feat: proper serde renames for Consequence and PutativeImpact (#214)

varfish-org · Oct 13, 2023 · 02286fa · 02286fa
1 parent cc61a66
commit 02286fa
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Showing 2 changed files with 15 additions and 2 deletions.
diff --git a/src/annotate/seqvars/ann.rs b/src/annotate/seqvars/ann.rs
@@ -29,6 +29,7 @@ use strum::IntoEnumIterator;
     strum::EnumIter,
 )]
 #[display(style = "UPPERCASE")]
+#[serde(rename_all = "UPPERCASE")]
 pub enum PutativeImpact {
     High,
     Moderate,
@@ -53,6 +54,7 @@ pub enum PutativeImpact {
     strum::EnumIter,
 )]
 #[display(style = "snake_case")]
+#[serde(rename_all = "snake_case")]
 pub enum Consequence {
     // high impact
     ChromosomeNumberVariation,
@@ -67,8 +69,10 @@ pub enum Consequence {
     TranscriptAblation,
     // moderate impact
     #[display("3_prime_UTR_truncation")]
+    #[serde(rename = "3_prime_UTR_truncation")]
     ThreePrimeUtrTruncation,
     #[display("5_prime_UTR_truncation")]
+    #[serde(rename = "5_prime_UTR_truncation")]
     FivePrimeUtrTruncaction,
     ConservativeInframeDeletion,
     ConservativeInframeInsertion,
@@ -78,18 +82,22 @@ pub enum Consequence {
     RegulatoryRegionAblation,
     SpliceRegionVariant,
     #[display("TFBS_ablation")]
+    #[serde(rename = "TFBS_ablation")]
     TbfsAblation,
     // low impact
     #[display("5_prime_UTR_premature_start_codon_gain_variant")]
+    #[serde(rename = "5_prime_UTR_premature_start_codon_gain_variant")]
     FivePrimeUtrPrematureStartCodonGainVariant,
     InitiatorCodonVariant,
     StartRetained,
     StopRetainedVariant,
     SynonymousVariant,
     // modifier
     #[display("3_prime_UTR_variant")]
+    #[serde(rename = "3_prime_UTR_variant")]
     ThreePrimeUtrVariant,
     #[display("5_prime_UTR_variant")]
+    #[serde(rename = "5_prime_UTR_variant")]
     FivePrimeUtrVariant,
     CodingSequenceVariant,
     ConservedIntergenicVariant,
@@ -102,18 +110,23 @@ pub enum Consequence {
     IntergenicVariant,
     IntronVariant,
     #[display("mature_miRNA_variant")]
+    #[serde(rename = "mature_miRNA_variant")]
     MatureMirnaVariant,
     #[display("miRNA")]
+    #[serde(rename = "miRNA")]
     Mirna,
     #[display("NMD_transcript_variant")]
+    #[serde(rename = "NMD_transcript_variant")]
     NmdTranscriptVariant,
     NonCodingTranscriptExonVariant,
     NonCodingTranscriptIntronVariant,
     RegulatoryRegionAmplification,
     RegulatoryRegionVariant,
     #[display("TF_binding_site_variant")]
+    #[serde(rename = "TF_binding_site_variant")]
     TfBindingSiteVariant,
     #[display("TFBS_amplification")]
+    #[serde(rename = "TFBS_amplification")]
     TfbsAmplification,
     TranscriptAmplification,
     TranscriptVariant,

diff --git a/...qvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap b/...qvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap
@@ -6,8 +6,8 @@ allele:
   Alt:
     alternative: C
 consequences:
-  - MissenseVariant
-putative_impact: Moderate
+  - missense_variant
+putative_impact: MODERATE
 gene_symbol: BRCA1
 gene_id: "HGNC:1100"
 feature_type: