Migrate package to Typescript and new build system

.github/workflows/test_ws_codecov.yml

@@ -16,18 +16,24 @@ jobs:
     - uses: actions/checkout@v3
       with:
         repository: biothings/biothings_explorer
+        ref: ${{ steps.branch-name.outputs.current_branch }}
 
-    - name: Use Node.js 16.x
-      uses: actions/setup-node@v1
+    - name: Use Node.js 18.x
+      uses: actions/setup-node@v3
       with:
-        node-version: 16.x
+        node-version: 18.x
 
-    - name: npm install, generate coverage report
+    - name: Use pnpm
+      uses: pnpm/action-setup@v2
+      with:
+        version: 8
+
+    - name: pnpm install, generate coverage report
       run: |
-        npm run clone
-        npm run git checkout ${{ steps.branch-name.outputs.current_branch }}
-        npm i || true && npm i
-        npm run test-cov --workspace=@biothings-explorer/call-apis
+        pnpm run clone
+        pnpm run git checkout ${{ steps.branch-name.outputs.current_branch }}
+        pnpm i
+        pnpm --filter call-apis test-cov
 
     - name: Send coverage report to codecov for visualization
       uses: codecov/codecov-action@v3

.gitignore

@@ -47,6 +47,9 @@ typings/
 # TypeScript cache
 *.tsbuildinfo
 
+# Turbo cache
+.turbo
+
 # Optional npm cache directory
 .npm
 

README.md

@@ -16,7 +16,7 @@ A nodejs module to make API calls in batch mode for BioThings Explorer
 ## Install
 
 ```sh
-npm i @biothings-explorer/call-apis
+pnpm i @biothings-explorer/call-apis
 ```
 
 ## Usage
@@ -30,7 +30,7 @@ npm i @biothings-explorer/call-apis
 ## Run tests
 
 ```sh
-npm run test
+pnpm run test
 ```
 
 ## Author

__test__/data/cooccurrence_example_edge.json

@@ -1,58 +1,37 @@
 {
-    "input": "MONDO:0005252",
-    "query_operation": {
-        "params": {
-            "fields": "subject,association",
-            "q": "object.MONDO:\"{inputs[0]}\" AND subject.type:ChemicalSubstance",
-            "size": 1000
-        },
-        "supportBatch": false,
-        "method": "get",
-        "pathParams": [],
-        "server": "https://biothings.ncats.io/text_mining_co_occurrence_kp",
-        "path": "/query",
-        "tags": [
-            "gene",
-            "chemical",
-            "association",
-            "annotation",
-            "query",
-            "translator",
-            "biothings",
-            "biothings_graph"
-        ]
+  "input": "MONDO:0005252",
+  "query_operation": {
+    "params": {
+      "fields": "subject,association",
+      "q": "object.MONDO:\"{inputs[0]}\" AND subject.type:ChemicalSubstance",
+      "size": 1000
     },
-    "association": {
-        "input_id": "MONDO",
-        "input_type": "Disease",
-        "output_id": "CHEBI",
-        "output_type": "ChemicalSubstance",
-        "predicate": "related_to",
-        "source": "Text Mining KP",
-        "api_name": "Text Mining CO-OCCURRENCE API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Text Mining Provider",
-                "Service Provider"
-            ]
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "CHEBI": "hits.subject.CHEBI",
-            "ngd": "hits.association.ngd"
-        }
-    },
-    "tags": [
-        "gene",
-        "chemical",
-        "association",
-        "annotation",
-        "query",
-        "translator",
-        "biothings",
-        "biothings_graph"
-    ]
-}
+    "supportBatch": false,
+    "method": "get",
+    "pathParams": [],
+    "server": "https://biothings.ncats.io/text_mining_co_occurrence_kp",
+    "path": "/query",
+    "tags": ["gene", "chemical", "association", "annotation", "query", "translator", "biothings", "biothings_graph"]
+  },
+  "association": {
+    "input_id": "MONDO",
+    "input_type": "Disease",
+    "output_id": "CHEBI",
+    "output_type": "ChemicalSubstance",
+    "predicate": "related_to",
+    "source": "Text Mining KP",
+    "api_name": "Text Mining CO-OCCURRENCE API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Text Mining Provider", "Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "CHEBI": "hits.subject.CHEBI",
+      "ngd": "hits.association.ngd"
+    }
+  },
+  "tags": ["gene", "chemical", "association", "annotation", "query", "translator", "biothings", "biothings_graph"]
+}

__test__/data/fake_error_edge.json

@@ -1,58 +1,37 @@
 {
-    "input": "MONDO:0005252",
-    "query_operation": {
-        "params": {
-            "fields": "subject,association",
-            "q": "object.MONDO:\"{inputs[0]}\" AND subject.type:ChemicalSubstance",
-            "size": 1000
-        },
-        "supportBatch": false,
-        "method": "get",
-        "pathParams": [],
-        "server": "https://biothings.ncats.io/text_mining_co_occurrence_kp1",
-        "path": "/query",
-        "tags": [
-            "gene",
-            "chemical",
-            "association",
-            "annotation",
-            "query",
-            "translator",
-            "biothings",
-            "biothings_graph"
-        ]
+  "input": "MONDO:0005252",
+  "query_operation": {
+    "params": {
+      "fields": "subject,association",
+      "q": "object.MONDO:\"{inputs[0]}\" AND subject.type:ChemicalSubstance",
+      "size": 1000
     },
-    "association": {
-        "input_id": "MONDO",
-        "input_type": "Disease",
-        "output_id": "CHEBI",
-        "output_type": "SmallMolecule",
-        "predicate": "related_to",
-        "source": "Text Mining KP",
-        "api_name": "Text Mining CO-OCCURRENCE API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Text Mining Provider",
-                "Service Provider"
-            ]
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "CHEBI": "hits.subject.CHEBI",
-            "ngd": "hits.association.ngd"
-        }
-    },
-    "tags": [
-        "gene",
-        "chemical",
-        "association",
-        "annotation",
-        "query",
-        "translator",
-        "biothings",
-        "biothings_graph"
-    ]
-}
+    "supportBatch": false,
+    "method": "get",
+    "pathParams": [],
+    "server": "https://biothings.ncats.io/text_mining_co_occurrence_kp1",
+    "path": "/query",
+    "tags": ["gene", "chemical", "association", "annotation", "query", "translator", "biothings", "biothings_graph"]
+  },
+  "association": {
+    "input_id": "MONDO",
+    "input_type": "Disease",
+    "output_id": "CHEBI",
+    "output_type": "SmallMolecule",
+    "predicate": "related_to",
+    "source": "Text Mining KP",
+    "api_name": "Text Mining CO-OCCURRENCE API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Text Mining Provider", "Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "CHEBI": "hits.subject.CHEBI",
+      "ngd": "hits.association.ngd"
+    }
+  },
+  "tags": ["gene", "chemical", "association", "annotation", "query", "translator", "biothings", "biothings_graph"]
+}