add string/:ac protion route;; modify and re-run build.js

meringlab · Sep 30, 2022 · 5f6fbc6 · 5f6fbc6
1 parent 30b20f4
commit 5f6fbc6
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
-#public/images/datasets/**svg
-public/images/scatter/**svg
+public/images/datasets/*svg
+public/images/scatter/*svg
 
 # Created by .gitignore support plugin (hsz.mobi)
 ### Emacs template

diff --git a/build.js b/build.js
@@ -5,7 +5,7 @@
 const PAYLOAD_VERSION = 22;
 const uniprotMappingFile = './data/paxdb_uniprot_linkins_ids.tsv';
 const PAXDB_URL = 'https://pax-db.org/';
-const PAXDB_API_URL = 'https://beta-api.pax-db.org/';
+const PAXDB_API_URL = 'https://api.pax-db.org/';
 const fs = require('fs');
 const async = require('async');
 const pg = require('pg');
@@ -75,6 +75,7 @@ function loadProteins(cb, createProteinModules = false) {
   const paxdbUniprotIdsMap = loadUniprotMapping();
   const uniprotPaxdbIdsMap = {};
   const speciesForProtein = {};
+  const externalToInternalMap = {};
 
   async.eachSeries(speciesIds, function (speciesId, callback) {
     console.log(`loading proteins for ${speciesId}`);
@@ -93,6 +94,7 @@ function loadProteins(cb, createProteinModules = false) {
         if (Object.prototype.hasOwnProperty.call(paxdbUniprotIdsMap, r.protein_external_id)) {
           const ac = paxdbUniprotIdsMap[r.protein_external_id];
           proteins[r.protein_id].uniprotId = ac;
+          externalToInternalMap[r.protein_external_id] = r.protein_id
           if (!Object.prototype.hasOwnProperty.call(uniprotPaxdbIdsMap, ac)) {
             uniprotPaxdbIdsMap[ac] = r.protein_id;
           } else {
@@ -121,7 +123,7 @@ function loadProteins(cb, createProteinModules = false) {
   }, function (err) {
     console.log(`loading proteins DONE`);
     if (err) throw err;
-    cb(speciesForProtein, uniprotPaxdbIdsMap);
+    cb(speciesForProtein, uniprotPaxdbIdsMap, externalToInternalMap);
   });
 }
 
@@ -305,7 +307,7 @@ function buildSpecies() {
 }
 
 function buildProteins() {
-  loadProteins(function(speciesForProtein, uniprotIdsMap) {
+  loadProteins(function(speciesForProtein, uniprotIdsMap, externalToInternalMap) {
     var writeStream = fs.createWriteStream('./lib/proteins_index.js');
     writeStream.write(`//FILE GENERATED BY build.js on ${new Date()}, DO NOT MODIFY!\n`);
     writeStream.write("const speciesForProtein = ");
@@ -319,6 +321,16 @@ function buildProteins() {
     writeStream.write('module.exports.uniprotIdsMap = uniprotIdsMap;\n');
     writeStream.end();
     console.log('./lib/proteins_index.js generated');
+
+    var writeStream = fs.createWriteStream('./lib/proteins_stringId_map.js');
+    writeStream.write(`//FILE GENERATED BY build.js on ${new Date()}, DO NOT MODIFY!\n`);
+    writeStream.write("const externalToInternalMap = ");
+    writeStream.write(JSON.stringify(externalToInternalMap));
+    writeStream.write(';\n');
+    writeStream.write('module.exports.externalToInternalMap = externalToInternalMap;\n');
+    writeStream.end();
+
+    console.log('./lib/proteins_stringId_map.js generated');
     client.on('drain', client.end.bind(client));
     client.end();
   }, true);
@@ -441,6 +453,9 @@ function build_proteins_index(){
   writeStream.write("const uniprotIdsMap = ");
   writeStream.write(JSON.stringify(uniprotIdsMap));
   writeStream.write(';\n');
+  writeStream.write("const externalToInternalMap = ");
+  writeStream.write(JSON.stringify(externalToInternalMap));
+  writeStream.write(';\n');
   writeStream.write('module.exports.speciesForProtein = speciesForProtein;');
   writeStream.write('module.exports.uniprotIdsMap = uniprotIdsMap;');
   writeStream.end();
@@ -480,6 +495,9 @@ function buildHistograms() {
     });
   });
   console.log('histograms generated');
+
+  client.on('drain', client.end.bind(client));
+  client.end();
 }
 
 
@@ -530,8 +548,6 @@ function buildPayload() {
 buildSpecies();
 buildDatasets();
 buildProteins();
-//TODO FIXME writing streams is async, so lib/species.js won' show up before buildPayload is called
+// TODO FIXME writing streams is async, so lib/species.js won' show up before buildPayload is called
 buildPayload();
 buildHistograms();
-
-
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