Merge pull request #28 from VariantEffect/feature/bencap/api-like-api-constant

New API values for protein categories

Author: bencap

src/dcd_mapping/schemas.py

@@ -21,9 +21,9 @@ class TargetSequenceType(str, Enum):
 class TargetType(str, Enum):
     """Define target gene types."""
 
-    PROTEIN_CODING = "Protein coding"
-    REGULATORY = "Regulatory"
-    OTHER_NC = "Other noncoding"
+    PROTEIN_CODING = "protein_coding"
+    REGULATORY = "regulatory"
+    OTHER_NC = "other_noncoding"
 
 
 class VrsVersion(str, Enum):

tests/fixtures/scoreset_metadata.json

@@ -3,7 +3,7 @@
     {
       "urn": "urn:mavedb:00000002-a-2",
       "target_gene_name": "hYAP65 WW domain",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "GACGTTCCACTGCCGGCTGGTTGGGAAATGGCTAAAACTAGTTCTGGTCAGCGTTACTTCCTGAACCACATCGACCAGACCACCACGTGGCAGGACCCGCGT",
       "target_sequence_type": "dna",
       "target_uniprot_ref": {
@@ -14,23 +14,23 @@
     {
       "urn": "urn:mavedb:00000099-a-1",
       "target_gene_name": "RHO",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA",
       "target_sequence_type": "dna",
       "target_uniprot_ref": null
     },
     {
       "urn": "urn:mavedb:00000103-c-1",
       "target_gene_name": "MAPK1",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS",
       "target_sequence_type": "protein",
       "target_uniprot_ref": null
     },
     {
       "urn": "urn:mavedb:00000041-a-1",
       "target_gene_name": "Src catalytic domain",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "CTGCGGCTGGAGGTCAAGCTGGGCCAGGGCTGCTTTGGCGAGGTGTGGATGGGGACCTGGAACGGTACCACCAGGGTGGCCATCAAAACCCTGAAGCCTGGCACGATGTCTCCAGAGGCCTTCCTGCAGGAGGCCCAGGTCATGAAGAAGCTGAGGCATGAGAAGCTGGTGCAGTTGTATGCTGTGGTTTCAGAGGAGCCCATTTACATCGTCACGGAGTACATGAGCAAGGGGAGTTTGCTGGACTTTCTCAAGGGGGAGACAGGCAAGTACCTGCGGCTGCCTCAGCTGGTGGACATGGCTGCTCAGATCGCCTCAGGCATGGCGTACGTGGAGCGGATGAACTACGTCCACCGGGACCTTCGTGCAGCCAACATCCTGGTGGGAGAGAACCTGGTGTGCAAAGTGGCCGACTTTGGGCTGGCTCGGCTCATTGAAGACAATGAGTACACGGCGCGGCAAGGTGCCAAATTCCCCATCAAGTGGACGGCTCCAGAAGCTGCCCTCTATGGCCGCTTCACCATCAAGTCGGACGTGTGGTCCTTCGGGATCCTGCTGACTGAGCTCACCACAAAGGGACGGGTGCCCTACCCTGGGATGGTGAACCGCGAGGTGCTGGACCAGGTGGAGCGGGGCTACCGGATGCCCTGCCCGCCGGAGTGTCCCGAGTCCCTGCACGACCTCATGTGCCAGTGCTGGCGGAAGGAGCCTGAGGAGCGGCCCACCTTCGAGTACCTGCAGGCCTTCCTG",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
@@ -42,7 +42,7 @@
     {
       "urn": "urn:mavedb:00000018-a-1",
       "target_gene_name": "HBB promoter",
-      "target_gene_category": "Regulatory",
+      "target_gene_category": "regulatory",
       "target_sequence": "GGTGTCTGTTTGAGGTTGCTAGTGAACACAGTTGTGTCAGAAGCAAATGTAAGCAATAGATGGCTCTGCCCTGACTTTTATGCCCAGCCCTGGCTCCTGCCCTCCCTGCTCCTGGGAGTAGATTGGCCAACCCTAGGGTGTGGCTCCACAGGGTGAGGTCTAAGTGATGACAGCCGTACCTGTCCTT",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
@@ -51,7 +51,7 @@
     {
       "urn": "urn:mavedb:00000001-a-4",
       "target_gene_name": "UBE2I",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
@@ -63,7 +63,7 @@
     {
       "urn": "urn:mavedb:00000113-a-2",
       "target_gene_name": "APP",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA",
       "target_sequence_type": "protein",
       "target_reference_genome": "hg38",
@@ -75,7 +75,7 @@
     {
       "urn": "urn:mavedb:00000098-a-1",
       "target_gene_name": "SCN5A",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "LFRVIRLARIGR",
       "target_sequence_type": "protein",
       "target_reference_genome": "hg38",
@@ -87,7 +87,7 @@
     {
       "urn": "urn:mavedb:00000061-h-1",
       "target_gene_name": "RAF",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
@@ -99,7 +99,7 @@
     {
       "urn": "urn:mavedb:00000068-a-1",
       "target_gene_name": "TP53 (P72R)",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTAG",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
@@ -108,7 +108,7 @@
     {
       "urn": "urn:mavedb:00000093-a-1",
       "target_gene_name": "BRCA1 translation start through RING domain",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAG",
       "target_sequence_type": "dna",
       "target_reference_genome": "hg19",
@@ -120,7 +120,7 @@
     {
       "urn": "urn:mavedb:00000001-b-2",
       "target_gene_name": "SUMO1",
-      "target_gene_category": "Protein coding",
+      "target_gene_category": "protein_coding",
       "target_sequence": "ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCATTGGACAGGATAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCAAAGAATCATACTGTCAAAGACAGGGTGTTCCAATGAATTCACTCAGGTTTCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGGGAATGGAGGAAGAAGATGTGATTGAAGTTTATCAGGAACAAACGGGGGGTCATTCAACAGTTTAG",
       "target_sequence_type": "dna",
       "target_uniprot_ref": {

tests/fixtures/scoreset_metadata_response.json

@@ -166,7 +166,7 @@
     "targetGenes": [
       {
         "name": "BRCA1 translation start through RING domain",
-        "category": "Protein coding",
+        "category": "protein_coding",
         "externalIdentifiers": [
           {
             "identifier": {