def show_reports():
form = FlaskForm()
if form.validate_on_submit():
vcf_id = request.form['vcfs'].split(',')[0]
url = urlparse.urlparse(request.form['url'])
args = MultiDict(urlparse.parse_qsl(url.query))
response = jsonapi.get_related(db, args, 'vcfs', vcf_id, 'calls')
title = request.form.get('title')
if response.status == requests.codes.ok:
report = Report(title)
report.vcfs = [VCF.query.get(vcf_id)]
report.creator = current_user
report.project = Project.query.get(request.form.get('project'))
report.panels = Panel.query.filter(Panel.id.in_(request.form.get('panels').split(','))).all()
report.fisher = request.form.get('fisher')
report.artifact = request.form.get('artifact')
report.frequency = request.form.get('frequency')
report.depth = request.form.get('depth')
report.content = cPickle.dumps(response.document)
db.add(report)
try:
db.commit()
except SQLAlchemyError:
flash("Error saving report: '{0}'. Please try again later.".format(title), category='danger')
else:
flash("Report: '{0}' saved successfully.".format(title), category='success')
admin = current_user.is_authenticated and PERMISSION.MANAGE_REPORT_REQUEST in current_user.permissions
return render_template('reports/index.html', admin=admin)
def get_project_categories(project_id):
response = jsonapi.get_related(db.session, request.args, 'project-categories', project_id, 'project')
return jsonify(response.document), response.status
def get_project(project_id):
response = jsonapi.get_related(db.session, request.args, 'projects', project_id, 'members')
return jsonify(response.document), response.status
def get_variant_gene_targets(variant_id):
response = jsonapi.get_related(db, request.args, 'variants', variant_id, 'targets')
return jsonify(response.document), response.status
def get_subject_vcfs(subject_id):
response = jsonapi.get_related(db, request.args, 'subjects', subject_id, 'vcfs')
return jsonify(response.document), response.status
def get_user_address(user_id):
response = jsonapi.get_related(db.session, request.args, 'users', user_id,
'address')
return jsonify(response.document), response.status
def get_vcf_calls(vcf_id):
response = jsonapi.get_related(db, request.args, 'vcfs', vcf_id, 'calls')
return jsonify(response.document), response.status
def get_project(project_id):
response = jsonapi.get_related(db.session, request.args, 'projects',
project_id, 'members')
return jsonify(response.document), response.status
def get_user_survey_checkbox_choices(user_survey_id):
response = jsonapi.get_related(db.session, request.args, 'user-surveys',
user_survey_id, 'checkbox-choices')
return jsonify(response.document), response.status
def get_project_reports(project_id):
response = jsonapi.get_related(db, request.args, 'projects', project_id, 'reports')
return jsonify(response.document), response.status
def get_user_survey_radio_fields(user_survey_id):
response = jsonapi.get_related(db.session, request.args, 'user-surveys',
user_survey_id, 'radio-fields')
return jsonify(response.document), response.status
def get_core_posts(core_id):
response = jsonapi.get_related(db.session, request.args, 'cores', core_id, 'posts')
return jsonify(response.document), response.status
def get_gene_gene_targets(gene_id):
response = jsonapi.get_related(db, request.args, 'genes', gene_id, 'targets')
return jsonify(response.document), response.status
def get_user_survey_radio_fields(user_survey_id):
response = jsonapi.get_related(db.session, request.args, 'user-surveys', user_survey_id, 'radio-fields')
return jsonify(response.document), response.status
def get_project_categories(project_id):
response = jsonapi.get_related(db.session, request.args,
'project-categories', project_id, 'project')
return jsonify(response.document), response.status
def get_user_survey_checkbox_choices(user_survey_id):
response = jsonapi.get_related(db.session, request.args, 'user-surveys', user_survey_id, 'checkbox-choices')
return jsonify(response.document), response.status
def get_user_address(user_id):
response = jsonapi.get_related(db.session, request.args, 'users', user_id, 'address')
return jsonify(response.document), response.status