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term-overview-section.html
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<link rel="import" href="external-scripts.html">
<link rel="import" href="nextprot-elements-shared-styles.html">
<link rel="import" href="atomic-formula-item.html">
<!--
`term-overview-section`
Term overview section
Specifications can be found in here:
https://swissprot.isb-sib.ch/wiki/display/cal/neXtProt+term+views+specs
https://docs.google.com/document/d/1NFWHy-M2K2qYrIePzRWulZi4UeJ2gp1Itrkpl2uEJec/edit
##### Example
<term-overview-section nx-config='{"term": "TS-0079"}'></term-overview-section>
@demo demo/term-overview-section-demo.html
-->
<dom-module id="term-overview-section" is="dom-if" if="[[accessionName]]">
<template>
<style include="nextprot-elements-shared-styles">
:host {
display: block;
background: #f8f8f8;
overflow-y: auto;
}
iron-collapse {
--iron-collapse-transition-duration: 500ms;
}
h3 {
text-align: left;
}
dd {<
margin-left: 15px;
}
dt {
font-weight: inherit;
}
dl {
margin: 0px;
}
.ec-link {
display: inline;
}
.multiple-prop {
padding: 0px;
}
.errorcomment {
font-size: 9px;
color: orange;
}
</style>
<div id="termOverview">
<div hidden id="noCvTermWarning" class='alert alert-warning noData'>Term '[[nxConfig.termAccession]]' not found.
Suggestions for updates are welcome! Please <a href="javascript:location='mailto:\u0073\u0075\u0070\u0070\u006f\u0072\u0074\u0040\u006e\u0065\u0078\u0074\u0070\u0072\u006f\u0074\u002e\u006f\u0072\u0067';void 0">contact us</a>.
</div>
<h3>
<template is="dom-if" if="[[term.name]]">
<template is="dom-if" if="[[_isEnzyme(term)]]">
[[term.name]] → [[term.description]]
</template>
<template is="dom-if" if="[[!_isEnzyme(term)]]">
[[term.accession]] → [[term.name]]
</template>
</template>
[[data.entryName]]
<template is="dom-if" if="[[data.recommendedProteinName]]">
<template is="dom-if" if="[[data.recommendedProteinName.EC.0]]">
[
<template is="dom-repeat" items="[[data.recommendedProteinName.EC]]" as="ec">
<div class="ec-link"><a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a></div>
<template is="dom-if" if="[[!_checkIfLast(data.recommendedProteinName.EC,index)]]">,
</template>
</template>
]
</template>
<template is="dom-if" if="[[data.recommendedProteinName.mainShortName]]">
([[data.recommendedProteinName.mainShortName]])
</template>
</template>
<paper-spinner-lite id="spinner" active></paper-spinner-lite>
</h3>
</div>
<div id="collapseInfosLess">
<div id="term-info">
<template is="dom-if" if="[[term.ontologyDisplayName]]">
<div id="term-ontology" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">ONTOLOGY :</div>
<template is="dom-if" if="[[!term.selfResolvedUrl]]">
<div class="col-md-9 col-xs-9"> [[term.ontologyDisplayName]] → [[term.accession]] </div>
</template>
<template is="dom-if" if="[[term.selfResolvedUrl]]">
<div class="col-md-9 col-xs-9"> [[term.ontologyDisplayName]] → <a class="ext-link" target='_blank' href="[[term.selfResolvedUrl]]">[[term.accession]]</a> </div>
</template>
</div>
</template>
<template is="dom-if" if="[[term.definition]]">
<div id="term-definition" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">DEFINITION :</div>
<div class="col-md-9 col-xs-9"> [[term.definition]] </div>
</div>
</template>
<template is="dom-if" if="[[_getValueProperties(term, 'abbreviation')]]">
<div id="term-abbreviation" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">ABBREVIATION :</div>
<div class="col-md-9 col-xs-9">
<dl>
<template is="dom-repeat" items="[[_getValueProperties(term, 'abbreviation')]]" as="property">
<dt class="col-md-9 col-xs-9 multiple-prop">[[property.propertyValue]]</dt>
</template>
</dl>
</div>
</div>
</template>
<template is="dom-if" if="[[term.synonyms]]">
<template is="dom-if" if="[[term.synonyms.0]]">
<div id="term-synonyms" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">SYNONYM :</div>
<div class="col-md-9 col-xs-9">
<dl>
<template is="dom-repeat" items="[[term.synonyms]]" as="synonym">
<dt>[[synonym]]</dt>
</template>
</dl>
</div>
</div>
</template>
</template>
<template is="dom-repeat" items="[[termprops]]" filter="_showInPropList" as="prop">
<template is="dom-if" if="[[_getValueProperties(term, prop.key)]]">
<div id="term-[[pro.key]]" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">[[prop.label]] :</div>
<div class="col-md-9 col-xs-9">
<dl>
<template is="dom-repeat" items="[[_getValueProperties(term, prop.key)]]" as="property">
<template is="dom-if" if="[[prop.taxonomicRange]]">
<dt class="col-md-9 col-xs-9 multiple-prop">
<template is="dom-repeat" items="[[_parseTaxonomicRange(property.propertyValue)]]" as="species">
[[species.label]] <a target="_blank" href="[[species.url]]" class="ext-link">[[species.taxon]]</a>
</template>
</dt>
</template>
<template is="dom-if" if="[[!prop.taxonomicRange]]">
<template is="dom-if" if="[[prop.atomicFormula]]">
<dt class="col-md-9 col-xs-9 multiple-prop"><atomic-formula-item formula=[[property.propertyValue]]></atomic-formula-item></dt>
</template>
<template is="dom-if" if="[[!prop.atomicFormula]]">
<dt class="col-md-9 col-xs-9 multiple-prop">[[property.propertyValue]]</dt>
</template>
</template>
</template>
</dl>
</div>
</div>
</template>
</template>
<template is="dom-if" if="[[term.relatedTerms]]">
<template is="dom-if" if="[[term.relatedTerms.0]]">
<div id="related-terms" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">RELATED TERM :</div>
<div class="col-md-9 col-xs-9">
<dl>
<template is="dom-repeat" items="[[term.relatedTerms]]" as="rto">
<dt>[[rto.name]] → [[rto.description]] <a href="[[rto.link]]">[[[rto.accession]]]</a></dt>
</template>
</dl>
</div>
</div>
</template>
</template>
<template is="dom-if" if="[[term.externalReferences]]">
<template is="dom-if" if="[[term.externalReferences.0]]">
<div id="external-references" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">EXTERNAL REFERENCES :</div>
<div class="col-md-9 col-xs-9">
<dl>
<template is="dom-repeat" items="[[term.externalReferences]]" as="xref">
<dt>[[_getDatabaseName(xref)]]: <a class="ext-link" target='_blank' href="[[xref.resolvedUrl]]">[[xref.accession]]</a></dt>
</template>
</dl>
</div>
</div>
</template>
</template>
</div>
</div>
</template>
<script>
Polymer({
is: 'term-overview-section',
properties: {
nxConfig: {
type: Object,
value: {}
},
noCvTerm : {
type: Boolean,
value: false,
notify: true
},
term: {
type: Object,
value: {}
},
termprops: {
type: Array,
value: [
{key: "Feature category", label: "CATEGORY"},
{key: "Category", label: "CATEGORY"},
{key: "abbreviation", label: "ABBREVIATION", show: false}, //Don't show because it will be shown at other place
{key: "Catalyst", label: "CATALYST"},
{key: "Reaction", label: "REACTION"},
{key: "Comment", label: "COMMENT"},
{key: "Target", label: "TARGETED AMINO ACID"},
{key: "Position of the modification", label: "POSITION OF THE MODIFICATION"},
{key: "Cellular location", label: "CELLULAR LOCATION"},
{key: "Taxonomic range", label: "TAXONOMIC RANGE", taxonomicRange: true},
{key: "Correction formula", label: "ATOMIC CORRECTION FORMULA", atomicFormula: true},
{key: "Average mass difference", label: "AVERAGE MASS DIFFERENCE"},
{key: "Monoisotopic mass difference", label: "MONOISOTONIC MASS DIFFERENCE"}
//FIXME Others from DB
/*
Cellular location 589
930
Feature key 632
Uniprot status 35
*/
]
}
},
ready: function () {
this._npClient = getNXClient(this.nxConfig);
var self = this;
// fetch data from overview
this._npClient.getTermByAccession(self.nxConfig.termAccession).then(function (term) {
if(term["cvTerm"]){
self.$.noCvTermWarning.hidden=true;
self.term = self._convertForTemplate(term["cvTerm"]);
self.noCvTerm = false;
}else {
self.$.noCvTermWarning.hidden=false;
self.noCvTerm = true;
}
self.$.spinner.active = false;
}, function (error) {
if(error.status = 404){
self.$.noCvTermWarning.hidden=false;
self.noCvTerm = true;
}else {
console.log("Some unexpected error occued", error);
}
self.$.spinner.active = false;
})
},
_parseTaxonomicRange: function(value) {
var realm = value.split(';')[0].trim();
var species = value.split(';')[1];
var speciesList= [];
var speciesArray = species.split(',');
for (idx in speciesArray) {
var data = speciesArray[idx].trim();
var species = {};
var spacePos = data.indexOf(' ');
species.taxon = data.substr(0,spacePos);
species.url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=" + species.taxon;
var label = data.substr(spacePos).trim();
// remove parentheses embedding the label
label = label.substr(1);
label = label.substr(0, label.length-1);
// build the label of the first species by prefixing it with the realm if different of label
if (idx==0 && label != realm) label = realm + " » " + label;
// build labels for species after the first one
if (idx>0) label = ' , ' + label;
species.label = label;
speciesList.push(species);
}
return speciesList;
},
_showInPropList: function(tp){
if (tp.show !== undefined) {
return tp.show;
}
else return true;
},
_isEnzyme: function(term){
return (term.ontology == "EnzymeClassificationCv")
},
_getTemplateUrl: function(term, prop, label){
if(prop.propertyName === "Taxonomic range"){
if(label === "label"){
return prop.propertyValue.split(" ")[0].slice(0, -1);
}else if(label === "urlLabel"){
return prop.propertyValue.split(" ")[1]
}else if(label === "url"){
var trid = prop.propertyValue.split(" ")[1].split(":")[1]
return ("https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=" + trid)
}
}
},
_getValueProperties : function (term, propertyKey){
if(term[propertyKey]){
return term[propertyKey];
}
},
_getProperty: function (propertyName, properties){
var result = []
var self = this;
if(properties && (properties.length > 0)) {
properties.forEach(function(prop){
var ploop = prop.propertyName.replace(/ /g,'').toLowerCase();
var parg = propertyName.replace(/ /g,'').toLowerCase();
if(ploop === parg){
var pv = prop.propertyValue;
prop.propertyValue = self._upperCaseFirstLetter(pv)
if(propertyName == "Reaction"){
prop.propertyValue = prop.propertyValue.replace("=", "⇄")
}
result.push(prop);
}
})
}
return result;
},
_upperCaseFirstLetter: function(string){
return string[0].toUpperCase() + string.substr(1);
},
_convertForTemplate: function (cvTerm) {
console.log(cvTerm);
var self = this;
var term = JSON.parse(JSON.stringify(cvTerm));
//Add capital letter
if(term.name)
term.name = self._upperCaseFirstLetter(term.name)
if(term.definition)
term.definition = self._upperCaseFirstLetter(term.definition)
if(term.description)
term.description = self._upperCaseFirstLetter(term.description)
if(term.name !== term.description && term.ontology != "EnzymeClassificationCv"){
term.definition = term.description;
}
if(term.synonyms && (term.synonyms.length > 0)){
term.synonyms = term.synonyms.sort(this._sort);
}
//Don't add any reference when it is None or when it is UniPathWay and evocontology (not maintained anymore)
if(term.selfXref && term.selfXref.resolvedUrl !== "None" && (term.selfXref.resolvedUrl.toLowerCase().indexOf("unipathway.org") === -1) && (term.selfXref.resolvedUrl.toLowerCase().indexOf("evocontology.org") === -1) ){
term.selfResolvedUrl = term.selfXref.resolvedUrl;
}
//remove synonym if equals to name or description, but CAREFUL WITH CASE SENSITVE! Chang Liver is not the same as Chang liver accoring to Amos and we need to keep both!
//Non, il n'y a jamais de diplication entre un nom et un synonyme ds le Cellosaurus (c'est vérifié par le Celloparser d'Alain).
//Il s'agit de differences de "casse" qui sont importante pour les cell lines, donc "Chang Liver" est différent de "Chang liver".
//Il ne faut en général pas essayer de faire une règle de ce genre. Si par hasard dans un CV ou une ontologie il y a une vrai
//duplication entre le nom et le synonyme: tant pis, on avertira les personnes qui le développed.
if(term.synonyms && term.synonyms.length > 0){
term.synonyms = term.synonyms.filter(function(s){return s.trim() !== term.name.trim()})
term.synonyms = term.synonyms.filter(function(s){return s.trim() !== term.description.trim()})
}
this.termprops.forEach(function (tp){
self._addPropertyToTermIfPresent(tp.key, term);
})
if(term.acsOfRelatedTerms && (term.acsOfRelatedTerms.length > 0)){
term.relatedTerms = []
term.acsOfRelatedTerms.forEach(function (rt){
term.xrefs.forEach(function (x){
if(x.accession === rt){
var rto = {}
x.properties.forEach(function (prop){
if(prop.name === "term_ontology_display_name"){
rto["name"] = prop.value
}else if(prop.name === "term_name"){
//Upper case first letter
rto["description"] = self._upperCaseFirstLetter(prop.value)
}
})
rto.accession = x.accession;
rto.link = "/term/" + x.accession;
term.relatedTerms.push(rto)
}}
)
})
term.relatedTerms = term.relatedTerms.sort(self._sort);
}
//Add external references which are not in related terms already
if(term.xrefs && (term.xrefs.length > 0 )){
term.externalReferences = [];
term.xrefs.forEach(function (x){
if(term.acsOfRelatedTerms.indexOf(x.accession) == -1){
term.externalReferences.push(x);
}
})
term.externalReferences = term.externalReferences.sort(this._sort);
}
return term;
},
_addPropertyToTermIfPresent: function (propertyName, term){
//DO NOT ADD Cellosaurus comments (part of specifications)
if(!(term.ontology === "NextprotCellosaurusCv" && propertyName === "Comment")){
var properties = this._getProperty(propertyName, term.properties);
if(properties && (properties.length > 0)){
if(!(propertyName in term)){
term[propertyName] = []
}
Array.prototype.push.apply(term[propertyName], properties)
var propsOrdered = term[propertyName].sort(this._sort);
term[propertyName] = propsOrdered;
}
}
},
_sort: function (a, b) {
if(a.databaseName) {
if(a.databaseName === b.databaseName){
return a.accession.trim().toLowerCase() < b.accession.trim().toLowerCase() ? -1 : 1;
}else return a.databaseName.trim().toLowerCase() < b.databaseName.trim().toLowerCase() ? -1 : 1;
}
else if(a["propertyValue"]) {
return a["propertyValue"].trim().toLowerCase() < b["propertyValue"].trim().toLowerCase() ? -1 : 1;
}
else if(a["name"]) {
var result = a["name"].trim().toLowerCase() < b["name"].trim().toLowerCase() ? -1 : 1;
if(a["name"].trim().toLowerCase() === b["name"].trim().toLowerCase() ){
if(a["description"]) {
return a["description"].trim().toLowerCase() < b["description"].trim().toLowerCase() ? -1 : 1;
}else {
return result;
}
}
return result;
}else {
return a.trim().toLowerCase() < b.trim().toLowerCase() ? -1 : 1;
}
},
_getDatabaseName: function(xref) {
if (xref.databaseName.includes("UniProt")) {
return xref.databaseName.replace("UniProt", "UniProtKB");
}
return xref.databaseName;
}
})
</script>
</dom-module>