#805 - rename VARIANT_CLASSIFICATION_ to CLASSIFICATION_

classification/autopopulate_evidence_keys/evidence_from_variant.py

@@ -381,7 +381,7 @@ def get_evidence_fields_from_preferred_transcript(
         data[SpecialEKeys.P_HGVS] = clingen_allele.get_p_hgvs(transcript_version.accession, match_version=False)
 
     # If we have a synonymous protein change, but a molecular consequence of splicing, change the "=" into "?"
-    if settings.VARIANT_CLASSIFICATION_AUTO_POPULATE_P_HGVS_SYNONYMOUS_SPLICE_CHANGE_TO_UNKNOWN:
+    if settings.CLASSIFICATION_AUTO_POPULATE_P_HGVS_SYNONYMOUS_SPLICE_CHANGE_TO_UNKNOWN:
         p_hgvs = data[SpecialEKeys.P_HGVS]
         if p_hgvs and "=" in p_hgvs and "splice" in transcript_data.get("consequence", ""):
             prefix, allele = p_hgvs.split(":", 1)

classification/classification_stats.py

@@ -58,7 +58,7 @@ def get_classification_counts_allele(qs: QuerySet[ClassificationModification], f
 def get_visible_classifications_qs(user: User) -> QuerySet[ClassificationModification]:
     # now excludes external labs (don't want to report on Shariant only data within SA Path for example)
 
-    shared = settings.VARIANT_CLASSIFICATION_STATS_USE_SHARED
+    shared = settings.CLASSIFICATION_STATS_USE_SHARED
     kwargs = {"classification__lab__external": False}
     if shared:
         kwargs["clinical_significance__isnull"] = False

classification/migrations/0112_one_off_check_variant_classification_settings.py

@@ -0,0 +1,33 @@
+# Generated by Django 4.2.2 on 2023-09-26 05:13
+import logging
+
+from django.conf import settings
+from django.db import migrations
+
+from manual.operations.manual_operations import ManualOperation
+
+def _check_settings_for_variant_classification(apps):
+    has_old_settings = False
+    for x in dir(settings):
+        if x.startswith("VARIANT_CLASSIFICATION"):
+            if not has_old_settings:  # Only show 1st time
+                logging.warning("Your developer settings has obsolete settings. Please rename:")
+                has_old_settings = True
+            old_setting = x
+            new_setting = x[len("VARIANT_"):]
+            logging.warning("settings.%s -> %s", old_setting, new_setting)
+    return has_old_settings
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('classification', '0111_alter_resolvedvariantinfo_options'),
+    ]
+
+    operations = [
+        ManualOperation.operation_other([
+            "Rename settings from VARIANT_CLASSIFICATION_X to CLASSIFICATION_X"
+        ], test=_check_settings_for_variant_classification),
+    ]
+

classification/models/classification.py

@@ -577,8 +577,8 @@ class Meta:
 
     @staticmethod
     def can_create_via_web_form(user: User):
-        can_create = settings.VARIANT_CLASSIFICATION_WEB_FORM_CREATE
-        return can_create and (user.is_superuser or settings.VARIANT_CLASSIFICATION_WEB_FORM_CREATE_BY_NON_ADMIN)
+        can_create = settings.CLASSIFICATION_WEB_FORM_CREATE
+        return can_create and (user.is_superuser or settings.CLASSIFICATION_WEB_FORM_CREATE_BY_NON_ADMIN)
 
     @staticmethod
     def dashboard_report_new_classifications(since) -> int:
@@ -691,7 +691,7 @@ def id_str(self):
 
     @property
     def cr_lab_id(self):
-        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+        if settings.CLASSIFICATION_ID_OVERRIDE_PREFIX:
             return f"CR_{self.id}"
         return self.lab_record_id
 
@@ -1033,7 +1033,7 @@ def process_option_values(cell: VCDataCell, values: List[Any]) -> Optional[List[
             matched_option = Classification.match_option(options, check_value)
             if matched_option:
                 results.append(matched_option.get('key'))
-                if settings.VARIANT_CLASSIFICATION_REQUIRE_OVERWRITE_NOTE and \
+                if settings.CLASSIFICATION_REQUIRE_OVERWRITE_NOTE and \
                         matched_option.get('override') and cell.note is None and cell.explain is None:
                     cell.add_validation(
                         code=ValidationCode.REQUIRES_NOTE,
@@ -1246,7 +1246,7 @@ def process_entry(self, cell: VCDataCell, source: str):
                                         message='Transcript should include version e.g. NM_001256799.1')
 
         elif e_key.key == SpecialEKeys.AGE:
-            if settings.VARIANT_CLASSIFICATION_AUTOFUZZ_AGE:
+            if settings.CLASSIFICATION_AUTOFUZZ_AGE:
                 cell.value = patch_fuzzy_age(value)
 
         # ensure we have one non None value before returning the structure
@@ -2200,7 +2200,7 @@ def __str__(self) -> str:
 
     @staticmethod
     def check_can_create_no_classification_via_web_form(_user: User):
-        if not settings.VARIANT_CLASSIFICATION_WEB_FORM_CREATE_ALLOW_NO_VARIANT:
+        if not settings.CLASSIFICATION_WEB_FORM_CREATE_ALLOW_NO_VARIANT:
             raise CreateNoClassificationForbidden()
 
 
@@ -2289,7 +2289,7 @@ def id_str(self) -> str:
 
     @property
     def cr_lab_id(self) -> str:
-        if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX:
+        if settings.CLASSIFICATION_ID_OVERRIDE_PREFIX:
             return f"CR_{self.classification.id_str}"
         return self.classification.lab_record_id
 

classification/models/classification_variant_fields_validation.py

@@ -24,7 +24,7 @@ def validate_variant_fields(sender, **kwargs) -> Optional[ValidationMerger]:  #
     """
     vm = ValidationMerger()
 
-    if not settings.VARIANT_CLASSIFICATION_MATCH_VARIANTS:
+    if not settings.CLASSIFICATION_MATCH_VARIANTS:
         # while this technically isn't about matching a variant, much of the work in get_variant_tuple -> pyhgvs
         # requires
         return vm

classification/models/classification_variant_info_models.py

@@ -131,7 +131,7 @@ def set_variant_and_save(self, variant: Variant) -> 'ResolvedVariantInfo':
             c_hgvs = hgvs_variant.format()
             c_hgvs_obj = CHGVS(c_hgvs)
             self.c_hgvs = c_hgvs
-            self.c_hgvs_full = hgvs_variant.format(max_ref_length=settings.VARIANT_CLASSIFICATION_MAX_REFERENCE_LENGTH)
+            self.c_hgvs_full = hgvs_variant.format(max_ref_length=settings.CLASSIFICATION_MAX_REFERENCE_LENGTH)
             self.transcript_version = c_hgvs_obj.transcript_version_model(genome_build=genome_build)
             self.gene_symbol = GeneSymbol.objects.filter(symbol=c_hgvs_obj.gene_symbol).first()
         except Exception as exception:
@@ -586,7 +586,7 @@ def issue_icon(self) -> Optional[IconWithTooltip]:
     def is_supported_transcript(transcript_or_hgvs: str):
         if not transcript_or_hgvs:
             return False
-        for transcript_type in settings.VARIANT_CLASSIFICATION_SUPPORTED_TRANSCRIPTS:
+        for transcript_type in settings.CLASSIFICATION_SUPPORTED_TRANSCRIPTS:
             if transcript_or_hgvs.startswith(transcript_type):
                 return True
         return False

classification/models/evidence_mixin.py

@@ -122,7 +122,7 @@ def loaded_citations(self) -> CitationFetchResponse:
 
     @property
     def is_likely_acmg(self) -> bool:
-        if non_standard_res := settings.VARIANT_CLASSIFICATION_NON_ACMG_ASSERTION_METHOD:
+        if non_standard_res := settings.CLASSIFICATION_NON_ACMG_ASSERTION_METHOD:
             if assertion_method := self.get(SpecialEKeys.ASSERTION_METHOD):
                 for non_standard_re in non_standard_res:
                     if non_standard_re.match(assertion_method):

classification/models/variant_resolver.py

@@ -26,7 +26,7 @@ def _classification_import_from(self, genome_build: GenomeBuild):
 
     def queue_resolve(self, imported_allele_info: ImportedAlleleInfo) -> bool:
         actually_queued = False
-        if settings.VARIANT_CLASSIFICATION_MATCH_VARIANTS:
+        if settings.CLASSIFICATION_MATCH_VARIANTS:
             if imported_allele_info.status == ImportedAlleleInfoStatus.PROCESSING and imported_allele_info.classification_import is None:
                 if genome_build_version := imported_allele_info.imported_genome_build_patch_version:
                     self.all_count += 1

classification/signals/classification_search.py

@@ -20,7 +20,7 @@
     search_type=Classification,
     example=SearchExample(
         note="The lab record ID",
-        examples=["CR_1545" if settings.VARIANT_CLASSIFICATION_ID_OVERRIDE_PREFIX else "vc1545"]
+        examples=["CR_1545" if settings.CLASSIFICATION_ID_OVERRIDE_PREFIX else "vc1545"]
     )
 )
 def classification_search(search_input: SearchInputInstance):

classification/tasks/classification_import_map_and_insert_task.py

@@ -26,7 +26,7 @@ class ClassificationImportMapInsertTask(Task):
 
     @property
     def data_dir(self) -> Path:
-        if data_dir_str := settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_DATA_DIR:
+        if data_dir_str := settings.CLASSIFICATION_OMNI_IMPORTER_DATA_DIR:
             data_dir = pathlib.Path(data_dir_str)
             data_dir.mkdir(parents=True, exist_ok=True)
             if not data_dir.exists():
@@ -35,15 +35,15 @@ def data_dir(self) -> Path:
 
     @property
     def omni_importer_dir(self) -> Path:
-        if omni_importer_dir_str := settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_APP_DIR:
+        if omni_importer_dir_str := settings.CLASSIFICATION_OMNI_IMPORTER_APP_DIR:
             omni_importer_dir = pathlib.Path(omni_importer_dir_str)
             if not omni_importer_dir.exists():
                 raise ValueError(f"{omni_importer_dir_str} does not exist")
             if not (omni_importer_dir / "main.py").exists():
-                raise ValueError(f"main.py doesn't exist inside OMNI IMPORTER DIR {settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_APP_DIR}")
+                raise ValueError(f"main.py doesn't exist inside OMNI IMPORTER DIR {settings.CLASSIFICATION_OMNI_IMPORTER_APP_DIR}")
             return omni_importer_dir
         else:
-            raise ValueError("Require settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_APP_DIR to be set to do automated imports")
+            raise ValueError("Require settings.CLASSIFICATION_OMNI_IMPORTER_APP_DIR to be set to do automated imports")
 
     @staticmethod
     def update_status(upload_file: UploadedClassificationsUnmapped, status: UploadedClassificationsUnmappedStatus):
@@ -99,8 +99,8 @@ def run(self, upload_classifications_unmapped_id: int, import_records: bool = Tr
             # and import it
             # --file data/path_west/sharmvl_grch38molecular_variants20220326_060243.json --publish logged_in_users --org path_west --lab unit_1 --env prod
 
-            publish = settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_PUBLISH_LEVEL
-            include_source = settings.VARIANT_CLASSIFICATION_OMNI_IMPORTER_INCLUDE_SOURCE
+            publish = settings.CLASSIFICATION_OMNI_IMPORTER_PUBLISH_LEVEL
+            include_source = settings.CLASSIFICATION_OMNI_IMPORTER_INCLUDE_SOURCE
 
             args: List[str] = [
                 settings.PYTHON_COMMAND, "main.py",

classification/templates/classification/classifications.html

@@ -150,10 +150,10 @@
 </script>
 {% endblock %}
 {% block content %}
-    {% settings_value 'VARIANT_CLASSIFICATION_GRID_SHOW_USERNAME' as VARIANT_CLASSIFICATION_GRID_SHOW_USERNAME %}
-    {% settings_value 'VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN' as VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN %}
-    {% settings_value 'VARIANT_CLASSIFICATION_ID_FILTER' as VARIANT_CLASSIFICATION_ID_FILTER %}
-    {% settings_value 'VARIANT_CLASSIFICATION_REDCAP_EXPORT' as VARIANT_CLASSIFICATION_REDCAP_EXPORT %}
+    {% settings_value 'CLASSIFICATION_GRID_SHOW_USERNAME' as CLASSIFICATION_GRID_SHOW_USERNAME %}
+    {% settings_value 'CLASSIFICATION_GRID_SHOW_ORIGIN' as CLASSIFICATION_GRID_SHOW_ORIGIN %}
+    {% settings_value 'CLASSIFICATION_ID_FILTER' as CLASSIFICATION_ID_FILTER %}
+    {% settings_value 'CLASSIFICATION_REDCAP_EXPORT' as CLASSIFICATION_REDCAP_EXPORT %}
 
     <div class="container">
         {% if labs.count > 0 and can_create_classification %}
@@ -177,10 +177,10 @@
                 </p>
             {% endif %}
             <p>
-            Export the grid below by clicking the CSV {% if VARIANT_CLASSIFICATION_REDCAP_EXPORT %} or Redcap {% endif %}buttons on the bottom left of the grid.<br/>
+            Export the grid below by clicking the CSV {% if CLASSIFICATION_REDCAP_EXPORT %} or Redcap {% endif %}buttons on the bottom left of the grid.<br/>
             The export will be using your default genome build.<br/>
             </p>
-            {% if VARIANT_CLASSIFICATION_REDCAP_EXPORT %}
+            {% if CLASSIFICATION_REDCAP_EXPORT %}
                 <p>
                 You can import into REDCap using this  <a href="/classification/redcap_data_dictionary.csv">data definition</a>.<br/>
                 Records will only be included in REDCap downloads if they have a value for <b>redcap_record_id</b>.
@@ -200,19 +200,19 @@
                 {% endif %}
                 {% crispy lab_form form_helper.horizontal_no_labels %}
             </div>
-            {% if VARIANT_CLASSIFICATION_GRID_SHOW_USERNAME %}
+            {% if CLASSIFICATION_GRID_SHOW_USERNAME %}
             <div class="col-md-4 col-lg-2">
                 <a class="hover-link" onclick="filterDefaultUser()">Filter : My Classifications</a>
                 {% crispy user_form form_helper.horizontal_no_labels %}
             </div>
             {% endif %}
-            {% if VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN %}
+            {% if CLASSIFICATION_GRID_SHOW_ORIGIN %}
             <div class="col-md-4 col-lg-2">
                 <br />
                 {% crispy allele_origin_form form_helper.horizontal_no_labels %}
             </div>
             {% endif %}
-            {% if VARIANT_CLASSIFICATION_ID_FILTER %}
+            {% if CLASSIFICATION_ID_FILTER %}
             <div class="col-md-4 col-lg-2">
                 <br/>
                 <input type="text" id="id_filter" placeholder="IDs filter" class="form-control" title="Filters on various ID evidence fields" />
@@ -241,7 +241,7 @@
                 <div>
                 Download as
                     <a class='hover-link download-link' href="javascript:downloadAs('csv')">CSV</a>
-                    {% if VARIANT_CLASSIFICATION_REDCAP_EXPORT %},
+                    {% if CLASSIFICATION_REDCAP_EXPORT %},
                     <a class='hover-link download-link' href="javascript:downloadAs('redcap')">REDCap</a>
                     {% endif %}
                 </div>

classification/templates/classification/create_classification_for_variant.html

@@ -9,7 +9,7 @@
 
 {% block title %}Variant Classification{% endblock %}
 {% block head %}
-{% settings_value 'VARIANT_CLASSIFICATION_WEB_FORM_CREATE_INITIALLY_REQUIRE_SAMPLE' as initially_require_sample %}
+{% settings_value 'CLASSIFICATION_WEB_FORM_CREATE_INITIALLY_REQUIRE_SAMPLE' as initially_require_sample %}
 
 <style>
     .pill {

classification/templates/classification/tags/classification_group_row.html

@@ -2,9 +2,9 @@
 {% load js_tags %}
 {% load settings_tags %}
 
-{% settings_value 'VARIANT_CLASSIFICATION_GRID_SHOW_USERNAME' as show_username %}
-{% settings_value 'VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN' as show_allele_origin %}
-{% settings_value 'VARIANT_CLASSIFICATION_SHOW_SPECIMEN_ID' as show_specimen_id %}
+{% settings_value 'CLASSIFICATION_GRID_SHOW_USERNAME' as show_username %}
+{% settings_value 'CLASSIFICATION_GRID_SHOW_ORIGIN' as show_allele_origin %}
+{% settings_value 'CLASSIFICATION_SHOW_SPECIMEN_ID' as show_specimen_id %}
 
 
 <tr class="{{ row_class }}" style="{% if group.clinical_grouping == "not-shared" %}opacity:0.5;{% endif %}{% if group.is_withdrawn %}text-decoration:line-through;{% endif %}cursor:pointer">

classification/templatetags/classification_tags.py

@@ -102,7 +102,7 @@ def classification_groups(
         "user": context.request.user,
         "genome_build": groups.genome_build,
         "table_id": str(uuid.uuid4()).replace("-", "_"),
-        "show_allele_origin": settings.VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN,
+        "show_allele_origin": settings.CLASSIFICATION_GRID_SHOW_ORIGIN,
         "sort_order_index": sort_order_index
     }
     ordered_classifications = list(groups.modifications)
@@ -338,7 +338,7 @@ def classification_modification_sort_score(vcm: ClassificationModification):
         "show_variant_link": show_variant_link,
         "show_clinical_context": show_clinical_context,
         "edit_clinical_groupings": edit_clinical_groupings,
-        "show_allele_origin": settings.VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN,
+        "show_allele_origin": settings.CLASSIFICATION_GRID_SHOW_ORIGIN,
         "user": user,
         "discordance_enabled": settings.DISCORDANCE_ENABLED
     }
@@ -410,7 +410,7 @@ def classification_row(
 
     c_hgvs = vc.c_hgvs_best(preferred_genome_build=genome_build)
     p_hgvs = None
-    if settings.VARIANT_CLASSIFICATION_GRID_SHOW_PHGVS:
+    if settings.CLASSIFICATION_GRID_SHOW_PHGVS:
         p_hgvs = record.get(SpecialEKeys.P_HGVS)
         if p_hgvs:
             p_dot = p_hgvs.find('p.')
@@ -431,8 +431,8 @@ def classification_row(
         "show_variant_link": show_variant_link,
         "show_clinical_context": show_clinical_context,
         "edit_clinical_context": edit_clinical_context,
-        "show_allele_origin": settings.VARIANT_CLASSIFICATION_GRID_SHOW_ORIGIN,
-        "show_specimen_id": settings.VARIANT_CLASSIFICATION_SHOW_SPECIMEN_ID
+        "show_allele_origin": settings.CLASSIFICATION_GRID_SHOW_ORIGIN,
+        "show_specimen_id": settings.CLASSIFICATION_SHOW_SPECIMEN_ID
     }
 
 

classification/tests/models/test_classification_validation.py

@@ -13,7 +13,7 @@ def setUp(self):
     def tearDown(self):
         ClassificationTestUtils.tearDown()
 
-    @override_settings(VARIANT_CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=False)
+    @override_settings(CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=False)
     def test_override_note_disabled(self):
         lab, user = ClassificationTestUtils.lab_and_user()
         vc = Classification.create(
@@ -30,7 +30,7 @@ def test_override_note_disabled(self):
         bp2 = vc.evidence.get('bp2')
         self.assertEqual(bp2, {'value': 'BA'})
 
-    @override_settings(VARIANT_CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=True)
+    @override_settings(CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=True)
     def test_override_note_enabled(self):
         lab, user = ClassificationTestUtils.lab_and_user()
         vc = Classification.create(
@@ -53,7 +53,7 @@ def test_override_note_enabled(self):
                             }]
         })
 
-    @override_settings(VARIANT_CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=True)
+    @override_settings(CLASSIFICATION_REQUIRE_OVERWRITE_NOTE=True)
     def test_external(self):
         lab, user = ClassificationTestUtils.external_lab_and_user()
         vc = Classification.create(

classification/tests/utils/test_clinvar_export.py

@@ -127,7 +127,7 @@ def mock_send_data(
 class TestClinVarExport(TestCase):
 
     @mock.patch('classification.models.clinvar_export_sync.ClinVarExportSync._send_data', side_effect=mock_send_data)
-    @override_settings(VARIANT_CLASSIFICATION_MATCH_VARIANTS=False, CLINVAR_EXPORT={"enabled": True, "mode": "prod", "api_key": "ABC123"})
+    @override_settings(CLASSIFICATION_MATCH_VARIANTS=False, CLINVAR_EXPORT={"enabled": True, "mode": "prod", "api_key": "ABC123"})
     def test_clinvar_setup(self, mocked_send_data):
 
         grch37 = GenomeBuild.get_name_or_alias("GRCh37")

classification/tests/views/test_classification_view.py

@@ -39,7 +39,7 @@ def request_post(self, data):
         request.data = data
         return ClassificationView().post(request=request)
 
-    @override_settings(VARIANT_CLASSIFICATION_MATCH_VARIANTS=False)
+    @override_settings(CLASSIFICATION_MATCH_VARIANTS=False)
     def test_return_data(self):
         lab, _user = ClassificationTestUtils.lab_and_user()
         response = self.request_post({
@@ -158,7 +158,7 @@ def test_return_data(self):
         self.maxDiff = None
         self.assertEqual(response, expected)
 
-    @override_settings(VARIANT_CLASSIFICATION_MATCH_VARIANTS=False)
+    @override_settings(CLASSIFICATION_MATCH_VARIANTS=False)
     def test_test_mode(self):
 
         lab, _user = ClassificationTestUtils.lab_and_user()
@@ -205,7 +205,7 @@ def test_test_mode(self):
         diffs = DeepDiff(t1=expected, t2=response_json)
         self.assertFalse(diffs)
 
-    @override_settings(VARIANT_CLASSIFICATION_MATCH_VARIANTS=False)
+    @override_settings(CLASSIFICATION_MATCH_VARIANTS=False)
     def test_bulk(self):
         lab, _user = ClassificationTestUtils.lab_and_user()
         response = self.request_post({"records": [{
@@ -229,7 +229,7 @@ def test_bulk(self):
         self.assertEqual(results[0]['lab_record_id'], "test_1")
         self.assertEqual(results[1]['lab_record_id'], "test_2")
 
-    @override_settings(VARIANT_CLASSIFICATION_MATCH_VARIANTS=False)
+    @override_settings(CLASSIFICATION_MATCH_VARIANTS=False)
     def test_basic_update(self):
         lab, _user = ClassificationTestUtils.lab_and_user()
         # all test that aliases work re foo BAAA -> bar