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Infobox text and URI change #762

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Merged
merged 7 commits into from
May 18, 2018
Merged

Infobox text and URI change #762

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7dd85ab
Infobox text and URI change
q4wen May 15, 2018
4beb66d
Removing space.
q4wen May 17, 2018
f5d1896
Merge branch 'development' into infobox-link
q4wen May 17, 2018
22e535d
Display name of NGNC change
q4wen May 17, 2018
3b4ca57
Add displayName to databases.
q4wen May 18, 2018
64fb91f
Fix typo "HGNC"
q4wen May 18, 2018
4143f5e
Coding style update.
q4wen May 18, 2018
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20 changes: 10 additions & 10 deletions src/client/features/interactions/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -51,12 +51,12 @@ class Interactions extends React.Component {
Phosphorylation:true,
Expression:true
}
};
};

const query = queryString.parse(props.location.search);
const sources=_.uniq(_.concat([],query.source));
const kind = sources.length>1?'PATHSBETWEEN':'Neighborhood';
ServerAPI.getNeighborhood(sources,kind).then(res=>{
ServerAPI.getNeighborhood(sources,kind).then(res=>{
const layoutConfig = getLayoutConfig('interactions');
const network= this.parse(res);
this.setState({
Expand All @@ -66,8 +66,8 @@ class Interactions extends React.Component {
loaded:_.assign(this.state.loaded,{network:true})
});
});
//get ids from uris
const geneIds = sources.map(source=>
//get ids from uris
const geneIds = sources.map(source=>
source.includes('pathwaycommons')?
ServerAPI.pcQuery('traverse',{uri:source,path:`${_.last(source.split('/')).split('_')[0]}/displayName`}).then(result=>result.json())
.then(id=> _.words(id.traverseEntry[0].value[0]).length===1 ? id.traverseEntry[0].value[0].split('_')[0] : ''):
Expand Down Expand Up @@ -102,7 +102,7 @@ class Interactions extends React.Component {
});
});
});

this.state.cy.on('trim', () => {
const state = this.state;
const ids = state.ids;
Expand All @@ -124,7 +124,7 @@ class Interactions extends React.Component {
const nodes = edges.connectedNodes();
edges.length?
categories.set(type,{edges:edges,nodes:nodes}):
(categories.delete(type),delete filters[type]);
(categories.delete(type),delete filters[type]);
});

_.tail(_.toPairs(filters)).map(pair=>this.filterUpdate(pair[0]));
Expand Down Expand Up @@ -170,7 +170,7 @@ class Interactions extends React.Component {
if(!nodeMap.has(node)){
const metadata=nodeMetadata.get(node);
nodeMap.set(node,true);
const links=_.uniqWith(_.flatten(metadata.slice(-2).map(entry => entry.split(';').map(entry=>entry.split(':')))),_.isEqual).filter(entry=>entry[0]!='intact');
const links=_.uniqWith(_.flatten(metadata.slice(-2).map(entry => entry.split(';').map(entry=>entry.split(':')))),_.isEqual).filter(entry=>entry[0]!='intact');
network.nodes.push({data:{class: "ball",id: node,label: node, queried: this.state.ids.indexOf(node)!=-1 ,
parsedMetadata:[['Type','bp:'+metadata[0].split(' ')[0].replace(/Reference/g,'').replace(/;/g,',')],['Database IDs', links]]}});
}
Expand Down Expand Up @@ -222,11 +222,11 @@ class Interactions extends React.Component {
cy.remove(edges);
cy.remove(nodes.filter(nodes=>nodes.connectedEdges().empty()));
}
else{
else{
edges.union(nodes).restore();
}
});

filters[type]=!filters[type];
this.setState({
filters:filters
Expand All @@ -246,7 +246,7 @@ class Interactions extends React.Component {
filterUpdate:(evt,type)=> this.filterUpdate(evt,type),
filters: state.filters,
download: {
types: downloadTypes.filter(ele=>ele.type==='png'||ele.type==='sif'),
types: downloadTypes.filter(ele=>ele.type==='png'||ele.type==='sif'),
promise: () => Promise.resolve(_.map(state.cy.edges(),edge=> edge.data().id).sort().join('\n'))
},
}):
Expand Down
23 changes: 16 additions & 7 deletions src/client/features/search/landing-box.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,10 @@ const Loader = require('react-loader');
const _ = require('lodash');
//usedDatabases=[['Uniprot lookup name',{configName:,gProfiler:}]]
const usedDatabases=new Map ([
['GeneCards',{configName:'Gene Cards',gProfiler:'HGNCSYMBOL'}],
['HGNC',{configName:'HGNC',gProfiler:'HGNC'}],
['GeneID',{configName:'NCBI Gene',gProfiler:'NCBIGene'}],
['Uniprot',{configName:'Uniprot',gProfiler:'Uniprot'}]
['GeneCards',{configName:'Gene Cards',gProfiler:'HGNCSYMBOL',displayName:'Gene Cards'}],
['HGNC Symbol',{configName:'HGNC Symbol',gProfiler:'HGNCSymbol',displayName:'HGNC'}],
['GeneID',{configName:'NCBI Gene',gProfiler:'NCBIGene',displayName:'NCBI Gene'}],
['Uniprot',{configName:'Uniprot',gProfiler:'Uniprot',displayName:'Uniprot'}]
]);

const linkBuilder= (source,geneQuery)=>{
Expand Down Expand Up @@ -47,9 +47,18 @@ const pcFallback = (unrecognized,genes) => {

const idToLinkConverter = (ids) =>{
const dbSet = databases.filter(databaseValue => ids[databaseValue.database]);
return _.assign({},
let dbs = _.assign({},
...dbSet.map(database=>({[database.database]:database.url+database.search+ids[database.database].replace(/[^a-zA-Z0-9:]/g)}))
);

let links = [];
usedDatabases.forEach((usedDatabase)=>{
let dbLink = dbs[usedDatabase.configName];
if (dbLink != null) {
links.push({link:dbLink,displayName:usedDatabase.displayName});
}
});
return links;
};

const getNcbiInfo = (ids,genes) => {
Expand Down Expand Up @@ -212,8 +221,8 @@ const landingBox = (props) => {
functions=expandableText(controller,landing,360, box.function,".",'span','search-landing-function','function',index);
}
let links=[];
_.forIn((box.links),(value,key)=>{
links.push(h('a.search-landing-link',{key: key, href: value},key));
box.links.forEach((link)=>{
links.push(h('a.search-landing-link',{key: link.displayName, href: link.link},link.displayName));
});
return [
h('div.search-landing-title',{key:'title',
Expand Down