def sv_variants(institute_id, case_name): """Display a list of structural variants.""" page = int(request.form.get("page", 1)) variant_type = request.args.get("variant_type", "clinical") category = "sv" # Define case and institute objects institute_obj, case_obj = institute_and_case(store, institute_id, case_name) if request.form.get("hpo_clinical_filter"): case_obj["hpo_clinical_filter"] = True if request.form.getlist("dismiss"): # dismiss a list of variants controllers.dismiss_variant_list( store, institute_obj, case_obj, "variant.sv_variant", request.form.getlist("dismiss"), request.form.getlist("dismiss_choices"), ) # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request) cytobands = store.cytoband_by_chrom(case_obj.get("genome_build")) variants_query = store.variants(case_obj["_id"], category=category, query=form.data) # Setup variant count session with variant count by category controllers.variant_count_session(store, institute_id, case_obj["_id"], variant_type, category) result_size = store.count_variants(case_obj["_id"], form.data, None, category) session["filtered_variants"] = result_size # if variants should be exported if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.sv_variants(store, institute_obj, case_obj, variants_query, result_size, page) return dict( institute=institute_obj, case=case_obj, dismiss_variant_options=DISMISS_VARIANT_OPTIONS, variant_type=variant_type, form=form, cytobands=cytobands, severe_so_terms=SEVERE_SO_TERMS, manual_rank_options=MANUAL_RANK_OPTIONS, page=page, expand_search=str(request.method == "POST"), **data, )
def variants(institute_id, case_name): """Display a list of SNV variants.""" page = int(request.form.get("page", 1)) category = "snv" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variant_type = request.args.get("variant_type", "clinical") if request.form.get("hpo_clinical_filter"): case_obj["hpo_clinical_filter"] = True user_obj = store.user(current_user.email) if request.method == "POST": form = controllers.populate_filters_form(store, institute_obj, case_obj, user_obj, category, request.form) else: form = FiltersForm(request.args) # set form variant data type the first time around form.variant_type.data = variant_type form.chrom.data = request.args.get("chrom", None) # populate filters dropdown available_filters = store.filters(institute_id, category) form.filters.choices = [(filter.get("_id"), filter.get("display_name")) for filter in available_filters] # populate available panel choices available_panels = case_obj.get("panels", []) + [{ "panel_name": "hpo", "display_name": "HPO" }] panel_choices = [(panel["panel_name"], panel["display_name"]) for panel in available_panels] form.gene_panels.choices = panel_choices # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) # upload gene panel if symbol file exists if request.files: file = request.files[form.symbol_file.name] if request.files and file and file.filename != "": LOG.debug("Upload file request files: {0}".format( request.files.to_dict())) try: stream = io.StringIO(file.stream.read().decode("utf-8"), newline=None) except UnicodeDecodeError as error: flash("Only text files are supported!", "warning") return redirect(request.referrer) hgnc_symbols_set = set(form.hgnc_symbols.data) LOG.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set)) new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream) hgnc_symbols_set.update(new_hgnc_symbols) form.hgnc_symbols.data = hgnc_symbols_set # reset gene panels form.gene_panels.data = "" # check if supplied gene symbols exist hgnc_symbols = [] non_clinical_symbols = [] not_found_symbols = [] not_found_ids = [] if (form.hgnc_symbols.data) and len(form.hgnc_symbols.data) > 0: is_clinical = form.data.get("variant_type", "clinical") == "clinical" clinical_symbols = store.clinical_symbols( case_obj) if is_clinical else None for hgnc_symbol in form.hgnc_symbols.data: if hgnc_symbol.isdigit(): hgnc_gene = store.hgnc_gene(int(hgnc_symbol), case_obj["genome_build"]) if hgnc_gene is None: not_found_ids.append(hgnc_symbol) else: hgnc_symbols.append(hgnc_gene["hgnc_symbol"]) elif sum(1 for i in store.hgnc_genes(hgnc_symbol)) == 0: not_found_symbols.append(hgnc_symbol) elif is_clinical and (hgnc_symbol not in clinical_symbols): non_clinical_symbols.append(hgnc_symbol) else: hgnc_symbols.append(hgnc_symbol) if not_found_ids: flash("HGNC id not found: {}".format(", ".join(not_found_ids)), "warning") if not_found_symbols: flash("HGNC symbol not found: {}".format(", ".join(not_found_symbols)), "warning") if non_clinical_symbols: flash( "Gene not included in clinical list: {}".format( ", ".join(non_clinical_symbols)), "warning", ) form.hgnc_symbols.data = hgnc_symbols # handle HPO gene list separately if "hpo" in form.data["gene_panels"]: hpo_symbols = list( set(term_obj["hgnc_symbol"] for term_obj in case_obj["dynamic_gene_list"])) current_symbols = set(hgnc_symbols) current_symbols.update(hpo_symbols) form.hgnc_symbols.data = list(current_symbols) cytobands = store.cytoband_by_chrom(case_obj.get("genome_build")) variants_query = store.variants(case_obj["_id"], query=form.data, category=category) # Setup variant count session with variant count by category controllers.variant_count_session(store, institute_id, case_obj["_id"], variant_type, category) session["filtered_variants"] = variants_query.count() if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.variants(store, institute_obj, case_obj, variants_query, page) return dict( institute=institute_obj, case=case_obj, form=form, manual_rank_options=MANUAL_RANK_OPTIONS, dismiss_variant_options=DISMISS_VARIANT_OPTIONS, cancer_tier_options=CANCER_TIER_OPTIONS, severe_so_terms=SEVERE_SO_TERMS, cytobands=cytobands, page=page, expand_search=str(request.method == "POST"), **data, )
def cancer_variants(institute_id, case_name): """Show cancer variants overview.""" category = "cancer" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) user_obj = store.user(current_user.email) if request.method == "POST": form = controllers.populate_filters_form(store, institute_obj, case_obj, user_obj, category, request.form) # if user is not loading an existing filter, check filter form if request.form.get( "load_filter") is None and form.validate_on_submit() is False: # Flash a message with errors for field, err_list in form.errors.items(): for err in err_list: flash(f"Content of field '{field}' has not a valid format", "warning") # And do not submit the form return redirect( url_for( ".cancer_variants", institute_id=institute_id, case_name=case_name, expand_search="True", ), ) page = int(request.form.get("page", 1)) else: page = int(request.args.get("page", 1)) form = CancerFiltersForm(request.args) form.chrom.data = request.args.get("chrom", None) # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) # populate filters dropdown available_filters = store.filters(institute_id, category) form.filters.choices = [(filter.get("_id"), filter.get("display_name")) for filter in available_filters] available_panels = case_obj.get("panels", []) + [{ "panel_name": "hpo", "display_name": "HPO" }] panel_choices = [(panel["panel_name"], panel["display_name"]) for panel in available_panels] form.gene_panels.choices = panel_choices cytobands = store.cytoband_by_chrom(case_obj.get("genome_build")) variant_type = request.args.get("variant_type", "clinical") variants_query = store.variants(case_obj["_id"], category="cancer", query=form.data) if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.cancer_variants(store, institute_id, case_name, variants_query, form, page=page) return dict( variant_type=variant_type, cytobands=cytobands, dismiss_variant_options={ **DISMISS_VARIANT_OPTIONS, **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS, }, expand_search=str(request.method == "POST"), **data, )
def managed_variants(request): """Create and return managed variants' data Args: request(werkzeug.local.LocalProxy): request containing form data Returns data(dict): data to be displayed in template page """ page = int(request.form.get("page", 1)) skip_count = VARS_PER_PAGE * max(page - 1, 0) # Retrieve form data for the 3 types of form present on the managed variants page filters_form = ManagedVariantsFilterForm(request.form) add_form = ManagedVariantAddForm() modify_form = ManagedVariantModifyForm() # Retrieve form data to compose variants query categories = request.form.getlist("category") or [ cat[0] for cat in CATEGORY_CHOICES ] query_options = {"sub_category": []} # Set variant sub-category in query_options for sub_cat in request.form.getlist("sub_category") or [ subcat[0] for subcat in SUBCATEGORY_CHOICES ]: query_options["sub_category"].append(sub_cat) if request.form.get("description") is not None and request.form.get( "description") != "": query_options["description"] = request.form["description"] # Set requested variant coordinates in query options set_query_coordinates(query_options, request.form) # Get all variants according to the selected fields in filter form managed_variants_query = store.managed_variants( category=categories, query_options=query_options) variant_count = store.count_managed_variants(category=categories, query_options=query_options) more_variants = True if variant_count > (skip_count + VARS_PER_PAGE) else False managed_variants_res = managed_variants_query.skip(skip_count).limit( VARS_PER_PAGE) managed_variants = [ managed_variant for managed_variant in managed_variants_res ] return { "page": page, "filters_form": filters_form, "add_form": add_form, "modify_form": modify_form, "managed_variants": managed_variants, "more_variants": more_variants, "cytobands_37": store.cytoband_by_chrom("37"), "cytobands_38": store.cytoband_by_chrom("38"), "chromosomes_37": CHROMOSOMES, "chromosomes_38": CHROMOSOMES_38, "subcategory_choices": [[choice[1], choice[0]] for choice in SUBCATEGORY_CHOICES], }
def variants(institute_id, case_name): """Display a list of SNV variants.""" page = int(Markup.escape(request.form.get("page", "1"))) category = "snv" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variant_type = request.args.get("variant_type", "clinical") variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False) if request.form.get("hpo_clinical_filter"): case_obj["hpo_clinical_filter"] = True user_obj = store.user(current_user.email) if request.method == "POST": if "dismiss_submit" in request.form: # dismiss a list of variants controllers.dismiss_variant_list( store, institute_obj, case_obj, "variant.variant", request.form.getlist("dismiss"), request.form.getlist("dismiss_choices"), ) form = controllers.populate_filters_form( store, institute_obj, case_obj, user_obj, category, request.form ) else: form = FiltersForm(request.args) # set form variant data type the first time around form.variant_type.data = variant_type # set chromosome to all chromosomes form.chrom.data = request.args.get("chrom", "") if form.gene_panels.data == [] and variant_type == "clinical": form.gene_panels.data = controllers.case_default_panels(case_obj) # populate filters dropdown available_filters = list(store.filters(institute_id, category)) form.filters.choices = [ (filter.get("_id"), filter.get("display_name")) for filter in available_filters ] # Populate chromosome select choices controllers.populate_chrom_choices(form, case_obj) # populate available panel choices form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj) # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) # upload gene panel if symbol file exists if request.files: file = request.files[form.symbol_file.name] if request.files and file and file.filename != "": LOG.debug("Upload file request files: {0}".format(request.files.to_dict())) try: stream = io.StringIO(file.stream.read().decode("utf-8"), newline=None) except UnicodeDecodeError as error: flash("Only text files are supported!", "warning") return redirect(request.referrer) hgnc_symbols_set = set(form.hgnc_symbols.data) LOG.debug("Symbols prior to upload: {0}".format(hgnc_symbols_set)) new_hgnc_symbols = controllers.upload_panel(store, institute_id, case_name, stream) hgnc_symbols_set.update(new_hgnc_symbols) form.hgnc_symbols.data = hgnc_symbols_set # reset gene panels form.gene_panels.data = "" controllers.update_form_hgnc_symbols(store, case_obj, form) cytobands = store.cytoband_by_chrom(case_obj.get("genome_build")) variants_query = store.variants(case_obj["_id"], query=form.data, category=category) result_size = store.count_variants(case_obj["_id"], form.data, None, category) if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.variants( store, institute_obj, case_obj, variants_query, result_size, page, query_form=form.data ) expand_search = request.method == "POST" and request.form.get("expand_search") in [ "True", "", ] return dict( institute=institute_obj, case=case_obj, form=form, filters=available_filters, manual_rank_options=MANUAL_RANK_OPTIONS, dismiss_variant_options=DISMISS_VARIANT_OPTIONS, cancer_tier_options=CANCER_TIER_OPTIONS, severe_so_terms=SEVERE_SO_TERMS, cytobands=cytobands, page=page, expand_search=expand_search, result_size=result_size, total_variants=variants_stats.get(variant_type, {}).get(category, "NA"), **data, )
def cancer_sv_variants(institute_id, case_name): """Display a list of cancer structural variants.""" page = int(Markup.escape(request.form.get("page", "1"))) variant_type = Markup.escape(request.args.get("variant_type", "clinical")) category = "cancer_sv" # Define case and institute objects institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False) if request.form.get("hpo_clinical_filter"): case_obj["hpo_clinical_filter"] = True if request.form.getlist("dismiss"): # dismiss a list of variants controllers.dismiss_variant_list( store, institute_obj, case_obj, "variant.sv_variant", request.form.getlist("dismiss"), request.form.getlist("dismiss_choices"), ) # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request) # populate filters dropdown available_filters = list(store.filters(institute_obj["_id"], category)) form.filters.choices = [ (filter.get("_id"), filter.get("display_name")) for filter in available_filters ] # Populate chromosome select choices controllers.populate_chrom_choices(form, case_obj) genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37" cytobands = store.cytoband_by_chrom(genome_build) controllers.update_form_hgnc_symbols(store, case_obj, form) variants_query = store.variants(case_obj["_id"], category=category, query=form.data) result_size = store.count_variants(case_obj["_id"], form.data, None, category) # if variants should be exported if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.sv_variants( store, institute_obj, case_obj, variants_query, result_size, page ) expand_search = request.method == "POST" and request.form.get("expand_search") in [ "True", "", ] return dict( institute=institute_obj, case=case_obj, dismiss_variant_options={ **DISMISS_VARIANT_OPTIONS, **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS, }, variant_type=variant_type, form=form, filters=available_filters, severe_so_terms=SEVERE_SO_TERMS, cancer_tier_options=CANCER_TIER_OPTIONS, manual_rank_options=MANUAL_RANK_OPTIONS, cytobands=cytobands, page=page, expand_search=expand_search, result_size=result_size, total_variants=variants_stats.get(variant_type, {}).get(category, "NA"), **data, )
def cancer_variants(institute_id, case_name): """Show cancer variants overview.""" category = "cancer" variant_type = Markup.escape(request.args.get("variant_type", "clinical")) institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False) user_obj = store.user(current_user.email) if request.method == "POST": if "dismiss_submit" in request.form: # dismiss a list of variants controllers.dismiss_variant_list( store, institute_obj, case_obj, "variant.variant", request.form.getlist("dismiss"), request.form.getlist("dismiss_choices"), ) form = controllers.populate_filters_form( store, institute_obj, case_obj, user_obj, category, request.form ) # if user is not loading an existing filter, check filter form if ( request.form.get("load_filter") is None and request.form.get("audit_filter") is None and form.validate_on_submit() is False ): # Flash a message with errors for field, err_list in form.errors.items(): for err in err_list: flash(f"Content of field '{field}' does not have a valid format", "warning") # And do not submit the form return redirect( url_for( ".cancer_variants", institute_id=institute_id, case_name=case_name, expand_search=True, ) ) page = int(Markup.escape(request.form.get("page", "1"))) else: page = int(Markup.escape(request.args.get("page", "1"))) form = CancerFiltersForm(request.args) # set chromosome to all chromosomes form.chrom.data = request.args.get("chrom", "") if form.gene_panels.data == []: form.gene_panels.data = controllers.case_default_panels(case_obj) # update status of case if visited for the first time controllers.activate_case(store, institute_obj, case_obj, current_user) # populate filters dropdown available_filters = list(store.filters(institute_id, category)) form.filters.choices = [ (filter.get("_id"), filter.get("display_name")) for filter in available_filters ] # Populate chromosome select choices controllers.populate_chrom_choices(form, case_obj) form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj) genome_build = "38" if "38" in str(case_obj.get("genome_build")) else "37" cytobands = store.cytoband_by_chrom(genome_build) controllers.update_form_hgnc_symbols(store, case_obj, form) variants_query = store.variants( case_obj["_id"], category="cancer", query=form.data, build=genome_build ) result_size = store.count_variants(case_obj["_id"], form.data, None, category) if request.form.get("export"): return controllers.download_variants(store, case_obj, variants_query) data = controllers.cancer_variants( store, institute_id, case_name, variants_query, result_size, form, page=page, ) expand_search = request.method == "POST" and request.form.get("expand_search") in [ "True", "", ] return dict( variant_type=variant_type, cytobands=cytobands, filters=available_filters, dismiss_variant_options={ **DISMISS_VARIANT_OPTIONS, **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS, }, expand_search=expand_search, result_size=result_size, total_variants=variants_stats.get(variant_type, {}).get(category, "NA"), **data, )
def str_variants(institute_id, case_name): """Display a list of STR variants.""" page = int(Markup.escape(request.form.get("page", "1"))) variant_type = Markup.escape(request.args.get("variant_type", "clinical")) category = "str" institute_obj, case_obj = institute_and_case(store, institute_id, case_name) variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False) user_obj = store.user(current_user.email) if request.method == "POST": form = controllers.populate_filters_form( store, institute_obj, case_obj, user_obj, category, request.form ) else: form = StrFiltersForm(request.args) if form.gene_panels.data == [] and variant_type == "clinical": form.gene_panels.data = controllers.case_default_panels(case_obj) # set form variant data type the first time around form.variant_type.data = variant_type # set chromosome to all chromosomes form.chrom.data = request.args.get("chrom", "") # populate filters dropdown available_filters = list(store.filters(institute_id, category)) form.filters.choices = [ (filter.get("_id"), filter.get("display_name")) for filter in available_filters ] # Populate chromosome select choices controllers.populate_chrom_choices(form, case_obj) # populate available panel choices form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj) controllers.activate_case(store, institute_obj, case_obj, current_user) cytobands = store.cytoband_by_chrom(case_obj.get("genome_build")) query = form.data query["variant_type"] = variant_type variants_query = store.variants(case_obj["_id"], category=category, query=query).sort( [ ("str_repid", pymongo.ASCENDING), ("chromosome", pymongo.ASCENDING), ("position", pymongo.ASCENDING), ] ) result_size = store.count_variants(case_obj["_id"], query, None, category) if request.form.get("export"): return controllers.download_str_variants(case_obj, variants_query) data = controllers.str_variants( store, institute_obj, case_obj, variants_query, result_size, page ) return dict( institute=institute_obj, case=case_obj, dismiss_variant_options=DISMISS_VARIANT_OPTIONS, variant_type=variant_type, manual_rank_options=MANUAL_RANK_OPTIONS, cytobands=cytobands, form=form, page=page, filters=available_filters, expand_search=str(request.method == "POST"), result_size=result_size, total_variants=variants_stats.get(variant_type, {}).get(category, "NA"), **data, )