@biothings-explorer/annotator - npm Package Compare versions

Comparing version 1.0.0 to 2.0.0

__test__/index.test.js

@@ -77,2 +77,39 @@ const annotate = require("../src/index");
     })
+
+    test("test with chemical ids", async () => {
+        const ids = {
+            "CHEBI:8863": {
+                "id": {
+                    "label": "RILUZOLE",
+                    "identifier": "CHEBI:8863"
+                },
+                "db_ids": {
+                    "CHEBI": [
+                        "CHEBI:8863"
+                    ],
+                    "CHEMBL.COMPOUND": [
+                        "CHEMBL744"
+                    ]
+                }
+            },
+            "CHEBI:133809": {
+                "id": {
+                    "label": "ANISINDIONE",
+                    "identifier": "CHEBI:133809"
+                },
+                "db_ids": {
+                    "CHEBI": [
+                        "CHEBI:133809"
+                    ],
+                    "CHEMBL.COMPOUND": [
+                        "CHEMBL712"
+                    ]
+                }
+            }
+        };
+        let res = await annotate("ChemicalSubstance", ids);
+        expect(res).toHaveProperty('CHEBI:133809');
+        expect(Object.keys(res).length).toBe(2);
+        expect(res["CHEBI:133809"]).toHaveProperty("max_phase")
+    })
 })

package.json

 {
   "name": "@biothings-explorer/annotator",
-  "version": "1.0.0",
+  "version": "2.0.0",
   "description": "A nodejs package providing batch annotating features for biomedical entities",
@@ -5,0 +5,0 @@ "main": "src/index.js",

README.md

@@ -25,5 +25,88 @@ [![Build Status](https://travis-ci.com/kevinxin90/annotator.js.svg?branch=master)](https://travis-ci.com/kevinxin90/annotator.js)
     ```javascript
-    const annotator = require("@biothings-explorer/annotator")
+    const annotate = require("@biothings-explorer/annotator")
     ```
 
+- Annotate Gene IDs
+
+    ```javascript
+    const gene_ids = {
+      "NCBIGene:4888": {
+          "db_ids": {
+              "NCBIGene": [
+                  "4888"
+              ],
+              "HGNC": [
+                  "7959"
+              ],
+              "SYMBOL": [
+                  "NPY6R"
+              ],
+              "UMLS": [
+                  "C1417819"
+              ]
+          }
+      },
+      "NCBIGene:4597": {
+          "db_ids": {
+              "NCBIGene": [
+                  "4597"
+              ],
+              "ENSEMBL": [
+                  "ENSG00000167508"
+              ],
+              "HGNC": [
+                  "7529"
+              ],
+              "SYMBOL": [
+                  "MVD"
+              ],
+              "UMLS": [
+                  "C1417507"
+              ]
+            }
+        }
+    }
+    let res = await annotate("Gene", gene_ids);
+    console.log(res);
+    // {"NCBIGene:4888": {"genomic_position": ..., "generif": ..., "biological_process": ...},"NCBIGene:4597": {"genomic_position": ..., "reactome": ..., "wikipathways": ...}}
+    ```
+
+- Annotate ChemicalSubstance IDs
+
+    ```javascript
+    const chemical_ids = {
+        "CHEBI:8863": {
+            "id": {
+                "label": "RILUZOLE",
+                "identifier": "CHEBI:8863"
+            },
+            "db_ids": {
+                "CHEBI": [
+                    "CHEBI:8863"
+                ],
+                "CHEMBL.COMPOUND": [
+                    "CHEMBL744"
+                ]
+            }
+        },
+        "CHEBI:133809": {
+            "id": {
+                "label": "ANISINDIONE",
+                "identifier": "CHEBI:133809"
+            },
+            "db_ids": {
+                "CHEBI": [
+                    "CHEBI:133809"
+                ],
+                "CHEMBL.COMPOUND": [
+                    "CHEMBL712"
+                ]
+            }
+        }
+    };
+    let res = await annotate("ChemicalSubstance", chemical_ids);
+    console.log(res);
+    // {"CHEBI:133809": {"max_phase": ..., "molecular_weight": ..., "molecular_type": ...}, "CHEBI:8863": {"max_phase": ..., "enzymes": ..., "targets": ...}}
+    ```
+
 ## Run tests
@@ -30,0 +113,0 @@

src/config.js

@@ -113,3 +113,3 @@ exports.APIMETA = {
             "molecular_weight": {
-                "fields": ["chembl.molecule_properties.full_mwt, drugbank.weight.average"],
+                "fields": ["chembl.molecule_properties.full_mwt", "drugbank.weight.average"],
                 "nested": false
@@ -122,3 +122,3 @@ },
             "ATC_classification": {
-                "fields": ["chembl.atc_classifications, drugbank.xrefs.atc_codes"],
+                "fields": ["chembl.atc_classifications", "drugbank.xrefs.atc_codes"],
                 "nested": false
@@ -177,6 +177,2 @@ },
                 "nested": false
-            },
-            "parent": {
-                "fields": ["drugbank.taxonomy.direct-parent"],
-                "nested": false
             }
@@ -187,2 +183,6 @@ }
 
-exports.MAX_CONCURRENT_QUERIES = 4;
+exports.MAX_CONCURRENT_QUERIES = 4;
+
+exports.CURIE = {
+    ALWAYS_PREFIXED: ["GO", "CHEBI", "HP", "MONDO", "DOID", "EFO", "UBERON", "MP", "CL", "MGI"]
+}

src/dispatch.js

@@ -47,3 +47,3 @@ const meta = require("./config");
         }
-        inputs = Array.from(inputs).join(',');
+        inputs = Array.from(inputs).map(item => "'" + item + "'").join(',');
         let apimeta = meta.APIMETA[this.semantic];
@@ -50,0 +50,0 @@ let fields = [];

src/parse.js

 const config = require("./config");
 const _ = require('lodash');
 const jp = require("jsonpath");
+const { method } = require("lodash");
 
@@ -18,3 +19,3 @@ module.exports = class {
         this.response.data.filter(rec => {
-            if (_.isEmpty(rec) || 'notfound' in rec) {
+            if (_.isEmpty(rec) || 'notfound' in rec || _.difference(Object.keys(rec), ['query', "_score", "_id"]).length === 0) {
                 return false
@@ -24,8 +25,20 @@ };
         }).map(rec => {
-            curie = this.prefix + ':' + rec['query'];
-            result[curie] = {};
+            if (config.CURIE.ALWAYS_PREFIXED.includes(this.prefix)) {
+                curie = rec['query'];
+            } else {
+                curie = this.prefix + ':' + rec['query'];
+            }
+            if (!(curie in result)) {
+                result[curie] = {};
+            }
             for (let [mapped_field, fields] of Object.entries(mapping)) {
                 for (let field of fields.fields) {
                     let path = "$." + field;
-                    let tmp = jp.query(rec, path);
+                    let tmp = [];
+                    try {
+                        tmp = jp.query(rec, path);
+                    } catch (e) {
+                        console.log(e)
+                    }
+
                     if (tmp.length !== 0) {
@@ -32,0 +45,0 @@ result[curie][mapped_field] = tmp;

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

23722

increased by18.93%

Lines of code

545

increased by9.44%

Number of lines in readme file

135

increased by159.62%

No dependency changes