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client/jsx/actions/search_actions.js

@@ -2,7 +2,7 @@ require('isomorphic-fetch');
 import { createPath } from '../lib/search_helpers';
 import _ from 'underscore';
 const queryString = require('query-string');
-const RESULTS_URL = '/backend/get_search_results';
+const RESULTS_URL = '/redirect_backend?param=get_search_results';
 const WRAPPED_PAGE_SIZE = 250;
 
 // helper methods

client/jsx/components/blast/search_form.jsx

@@ -927,7 +927,9 @@ BLAST Help at NCBI</a>.</p><hr>';
       // check to make sure sequence type matches the program
 
     // let tmpseq = seq.replace(/[ATCGU]/gi, '');
-    let tmpseq = seq.replace(/[ATCGUXN]/gi, '');
+    // let tmpseq = seq.replace(/[ATCGUXN]/gi, '');
+    // https://droog.gs.washington.edu/mdecode/images/iupac.html
+    let tmpseq = seq.replace(/[ATCGUMRWSYKVHDBNX]/gi, '');
 
     if (tmpseq == '') {
       if (program == 'blastp' || program == 'tblastn') {

client/jsx/components/colleagues/colleagues_form_show.jsx

@@ -16,16 +16,16 @@ import {
 import PropTypes from 'prop-types';
 
 const COLLEAGUES_AUTOCOMPLETE_URL =
-  '/backend/autocomplete_results?category=colleague&q=';
-const GENES_URL = '/backend/autocomplete_results?category=locus&q=';
+  '/redirect_backend?param=autocomplete_results?category=colleague&q=';
+const GENES_URL = '/redirect_backend?param=autocomplete_results?category=locus&q=';
 const KEYWORDS_AUTOCOMPLETE_URL =
-  '/backend/autocomplete_results?category=colleague&field=keywords&q=';
+  '/redirect_backend?param=autocomplete_results?category=colleague&field=keywords&q=';
 const INSTITUTION_URL =
-  '/backend/autocomplete_results?category=colleague&field=institution&q=';
+  '/redirect_backend?param=autocomplete_results?category=colleague&field=institution&q=';
 
 const TRIAGED_COLLEAGUE_URL = '/colleagues/triage';
 const COLLEAGUE_GET_URL = '/colleagues';
-const USER_COLLEAGUE_UPDATE_URL = '/backend/colleagues';
+const USER_COLLEAGUE_UPDATE_URL = '/redirect_backend?param=colleagues';
 const CURATOR_COLLEAGUE_UPDATE_URL = TRIAGED_COLLEAGUE_URL;
 
 const ColleaguesFormShow = createReactClass({

client/jsx/components/gotools/goslimmapper_form.jsx

@@ -17,8 +17,8 @@ const style = {
 };
 
 const GOtoolsUrl = '/run_gotools';
-const GOslimUrl = '/backend/goslim';
-const GeneChkUrl = '/backend/ambiguous_names';
+const GOslimUrl = '/redirect_backend?param=goslim';
+const GeneChkUrl = '/redirect_backend?param=ambiguous_names';
 
 const goSet = [
   'Yeast GO-Slim: process',

client/jsx/components/gotools/gotermfinder_form.jsx

@@ -18,7 +18,7 @@ const style = {
 };
 
 const GOtoolsUrl = '/run_gotools';
-const GeneChkUrl = '/backend/ambiguous_names';
+const GeneChkUrl = '/redirect_backend?param=ambiguous_names';
 
 const evidenceCode = [
   'HDA',

client/jsx/components/primer3/primer3.jsx

@@ -5,7 +5,7 @@ import t from 'tcomb-form';
 import createReactClass from 'create-react-class';
 const DataTable = require('../widgets/data_table.jsx');
 import PropTypes from 'prop-types';
-const PRIMER3URL = '/backend/primer3';
+const PRIMER3URL = '/redirect_backend?param=primer3';
 const queryString = require('query-string');
 
 const Primer3 = createReactClass({

client/jsx/containers/app_search_bar.jsx

@@ -9,7 +9,7 @@ import Typeahead from '../lib/react-typeahead-component';
 import { setUserInput } from '../actions/search_actions';
 import { getCategoryDisplayName } from '../lib/search_helpers';
 
-const AUTOCOMPLETE_URL = '/backend/autocomplete_results';
+const AUTOCOMPLETE_URL = '/redirect_backend?param=autocomplete_results';
 const AUTOCOMPLETE_FETCH_DEBOUNCE_WAIT = 200;
 import createReactClass from 'create-react-class';
 import PropTypes from 'prop-types';

client/jsx/containers/layout/header.jsx

@@ -322,6 +322,14 @@ class Header extends Component {
                         YGOB (Trinity College)
                       </a>
                     </li>
+		    <li>
+                      <a
+                        className="disabled-header-a"
+                        href="https://alphafold.ebi.ac.uk/"
+                      >
+                        AlphaFold
+                      </a>
+                    </li>
                   </ul>
                 </li>
               </ul>

client/jsx/models/alignment_index_model.jsx

@@ -7,13 +7,13 @@ var BaseModel = require('./base_model.jsx');
 module.exports = class AlignmentIndexModel extends BaseModel {
   constructor(options) {
     var options = options || {};
-    options.url = options.url || '/backend/alignments';
+    options.url = options.url || '/redirect_backend?param=alignments';
     super(options);
   }
 
   // cache from local storage, otherwise normal fetch
   fetch(callback) {
-    var storageKey = '/backend/alignments';
+    var storageKey = '/redirect_backend?param=alignments';
     var maybeCachedResponse = JSON.parse(localStorage.getItem(storageKey));
 
     // cached data available, use

client/jsx/models/genome_snapshot_model.jsx

@@ -8,7 +8,7 @@ var QUALIFICATION_STATUSES = ['Verified', 'Uncharacterized', 'Dubious'];
 module.exports = class GenomeSnapshotModel extends BaseModel {
   constructor(options) {
     var options = options || {};
-    options.url = options.url || '/backend/snapshot';
+    options.url = options.url || '/redirect_backend?param=snapshot';
     super(options);
   }
 

client/jsx/models/sequence_details_model.jsx

@@ -10,7 +10,7 @@ var MAIN_STRAIN_NAME = 'S288C';
 module.exports = class SequenceDetailsModel extends BaseModel {
   constructor(options) {
     options = options || {};
-    options.url = `/backend/locus/${options.id}/sequence_details`;
+    options.url = `/redirect_backend?param=locus/${options.id}/sequence_details`;
     super(options);
     this.baseAttributes = options;
   }

client/jsx/models/sequence_neighbors_model.jsx

@@ -10,7 +10,7 @@ var MAIN_STRAIN_NAME = 'S288C';
 module.exports = class SequenceNeighborsModel extends BaseModel {
   constructor(options) {
     options = options || {};
-    options.url = `/backend/locus/${options.id}/neighbor_sequence_details`;
+    options.url = `/redirect_backend?param=locus/${options.id}/neighbor_sequence_details`;
     super(options);
     if (options.id) this.id = parseInt(options.id);
     if (options.mainStrain) this.mainStrain = options.mainStrain;

client/jsx/store/search_store.jsx

@@ -1,7 +1,7 @@
 'use strict';
 var $ = require('jquery');
 
-var AUTOCOMPLETE_URL = '/backend/autocomplete_results';
+var AUTOCOMPLETE_URL = '/redirect_backend?param=autocomplete_results';
 
 var autocompleteQuery = '';
 var query = '';

client/jsx/stores/variant_viewer_store.jsx

@@ -6,8 +6,8 @@ var ClusterStrainsWorker = require('./cluster_strains.jsx');
 var staticStrainMetadata = require('./strain_metadata.jsx');
 var work = require('webworkify');
 
-var LOCI_SEARCH_BASE_URL = '/backend/search_sequence_objects';
-var LOCUS_SHOW_BASE_URL = '/backend/get_sequence_object';
+var LOCI_SEARCH_BASE_URL = '/redirect_backend?param=search_sequence_objects';
+var LOCUS_SHOW_BASE_URL = '/redirect_backend?param=get_sequence_object';
 var REFERENCE_STRAIN_ID = 1;
 
 // internal data, initial state

client/jsx/views/snapshot_view.jsx

@@ -31,7 +31,7 @@ snapshotView.render = function () {
 
   // init the model and fetch data
   var genomeModel = new GenomeSnapshotModel({
-    url: '/backend/genomesnapshot',
+    url: '/redirect_backend?param=genomesnapshot',
   });
   genomeModel.fetch((err, nestedData) => {
     // features visualization and table alt

config/deploy.rb

@@ -3,7 +3,7 @@
 set :application, 'SGDFrontend'
 set :ssh_options, {:forward_agent => true}
 
-set :repo_url, 'git://github.com/yeastgenome/SGDFrontend.git'
+set :repo_url, 'https://github.com/yeastgenome/SGDFrontend.git'
 set :branch, ENV['BRANCH'] || $1 if `git branch` =~ /\* (\S+)\s/m
 
 set :deploy_to, '/data/www/' + fetch(:application)

src/sgd/frontend/__init__.py

@@ -3,6 +3,7 @@
 from src.sgd.frontend import config
 from pyramid.view import notfound_view_config
 from src.sgd.frontend.yeastgenome import send_message
+from src.sgd.redirect import direct_backend
 from src.sgd.tools.blast import do_blast
 from src.sgd.tools.patmatch import do_patmatch
 from src.sgd.tools.seqtools import do_seq_analysis
@@ -27,7 +28,10 @@ def prep_views(chosen_frontend, config):
     config.add_route('gotermfinder', '/goTermFinder')
     config.add_route('goslimmapper', '/goSlimMapper')
     config.add_route('strain_alignment', '/strainAlignment')
+    config.add_route('redirect_backend', '/redirect_backend')
     config.add_route('complex', '/complex/{identifier}')
+    config.add_route('complex_literature_details', '/complex/{identifier}/literature')
+    config.add_route('complex_go_details', '/complex/{identifier}/go')
     config.add_route('allele', '/allele/{identifier}')
     config.add_route('allele_literature_details', '/allele/{identifier}/literature')
     config.add_route('blog_post', '/blog/{slug}')

src/sgd/frontend/yeastgenome/static/js/allele.js

@@ -1,17 +1,17 @@
 $(document).ready(function() {
 
-	$.getJSON('/backend/allele/' + allele['sgdid']  + '/phenotype_details', function(data) {
+	$.getJSON('/redirect_backend?param=allele/' + allele['sgdid']  + '/phenotype_details', function(data) {
 	    var phenotype_table = create_phenotype_table(data);
   	    create_download_button("phenotype_table_download", phenotype_table, allele['display_name'] + "_phenotype_annotations");
 	});
 
-        $.getJSON('/backend/allele/' + allele['sgdid']  + '/interaction_details', function(data) {
+        $.getJSON('/redirect_backend?param=allele/' + allele['sgdid']  + '/interaction_details', function(data) {
             var interaction_table = create_interaction_table(data, allele['name']['display_text']);
             create_download_button("interaction_table_download", interaction_table, allele['name']['display_text'] + "_interaction_annotations");
 	    create_analyze_button("interaction_table_analyze", interaction_table, "<a href='' class='gene_name'>" + allele['name']['display_name'] + "</a> interactors", true);
         });
 
-        $.getJSON('/backend/allele/' + allele['sgdid']  + '/network_graph', function(data) {
+        $.getJSON('/redirect_backend?param=allele/' + allele['sgdid']  + '/network_graph', function(data) {
 
                 if (data != null && data["nodes"].length > 1) {
 

src/sgd/frontend/yeastgenome/static/js/chemical.js

@@ -1,24 +1,24 @@
 
 $(document).ready(function() {
 
-	$.getJSON('/backend/chemical/' + chemical['id']  + '/phenotype_details', function(data) {
+	$.getJSON('/redirect_backend?param=chemical/' + chemical['id']  + '/phenotype_details', function(data) {
 	  	var phenotype_table = create_phenotype_table(data);
 	  	create_analyze_button("phenotype_table_analyze", phenotype_table, "<a href='" + chemical['link'] + "' class='gene_name'>" + chemical['display_name'] + "</a> Genes", true);
   	    create_download_button("phenotype_table_download", phenotype_table, chemical['display_name'] + "_phenotype_annotations");
 	});
 
-	$.getJSON('/backend/chemical/' + chemical['id']  + '/go_details', function(data) {
+	$.getJSON('/redirect_backend?param=chemical/' + chemical['id']  + '/go_details', function(data) {
                 var go_table = create_go_table(data);
                 create_analyze_button("go_table_analyze", go_table, "<a href='" + chemical['link'] + "' class='gene_name'>" + chemical['display_name'] + "</a> Genes", true);
 		create_download_button("go_table_download", go_table, chemical['display_name'] + "_go_annotations");
 	});
 
-        $.getJSON('/backend/chemical/' + chemical['id']  + '/proteinabundance_details', function(data) {
+        $.getJSON('/redirect_backend?param=chemical/' + chemical['id']  + '/proteinabundance_details', function(data) {
                 var protein_abundance_table = create_protein_abundance_table(data);
                 create_download_button("protein_abundance_table_download", protein_abundance_table, chemical['display_name'] + "_protein_abundance");
         });
 
-	$.getJSON('/backend/chemical/' + chemical['id']  + '/network_graph', function(data) {
+	$.getJSON('/redirect_backend?param=chemical/' + chemical['id']  + '/network_graph', function(data) {
 
 	        if (data != null && data["nodes"].length > 1) {
 
@@ -196,15 +196,15 @@ function create_go_table(data) {
 	    {"bSearchable":false, "bVisible":false,"aTargets":[1],"mData":1}, //analyze_id
 	    {"aTargets":[2],"mData":2}, //gene                                                           
             {"bSearchable":false, "bVisible":false,"aTargets":[3],"mData":3}, //gene systematic name     
-            {"aTargets":[4],"mData":6}, //gene ontology term  -----> qualifier                           
+            {"aTargets":[4],"mData":4}, //gene ontology term  -----> qualifier                           
             {"bSearchable":false, "bVisible":false,"aTargets":[5],"mData":5}, //gene ontology term id    
-            {"aTargets":[6],"mData":4}, //qualifier   -----> gene ontology term  
+            {"aTargets":[6],"mData":6}, //qualifier   -----> gene ontology term  
 	    {"bSearchable":false, "bVisible":false,"aTargets":[7],"mData":7}, //aspect                   
-            {"aTargets":[8],"mData":12}, //evidence   -----> annotation_extension                        
-            {"aTargets":[9],"mData":8}, //method -----> evidence                                         
-            {"bSearchable":false,"bVisible":false,"aTargets":[10],"mData":9}, //source -----> method     
-            {"aTargets":[11],"mData":10}, //assigned on -----> source                                    
-            {"aTargets":[12],"mData":11}, //annotation_extension -----> assigned on                      
+            {"aTargets":[8],"mData":8}, //evidence   -----> annotation_extension                        
+            {"aTargets":[9],"mData":9}, //method -----> evidence                                         
+            {"bSearchable":false,"bVisible":false,"aTargets":[10],"mData":10}, //source -----> method     
+            {"aTargets":[11],"mData":11}, //assigned on -----> source                                    
+            {"aTargets":[12],"mData":12}, //annotation_extension -----> assigned on                      
             {"aTargets":[13],"mData":13} // reference  
 	];
     }

src/sgd/frontend/yeastgenome/static/js/complex.js

@@ -1,9 +1,9 @@
 
 $(document).ready(function() {
 
-    $.getJSON('/backend/complex/' + complex['complex_accession'], function(data) {
+    $.getJSON('/redirect_backend?param=complex/' + complex['complex_accession'], function(data) {
 
-	document.getElementById("summary_paragraph").innerHTML = data['description'] + "<p></p>" + data['properties']
+//	document.getElementById("summary_paragraph").innerHTML = data['description'] + "<p></p>" + data['properties']
 
         var complex_table = create_complex_table(data);
 

src/sgd/frontend/yeastgenome/static/js/complex_go.js

@@ -0,0 +1,99 @@
+
+$(document).ready(function() {
+
+    $.getJSON('/redirect_backend?param=complex/' + complex['complex_accession'], function(data) {
+
+	if (data["process"].length > 0) {
+	    var complex_bp_go_table = create_go_table("complex_bp", data["process"]);
+            create_download_button("complex_bp_go_table_download", complex_bp_go_table, complex['complex_accession'] + "_complex_bp_go");
+	}
+	if (data["function"].length > 0) {
+	    var complex_mf_go_table = create_go_table("complex_mf", data["function"]);
+            create_download_button("complex_mf_go_table_download", complex_mf_go_table, complex['complex_accession'] +"_complex_mf_go");
+	}
+	if (data["component"].length > 0) {
+	    var complex_cc_go_table = create_go_table("complex_cc", data["component"]);
+            create_download_button("complex_cc_go_table_download", complex_cc_go_table, complex['complex_accession'] +"_complex_cc_go");
+	}
+
+	all_data = [];
+	var p = data["process"];
+	for (var i=0; i < p.length; i++) {
+	    all_data.push(go_data_to_table(p[i], i));
+	}
+	var f = data["function"];
+        for (var i=0; i < f.length; i++) {
+            all_data.push(go_data_to_table(f[i], i));
+	}
+	var c = data["component"];
+        for (var i=0; i < c.length; i++) {
+            all_data.push(go_data_to_table(c[i], i));
+	}
+
+	var headers = ["Evidence ID", "Analyze ID", "Complex Name",  "Complex Accession", "Qualifier", "Gene Ontology Term ID", "Gene Ontology Term ", "Aspect", "Annotation Extension", "Evidence", "Method", "Source", "Assigned On", "Reference"]
+	create_download_button_no_table("complex_go_download_all", headers, all_data, complex['complex_accession'] + "_go_annotations")
+
+	//if (data != null && data["go_network_graph"]["nodes"].length > 1) {
+	if (data["go_network_graph"]["nodes"].length > 1) {  
+	    var _categoryColors = {
+                'FOCUS': 'black',
+                'GO': '#2ca02c',
+                'complex': '#E6AB03'
+            };
+	    views.network.render(data["go_network_graph"], _categoryColors, "j-complex-network");
+        } else {
+            hide_section("network");
+        }
+
+
+    });
+
+});
+
+function create_go_table(prefix, data) {
+    var options = {};
+    options["aoColumns"] = [
+        {"bSearchable":false, "bVisible":false,"aTargets":[0],"mData":0}, // evidence_id
+        {"bSearchable":false, "bVisible":false,"aTargets":[1],"mData":1}, // analyze_id
+        {"bSearchable":false, "bVisible":false,"aTargets":[2],"mData":2}, // complex name
+        {"bSearchable":false, "bVisible":false,"aTargets":[3],"mData":3}, // complex accession
+        {"aTargets":[4],"mData":4},                                       // qualifier       
+	{"bSearchable":false, "bVisible":false,"aTargets":[5],"mData":5}, // gene ontology term id
+        {"aTargets":[6],"mData":6},                                       // gene ontology term
+        {"bSearchable":false, "bVisible":false,"aTargets":[7],"mData":7}, // aspect
+        {"aTargets":[8],"mData":8},                                      // annotation_extension
+        {"aTargets":[9],"mData":9},                                       // evidence
+	{"bSearchable":false, "bVisible":false, "aTargets":[10],"mData":9}, // annotation type
+        {"aTargets":[11],"mData":11},                                     // source
+        {"aTargets":[12],"mData":12},                                     // assigned on
+        {"aTargets":[13],"mData":13}                                      // reference
+    ];
+    options["bPaginate"] = true;
+    options["aaSorting"] = [[5, "asc"]];
+    if("Error" in data) {
+        options["oLanguage"] = {"sEmptyTable": data["Error"]};
+        options["aaData"] = [];
+    }
+    else {
+        var datatable = [];
+        var gos = {};
+        for (var i=0; i < data.length; i++) {    
+            datatable.push(go_data_to_table(data[i], i));
+	    gos[data[i]['go']['id']] = true;
+	    //console.log(prefix + ": " + data[i]["go"]["display_name"])
+        }
+	set_up_header(prefix + '_go_table', datatable.length, 'entry', 'entries', Object.keys(gos).length, 'Gene Ontology term', 'Gene Ontology terms');
+
+	options["oLanguage"] = {"sEmptyTable": ''};
+        options["aaData"] = datatable;
+
+        if(Object.keys(gos).length == 0) {
+            $("#" + prefix + "_go").hide();
+            $("#" + prefix + "_subsection").hide();
+        }
+    }
+    $("#" + prefix + "_go_table_analyze").hide();
+    return create_table(prefix + "_go_table", options);
+
+}
+

src/sgd/frontend/yeastgenome/static/js/contig.js

@@ -19,7 +19,7 @@ $(document).ready(function () {
         }
     });
 
-    $.getJSON('/backend/contig/' + contig['id'] + '/sequence_details', function (data) {
+    $.getJSON('/redirect_backend?param=contig/' + contig['id'] + '/sequence_details', function (data) {
         var feature_table = create_feature_table(data['genomic_dna']);
         create_download_button("chromosomal_coord_table_download", feature_table, contig['display_name'] + '_features');
         create_analyze_button("chromosomal_coord_table_analyze", feature_table, "<a href='" + contig['link'] + "' class='gene_name'>" + contig['display_name'] + "</a> genes", true);