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Co-authored-by: Manuel Holtgrewe <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| diff --git a/variants/vueapp/src/components/FilterResultsTable.vue b/variants/vueapp/src/components/FilterResultsTable.vue | ||
| index b3fb41de..84185be0 100644 | ||
| --- a/variants/vueapp/src/components/FilterResultsTable.vue | ||
| +++ b/variants/vueapp/src/components/FilterResultsTable.vue | ||
| @@ -224,6 +224,42 @@ const tableRows = ref([]) | ||
| /** Whether the Vue3EasyDataTable is loading. */ | ||
| const tableLoading = ref(false) | ||
|
|
||
| +const getAcmgRating = (payload) => { | ||
| + return acmgRatingStore.getAcmgRating( | ||
| + new SeqvarImpl( | ||
| + payload.release === 'GRCh37' ? 'grch37' : 'grch38', | ||
| + payload.chromosome, | ||
| + payload.start, | ||
| + payload.reference, | ||
| + payload.alternative, | ||
| + ), | ||
| + ) | ||
| +} | ||
| + | ||
| +const getFlags = (payload) => { | ||
| + return flagsStore.getFlags( | ||
| + new SeqvarImpl( | ||
| + payload.release === 'GRCh37' ? 'grch37' : 'grch38', | ||
| + payload.chromosome, | ||
| + payload.start, | ||
| + payload.reference, | ||
| + payload.alternative, | ||
| + ), | ||
| + ) | ||
| +} | ||
| + | ||
| +const hasComments = (payload) => { | ||
| + return commentsStore.hasComments( | ||
| + new SeqvarImpl( | ||
| + payload.release === 'GRCh37' ? 'grch37' : 'grch38', | ||
| + payload.chromosome, | ||
| + payload.start, | ||
| + payload.reference, | ||
| + payload.alternative, | ||
| + ), | ||
| + ) | ||
| +} | ||
| + | ||
| /** | ||
| * Configuration for the row to color them based on flags. | ||
| */ | ||
| @@ -232,15 +268,7 @@ const tableRowClassName = (item, _rowNumber) => { | ||
| return '' | ||
| } | ||
| const flagColors = ['positive', 'uncertain', 'negative'] | ||
| - const flags = flagsStore.getFlags( | ||
| - new SeqvarImpl( | ||
| - item.payload.genome_build == 'GRCh37' ? 'grch37' : 'grch38', | ||
| - item.payload.chromosome, | ||
| - item.payload.start, | ||
| - item.payload.reference, | ||
| - item.payload.alternative, | ||
| - ), | ||
| - ) | ||
| + const flags = getFlags(item.payload) | ||
| if (!flags) { | ||
| return '' | ||
| } | ||
| @@ -591,7 +619,7 @@ watch( | ||
| @click="showVariantDetails(sodar_uuid)" | ||
| /> | ||
| <i-fa-solid-bookmark | ||
| - v-if="flagsStore.getFlags(payload)" | ||
| + v-if="getFlags(payload)" | ||
| class="text-muted ml-1" | ||
| title="flags & bookmarks" | ||
| role="button" | ||
| @@ -606,7 +634,7 @@ watch( | ||
| /> | ||
|
|
||
| <i-fa-solid-comment | ||
| - v-if="commentsStore.hasComments(payload)" | ||
| + v-if="hasComments(payload)" | ||
| class="text-muted ml-1" | ||
| role="button" | ||
| @click="showVariantDetails(sodar_uuid, 'comments')" | ||
| @@ -621,11 +649,11 @@ watch( | ||
| <span | ||
| title="ACMG rating" | ||
| :class=" | ||
| - getAcmgBadgeClasses(acmgRatingStore.getAcmgRating(payload)) | ||
| + getAcmgBadgeClasses(getAcmgRating(payload)) | ||
| " | ||
| role="button" | ||
| @click="showVariantDetails(sodar_uuid, 'acmg-rating')" | ||
| - >{{ acmgRatingStore.getAcmgRating(payload) || '-' }}</span | ||
| + >{{ getAcmgRating(payload) || '-' }}</span | ||
| > | ||
|
|
||
| <a |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,219 @@ | ||
| from collections import defaultdict | ||
| from itertools import chain | ||
| import sys | ||
| import uuid | ||
|
|
||
| from django.core.exceptions import ValidationError | ||
| from django.core.management.base import BaseCommand | ||
| from django.db import transaction | ||
| from projectroles.models import Project | ||
|
|
||
| from variants.models.case import Case | ||
| from variants.models.userannos import AcmgCriteriaRating, SmallVariantComment, SmallVariantFlags | ||
|
|
||
|
|
||
| class RollbackException(Exception): | ||
| pass | ||
|
|
||
|
|
||
| class Command(BaseCommand): | ||
| """Implementation repairing result sets.""" | ||
|
|
||
| #: Help message displayed on the command line. | ||
| help = "Repair query result set for case." | ||
|
|
||
| def add_arguments(self, parser): | ||
| """Add the command's argument to the ``parser``.""" | ||
| parser.add_argument("--write", help="Perform the actual action.", action="store_true") | ||
| parser.add_argument("--case-uuid", help="UUID of the case to create the query set for.") | ||
| parser.add_argument( | ||
| "--project-uuid", help="UUID of the project to create the query set for all cases." | ||
| ) | ||
| parser.add_argument("--all", help="Create query set for all cases.", action="store_true") | ||
|
|
||
| def check_arguments(self, options): | ||
| if bool(options["case_uuid"]) + bool(options["project_uuid"]) + bool(options["all"]) != 1: | ||
| self.stderr.write(self.style.ERROR("Please specify exactly one of the options.")) | ||
| sys.exit(1) | ||
|
|
||
| if options["case_uuid"]: | ||
| try: | ||
| Case.objects.get(sodar_uuid=options["case_uuid"]) | ||
| msg = "Fixing case {}.".format(options["case_uuid"]) | ||
| except Case.DoesNotExist: | ||
| self.stderr.write( | ||
| self.style.ERROR(f"Case with UUID {options['case_uuid']} not found.") | ||
| ) | ||
| sys.exit(1) | ||
| except ValidationError as e: | ||
| self.stderr.write(self.style.ERROR(" ".join(e))) | ||
| sys.exit(1) | ||
| elif options["project_uuid"]: | ||
| try: | ||
| Project.objects.get(sodar_uuid=options["project_uuid"]) | ||
| msg = "Fixing cases of project {}.".format(options["project_uuid"]) | ||
| except Project.DoesNotExist: | ||
| self.stderr.write( | ||
| self.style.ERROR(f"Project with UUID {options['project_uuid']} not found.") | ||
| ) | ||
| sys.exit(1) | ||
| except ValidationError as e: | ||
| self.stderr.write(self.style.ERROR(" ".join(e))) | ||
| sys.exit(1) | ||
| elif options["all"]: | ||
| msg = "Creating query set for all cases." | ||
| else: | ||
| self.stderr.write(self.style.ERROR("Please specify exactly one of the options.")) | ||
| sys.exit(1) | ||
|
|
||
| self.stdout.write(self.style.NOTICE(msg)) | ||
|
|
||
| def handle(self, *args, **options): | ||
| """Generate and fill result sets.""" | ||
| self.check_arguments(options) | ||
|
|
||
| try: | ||
| with transaction.atomic(): | ||
| if options["case_uuid"]: | ||
| _case = Case.objects.get(sodar_uuid=options["case_uuid"]) | ||
| self._handle_case(_case) | ||
| elif options["project_uuid"]: | ||
| for _case in Case.objects.filter(project__sodar_uuid=options["project_uuid"]): | ||
| self._handle_case(_case) | ||
| elif options["all"]: | ||
| for _case in Case.objects.all(): | ||
| self._handle_case(_case) | ||
|
|
||
| if not options["write"]: | ||
| raise RollbackException("Rolling back transaction.") | ||
| self.stderr.write(self.style.SUCCESS("Successfully repaired result set.")) | ||
|
|
||
| except RollbackException as e: | ||
| self.stderr.write(self.style.ERROR(e)) | ||
| sys.exit(1) | ||
|
|
||
| def _handle_case(self, case): # noqa: C901 | ||
| try: | ||
| case_result_set = case.smallvariantqueryresultset_set.get(smallvariantquery=None) | ||
| except Exception: | ||
| self.stderr.write(self.style.ERROR("No result set for case.")) | ||
| sys.exit(1) | ||
|
|
||
| query_result_sets = case.smallvariantqueryresultset_set.filter( | ||
| smallvariantquery__isnull=False | ||
| ) | ||
| self.stderr.write(self.style.NOTICE("Deleting old result set.")) | ||
| case_result_set.smallvariantqueryresultrow_set.all().delete() | ||
| case_result_set.result_row_count = 0 | ||
| case_result_set.save() | ||
|
|
||
| comments = SmallVariantComment.objects.filter(case=case) | ||
| flags = SmallVariantFlags.objects.filter(case=case) | ||
| acmg_ratings = AcmgCriteriaRating.objects.filter(case=case) | ||
|
|
||
| dict_query_result_rows = {} | ||
| for query_result_set in query_result_sets: | ||
| query_result_rows = query_result_set.smallvariantqueryresultrow_set.all() | ||
| for row in query_result_rows: | ||
| key = ( | ||
| f"{row.release}-{row.chromosome}-{row.start}-{row.reference}-{row.alternative}" | ||
| ) | ||
| if key not in dict_query_result_rows: | ||
| dict_query_result_rows[key] = row | ||
|
|
||
| dict_comments = defaultdict(int) | ||
| for comment in comments: | ||
| dict_comments[ | ||
| f"{comment.release}-{comment.chromosome}-{comment.start}-{comment.reference}-{comment.alternative}" | ||
| ] += 1 | ||
|
|
||
| dict_flags = { | ||
| f"{flag.release}-{flag.chromosome}-{flag.start}-{flag.reference}-{flag.alternative}": flag | ||
| for flag in flags | ||
| } | ||
|
|
||
| dict_acmg_ratings = { | ||
| f"{acmg_rating.release}-{acmg_rating.chromosome}-{acmg_rating.start}-{acmg_rating.reference}-{acmg_rating.alternative}": acmg_rating | ||
| for acmg_rating in acmg_ratings | ||
| } | ||
|
|
||
| dict_query_result_rows_keys = set(dict_query_result_rows.keys()) | ||
| dict_comments_keys = set(dict_comments.keys()) | ||
| dict_flags_keys = set(dict_flags.keys()) | ||
| dict_acmg_ratings_keys = set(dict_acmg_ratings.keys()) | ||
|
|
||
| dict_case_result_rows = {} | ||
| for key in dict_query_result_rows_keys: | ||
| if key not in chain(dict_comments_keys, dict_flags_keys, dict_acmg_ratings_keys): | ||
| continue | ||
| self.stderr.write( | ||
| self.style.NOTICE(f"Creating new result row in case result set {key}.") | ||
| ) | ||
|
|
||
| row = dict_query_result_rows[key] | ||
| row.pk = None | ||
| row.sodar_uuid = uuid.uuid4() | ||
| row.smallvariantqueryresultset = case_result_set | ||
| row.payload["comment_count"] = 0 | ||
| row.payload["flag_count"] = 0 | ||
| row.save() | ||
|
|
||
| case_result_set.result_row_count += 1 | ||
| case_result_set.save() | ||
| dict_case_result_rows[key] = row | ||
|
|
||
| for key, comment_count in dict_comments.items(): | ||
| self.stderr.write(self.style.NOTICE(f"Adding comment to row in case result set {key}.")) | ||
| try: | ||
| dict_case_result_rows[key].payload["comment_count"] += comment_count | ||
| dict_case_result_rows[key].save() | ||
| except KeyError: | ||
| self.stderr.write( | ||
| self.style.ERROR( | ||
| f"Comment with key {key} not found in case result set {case_result_set.sodar_uuid}." | ||
| ) | ||
| ) | ||
|
|
||
| for key, flag in dict_flags.items(): | ||
| self.stderr.write(self.style.NOTICE(f"Adding flag to row in case result set {key}.")) | ||
| try: | ||
| for field in ( | ||
| "flag_visual", | ||
| "flag_summary", | ||
| "flag_candidate", | ||
| "flag_molecular", | ||
| "flag_bookmarked", | ||
| "flag_segregates", | ||
| "flag_validation", | ||
| "flag_for_validation", | ||
| "flag_final_causative", | ||
| "flag_phenotype_match", | ||
| "flag_doesnt_segregate", | ||
| "flag_no_disease_association", | ||
| ): | ||
| dict_case_result_rows[key].payload[field] = getattr(flag, field) | ||
| dict_case_result_rows[key].payload["flag_count"] += 1 | ||
| dict_case_result_rows[key].save() | ||
| except KeyError: | ||
| self.stderr.write( | ||
| self.style.ERROR( | ||
| f"Flag with key {key} not found in case result set {case_result_set.sodar_uuid}." | ||
| ) | ||
| ) | ||
|
|
||
| for key, acmg_rating in dict_acmg_ratings.items(): | ||
| self.stderr.write( | ||
| self.style.NOTICE(f"Adding acmg rating to row in case result set {key}.") | ||
| ) | ||
| try: | ||
| dict_case_result_rows[key].payload["acmg_class_auto"] = acmg_rating.class_auto | ||
| dict_case_result_rows[key].payload[ | ||
| "acmg_class_override" | ||
| ] = acmg_rating.class_override | ||
| dict_case_result_rows[key].save() | ||
| except KeyError: | ||
| self.stderr.write( | ||
| self.style.ERROR( | ||
| f"Acmg rating with key {key} not found in case result set {case_result_set.sodar_uuid}." | ||
| ) | ||
| ) |
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