def withdraw_sequence(id):
seq = check_seq_withdraw(id)
if seq is not None:
add_history(current_user, 'Published version %s withdrawn' % seq.release_version, seq, db, body = '')
send_mail('Sequence %s version %d withdrawn by the IARC %s Committee' % (seq.description_id, seq.release_version, seq.species), [seq.species], 'iarc_sequence_withdrawn', reviewer=current_user, user_name=seq.maintainer, sequence=seq, comment='')
seq.status = 'withdrawn'
db.session.commit()
seq.duplicate_sequences = list()
flash('Sequence %s withdrawn' % seq.sequence_name)
related_subs = []
for inf in seq.inferred_sequences:
related_subs.append(inf.submission)
# un-publish any related submissions that now don't have published sequences
published_seqs = db.session.query(GeneDescription).filter_by(species=seq.species, status='published').all()
for related_sub in related_subs:
other_published = False
for ps in published_seqs:
for inf in ps.inferred_sequences:
if inf.submission == related_sub:
other_published = True
break
if not other_published:
related_sub.submission_status = 'reviewing'
related_sub.public = False
add_history(current_user, 'Status changed from published to reviewing as submission %s was withdrawn.' % seq.description_id, related_sub, db, body = '')
db.session.commit()
return ''
def sequence_imgt_name():
if request.is_json:
content = request.get_json()
seq = check_seq_draft(content['id'])
if seq is not None:
seq.imgt_name = content['imgt_name']
add_history(current_user, 'IMGT Name updated to %s' % seq.imgt_name, seq, db, body='IMGT Name updated.')
send_mail('Sequence %s version %d: IMGT name updated to %s by the IARC %s Committee' % (seq.description_id, seq.release_version, seq.imgt_name, seq.species), [seq.species], 'iarc_sequence_released', reviewer=current_user, user_name=seq.maintainer, sequence=seq, comment='IMGT Name updated to %s' % seq.imgt_name)
db.session.commit()
return json.dumps({'success':True}), 200, {'ContentType':'application/json'}
return ''
def new_germline_set(species):
if not current_user.has_role(species):
return redirect('/')
form = NewGermlineSetForm()
form.locus.choices = ['IGH', 'IGK', 'IGL', 'TRA', 'TRB', 'TRG', 'TRD']
if request.method == 'POST':
if form.cancel.data:
return redirect('/germline_sets')
if form.validate():
try:
if db.session.query(GermlineSet).filter(
and_(
GermlineSet.species == species,
GermlineSet.germline_set_name == form.name.data,
~GermlineSet.status.in_(
['withdrawn', 'superceded']))).count() > 0:
form.new_name.errors = [
'A germline set already exists with that name.'
]
raise ValidationError()
germline_set = GermlineSet()
germline_set.species = species
germline_set.status = 'draft'
germline_set.author = current_user.name
germline_set.lab_address = current_user.address
germline_set.release_version = 0
germline_set.locus = form.locus.data
germline_set.germline_set_name = form.name.data
db.session.add(germline_set)
db.session.commit()
germline_set.germline_set_id = "G%05d" % germline_set.id
add_history(
current_user, '%s germline set %s (%s) created' %
(germline_set.species, germline_set.germline_set_id,
germline_set.germline_set_name), germline_set, db)
db.session.commit()
return redirect('/germline_sets')
except ValidationError as e:
return render_template('germline_set_new.html',
form=form,
species=species)
return render_template('germline_set_new.html', form=form, species=species)
def publish_sequence(seq, notes, email):
old_seq = db.session.query(GeneDescription).filter_by(description_id=seq.description_id,
status='published').one_or_none()
if old_seq:
old_seq.status = 'superceded'
old_seq.duplicate_sequences = list()
seq.release_version = old_seq.release_version + 1
else:
seq.release_version = 1
# Mark any referenced submissions as public
for inferred_sequence in seq.inferred_sequences:
sub = inferred_sequence.submission
if not inferred_sequence.submission.public:
inferred_sequence.submission.public = True
db.session.commit()
add_history(current_user, 'Submission published', sub, db)
send_mail(
'Submission %s accepted and published by the IARC %s Committee' % (sub.submission_id, sub.species),
[sub.submitter_email], 'user_submission_published', reviewer=current_user, user_name=sub.submitter_name,
submission=sub, sequence=seq)
send_mail(
'Submission %s accepted and published by the IARC %s Committee' % (sub.submission_id, sub.species),
[sub.species], 'iarc_submission_published', reviewer=current_user, user_name=sub.submitter_name,
submission=sub, sequence=seq)
# Make a note in submission history if we haven't already
title = 'Sequence %s listed in affirmation' % inferred_sequence.sequence_details.sequence_id
entry = db.session.query(JournalEntry).filter_by(type='note', submission=sub, title=title).all()
if not entry:
add_note(current_user, title, safe_textile(
'* Sequence: %s\n* Genotype: %s\n* Subject ID: %s\nis referenced in affirmation %s (sequence name %s)' %
(inferred_sequence.sequence_details.sequence_id, inferred_sequence.genotype_description.genotype_name,
inferred_sequence.genotype_description.genotype_subject_id, seq.description_id, seq.sequence_name)),
sub, db)
seq.release_date = datetime.date.today()
add_history(current_user, 'Version %s published' % seq.release_version, seq, db, body=notes)
if email:
send_mail('Sequence %s version %d published by the IARC %s Committee' % (
seq.description_id, seq.release_version, seq.species), [seq.species], 'iarc_sequence_released',
reviewer=current_user, user_name=seq.maintainer, sequence=seq, comment=notes)
seq.release_description = notes
seq.status = 'published'
db.session.commit()
def withdraw_germline_set(id):
set = check_set_withdraw(id)
if set is not None:
add_history(current_user,
'Published version %s withdrawn' % set.release_version,
set,
db,
body='')
send_mail(
'Germline set %s version %d withdrawn by the IARC %s Committee' %
(set.germline_set_id, set.release_version, set.species),
[set.species],
'iarc_germline_set_withdrawn',
reviewer=current_user,
user_name=set.author,
germline_set=set,
comment='')
set.status = 'withdrawn'
db.session.commit()
flash('Germline set %s withdrawn' % set.germline_set_name)
db.session.commit()
return ''
def submission(id):
sub = db.session.query(Submission).filter_by(
submission_id=id).one_or_none()
if sub is None or not (sub.can_see(current_user)
or current_user.has_role('Admin')):
flash('Submission not found')
return redirect('/submissions')
(form, tables) = setup_submission_view_forms_and_tables(
sub, db, sub.can_see_private(current_user))
reviewer = (current_user.has_role(sub.species)
or current_user in sub.delegates)
if request.method == 'GET':
return render_template(
'submission_view.html',
sub=sub,
tables=tables,
form=form,
reviewer=reviewer,
id=id,
jump="",
status=sub.submission_status,
attachment=len(sub.notes_entries[0].attached_files) > 0)
else:
if not reviewer:
flash('Submission not found')
return redirect('/submissions')
# Check for additions/deletions to editable tables, and any errors flagged up by validation in check_add_item
editable_tables = {'delegate_table': tables['delegate_table']}
validation_result = process_table_updates(editable_tables, request, db)
if validation_result.tag:
if validation_result.valid: # rebuild tables if something has changed
(form, tables) = setup_submission_view_forms_and_tables(
sub, db, sub.can_see_private(current_user))
return render_template('submission_view.html',
sub=sub,
tables=tables,
form=form,
reviewer=reviewer,
id=id,
jump=validation_result.tag,
status=sub.submission_status)
if form.validate():
if form.action.data == 'draft':
add_note(
current_user, form.title.data,
safe_textile(
'Submission returned to Submitter with the following message:\r\n\r\n'
+ form.body.data), sub, db)
add_history(current_user, 'Submission returned to Submitter',
sub, db)
send_mail(
'Submission %s returned to you from the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.submitter_email],
'user_submission_returned',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
send_mail(
'Submission %s returned to Submitter by the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.species],
'iarc_submission_returned',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
sub.submission_status = 'draft'
db.session.commit()
flash('Submission returned to Submitter')
return redirect('/submissions')
elif form.action.data == 'complete':
add_note(
current_user, form.title.data,
safe_textile(
'Submission completed with the following message to the Submitter:\n\n'
+ form.body.data), sub, db)
add_history(current_user, 'Submission completed', sub, db)
send_mail(
'Submission %s completed review by the IARC %s Committee' %
(sub.submission_id, sub.species), [sub.submitter_email],
'user_submission_completed',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
send_mail(
'Submission %s completed review by the IARC %s Committee' %
(sub.submission_id, sub.species), [sub.species],
'iarc_submission_completed',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
sub.submission_status = 'complete'
db.session.commit()
flash('Submission marked as complete')
return redirect('/submissions')
elif form.action.data == 'withdraw':
referenced_gds = []
for inf in sub.inferred_sequences:
for gd in inf.gene_descriptions:
if gd.status not in ('superceded', 'withdrawn'):
referenced_gds.append(gd.description_id)
if len(referenced_gds) > 0:
flash(
'Please remove references to this submission in sequence(s) %s first.'
% ','.join(referenced_gds))
return render_template('submission_view.html',
sub=sub,
tables=tables,
form=form,
reviewer=reviewer,
id=id,
jump=validation_result.tag,
status=sub.submission_status)
add_note(
current_user, form.title.data,
safe_textile(
'Submission withdrawn with the following message to the Submitter:\n\n'
+ form.body.data), sub, db)
add_history(current_user, 'Submission withdrawn', sub, db)
send_mail(
'Submission %s has been marked as withdrawn by the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.submitter_email],
'user_submission_withdrawn',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
send_mail(
'Submission %s has been marked as withdrawn by the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.species],
'iarc_submission_withdrawn',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
sub.submission_status = 'withdrawn'
db.session.commit()
flash('Submission marked as withdrawn')
return redirect('/submissions')
elif form.action.data == 'review':
add_note(
current_user, form.title.data,
safe_textile(
'Submission returned to IARC Review with the following message to the Submitter:\n\n'
+ form.body.data), sub, db)
add_history(current_user, 'Submission returned to Review', sub,
db)
send_mail(
'Submission %s returned to review by the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.submitter_email],
'user_submission_re_review',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
send_mail(
'Submission %s returned to review by the IARC %s Committee'
% (sub.submission_id, sub.species), [sub.species],
'iarc_submission_re_review',
reviewer=current_user,
user_name=sub.submitter_name,
submission=sub,
comment=form.body.data)
sub.submission_status = 'reviewing'
db.session.commit()
flash('Submission returned to Review')
return redirect('/submissions')
elif form.action.data == 'note':
add_note(current_user, form.title.data, form.body.data, sub,
db)
db.session.commit()
flash('Note Added')
return redirect(url_for('submission', id=id, _anchor='review'))
elif form.type.data == 'note': #reply to thread
head = db.session.query(JournalEntry).filter_by(
submission_id=sub.id,
type='note',
id=int(form.action.data)).one_or_none()
add_note(current_user,
head.title,
form.body.data,
sub,
db,
parent_id=int(form.action.data))
db.session.commit()
flash('Note Added')
return redirect(url_for('submission', id=id, _anchor='review'))
else:
return redirect('/submissions')
else:
return render_template('submission_view.html',
sub=sub,
tables=tables,
form=form,
reviewer=reviewer,
id=id,
jump=validation_result.tag,
status=sub.submission_status)
def edit_submission(id):
sub = check_sub_edit(id)
if sub is None:
return redirect('/submissions')
(tables, form) = setup_submission_edit_forms_and_tables(sub, db)
if request.method == 'GET':
populate_Submission(db, sub, form)
populate_Repertoire(db, sub.repertoire[0], form)
form.repository_select.data = sub.repertoire[
0].repository_name if sub.repertoire[0].repository_name in (
'NCBI SRA', 'ENA') else 'Other'
return render_template(
'submission_edit.html',
form=form,
id=id,
tables=tables,
attachment=len(sub.notes_entries[0].attached_files) > 0)
validation_result = ValidationResult()
try:
if 'save_btn' in request.form or 'save_close_btn' or 'submit_btn' in request.form:
if not form.validate():
if 'submit_btn' in request.form:
raise ValidationError()
# Overlook empty field errors when saving to draft
nonblank_errors = False
for field in form._fields:
if len(form._fields[field].errors) > 0:
if len(form._fields[field].data) == 0:
form._fields[field].errors = []
else:
nonblank_errors = True
if nonblank_errors:
raise ValidationError()
# Check if this is an NCBI related repertoire, and, if so, validate accession number and update related fields
choice = form.repository_select.data
update_sra_rep_details(form)
# Check for additions/deletions to editable tables, and any errors flagged up by validation in check_add_item
validation_result = process_table_updates(tables, request, db)
if not validation_result.valid:
raise ValidationError()
if 'submit_btn' in request.form:
check_submission_complete(sub, validation_result)
sub.submission_status = 'reviewing'
add_history(
current_user,
'Submission submitted to IARC %s Committee for review' %
sub.species, sub, db)
send_mail(
'Submission %s submitted to IARC %s Committee for review' %
(sub.submission_id, sub.species), [current_user.email],
'user_submission_submitted',
user=current_user,
submission=sub)
send_mail(
'Submission %s submitted to IARC %s Committee for review' %
(sub.submission_id, sub.species), [sub.species],
'iarc_submission_received',
user=current_user,
submission=sub)
db.session.commit()
flash('Submission %s has been submitted to IARC for review.' % id)
return redirect(url_for('submissions'))
# We've gone too far off-piste to use form initialisation or process() to push field values into the object
# The main problem is that not all object attributes are represented in the form, for example submission_id
# if these were present as hidden fields, maybe we could use process()
if ('save_btn' in request.form or 'save_close_btn'
or 'submit_btn' in request.form
or 'upload_btn' in request.form):
for (k, v) in request.form.items():
if hasattr(sub, k):
setattr(sub, k, v)
elif hasattr(sub.repertoire[0], k):
setattr(sub.repertoire[0], k, v)
# update fields that may have been fetched from NCBI
sub.repertoire[0].repository_name = form.repository_name.data
sub.repertoire[0].dataset_url = form.dataset_url.data
sub.repertoire[0].rep_title = form.rep_title.data
db.session.commit()
if 'notes_attachment' in request.files:
for file in form.notes_attachment.data:
if file.filename != '':
af = None
for at in sub.notes_entries[0].attached_files:
if at.filename == file.filename:
af = at
break
if af is None:
af = AttachedFile()
af.notes_entry = sub.notes_entries[0]
af.filename = file.filename
db.session.add(af)
db.session.commit()
dirname = attach_path + sub.submission_id
try:
if not isdir(dirname):
mkdir(dirname)
with open(dirname + '/multi_attachment_%s' % af.id,
'wb') as fo:
fo.write(file.stream.read())
except:
info = sys.exc_info()
flash('Error saving attachment: %s' % (info[1]))
app.logger.error(format_exc())
return redirect(
url_for('edit_submission',
id=sub.submission_id))
if 'notes_text' in request.form:
sub.notes_entries[0].notes_text = request.form[
'notes_text'].encode('utf-8')
db.session.commit()
form.repository_select.data = sub.repertoire[
0].repository_name if sub.repertoire[0].repository_name in (
'NCBI SRA', 'ENA') else 'Other'
if validation_result.route:
return redirect(
url_for(validation_result.route, id=validation_result.id))
if validation_result.tag:
return redirect(
url_for('edit_submission',
id=id,
_anchor=validation_result.tag))
if 'save_btn' in request.form or 'upload_btn' in request.form:
tag = request.form['current_tab'].split(
'#')[1] if '#' in request.form['current_tab'] else '#sub'
return redirect(url_for('edit_submission', id=id, _anchor=tag))
else:
return redirect(url_for('submissions'))
except ValidationError as e:
# If we don't have a tag, find an error to jump to
if not validation_result.tag:
repform = type(RepertoireForm())
for subform in form.subforms:
if type(subform) is repform:
for field in subform:
if len(field.errors) > 0:
validation_result.tag = 'rep'
break
break
if not validation_result.tag:
for table in tables.values():
for field in table.form:
if len(field.errors) > 0:
validation_result.tag = table.name
break
return render_template('submission_edit.html',
form=form,
id=id,
tables=tables,
jump=validation_result.tag)
def edit_germline_set(id):
germline_set = check_set_edit(id)
if germline_set is None:
return redirect('/germline_sets')
if len(germline_set.notes_entries) == 0:
germline_set.notes_entries.append(NotesEntry())
db.session.commit()
update_germline_set_seqs(germline_set)
db.session.commit()
tables = setup_germline_set_edit_tables(db, germline_set)
tables['genes'].table_id = "genetable"
tables['genes'].html_attrs = {'style': 'width: 100%'}
germline_set_form = GermlineSetForm(obj=germline_set)
notes_entry_form = NotesEntryForm(obj=germline_set.notes_entries[0])
history_form = JournalEntryForm()
hidden_return_form = HiddenReturnForm()
changes = list_germline_set_changes(germline_set)
form = AggregateForm(germline_set_form, notes_entry_form, history_form,
hidden_return_form, tables['ack'].form,
tables['pubmed_table'].form)
if request.method == 'POST':
form.validate()
valid = True
for field in form._fields:
if len(form[field].errors) > 0:
if field in history_form._fields and 'history_btn' not in request.form:
form[field].errors = []
else:
valid = False
if form.action.data == 'published':
if len(germline_set.gene_descriptions) < 1:
flash("Please add at least one gene to the set!")
form.action.data = ''
valid = False
for gene_description in germline_set.gene_descriptions:
if gene_description.status == 'draft':
publish_sequence(gene_description, form.body.data, False)
if gene_description.status == 'published' and gene_description.affirmation_level == 0:
flash(
"Can't publish this set while gene %s is at affirmation level 0."
% gene_description.sequence_name)
form.action.data = ''
valid = False
if gene_description.status == 'withdrawn':
flash(
"Can't publish this set while gene %s is withdrawn." %
gene_description.sequence_name)
form.action.data = ''
valid = False
if gene_description.species_subgroup != germline_set.species_subgroup or gene_description.species_subgroup_type != germline_set.species_subgroup_type:
flash(
"Can't publish this set while gene %s species subgroup/subgroup type disagreees with the germline set values."
% gene_description.sequence_name)
form.action.data = ''
valid = False
if valid:
try:
validation_result = process_table_updates(
{
'ack': tables['ack'],
'pubmed_table': tables['pubmed_table']
}, request, db)
if not validation_result.valid:
raise ValidationError()
save_GermlineSet(db, germline_set, form)
if 'add_gene_btn' in request.form:
return redirect(url_for('add_gene_to_set', id=id))
if form.action.data == 'published':
old_set = db.session.query(GermlineSet).filter_by(
germline_set_id=germline_set.germline_set_id,
status='published').one_or_none()
if old_set:
old_set.status = 'superceded'
max_version = db.session.query(func.max(GermlineSet.release_version))\
.filter(GermlineSet.germline_set_id == germline_set.germline_set_id)\
.filter(or_(GermlineSet.status == 'withdrawn', GermlineSet.status == 'superceded'))\
.one_or_none()
germline_set.release_version = max_version[
0] + 1 if max_version[0] else 1
germline_set.release_date = datetime.date.today()
hist_notes = form.body.data
changes = list_germline_set_changes(
germline_set) # to get updated versions
if changes != '':
hist_notes += Markup('<br>') + changes
add_history(current_user,
'Version %s published' %
(germline_set.release_version),
germline_set,
db,
body=hist_notes)
send_mail(
'Sequence %s version %d published by the IARC %s Committee'
% (germline_set.germline_set_id,
germline_set.release_version, germline_set.species),
[germline_set.species],
'iarc_germline_set_released',
reviewer=current_user,
user_name=germline_set.author,
germline_set=germline_set,
comment=form.body.data)
germline_set.status = 'published'
db.session.commit()
flash('Germline set published')
return redirect('/germline_sets')
if 'notes_attachment' in request.files:
for file in form.notes_attachment.data:
if file.filename != '':
af = None
for at in germline_set.notes_entries[
0].attached_files:
if at.filename == file.filename:
af = at
break
if af is None:
af = AttachedFile()
af.notes_entry = germline_set.notes_entries[0]
af.filename = file.filename
db.session.add(af)
db.session.commit()
dirname = attach_path + germline_set.germline_set_id
try:
if not isdir(dirname):
mkdir(dirname)
with open(
dirname +
'/multi_attachment_%s' % af.id,
'wb') as fo:
fo.write(file.stream.read())
except:
info = sys.exc_info()
flash('Error saving attachment: %s' %
(info[1]))
app.logger.error(format_exc())
return redirect(
url_for('edit_submission',
id=germline_set.germline_set_id))
db.session.commit()
validation_result.tag = 'notes'
if 'notes_text' in request.form and germline_set.notes_entries[
0].notes_text is None or germline_set.notes_entries[
0].notes_text != request.form['notes_text'].encode(
'utf-8'):
germline_set.notes_entries[0].notes_text = request.form[
'notes_text'].encode('utf-8')
db.session.commit()
except ValidationError:
return render_template(
'germline_set_edit.html',
form=form,
germline_set_name=germline_set.germline_set_name,
id=id,
set_id=germline_set.germline_set_id,
tables=tables,
changes=changes,
jump=validation_result.tag,
version=germline_set.release_version)
if validation_result.tag:
return redirect(
url_for('edit_germline_set',
id=id,
_anchor=validation_result.tag))
else:
return redirect(url_for('germline_sets'))
else:
for field in tables['ack'].form:
if len(field.errors) > 0:
return render_template(
'germline_set_edit.html',
form=form,
germline_set_name=germline_set.germline_set_name,
id=id,
set_id=germline_set.germline_set_id,
tables=tables,
changes=changes,
jump='ack',
version=germline_set.release_version)
return render_template(
'germline_set_edit.html',
form=form,
germline_set_name=germline_set.germline_set_name,
id=id,
set_id=germline_set.germline_set_id,
tables=tables,
version=germline_set.release_version,
changes=changes,
)
