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 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,
)
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 variants(
user: str,
case_id: str,
status: list,
older_than: int,
analysis_type: list,
rank_threshold: int,
variants_threshold: int,
keep_ctg: list,
dry_run: bool,
) -> None:
"""Delete variants for one or more cases"""
user_obj = store.user(user)
if user_obj is None:
click.echo(f"Could not find a user with email '{user}' in database")
return
total_deleted = 0
items_name = "deleted variants"
if dry_run:
click.echo("--------------- DRY RUN COMMAND ---------------")
items_name = "estimated deleted variants"
else:
click.confirm(
"Variants are going to be deleted from database. Continue?",
abort=True)
case_query = store.build_case_query(case_id, status, older_than,
analysis_type)
# Estimate the average size of a variant document in database
avg_var_size = store.collection_stats("variant").get("avgObjSize",
0) # in bytes
# Get all cases where case_query applies
n_cases = store.case_collection.count_documents(case_query)
cases = store.cases(query=case_query)
filters = (
f"Rank-score threshold:{rank_threshold}, case n. variants threshold:{variants_threshold}."
)
click.echo("\t".join(DELETE_VARIANTS_HEADER))
for nr, case in enumerate(cases, 1):
case_id = case["_id"]
institute_id = case["owner"]
case_n_variants = store.variant_collection.count_documents(
{"case_id": case_id})
# Skip case if user provided a number of variants to keep and this number is less than total number of case variants
if variants_threshold and case_n_variants < variants_threshold:
continue
# Get evaluated variants for the case that haven't been dismissed
case_evaluated = store.evaluated_variants(case_id=case_id,
institute_id=institute_id)
evaluated_not_dismissed = [
variant["_id"] for variant in case_evaluated
if "dismiss_variant" not in variant
]
# Do not remove variants that are either pinned, causative or evaluated not dismissed
variants_to_keep = (case.get("suspects", []) +
case.get("causatives", []) +
evaluated_not_dismissed or [])
variants_query = store.delete_variants_query(case_id, variants_to_keep,
rank_threshold, keep_ctg)
if dry_run:
# Just print how many variants would be removed for this case
remove_n_variants = store.variant_collection.count_documents(
variants_query)
total_deleted += remove_n_variants
click.echo("\t".join([
str(nr),
str(n_cases),
case["owner"],
case["display_name"],
case_id,
case.get("track", ""),
str(case["analysis_date"]),
case.get("status", ""),
str(case.get("is_research", "")),
str(case_n_variants),
str(remove_n_variants),
]))
continue
# delete variants specified by variants_query
result = store.variant_collection.delete_many(variants_query)
total_deleted += result.deleted_count
click.echo("\t".join([
str(nr),
str(n_cases),
case["owner"],
case["display_name"],
case_id,
case.get("track", ""),
str(case["analysis_date"]),
case.get("status", ""),
str(case.get("is_research", "")),
str(case_n_variants),
str(result.deleted_count),
]))
# Create event in database
institute_obj = store.institute(case["owner"])
with current_app.test_request_context("/cases"):
url = url_for(
"cases.case",
institute_id=institute_obj["_id"],
case_name=case["display_name"],
)
store.remove_variants_event(
institute=institute_obj,
case=case,
user=user_obj,
link=url,
content=filters,
)
# Update case variants count
store.case_variants_count(case_id, institute_obj["_id"], True)
click.echo(f"Total {items_name}: {total_deleted}")
click.echo(
f"Estimated space freed (GB): {round((total_deleted * avg_var_size) / BYTES_IN_ONE_GIGABYTE, 4)}"
)