {}".format(hgnc_symbol),
'warning')
elif is_clinical and (hgnc_symbol not in clinical_symbols):
flash(
"Gene not included in clinical list: {}".format(
hgnc_symbol), 'warning')
else:
hgnc_symbols.append(hgnc_symbol)
form.hgnc_symbols.data = hgnc_symbols
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.args.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(
store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition',
'attachment',
filename=str(case_obj['_id']) + '-filtered_variants.csv')
return Response(
generate(",".join(document_header), export_lines),
mimetype='text/csv',
headers=headers) # return a csv with the exported variants
else:
data = controllers.variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.args.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
form = FiltersForm(request.args)
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in case_obj.get('panels', [])]
form.gene_panels.choices = panel_choices
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case',
institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active',
case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
if 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:
flash("HGNC id not found: {}".format(hgnc_symbol),
'warning')
else:
hgnc_symbols.append(hgnc_gene['hgnc_symbol'])
elif store.hgnc_genes(hgnc_symbol).count() == 0:
flash("HGNC symbol not found: {}".format(hgnc_symbol),
'warning')
elif is_clinical and (hgnc_symbol not in clinical_symbols):
flash(
"Gene not included in clinical list: {}".format(
hgnc_symbol), 'warning')
else:
hgnc_symbols.append(hgnc_symbol)
form.hgnc_symbols.data = hgnc_symbols
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(
set(term_obj['hgnc_symbol']
for term_obj in case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = controllers.variants(store, institute_obj, case_obj, variants_query,
page)
return dict(institute=institute_obj,
case=case_obj,
form=form,
severe_so_terms=SEVERE_SO_TERMS,
page=page,
**data)
def variants(institute_id, case_name):
"""Display a list of SNV variants."""
page = int(request.form.get('page', 1))
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_type = request.args.get('variant_type', 'clinical')
# Update filter settings if Clinical Filter was requested
default_panels = []
for panel in case_obj['panels']:
if panel.get('is_default'):
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'clinsig': [4,5],
'clinsig_confident_always_returned': True,
'gnomad_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = FiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = FiltersForm(request.form)
else:
form = FiltersForm(request.args)
# populate available panel choices
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
# upload gene panel if symbol file exists
if (request.files):
file = request.files[form.symbol_file.name]
if request.files and file and file.filename != '':
log.debug("Upload file request files: {0}".format(request.files.to_dict()))
try:
stream = io.StringIO(file.stream.read().decode('utf-8'), newline=None)
except UnicodeDecodeError as error:
flash("Only text files are supported!", 'warning')
return redirect(request.referrer)
hgnc_symbols_set = set(form.hgnc_symbols.data)
log.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set))
new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream)
hgnc_symbols_set.update(new_hgnc_symbols)
form.hgnc_symbols.data = hgnc_symbols_set
# reset gene panels
form.gene_panels.data = ''
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
# check if supplied gene symbols exist
hgnc_symbols = []
non_clinical_symbols = []
not_found_symbols = []
not_found_ids = []
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
# handle HPO gene list separately
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
variants_query = store.variants(case_obj['_id'], query=form.data)
data = {}
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
if form.data['chrom'] == 'MT':
# Return all MT variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query)
else:
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_variants.csv')
# return a csv with the exported variants
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv',
headers=headers)
data = controllers.variants(store, institute_obj, case_obj, variants_query, page)
return dict(institute=institute_obj, case=case_obj, form=form,
severe_so_terms=SEVERE_SO_TERMS, page=page, **data)
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')
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
form = SvFiltersForm(request.form)
default_panels = []
for panel in case_obj['panels']:
if panel['is_default']:
default_panels.append(panel['panel_name'])
request.form.get('gene_panels')
if bool(request.form.get('clinical_filter')):
clinical_filter = MultiDict({
'variant_type': 'clinical',
'region_annotations': ['exonic','splicing'],
'functional_annotations': SEVERE_SO_TERMS,
'thousand_genomes_frequency': str(institute_obj['frequency_cutoff']),
'variant_type': 'clinical',
'clingen_ngi': 10,
'swegen': 10,
'size': 100,
'gene_panels': default_panels
})
if(request.method == "POST"):
if bool(request.form.get('clinical_filter')):
form = SvFiltersForm(clinical_filter)
form.csrf_token = request.args.get('csrf_token')
else:
form = SvFiltersForm(request.form)
else:
form = SvFiltersForm(request.args)
available_panels = case_obj.get('panels', []) + [
{'panel_name': 'hpo', 'display_name': 'HPO'}]
panel_choices = [(panel['panel_name'], panel['display_name'])
for panel in available_panels]
form.gene_panels.choices = panel_choices
if form.data['gene_panels'] == ['hpo']:
hpo_symbols = list(set(term_obj['hgnc_symbol'] for term_obj in
case_obj['dynamic_gene_list']))
form.hgnc_symbols.data = hpo_symbols
# update status of case if vistited for the first time
if case_obj['status'] == 'inactive' and not current_user.is_admin:
flash('You just activated this case!', 'info')
user_obj = store.user(current_user.email)
case_link = url_for('cases.case', institute_id=institute_obj['_id'],
case_name=case_obj['display_name'])
store.update_status(institute_obj, case_obj, user_obj, 'active', case_link)
variants_query = store.variants(case_obj['_id'], category='sv',
query=form.data)
data = {}
# if variants should be exported
if request.form.get('export'):
document_header = controllers.variants_export_header(case_obj)
export_lines = []
# Return max 500 variants
export_lines = controllers.variant_export_lines(store, case_obj, variants_query.limit(500))
def generate(header, lines):
yield header + '\n'
for line in lines:
yield line + '\n'
headers = Headers()
headers.add('Content-Disposition','attachment', filename=str(case_obj['display_name'])+'-filtered_sv-variants.csv')
return Response(generate(",".join(document_header), export_lines), mimetype='text/csv', headers=headers) # return a csv with the exported variants
else:
data = controllers.sv_variants(store, institute_obj, case_obj,
variants_query, page)
return dict(institute=institute_obj, case=case_obj, variant_type=variant_type,
form=form, severe_so_terms=SEVERE_SO_TERMS, page=page, **data)
