def variant(institute_id, case_id, variant_id):
"""View a single variant in a single case."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
comments = store.events(institute, case=case_model, variant_id=variant_model.variant_id, comments=True)
events = store.events(institute, case=case_model, variant_id=variant_model.variant_id)
individuals = {individual.individual_id: individual for individual in case_model.individuals}
prev_variant = store.previous_variant(document_id=variant_id)
next_variant = store.next_variant(document_id=variant_id)
return dict(
institute=institute,
institute_id=institute_id,
case=case_model,
case_id=case_id,
variant=variant_model,
variant_id=variant_id,
comments=comments,
events=events,
prev_variant=prev_variant,
next_variant=next_variant,
manual_rank_options=Variant.manual_rank.choices,
individuals=individuals,
)
def variant(institute_id, case_id, variant_id):
"""View a single variant in a single case."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
comments = store.events(institute,
case=case_model,
variant_id=variant_model.variant_id,
comments=True)
events = store.events(institute,
case=case_model,
variant_id=variant_model.variant_id)
prev_variant = store.previous_variant(document_id=variant_id)
next_variant = store.next_variant(document_id=variant_id)
return dict(institute=institute,
institute_id=institute_id,
case=case_model,
case_id=case_id,
variant=variant_model,
variant_id=variant_id,
comments=comments,
events=events,
prev_variant=prev_variant,
next_variant=next_variant,
manual_rank_options=Variant.manual_rank.choices)
def email_sanger(institute_id, case_id, variant_id):
# very basic security check
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
recipients = institute.sanger_recipients
if len(recipients) == 0:
flash('No sanger recipients added to the institute.')
return abort(403)
# build variant page URL
variant_url = url_for('.variant', institute_id=institute_id,
case_id=case_id, variant_id=variant_id)
hgnc_symbol = ', '.join(variant_model.hgnc_symbols)
functions = ["<li>{}</li>".format(function) for function in
variant_model.protein_changes]
gtcalls = ["<li>{}: {}</li>".format(individual.display_name,
individual.genotype_call)
for individual in variant_model.samples]
html = """
<p>Case {case_id}: <a href='{url}'>{variant_id}</a></p>
<p>HGNC symbol: {hgnc_symbol}</p>
<p>Database: {database_id}</p>
<p>Chr position: {chromosome_position}</p>
<p>Amino acid change(s): <br> <ul>{functions}</ul></p><br>
<p>GT-call: <br> <ul>{gtcalls}</ul></p><br>
<p>Ordered by: {name}</p>
""".format(
case_id=case_id,
url=variant_url,
variant_id=variant_id,
hgnc_symbol=hgnc_symbol,
database_id='coming soon',
chromosome_position=variant_model.display_name,
functions=''.join(functions),
gtcalls=''.join(gtcalls),
name=current_user.name
)
kwargs = dict(
subject="SCOUT: Sanger sequencing of %s" % hgnc_symbol,
html=html,
sender=current_app.config['MAIL_USERNAME'],
recipients=recipients,
# cc the sender of the email for confirmation
cc=[current_user.email]
)
# compose and send the email message
msg = Message(**kwargs)
mail.send(msg)
link = url_for('.case', institute_id=institute_id, case_id=case_id)
store.order_sanger(institute, case_model, current_user, link, variant_model)
return redirect(variant_url)
def unpin_variant(institute_id, case_id, variant_id):
"""Pin or unpin a variant from the list of suspects."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
link = url_for(".variant", institute_id=institute_id, case_id=case_id, variant_id=variant_id)
store.unpin_variant(institute, case_model, current_user, link, variant_model)
return redirect(request.args.get("next") or request.referrer or link)
def mark_causative(institute_id, case_id, variant_id):
"""Mark a variant as confirmed causative."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
link = url_for(".variant", institute_id=institute_id, case_id=case_id, variant_id=variant_id)
case_url = url_for(".case", institute_id=institute_id, case_id=case_id)
store.mark_causative(institute, case_model, current_user, link, variant_model)
# send the user back to the case the was marked as solved
return redirect(case_url)
def unpin_variant(institute_id, case_id, variant_id):
"""Pin or unpin a variant from the list of suspects."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
link = url_for('.variant',
institute_id=institute_id,
case_id=case_id,
variant_id=variant_id)
store.unpin_variant(institute, case_model, current_user, link,
variant_model)
return redirect(request.args.get('next') or request.referrer or link)
def unmark_causative(institute_id, case_id, variant_id):
"""Remove a variant as confirmed causative for a case."""
# very basic security check
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
case_url = url_for(".case", institute_id=institute_id, case_id=case_id)
# skip the host part of the URL to make it more flexible
link = request.referrer.replace(request.host_url, "/")
variant_model = store.variant(document_id=variant_id)
store.unmark_causative(institute, case_model, current_user, link, variant_model)
# send the user back to the case the was marked as solved
return redirect(request.referrer or case_url)
def mark_causative(institute_id, case_id, variant_id):
"""Mark a variant as confirmed causative."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
link = url_for('.variant',
institute_id=institute_id,
case_id=case_id,
variant_id=variant_id)
case_url = url_for('.case', institute_id=institute_id, case_id=case_id)
store.mark_causative(institute, case_model, current_user, link,
variant_model)
# send the user back to the case the was marked as solved
return redirect(case_url)
def email_sanger(institute_id, case_id, variant_id):
# very basic security check
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
variant_model = store.variant(document_id=variant_id)
recipients = institute.sanger_recipients
if len(recipients) == 0:
flash('No sanger recipients added to the institute.')
return abort(403)
# build variant page URL
variant_url = url_for('.variant',
institute_id=institute_id,
case_id=case_id,
variant_id=variant_id)
hgnc_symbol = ', '.join(variant_model.hgnc_symbols)
functions = [
"<li>{}</li>".format(function)
for function in variant_model.protein_changes
]
gtcalls = [
"<li>{}: {}</li>".format(individual.display_name,
individual.genotype_call)
for individual in variant_model.samples
]
html = """
<p>Case {case_id}: <a href='{url}'>{variant_id}</a></p>
<p>HGNC symbol: {hgnc_symbol}</p>
<p>Database: {database_id}</p>
<p>Chr position: {chromosome_position}</p>
<p>Amino acid change(s): <br> <ul>{functions}</ul></p><br>
<p>GT-call: <br> <ul>{gtcalls}</ul></p><br>
<p>Ordered by: {name}</p>
""".format(case_id=case_id,
url=variant_url,
variant_id=variant_id,
hgnc_symbol=hgnc_symbol,
database_id='coming soon',
chromosome_position=variant_model.display_name,
functions=''.join(functions),
gtcalls=''.join(gtcalls),
name=current_user.name)
kwargs = dict(
subject="SCOUT: Sanger sequencing of %s" % hgnc_symbol,
html=html,
sender=current_app.config['MAIL_USERNAME'],
recipients=recipients,
# cc the sender of the email for confirmation
cc=[current_user.email])
# compose and send the email message
msg = Message(**kwargs)
mail.send(msg)
link = url_for('.case', institute_id=institute_id, case_id=case_id)
store.order_sanger(institute, case_model, current_user, link,
variant_model)
return redirect(variant_url)