CTD,biolink/monarch,ebi-proteins,litvar: adjust nunjucks templating used

reference: biothings/call-apis.js#30 due to code on some instances keeping the ID prefix from the TRAPI query
NCATS-Tangerine · Mar 18, 2023 · 7b918f8 · 7b918f8
1 parent da81308
commit 7b918f8
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Showing 5 changed files with 29 additions and 28 deletions.
diff --git a/CTD/smartapi.yaml b/CTD/smartapi.yaml
@@ -197,7 +197,7 @@ components:
         semantic: SmallMolecule
       parameters:
         inputType: gene
-        inputTerms: "{{ queryInputs }}"  ## no prefix
+        inputTerms: "{{ queryInputs | rmPrefix() }}"  ## no prefix
         inputTermSearchType: directAssociations
         report: chems_curated
         format: json
@@ -240,7 +240,7 @@ components:
         semantic: SmallMolecule
       parameters:
         inputType: disease
-        inputTerms: "{{ queryInputs | addPrefix('MESH') }}"  ## HAS PREFIX
+        inputTerms: "{{ queryInputs | replPrefix('MESH') }}"  ## HAS PREFIX
         inputTermSearchType: directAssociations
         report: chems_curated
         format: json
@@ -282,7 +282,7 @@ components:
         semantic: SmallMolecule
       parameters:
         inputType: disease
-        inputTerms: "{{ queryInputs | addPrefix('OMIM') }}"  ## HAS PREFIX
+        inputTerms: "{{ queryInputs | replPrefix('OMIM') }}"  ## HAS PREFIX
         inputTermSearchType: directAssociations
         report: chems_curated
         format: json
@@ -376,7 +376,7 @@ components:
         semantic: Gene
       parameters:
         inputType: disease
-        inputTerms: "{{ queryInputs | addPrefix('MESH') }}"  ## HAS PREFIX
+        inputTerms: "{{ queryInputs | replPrefix('MESH') }}"  ## HAS PREFIX
         inputTermSearchType: directAssociations
         report: genes_curated
         format: json
@@ -397,7 +397,7 @@ components:
     #     semantic: Disease
     #   parameters:
     #     inputType: gene
-    #     inputTerms: "{{ queryInputs }}"  ## no prefix
+    #     inputTerms: "{{ queryInputs | rmPrefix() }}"  ## no prefix
     #     inputTermSearchType: directAssociations
     #     report: diseases_curated
     #     format: json
@@ -418,7 +418,7 @@ components:
         semantic: Gene
       parameters:
         inputType: disease
-        inputTerms: "{{ queryInputs | addPrefix('OMIM') }}"  ## HAS PREFIX
+        inputTerms: "{{ queryInputs | replPrefix('OMIM') }}"  ## HAS PREFIX
         inputTermSearchType: directAssociations
         report: genes_curated
         format: json
@@ -439,7 +439,7 @@ components:
     #     semantic: Disease
     #   parameters:
     #     inputType: gene
-    #     inputTerms: "{{ queryInputs }}"  ## no prefix
+    #     inputTerms: "{{ queryInputs | rmPrefix() }}"  ## no prefix
     #     inputTermSearchType: directAssociations
     #     report: diseases_curated
     #     format: json
@@ -461,7 +461,7 @@ components:
     #     semantic: Pathway
     #   parameters:
     #     inputType: gene
-    #     inputTerms: "{{ queryInputs }}"  ## no prefix
+    #     inputTerms: "{{ queryInputs | rmPrefix() }}"  ## no prefix
     #     inputTermSearchType: directAssociations
     #     report: pathways_curated
     #     format: json
@@ -482,7 +482,7 @@ components:
         semantic: Gene
       parameters:
         inputType: pathway
-        inputTerms: "{{ queryInputs | addPrefix('REACT') }}"  ## HAS PREFIX
+        inputTerms: "{{ queryInputs | replPrefix('REACT') }}"  ## HAS PREFIX
         inputTermSearchType: directAssociations
         report: genes_curated
         format: json
@@ -503,7 +503,7 @@ components:
     #     semantic: Pathway
     #   parameters:
     #     inputType: gene
-    #     inputTerms: "{{ queryInputs }}"  ## no prefix
+    #     inputTerms: "{{ queryInputs | rmPrefix() }}"  ## no prefix
     #     inputTermSearchType: directAssociations
     #     report: pathways_curated
     #     format: json
@@ -524,7 +524,7 @@ components:
         semantic: Gene
       parameters:
         inputType: pathway
-        inputTerms: "{{ queryInputs | addPrefix('KEGG') }}"  ## HAS PREFIX (not biolink-model spelling)
+        inputTerms: "{{ queryInputs | replPrefix('KEGG') }}"  ## HAS PREFIX (not biolink-model spelling)
         inputTermSearchType: directAssociations
         report: genes_curated
         format: json

diff --git a/biolink/openapi.yml b/biolink/openapi.yml
@@ -1111,7 +1111,7 @@ components:
       - id: HGNC   ## Monarch seems to prefer HGNC IDs for human genes
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1136,7 +1136,7 @@ components:
       - id: HGNC
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1162,7 +1162,7 @@ components:
       - id: HGNC
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1187,7 +1187,7 @@ components:
       - id: HGNC
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         rows: -1
         direct: true
         unselect_evidence: true
@@ -1219,7 +1219,7 @@ components:
       - id: HGNC
         semantic: Gene  ## aka start with human gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1249,7 +1249,7 @@ components:
       - id: HGNC
         semantic: Gene  ## aka start with human gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1277,7 +1277,7 @@ components:
       - id: HGNC
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         rows: -1
         direct: true
         unselect_evidence: true
@@ -1301,7 +1301,7 @@ components:
       - id: HGNC
         semantic: Gene
       parameters:
-        id: "{{ queryInputs | addPrefix('HGNC') }}"
+        id: "{{ queryInputs | replPrefix('HGNC') }}"
         rows: -1
         direct: true
         unselect_evidence: true
@@ -1324,7 +1324,7 @@ components:
       - id: REACT
         semantic: Pathway
       parameters:
-        id: "{{ queryInputs | addPrefix('REACT') }}"
+        id: "{{ queryInputs | replPrefix('REACT') }}"
         ## add prefix since Monarch expects this, while BTE automatically removes
         rows: -1
         direct: true
@@ -1423,7 +1423,7 @@ components:
       - id: DBSNP
         semantic: SequenceVariant
       parameters:
-        id: "{{ queryInputs | addPrefix('dbSNP') }}"
+        id: "{{ queryInputs | replPrefix('dbSNP') }}"
         ## add prefix since Monarch expects this in this form, while BTE automatically removes
         rows: -1
         direct: true
@@ -1450,7 +1450,7 @@ components:
       - id: DBSNP
         semantic: SequenceVariant
       parameters:
-        id: "{{ queryInputs | addPrefix('dbSNP') }}"
+        id: "{{ queryInputs | replPrefix('dbSNP') }}"
         # id: "dbSNP:{inputs[0]}"
         ## add prefix since Monarch expects this in this form, while BTE automatically removes
         rows: -1
@@ -1475,7 +1475,7 @@ components:
       - id: DBSNP
         semantic: SequenceVariant
       parameters:
-        id: "{{ queryInputs | addPrefix('dbSNP') }}"
+        id: "{{ queryInputs | replPrefix('dbSNP') }}"
         ## add prefix since Monarch expects this in this form, while BTE automatically removes
         rows: -1
         direct: true
@@ -1492,4 +1492,5 @@ components:
       # testExamples:
       #   - qInput: "DBSNP:rs115165302" 
       #     oneOutput: "HP:0002944"  ## Thoracolumbar scoliosis
-      ## another possible input: "DBSNP:rs771684665"
+      ## another possible input: "DBSNP:rs771684665"
+
diff --git a/ebi_proteins/openapi.yml b/ebi_proteins/openapi.yml
@@ -3248,7 +3248,7 @@ components:
       - id: UniProtKB
         semantic: Gene
       parameters:
-        accession: "{{ queryInputs }}"  ## no prefix
+        accession: "{{ queryInputs | rmPrefix() }}"  ## no prefix
       outputs:
       - id: RHEA
         semantic: MolecularActivity

diff --git a/litvar/smartapi.yaml b/litvar/smartapi.yaml
@@ -53,7 +53,7 @@ components:
       - id: DBSNP
         semantic: SequenceVariant
       parameters:
-        variantid: "{{ queryInputs }}%23%23"  ## no prefix
+        variantid: "{{ queryInputs | rmPrefix() }}%23%23"  ## no prefix
       outputs:
       - id: NCBIGene
         semantic: Gene

diff --git a/ols/smartapi.yaml b/ols/smartapi.yaml
@@ -63,8 +63,8 @@ components:
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease_has_subclass_disease"
       # testExamples:
-      #   - qInput: "DOID:0050686"   ## organ system cancer
-      #     oneOutput: "DOID:1725"    ##  peritoneum cancer
+      #   - qInput: "DOID:10123"          ## skin pigmentation disorder
+      #     oneOutput: "MONDO:0007483"    ##  dyschromatosis symmetrica hereditaria
   x-bte-response-mapping:
     disease_has_subclass_disease:
       DOID: _embedded.terms.obo_id  ## HAS PREFIX (DOID)