refactor: consolidating models with worker (#1956)

varfish-org · Oct 28, 2024 · 3f43423 · 3f43423
1 parent a02cf55
commit 3f43423
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Showing 30 changed files with 1,933 additions and 2,002 deletions.
diff --git a/backend/Makefile b/backend/Makefile
@@ -146,9 +146,9 @@ protos-download:
 	rm -f protos/seqvars/protos/*_p*2*.py
 
 	wget -O protos/seqvars/protos/output.proto \
-		https://raw.githubusercontent.com/varfish-org/varfish-server-worker/main/protos/varfish/v1/seqvars/output.proto
+		https://raw.githubusercontent.com/varfish-org/varfish-server-worker/refactor-more-protobuf-cleaning-2/protos/varfish/v1/seqvars/output.proto
 	wget -O protos/seqvars/protos/query.proto \
-		https://raw.githubusercontent.com/varfish-org/varfish-server-worker/main/protos/varfish/v1/seqvars/query.proto
+		https://raw.githubusercontent.com/varfish-org/varfish-server-worker/refactor-more-protobuf-cleaning-2/protos/varfish/v1/seqvars/query.proto
 
 	mkdir -p seqvars/protos
 	touch seqvars/protos/__init__.py

diff --git a/backend/protos/seqvars/protos/output.proto b/backend/protos/seqvars/protos/output.proto
@@ -335,9 +335,9 @@ message FrequencyAnnotation {
   // gnomAD-genomes filter
   optional NuclearFrequency gnomad_genomes = 2;
   // gnomAD-MT filter
-  optional GnomadMitochondrialFrequency gnomad_mtdna = 3;
+  optional MitochondrialFrequency gnomad_mtdna = 3;
   // HelixMtDb filter
-  optional HelixMtDbFrequency helixmtdb = 4;
+  optional MitochondrialFrequency helixmtdb = 4;
   // In-house filter
   optional NuclearFrequency inhouse = 5;
 }
@@ -356,8 +356,8 @@ message NuclearFrequency {
   float af = 5;
 }
 
-// gnomAD mitochondrial frequency information.
-message GnomadMitochondrialFrequency {
+// Mitochondrial frequency information.
+message MitochondrialFrequency {
   // Number of covered alleles.
   int32 an = 1;
   // Number of heteroplasmic carriers.
@@ -368,18 +368,6 @@ message GnomadMitochondrialFrequency {
   float af = 4;
 }
 
-// HelixMtDb frequency information.
-message HelixMtDbFrequency {
-  // Number of covered alleles.
-  int32 an = 1;
-  // Number of heterozygous carriers in HelixMtDb
-  int32 het = 2;
-  // Number of homozygous carriers in HelixMtDb
-  int32 homalt = 3;
-  // Frequency in HelixMtDb
-  float af = 4;
-}
-
 // Database identifiers.
 message DbIds {
   // dbSNP ID.

diff --git a/backend/protos/seqvars/protos/query.proto b/backend/protos/seqvars/protos/query.proto
@@ -88,57 +88,58 @@ message QuerySettingsQuality {
   repeated SampleQualitySettings sample_qualities = 1;
 }
 
-// gnomAD and In-house nuclear filter options.
+// gnomAD filter options.
 message NuclearFrequencySettings {
-  // Whether to enable filtration by 1000 Genomes.
+  // Whether to enable filtration.
   bool enabled = 1;
-  // Maximal number of in-house heterozygous carriers
-  optional int32 heterozygous = 2;
-  // Maximal number of in-house homozygous carriers
-  optional int32 homozygous = 3;
-  // Maximal number of in-house hemizygous carriers
-  optional int32 hemizygous = 4;
+  // Maximal number of heterozygous carriers
+  optional int32 max_het = 2;
+  // Maximal number of homozygous carriers
+  optional int32 max_hom = 3;
+  // Maximal number of hemizygous carriers
+  optional int32 max_hemi = 4;
   // Maximal allele frequency.
-  optional float frequency = 5;
+  optional float max_af = 5;
 }
 
-// gnomAD mitochondrial filter options.
-message GnomadMitochondrialFrequencySettings {
-  // Whether to enable filtration by 1000 Genomes.
+// Mitochondrial filter options.
+message MitochondrialFrequencySettings {
+  // Whether to enable filtration.
   bool enabled = 1;
   // Maximal number of heteroplasmic carriers.
-  optional int32 heteroplasmic = 2;
+  optional int32 max_het = 2;
   // Maximal number of homoplasmic carriers.
-  optional int32 homoplasmic = 3;
+  optional int32 max_hom = 3;
   // Maximal allele frequency.
-  optional float frequency = 4;
+  optional float max_af = 4;
 }
 
-// HelixMtDb filter options.
-message HelixMtDbFrequencySettings {
-  // Whether to enable filtration by mtDB
+// In-house filter options.
+message InhouseFrequencySettings {
+  // Whether to enable filtration.
   bool enabled = 1;
-  // Maximal number of heterozygous carriers in HelixMtDb
-  optional int32 heteroplasmic = 2;
-  // Maximal number of homozygous carriers in HelixMtDb
-  optional int32 homoplasmic = 3;
-  // Maximal frequency in HelixMtDb
-  optional float frequency = 4;
+  // Maximal number of heterozygous carriers
+  optional int32 max_het = 2;
+  // Maximal number of homozygous carriers
+  optional int32 max_hom = 3;
+  // Maximal number of hemizygous carriers
+  optional int32 max_hemi = 4;
+  // Maximal number of total carriers.
+  optional int32 max_carriers = 5;
 }
 
-
 // Population frequency filter options.
 message QuerySettingsFrequency {
   // gnomAD-exomes filter
   NuclearFrequencySettings gnomad_exomes = 1;
   // gnomAD-genomes filter
   NuclearFrequencySettings gnomad_genomes = 2;
   // gnomAD-MT filter
-  GnomadMitochondrialFrequencySettings gnomad_mtdna = 3;
+  MitochondrialFrequencySettings gnomad_mtdna = 3;
   // HelixMtDb filter
-  HelixMtDbFrequencySettings helixmtdb = 4;
+  MitochondrialFrequencySettings helixmtdb = 4;
   // In-house filter
-  NuclearFrequencySettings inhouse = 5;
+  InhouseFrequencySettings inhouse = 5;
 }
 
 // The variant types.
@@ -284,7 +285,7 @@ message Range {
   // 1-based start position.
   int32 start = 1;
   // 1-based end position.
-  int32 end = 2;
+  int32 stop = 2;
 }
 
 // Genomic region.