fix: rename url to route

cheminfo · Dec 5, 2023 · d894dc5 · d894dc5
1 parent abe947e
commit d894dc5
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Showing 7 changed files with 18 additions and 18 deletions.
diff --git a/packages/octochemdb/src/activeOrNaturalDetails.js b/packages/octochemdb/src/activeOrNaturalDetails.js
@@ -6,19 +6,19 @@ import { normalizeActivities } from './utils/normalizeActivities.js';
  * Search for a specific natural or active compound using its ID
  * @param {object} [options={}]
  * @param {string} [options.fields='_id,data'] - List of fields to retrieve
- * @param {string} [options.url='activesOrNaturals/v1/id'] - URL of the webservice
+ * @param {string} [options.route='activesOrNaturals/v1/id'] - URL of the webservice
  * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
  */
 
 export async function activeOrNaturalDetails(id, options = {}) {
   const {
-    url = 'activesOrNaturals/v1/id',
+    route = 'activesOrNaturals/v1/id',
     baseURL = 'https://octochemdb.cheminfo.org/',
     fields = '_id,data',
   } = options;
 
   const activeOrNatural = await fetchActiveOrNatural(id, {
-    url: new URL(url, baseURL).toString(),
+    url: new URL(route, baseURL).toString(),
     fields,
   });
 

diff --git a/packages/octochemdb/src/activesOrNaturals.js b/packages/octochemdb/src/activesOrNaturals.js
@@ -19,19 +19,19 @@ import { searchWithIonizations } from './utils/searchWithIonizations.js';
  * @param {string} [options.kwTitles=''] - Comma separated list of keyword from the compound title
  * @param {string} [options.minNbMassSpectra] - Minimal number of mass spectra
  * @param {number} [options.limit=1000] - Maximal number of entries to return
- * @param {string} [options.url='activesOrNaturals/v1/search'] - URL of the webservice
+ * @param {string} [options.route='activesOrNaturals/v1/search'] - Route to this specific webservice
  * @param {string[]|undefined} [options.includes] - Array of DBref collections to include
- * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
+ * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - Base URL of the webservice
  */
 
 export async function activesOrNaturals(options = {}) {
   const {
-    url = 'activesOrNaturals/v1/search',
+    route = 'activesOrNaturals/v1/search',
     baseURL = 'https://octochemdb.cheminfo.org/',
     includes,
   } = options;
 
-  const realURL = new URL(url, baseURL).toString();
+  const realURL = new URL(route, baseURL).toString();
 
   const searchParams = prepareSearchParams(options);
 

diff --git a/packages/octochemdb/src/activesOrNaturalsByMF.js b/packages/octochemdb/src/activesOrNaturalsByMF.js
@@ -14,7 +14,7 @@ import { activesOrNaturals } from './activesOrNaturals.js';
  * @param {string} [options.kwMeshTerms=''] - Comma separated list of keyword from the medline MeshTerms
  * @param {string} [options.kwTitles=''] - Comma separated list of keyword from compound title
  * @param {number} [options.limit=1000] - Maximal number of entries to return
- * @param {string} [options.url='activesOrNaturals/v1/search'] - URL of the webservice
+ * @param {string} [options.route='activesOrNaturals/v1/search'] - URL of the webservice
  * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
  */
 

diff --git a/packages/octochemdb/src/compoundsFromMF.js b/packages/octochemdb/src/compoundsFromMF.js
@@ -8,14 +8,14 @@ import { postFetchJSON } from './utils/postFetchJSON.js';
  * @param {object} [options={}]
  * @param {string} [options.fields] - Fields to retrieve from the database
  * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
- * @param {string} [options.url='mfs/v1/fromMF'] - URL of the webservice
+ * @param {string} [options.route='mfs/v1/fromMF'] - URL of the webservice
  * @param {string} [options.titleCompoundsURL='titleCompounds/v1/ids'] - URL of the webservice
  * @param {number} [options.limit=50000] - Maximal number of entries to return
  */
 
 export async function compoundsFromMF(mf, options = {}) {
   const {
-    url = 'compounds/v1/fromMF',
+    route = 'compounds/v1/fromMF',
     baseURL = 'https://octochemdb.cheminfo.org/',
     limit = 50000,
     fields = 'data.ocl.idCode,data.ocl.index,data.iupac',
@@ -27,7 +27,7 @@ export async function compoundsFromMF(mf, options = {}) {
     mf,
   };
 
-  const realURL = new URL(url, baseURL).toString();
+  const realURL = new URL(route, baseURL).toString();
   const data = (await fetchJSON(realURL, searchParams)).data;
 
   const ids = data.map((datum) => datum._id);

diff --git a/packages/octochemdb/src/massSpectra.js b/packages/octochemdb/src/massSpectra.js
@@ -52,7 +52,7 @@ export async function massSpectra(options = {}) {
       promises.push(
         searchMasses({
           ...options,
-          url: route.url,
+          route: route.url,
           link: route.link,
         }).then((entries) =>
           entries.map((entry) => ({ ...entry, database: route.name })),

diff --git a/packages/octochemdb/src/mfsFromEMs.js b/packages/octochemdb/src/mfsFromEMs.js
@@ -12,19 +12,19 @@ import { searchWithIonizations } from './utils/searchWithIonizations.js';
  * @param {number} [options.minCount=5] - Minimal number of molecules having a specific MF
  * @param {number} [options.fields] - Fields to retrieve from the database
  * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
- * @param {string} [options.url='mfs/v1/fromEM'] - URL of the webservice
+ * @param {string} [options.route='mfs/v1/fromEM'] - URL of the webservice
  * @param {string} [options.compoundsURL='mfs/v1/fromMF'] - URL to retrieve corresponding compounds
  */
 
 export async function mfsFromEMs(masses, options = {}) {
   const {
-    url = 'mfs/v1/fromEM',
+    route = 'mfs/v1/fromEM',
     compoundsURL = 'compounds/v1/fromMF',
     baseURL = 'https://octochemdb.cheminfo.org/',
     minCount = 5,
   } = options;
 
-  const realURL = new URL(url, baseURL).toString();
+  const realURL = new URL(route, baseURL).toString();
 
   const searchParams = {};
   searchParams.minCount = String(minCount);

diff --git a/packages/octochemdb/src/pubmedCompounds.js b/packages/octochemdb/src/pubmedCompounds.js
@@ -5,19 +5,19 @@ import { includeDBRefs } from './utils/includeDBRefs.js';
  * Retrieve the compounds from a pubmedID
  * @param {string} pubmedID
  * @param {object} [options={}]
- * @param {string} [options.url='pubmeds/v1/id'] - relative URL of the webservice
+ * @param {string} [options.route='pubmeds/v1/id'] - relative URL of the webservice
  * @param {string} [options.baseURL='https://octochemdb.cheminfo.org/'] - URL of the webservice
  * @param {number} [options.limit=1000] - Maximal number of entries to return
  * @returns
  */
 export async function pubmedCompounds(pubmedID, options = {}) {
   const {
-    url = 'pubmeds/v1/id',
+    route = 'pubmeds/v1/id',
     baseURL = 'https://octochemdb.cheminfo.org/',
     limit = 1000,
   } = options;
 
-  const realURL = new URL(url, baseURL).toString();
+  const realURL = new URL(route, baseURL).toString();
 
   const searchParams = {
     id: pubmedID,