def open_research(institute_id, case_id):
"""Open the research list for a case."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
# send email to trigger manual load of research variants
main_recipient = current_app.config['RESEARCH_MODE_RECIPIENT']
# this should send a JSON document to the SuSy API in the future
html = """
<p>{institute}: {case} ({case_id})</p>
<p>Requested by: {name}</p>
""".format(institute=institute.display_name, case=case_model.display_name,
case_id=case_model.id, name=current_user.name)
# compose and send the email message
msg = Message(subject=("SCOUT: open research mode for {}"
.format(case_model.display_name)),
html=html,
sender=current_app.config['MAIL_USERNAME'],
recipients=[main_recipient],
# cc the sender of the email for confirmation
cc=[current_user.email])
mail.send(msg)
link = url_for('.case', institute_id=institute_id, case_id=case_id)
store.open_research(institute, case_model, current_user, link)
return redirect(url_for('.case', institute_id=institute_id, case_id=case_id))
def open_research(institute_id, case_id):
"""Open the research list for a case."""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
# send email to trigger manual load of research variants
main_recipient = current_app.config['RESEARCH_MODE_RECIPIENT']
# this should send a JSON document to the SuSy API in the future
html = """
<p>{institute}: {case} ({case_id})</p>
<p>Requested by: {name}</p>
""".format(institute=institute.display_name,
case=case_model.display_name,
case_id=case_model.id,
name=current_user.name)
# compose and send the email message
msg = Message(
subject=("SCOUT: open research mode for {}".format(
case_model.display_name)),
html=html,
sender=current_app.config['MAIL_USERNAME'],
recipients=[main_recipient],
# cc the sender of the email for confirmation
cc=[current_user.email])
mail.send(msg)
link = url_for('.case', institute_id=institute_id, case_id=case_id)
store.open_research(institute, case_model, current_user, link)
return redirect(
url_for('.case', institute_id=institute_id, case_id=case_id))
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 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)
