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_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