Refs PR #885 and fixed #876.

Author: IgorRodchenkov

README.md

@@ -34,7 +34,6 @@ The following environment variables can be used to configure the server:
 
 - `NODE_ENV` : the environment mode, either `production` or `development` (default)
 - `PC_URL` : actual Pathway Commons web service endpoint URL (default: 'http://www.pathwaycommons.org/pc2/')
-- `PC_XMLBASE` : actual Pathway Commons BioPAX xml:base (e.g., 'http://pathwaycommons.org/pc2/' for the v9; it's not address)
 - `PORT` : the port on which the server runs (default 3000)
 
 ### Configure RethinkDB
@@ -46,7 +45,7 @@ The following environment variables can be used to configure the server:
 ### Switching Pathway Commons Versions (release/other)
 
 If Pathway Commons data and files have been updated since this app's last built and run,
-or you simply want to connect to a different PC2 instance (don't forget to set PC_URL and PC_XMLBASE), 
+or you simply want to connect to a different PC2 instance (don't forget to set PC_URL), 
 then the file `src/server/graph-generation/biopax-metadata/generic-physical-entity-map.json` 
 needs to be updated. Also, purge the RethinkDb db tables or simply switch the database.
 

src/client/features/enrichment/index.js

@@ -71,7 +71,8 @@ class Enrichment extends React.Component {
   }
 
   handleGenes( genes ) {
-    this.setState( { genes } );console.log(genes);
+    this.setState( { genes } );
+    // console.log(genes);
   }
 
   render() {

src/config.js

@@ -5,7 +5,6 @@ let defaults = {
   PORT: 3000,
   MASTER_PASSWORD: '',
   PC_URL: 'http://www.pathwaycommons.org/pc2/',
-  PC_XMLBASE: 'http://pathwaycommons.org/pc2/',
   GPROFILER_URL: "http://biit.cs.ut.ee/gprofiler_archive3/r1741_e90_eg37/web/",
   PC_CACHE_MAX_SIZE: 1000
 };

src/server/graph-generation/biopax-metadata/index.js

@@ -1,7 +1,6 @@
 const fs = require('fs');
 const metadataParser = require('./metadataParserJson');
 const _ = require('lodash');
-// const config = require('../../../config');
 
 var biopaxMap = null;
 

src/server/pathway-commons/index.js

@@ -107,7 +107,6 @@ const _datasources = () => {
         hasPathways: (ds.numPathways>0)?true:false
       };
     });
-    // console.log(output);
     return output; //filtered, simplified map
   })
   .catch(() => {