List models and admins for the sake of DJango Structure in PyCharm

analysis/admin.py

@@ -3,6 +3,7 @@
 from guardian.admin import GuardedModelAdmin
 
 from analysis import models
+from snpdb.admin_utils import ModelAdminBasics
 
 
 class AnalysisUserFilter(admin.SimpleListFilter):
@@ -20,15 +21,33 @@ def queryset(self, request, queryset):
         return queryset
 
 
+@admin.register(models.Analysis)
 class AnalysisAdmin(GuardedModelAdmin):
     list_display = ['id', 'user', 'name', 'description', 'template_type', 'visible', 'created']
     list_filter = (AnalysisUserFilter,)
     search_fields = ('id', 'lab_record_id')
 
 
-admin.site.register(models.Analysis, AnalysisAdmin)
-admin.site.register(models.AnalysisTemplate)
-admin.site.register(models.AnalysisTemplateRun)
-admin.site.register(models.AnalysisTemplateVersion)
-admin.site.register(models.VariantTag)
-admin.site.register(models.VariantTagsImport)
+@admin.register(models.AnalysisTemplate)
+class AnalysisTemplateAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.AnalysisTemplateRun)
+class AnalysisTemplateRunAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.AnalysisTemplateVersion)
+class AnalysisTemplateRunAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.VariantTag)
+class VariantTagAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.VariantTagsImport)
+class VariantTagsImportAdmin(ModelAdminBasics):
+    pass

analysis/models.py

@@ -0,0 +1,29 @@
+# This file exists for PyCharm's Django Structure plugin
+from analysis.models.models_analysis import Analysis, AnalysisLock, AnalysisNodeCountConfiguration, AnalysisNodeCountConfigRecord, AnalysisVariable, AnalysisTemplate, AnalysisTemplateVersion, AnalysisTemplateRun, AnalysisTemplateRunArgument, CohortAnalysisTemplateRun, SampleAnalysisTemplateRun
+from analysis.models.models_karyomapping import KaryomappingAnalysis, KaryomappingGene, GenomeKaryomappingCounts, ContigKaryomappingCounts
+from analysis.models.nodes.analysis_node import AnalysisNode, AnalysisEdge, NodeTask, NodeWiki, AnalysisNodeAlleleSource, NodeVersion, NodeCache, NodeCount, NodeColumnSummaryCacheCollection, NodeColumnSummaryData, NodeVCFFilter, NodeAlleleFrequencyFilter, NodeAlleleFrequencyRange, AnalysisClassification
+from analysis.models.models_variant_tag import VariantTagsImport, ImportedVariantTag, VariantTag
+from analysis.models.mutational_signatures import MutationalSignatureCalculator, MutationalSignature, MutationalSignatureMinimisationResult, MutationalSignatureMutationCount
+from analysis.models.nodes.filters.allele_frequency_node import AlleleFrequencyNode
+from analysis.models.nodes.filters.built_in_filter_node import BuiltInFilterNode
+from analysis.models.nodes.filters.damage_node import DamageNode
+from analysis.models.nodes.filters.filter_node import FilterNode, FilterNodeItem
+from analysis.models.nodes.filters.gene_list_node import GeneListNode, GeneListNodeGeneList, GeneListNodePanelAppPanel
+from analysis.models.nodes.filters.intersection_node import IntersectionNode
+from analysis.models.nodes.filters.merge_node import MergeNode
+from analysis.models.nodes.filters.moi_node import MOINode, MOINodeOntologyTerm, MOINodeModeOfInheritance, MOINodeSubmitter
+from analysis.models.nodes.filters.phenotype_node import PhenotypeNode, PhenotypeNodeOntologyTerm
+from analysis.models.nodes.filters.population_node import PopulationNode, PopulationNodeGnomADPopulation
+from analysis.models.nodes.filters.selected_in_parent_node import SelectedInParentNode, NodeVariant
+from analysis.models.nodes.filters.tag_node import TagNode, TagNodeTag
+from analysis.models.nodes.filters.tissue_node import TissueNode
+from analysis.models.nodes.filters.venn_node import VennNode, VennNodeCache
+from analysis.models.gene_counts import NodeGenesCountCollection, NodeGenesCount
+from analysis.models.nodes.filters.zygosity_node import ZygosityNode
+from analysis.models.nodes.node_types import NodeGraphType
+from analysis.models.nodes.sources.all_variants_node import AllVariantsNode
+from analysis.models.nodes.sources.classifications_node import ClassificationsNode, ClassificationsNodeLab
+from analysis.models.nodes.sources.cohort_node import CohortNode, CohortNodeZygosityFiltersCollection, CohortNodeZygosityFilter
+from analysis.models.nodes.sources.pedigree_node import PedigreeNode
+from analysis.models.nodes.sources.sample_node import SampleNode
+from analysis.models.nodes.sources.trio_node import TrioNode

annotation/models.py

@@ -0,0 +1,7 @@
+# This file exists for PyCharm's Django Structure plugin
+from annotation.models.models_citations import Citation
+from annotation.models.models import ClinVarVersion, ClinVar, ClinVarRecordCollection, ClinVarRecord, ClinVarCitationsCollection, ClinVarCitation, DBNSFPGeneAnnotationVersion, DBNSFPGeneAnnotation, GeneAnnotationVersion, GeneAnnotation, HumanProteinAtlasAnnotationVersion, HumanProteinAtlasTissueSample, HumanProteinAtlasAnnotation, ColumnVEPField, VariantAnnotationVersion, VCFAnnotationStats, AnnotationRangeLock, AnnotationRun, VariantAnnotation, VariantTranscriptAnnotation, VariantGeneOverlap, ManualVariantEntryCollection, ManualVariantEntry, CreatedManualVariant, AnnotationVersion, CachedWebResource, GeneSymbolCitation, GeneSymbolPubMedCount, MutationalSignatureInfo
+from annotation.models.models_gene_counts import VariantSource, SampleAnnotationVersionVariantSource, GeneCountType, GeneValue, GeneValueCountCollection, GeneValueCount, CohortGeneCounts
+from annotation.models.models_phenotype_match import DescriptionProcessingStatus, PhenotypeDescription, TextPhenotype, TextPhenotypeSentence, TextPhenotypeMatch, PatientTextPhenotype
+from annotation.models.models_sample_stats import SampleVariantAnnotationStats, SampleVariantAnnotationStatsPassingFilter, SampleGeneAnnotationStats, SampleGeneAnnotationStatsPassingFilter, SampleClinVarAnnotationStats, SampleClinVarAnnotationStatsPassingFilter
+from annotation.models.models_version_diff import VersionDiff, VersionDiffFromToResult, VersionDiffChangeCountResult, VariantAnnotationVersionDiff

classification/admin.py

@@ -1,2 +1,4 @@
+# File for PyCharm DJango Structure plugin
 # noinspection PyUnresolvedReferences
-import classification.admin  # just need these to trigger the decorators
+from classification.admin import ClassificationImportRunAdmin, ClassificationAdmin, ClassificationImportAdmin, ClinicalContextAdmin, EvidenceKeyAdmin, ClassificationReportTemplateAdmin, DiscordanceReportAdmin, DiscordanceReportTriageAdmin, DiscordanceNotificationAdmin, UploadedClassificationsUnmappedAdmin, ResolvedVariantInfoAdmin, ImportedAlleleInfoAdmin, ImportedAlleleInfoValidationAdmin, ClinVarExportAdmin, ClinVarAlleleAdmin, ClinVarExportBatchAdmin, ConditionTextAdmin
+

classification/models.py

@@ -0,0 +1,12 @@
+# This file exists for PyCharm's Django Structure plugin
+from classification.models.uploaded_classifications_unmapped import UploadedClassificationsUnmapped
+from classification.models.classification_import_run import ClassificationImportRun
+from classification.models.classification_variant_info_models import HGVSConverterVersion, ResolvedVariantInfo, ImportedAlleleInfoValidation, ImportedAlleleInfo
+from classification.models.evidence_key import EvidenceKey
+from classification.models.classification import ClassificationImport, ClassificationImportAlleleSource, AllClassificationsAlleleSource, Classification, ClassificationModification
+from classification.models.clinical_context_models import DiscordanceNotification, ClinicalContext
+from classification.models.discordance_models import DiscordanceReport, DiscordanceReportClassification, DiscordanceReportTriage
+from classification.models.variant_models import ClassificationAttachment
+from classification.models.condition_text_matching import ConditionText, ConditionTextMatch
+from classification.models.clinvar_export_models import ClinVarAllele, ClinVarExport, ClinVarExportBatch, ClinVarExportSubmission, ClinVarExportRequest
+from classification.models.classification_report_models import ClassificationReportTemplate

classification/models/__init__.py

@@ -1,8 +1,8 @@
 from classification.models.discordance_models import *
 from classification.models.classification import *
 from classification.models.classification_ref import *
-
 from classification.models.classification_variant_fields_validation import *  # so we load the receivers
+from classification.models.classification_variant_info_models import *
 from classification.models.variant_models import *
 from classification.models.condition_text_matching import *
 from classification.models.clinvar_export_models import *

email_manager/models.py

@@ -0,0 +1,2 @@
+# This file exists for PyCharm's Django Structure plugin
+from email_manager.models.email_model import EmailLog

eventlog/views.py

@@ -5,6 +5,7 @@
 from django.shortcuts import render
 from django.utils import timezone
 from django.views.decorators.http import require_POST
+from django.views.generic import ListView
 
 from eventlog.models import Event
 from library.enums.log_level import LogLevel

flags/models.py

@@ -0,0 +1,2 @@
+# This file exists for PyCharm's Django Structure plugin
+from flags.models.models import FlagResolution, FlagTypeContext, FlagType, FlagTypeResolution, Flag, FlagCollection, FlagComment

genes/admin.py

@@ -40,11 +40,41 @@ def panelapp_au_refresh(self, request, queryset: QuerySet[GeneSymbol]):
             update_gene_relations(gene_symbol)
 
 
-admin.site.register(models.ActiveSampleGeneList)
-admin.site.register(models.GeneAnnotationRelease)
-admin.site.register(models.GeneInfo)
-admin.site.register(models.GeneListGeneSymbol)
-admin.site.register(models.GeneSymbolAlias)
-admin.site.register(models.PanelAppPanel)
-admin.site.register(models.PanelAppPanelLocalCache)
-admin.site.register(models.SampleGeneList)
+@admin.register(models.ActiveSampleGeneList)
+class ActiveSampleGeneListAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.GeneAnnotationRelease)
+class GeneAnnotationReleaseAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.GeneInfo)
+class GeneInfoAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.GeneListGeneSymbol)
+class GeneListGeneSymbolAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.GeneSymbolAlias)
+class GeneSymbolAliasAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PanelAppPanel)
+class PanelAppPanelAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PanelAppPanelLocalCache)
+class PanelAppPanelLocalCacheAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.SampleGeneList)
+class SampleGeneListAdmin(ModelAdminBasics):
+    pass

manual/models.py

@@ -0,0 +1,3 @@
+# This file exists for PyCharm's Django Structure plugin
+from manual.models.deployment_models import Deployment
+from manual.models.manual_migration_models import ManualMigrationTask, ManualMigrationRequired, ManualMigrationAttempt

ontology/models.py

@@ -0,0 +1,2 @@
+# This file exists for PyCharm's Django Structure plugin
+from ontology.models.models_ontology import OntologyImport, OntologyTerm, OntologyTermRelation, OntologyVersion

patients/admin.py

@@ -1,13 +1,49 @@
 from django.contrib import admin
 
 from patients import models
+from snpdb.admin_utils import ModelAdminBasics
 
-admin.site.register(models.Patient)
-admin.site.register(models.Tissue)
-admin.site.register(models.Specimen)
-admin.site.register(models.PatientImport)
-admin.site.register(models.PatientModification)
-admin.site.register(models.PatientComment)
-admin.site.register(models.Clinician)
-admin.site.register(models.PatientRecords)
-admin.site.register(models.PatientRecord)
+
+@admin.register(models.Patient)
+class PatientAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.Tissue)
+class TissueAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.Specimen)
+class SpecimenAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PatientImport)
+class PatientImportAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PatientModification)
+class PatientModificationAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PatientComment)
+class PatientCommentAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.Clinician)
+class ClinicianAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PatientRecords)
+class PatientRecordsAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.PatientRecord)
+class PatientRecordAdmin(ModelAdminBasics):
+    pass

review/admin.py

@@ -0,0 +1,3 @@
+# File for PyCharm DJango Structure plugin
+# noinspection PyUnresolvedReferences
+from review.admin import ReviewTopicAdmin, ReviewAdmin

review/admin/review_admin.py

@@ -32,7 +32,7 @@ def has_change_permission(self, request, obj=None):
 
 
 @admin.register(ReviewTopic)
-class ReviewQuestionTopicAdmin(ModelAdminBasics):
+class ReviewTopicAdmin(ModelAdminBasics):
     inlines = (ReviewQuestionInline,)
 
     def widget_overrides(self):

review/models.py

@@ -0,0 +1,2 @@
+# This file exists for PyCharm's Django Structure plugin
+from review.models.review_models import ReviewTopic, ReviewQuestion, ReviewedObject, Review_reviewing_labs, Review

seqauto/admin.py

@@ -17,17 +17,66 @@ def is_readonly_field(self, f) -> bool:
         return super().is_readonly_field(f)
 
 
-# Register your models here.
-admin.site.register(models.Sequencer)
-admin.site.register(models.SequencerModel)
-admin.site.register(models.SeqAutoRun)
-admin.site.register(models.SequencingRun)
-admin.site.register(models.IlluminaFlowcellQC)
-admin.site.register(models.Fastq)
-admin.site.register(models.FastQC)
-admin.site.register(models.UnalignedReads)
-admin.site.register(models.BamFile)
-admin.site.register(models.Flagstats)
-admin.site.register(models.VCFFile)
-admin.site.register(models.QC)
-admin.site.register(models.QCExecSummary)
+@admin.register(models.Sequencer)
+class SequencerAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.SequencerModel)
+class SequencerModelAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.SeqAutoRun)
+class SeqAutoRunAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.SequencingRun)
+class SequencingRunAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.IlluminaFlowcellQC)
+class IlluminaFlowcellQCAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.Fastq)
+class FastqAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.FastQC)
+class FastQCAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.UnalignedReads)
+class UnalignedReadsAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.BamFile)
+class BamFileAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.Flagstats)
+class FlagstatsAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.VCFFile)
+class VCFFileAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.QC)
+class QCAdmin(ModelAdminBasics):
+    pass
+
+
+@admin.register(models.QCExecSummary)
+class QCExecSummaryAdmin(ModelAdminBasics):
+    pass

seqauto/models.py

@@ -0,0 +1,4 @@
+# This file exists for PyCharm's Django Structure plugin
+from seqauto.models.models_sequencing import SequencerModel, Sequencer, EnrichmentKit, Library, Assay, Experiment, SequencingInfo
+from seqauto.models.models_software import VariantCaller, Aligner, VariantCallingPipeline, SoftwarePipeline, SoftwarePipelineNode, SoftwarePipelineEdge
+from seqauto.models.models_seqauto import SeqAutoRun, SeqAutoRecord, SeqAutoMessage, SequencingRun, SequencingRunWiki, SampleSheet, SequencingRunCurrentSampleSheet, SequencingSample, SequencingSampleData, SampleFromSequencingSample, VCFFromSequencingRun, IlluminaFlowcellQC, ReadQ30, IlluminaIndexQC, Fastq, FastQC, UnalignedReads, BamFile, Flagstats, VCFFile, SampleSheetCombinedVCFFile, QC, QCGeneList, QCExecSummary, ExecSummaryReferenceRange, QCGeneCoverage, GoldReference, GoldGeneCoverageCollection, GoldCoverageSummary, QCType, QCColumn, JobScript

snpdb/models.py

@@ -0,0 +1,13 @@
+# This file exists for PyCharm's Django Structure plugin
+from snpdb.models.models import Tag, CachedGeneratedFile, Company, Manufacturer, Wiki, ImportedWikiCollection, ImportedWiki, Organization, ClinVarKey, ClinVarKeyExcludePattern, Country, State, Lab, LabHead, UserAward, LabProject, SiteMessage
+from snpdb.models.models_genome import GenomeBuild, GenomeBuildPatchVersion, Contig, GenomeBuildContig, GenomeFasta, GenomeFastaContig
+from snpdb.models.models_clingen_allele import ClinGenAllele
+from snpdb.models.models_variant import Allele, AlleleMergeLog, Sequence, Locus, Variant, VariantWiki, VariantAllele, VariantCollection, VariantCollectionRecord, AlleleSource, VariantAlleleSource, VariantAlleleCollectionSource, VariantAlleleCollectionRecord, LiftoverRun, AlleleLiftover
+from snpdb.models.models_genomic_interval import GenomicIntervalsCategory, GenomicIntervalsCollection, GenomicInterval
+from snpdb.models.models_vcf import Project, VCF, VCFFilter, VCFTag, Sample, SampleFilePath, SampleTag, VCFAlleleSource, SampleStatsCodeVersion, SampleStats, SampleStatsPassingFilter, SampleLocusCount, SampleLabProject, VCFSourceSettings, VCFBedIntersection
+from snpdb.models.models_cohort import Cohort, CohortSample, CohortGenotypeTaskVersion, CohortGenotypeCommonFilterVersion, CommonVariantClassified, CohortGenotypeCollection, CohortGenotype, Trio
+from snpdb.models.models_columns import VariantGridColumn, ColumnVCFInfo, CustomColumnsCollection, CustomColumn
+from snpdb.models.models_dbsnp import DbSNP
+from snpdb.models.models_somalier import SomalierVCFExtract, SomalierSampleExtract, SomalierAncestryRun, SomalierAncestry, SomalierCohortRelate, SomalierTrioRelate, SomalierAllSamplesRelate, SomalierRelatePairs
+from snpdb.models.models_user_settings import UserDataPrefix, TagColorsCollection, TagColor, UserPageAck, UserGridConfig, SettingsOverride, GlobalSettings, OrganizationUserSettingsOverride, LabUserSettingsOverride, UserSettingsOverride, SettingsInitialGroupPermission, NodeCountSettingsCollection, NodeCountSettings, UserContact
+from snpdb.models.models_zygosity_counts import VariantZygosityCountCollection, VariantZygosityCount, VariantZygosityCountForVCF, VariantZygosityCountForSample

sync/models.py

@@ -0,0 +1,3 @@
+# This file exists for PyCharm's Django Structure plugin
+from sync.models.models import SyncDestination, SyncRun
+from sync.models.models_classification_sync import ClassificationModificationSyncRecord

upload/models.py

@@ -0,0 +1,3 @@
+# This file exists for PyCharm's Django Structure plugin
+from upload.models.models import UploadedFile, UploadPipeline, ToolVersion, UploadStep, UploadStepMultiFileOutput, VCFImporter, UploadedVCF, UploadedVCFPendingAnnotation, BackendVCF, VCFImportInfo, SimpleVCFImportInfo, ModifiedImportedVariants, ModifiedImportedVariant, VCFSkippedContigs, VCFSkippedContig, UploadSettings, UploadSettingsFileType
+from upload.models.models_uploaded_files import UploadedGeneList, UploadedBed, UploadedPedFile, UploadedPatientRecords, UploadedGeneCoverage, UploadedManualVariantEntryCollection, UploadedClassificationImport, UploadedLiftover, UploadedWikiCollection, UploadedClinVarVersion, UploadedVariantTags