Use sequence id instead of accession for sequence retrieval

With V4 databases it was possible to use accession for retrieving
sequences. So we used accession. Thus freeing us from the need to
encode sequence ids which may contain the pipe special character.

However, with V5 databases, the entire sequence id must be used.
This is problematic if databases use sequence id of the format
'gnl|foo|bar' (#475), and potentially for other id formats too.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

Author: yeban

lib/sequenceserver/sequence.rb

@@ -42,7 +42,7 @@ def initialize(*args)
       # If hit comes from a non -parse_seqids
       # database, obtain seqid and title from
       # defline.
-      if args[1] =~ /^gnl\|/
+      if args[1] =~ /^gnl\|BL_ORD_ID\|\d+/
         defline = args[3].split
         args[1] = defline.shift
         args[3] = defline.join(' ')

public/js/hit.js

@@ -16,6 +16,13 @@ export default React.createClass({
         return this.props.hit.accession;
     },
 
+    /**
+     * Returns id of the hit sequence.
+     */
+    sequenceID: function () {
+        return this.props.hit.id;
+    },
+
     /**
      * Returns length of the hit sequence.
      */
@@ -41,12 +48,12 @@ export default React.createClass({
     },
 
     viewSequenceLink: function () {
-        return encodeURI(`get_sequence/?sequence_ids=${this.accession()}&database_ids=${this.databaseIDs()}`);
+        return encodeURI(`get_sequence/?sequence_ids=${this.sequenceID()}&database_ids=${this.databaseIDs()}`);
     },
 
     downloadFASTA: function (event) {
-        var accessions = [this.accession()];
-        downloadFASTA(accessions, this.databaseIDs());
+        var sequenceIDs = [this.sequenceID()];
+        downloadFASTA(sequenceIDs, this.databaseIDs());
     },
 
     // Event-handler for exporting alignments.
@@ -129,7 +136,7 @@ export default React.createClass({
             <div className="hit-links">
                 <label>
                     <input type="checkbox" id={this.domID() + '_checkbox'}
-                        value={this.accession()} onChange={function () {
+                        value={this.sequenceID()} onChange={function () {
                             this.props.selectHit(this.domID() + '_checkbox');
                         }.bind(this)} data-target={'#' + this.domID()}
                     /> Select

public/js/sidebar.js

@@ -16,7 +16,7 @@ export default React.createClass({
         var sequence_ids = [];
         this.props.data.queries.forEach(
             (query) => query.hits.forEach(
-                (hit) => sequence_ids.push(hit.accession)));
+                (hit) => sequence_ids.push(hit.id)));
         var database_ids = this.props.data.querydb.map((querydb) => querydb.id);
         downloadFASTA(sequence_ids, database_ids);
         return false;
@@ -66,7 +66,7 @@ export default React.createClass({
         console.log('check '+sequence_ids.toString());
         _.each(this.props.data.queries, _.bind(function (query) {
             _.each(query.hits, function (hit) {
-                if (_.indexOf(sequence_ids, hit.accession) != -1) {
+                if (_.indexOf(sequence_ids, hit.id) != -1) {
                     _.each(hit.hsps, function (hsp) {
                         hsp.hit_id = hit.id;
                         hsp.query_id = query.id;