Refactor cancer SNVs code to use shared routines

CHANGELOG.md

@@ -14,7 +14,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 - Rework rank model file loading, allowing full URI (#6090)
 - Refactored `scout delete` commands and relative tests into separate modules (#6102)
 - The gens extension now generates version appropriate links (#6105)
-- Refactored snv variants code to share same routines as other variant categories (#6116)
+- Refactored snv and cancer snv variants code to share same routines as other variant categories (#6116 and #6128)
 - On managed variants page, print maintainers names instead of emails/ids (#6121)
 ### Fixed
 - Comments' text wrapping in ACMG classifications exported as PDF (#6086)

scout/server/blueprints/variants/controllers.py

@@ -72,12 +72,14 @@
 
 SV_VARIANT_PAGE = "variant.sv_variant"
 VARIANT_PAGE = "variant.variant"
+CANCER_VARIANT_PAGE = "variant.cancer_variant"
 DISMISS_VARIANT_LINK = {
     "sv": SV_VARIANT_PAGE,
     "cancer_sv": SV_VARIANT_PAGE,
     "mei": SV_VARIANT_PAGE,
     "str": VARIANT_PAGE,
     "snv": VARIANT_PAGE,
+    "cancer": CANCER_VARIANT_PAGE,
 }
 
 LOG = logging.getLogger(__name__)
@@ -301,14 +303,14 @@ def render_variants_page(
         return data_exporter(store, case_obj, variants_query)
 
     args = [store, institute_obj, case_obj, variants_query, page]
-    if category in ["snv", "snv_research"]:
+    if category in ["snv", "cancer"]:
         args.append(request.form)
 
     data = decorator(*args)
 
     dismiss_variant_options = (
         {**DISMISS_VARIANT_OPTIONS, **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS}
-        if category == "cancer_sv"
+        if category in ["cancer_sv", "cancer"]
         else DISMISS_VARIANT_OPTIONS
     )
 
@@ -1852,7 +1854,7 @@ def _populate_form_genes_from_file(
         form.hgnc_symbols.data = hgnc_symbols_set
 
 
-def populate_snv_sv_mei_str_filters_form(
+def populate_variants_filters_form(
     store: MongoAdapter, institute_obj: dict, case_obj: dict, category: str, request_obj: LocalProxy
 ) -> Union[StrFiltersForm, SvFiltersForm, CancerSvFiltersForm, MeiFiltersForm]:
     """Populate a filters form for SVs, cancer SVs, MEIs and STRs pages."""

scout/server/blueprints/variants/views.py

@@ -24,7 +24,7 @@
 )
 
 from . import controllers
 from .forms import (
     CancerFiltersForm,
     FiltersForm,
     FusionFiltersForm,
@@ -57,9 +57,9 @@
 def variants(institute_id, case_name):
     """Display a list of SNV variants."""
 
     def form_builder(store, inst, case, cat, vtype):
         """Builds the SNVs filters form."""
-        return controllers.populate_snv_sv_mei_str_filters_form(
+        return controllers.populate_variants_filters_form(
             store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
@@ -91,9 +91,9 @@
 def str_variants(institute_id: str, case_name: str):
     """Display a list of STR variants (STRs)."""
 
     def form_builder(store, inst, case, cat, vtype):
         """Builds the STRs filters form."""
-        return controllers.populate_snv_sv_mei_str_filters_form(
+        return controllers.populate_variants_filters_form(
             store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
@@ -124,9 +124,9 @@
 def sv_variants(institute_id: str, case_name: str):
     """Display a list of structural variants (SV)."""
 
     def form_builder(store, inst, case, cat, vtype):
         """Builds the SV filters form."""
-        return controllers.populate_snv_sv_mei_str_filters_form(
+        return controllers.populate_variants_filters_form(
             store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
@@ -157,9 +157,9 @@
 def cancer_sv_variants(institute_id: str, case_name: str):
     """Display a list of cancer structural variants."""
 
     def form_builder(store, inst, case, cat, vtype):
         """Builds the cancer SV filters form."""
-        return controllers.populate_snv_sv_mei_str_filters_form(
+        return controllers.populate_variants_filters_form(
             store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
@@ -184,9 +184,9 @@
 def mei_variants(institute_id: str, case_name: str):
     """Display a list of MEI variants."""
 
     def form_builder(store, inst, case, cat, vtype):
         """Builds the cancer SV filters form."""
-        return controllers.populate_snv_sv_mei_str_filters_form(
+        return controllers.populate_variants_filters_form(
             store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
@@ -211,110 +211,32 @@
 def cancer_variants(institute_id, case_name):
     """Show cancer variants overview."""
 
-    page = controllers.get_variants_page(request.form)
-
-    category = "cancer"
-    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
-    variant_type = Markup.escape(
-        request.args.get("variant_type", request.form.get("variant_type", "clinical"))
-    )
-    if variant_type not in ["clinical", "research"]:
-        variant_type = "clinical"
-    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_PAGE,
-                request.form.getlist("dismiss"),
-                request.form.getlist("dismiss_choices"),
-            )
-
-        form = controllers.populate_filters_form(
-            store, institute_obj, case_obj, user_obj, category, request.form
+    def form_builder(store, inst, case, cat, vtype):
+        """Builds the cancer SNVs filters form."""
+        return controllers.populate_variants_filters_form(
+            store=store, institute_obj=inst, case_obj=case, category=cat, request_obj=request
         )
 
-        # 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)
-            )
-    else:
-        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)
-
-    controllers.populate_force_show_unaffected_vars(institute_obj, form)
-
-    # update status of case if visited for the first time
-    controllers.activate_case(store, institute_obj, case_obj, current_user)
-
-    # Populate chromosome select choices
-    controllers.populate_chrom_choices(form, case_obj)
-
-    # Populate custom soft filters
-    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
-
-    form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
-
-    genome_build = get_case_genome_build(case_obj)
-    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, build=genome_build
-    )
+    def data_exporter(store, case, variants_query):
+        return controllers.download_variants(store, case, variants_query)
 
-    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,
-    )
+    def decorator(store, institute, case, variants_query, page, query_form):
+        return controllers.variants(
+            store=store,
+            institute_obj=institute,
+            case_obj=case,
+            variants_query=variants_query,
+            page=page,
+            query_form=query_form,
+        )
 
-    return dict(
-        cytobands=cytobands,
-        dismiss_variant_options={
-            **DISMISS_VARIANT_OPTIONS,
-            **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
-        },
-        scroll_pos=int(float(request.values.get("scroll_pos", 0) or 0)),
-        expand_search=controllers.get_expand_search(request.form),
-        filters=controllers.populate_persistent_filters_choices(
-            institute_id=institute_id, category=category, form=form
-        ),
-        result_size=result_size,
-        show_dismiss_block=controllers.get_show_dismiss_block(),
-        total_variants=variants_stats.get(variant_type, {}).get(category, "NA"),
-        variant_type=variant_type,
-        **data,
+    return controllers.render_variants_page(
+        category="cancer",
+        institute_id=institute_id,
+        case_name=case_name,
+        form_builder=form_builder,
+        data_exporter=data_exporter,
+        decorator=decorator,
     )
 
 

tests/server/blueprints/variants/test_variants_views.py

@@ -401,30 +401,6 @@ def test_cancer_variants(app, institute_obj, case_obj):
     assert resp.status_code == 200
 
 
-def test_filter_cancer_variants_wrong_params(app, institute_obj, case_obj):
-    """test filter cancer SNV variants with filter form filled with parameters having the wrong format"""
-
-    # GIVEN an initialized app
-    with app.test_client() as client:
-        # GIVEN that the user could be logged in
-        resp = client.get(url_for("auto_login"))
-
-        # When a POST request with filter containing wrongly formatted parameters is sent
-        form_data = {
-            "control_frequency": "not a number!",
-        }
-        resp = client.post(
-            url_for(
-                "variants.cancer_variants",
-                institute_id=institute_obj["internal_id"],
-                case_name=case_obj["display_name"],
-            ),
-            data=form_data,
-        )
-        # THEN it should return a redirected page
-        assert resp.status_code == 302
-
-
 def test_filter_cancer_variants_by_vaf(app, institute_obj, cancer_case_obj, cancer_variant_obj):
     """Tests the cancer form filter by VAF"""