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soba.js
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// javascript for form at ~azurebrd/public_html/cgi-bin/forms/community_gene_description.cgi
// autocomplete (not forced) on genes and species, enter PMIDs and use those plus previous matches of pmid-title to look up new pmid titles to add to list of pmid-titles in readonly textarea. 2013 06 02
//
// changed tazendra.caltech.edu/~azurebrd/cgi-bin/forms/datatype_objects.cgi to caltech-curation.textpressolab.com/pub/cgi-bin/forms/datatype_objects.cgi 2024 10 18
var cgiUrl = 'soba.cgi';
YAHOO.util.Event.addListener(window, "load", function() { // on load assign listeners
setAutocompleteListeners(); // add listener for gene, species, pmids
}); // YAHOO.util.Event.addListener(window, "load", function()
// window.onscroll = function () {
// // delay(function(){
// var termInfoBox = document.getElementById("term_info_box");
// var bodyTop = window.pageYOffset; // vertical offset of window
// if (bodyTop > 20) { // scrolled more than 20
// var setTop = 95 - bodyTop; // from default 95 minus the offset, move it
// if (setTop < 20) { setTop = 20; } // move no less than 20px from the top
// termInfoBox.style.top = setTop + 'px';
// }
// else {
// termInfoBox.style.top = '95px'; // if window not scrolled much, set to default 95px
// }
// // }, 5 );
// };
function setAutocompleteListeners() { // add listener for gene, species, pmids
var whichPage = document.getElementById('which_page').value;
if (whichPage === 'pickOneGenePage') {
var field = 'Gene';
settingAutocompleteListeners = function() {
var taxons = [];
var arrCheckbox = document.getElementsByClassName("taxon");
for (var i = 0; arrCheckbox[i]; i++) {
if (arrCheckbox[i].checked) {
taxons.push('taxon_label:"'+ arrCheckbox[i].value + '"');
}
} // for (i = arrCheckbox.length - 1; i > -1; i--)
var taxonFq = taxons.join('+OR+');
// alert(taxonFq);
var datatypeValue = 'phenotype';
var radioDatatypeElements = document.getElementsByName("radio_datatype");
for (var i = 0, length = radioDatatypeElements.length; i < length; i++) {
if (radioDatatypeElements[i].checked) {
datatypeValue = radioDatatypeElements[i].value; } }
// var sUrl = cgiUrl + "?action=autocompleteXHR&taxonFq=" + taxonFq + "&field=" + field + "&"; // ajax calls need curator and datatype
// var sUrl = cgiUrl + "?action=autocompleteXHR&datatype=" + datatypeValue + "&taxonFq=" + taxonFq + "&field=Gene&"; // good until 2019 11 01
// var sUrl = cgiUrl + "?action=autocompleteTazendraXHR&objectType=gene&"; // to try to get from tazendra OA through cgi
// var sUrl = "https://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/datatype_objects.cgi?action=autocompleteXHR&objectType=gene&"; // to try to get from tazendra OA
var sUrl = "https://caltech-curation.textpressolab.com/pub/cgi-bin/forms/datatype_objects.cgi?action=autocompleteXHR&objectType=gene&"; // to try to get from tazendra OA
var oDS = new YAHOO.util.XHRDataSource(sUrl); // Use an XHRDataSource
oDS.responseType = YAHOO.util.XHRDataSource.TYPE_TEXT; // Set the responseType
oDS.responseSchema = { // Define the schema of the delimited results
recordDelim: "\n",
fieldDelim: "\t"
};
oDS.maxCacheEntries = 5; // Enable caching
var forcedOrFree = "forced";
var inputElement = document.getElementById('input_'+field);
var containerElement = document.getElementById(forcedOrFree + field + "Container");
var forcedOAC = new YAHOO.widget.AutoComplete(inputElement, containerElement, oDS);
forcedOAC.queryQuestionMark = false; // don't add a ? to the sUrl query since it's been built with some other values
forcedOAC.queryDelay = 0.1; // add a delay to wait for user to stop typing
forcedOAC.maxResultsDisplayed = 500;
forcedOAC.forceSelection = true;
forcedOAC.generateRequest = function(sQuery) { return "userValue=" + sQuery ; }; // instead of sending 'query' to form, use 'userValue'
forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelect);
// Don't needs this because don't need action on these, if it was necessary, would have to create functions like in the OA
// forcedOAC.selectionEnforceEvent.subscribe(onAutocompleteSelectionEnforce);
// forcedOAC.itemArrowToEvent.subscribe(onAutocompleteItemHighlight);
// forcedOAC.itemMouseOverEvent.subscribe(onAutocompleteItemHighlight);
return {
oDS: oDS,
forcedOAC: forcedOAC
}
}();
} // if (whichPage === 'pickOneGenePage')
else if (whichPage === 'pickOneGeneBiggoPage') {
var field = 'Gene';
settingAutocompleteListeners = function() {
// to select from checkboxes instead of drop down
// var taxons = [];
// var arrCheckbox = document.getElementsByClassName("taxon");
// for (var i = 0; arrCheckbox[i]; i++) {
// if (arrCheckbox[i].checked) {
// taxons.push('taxon_label:"'+ arrCheckbox[i].value + '"'); } }
// var taxonFq = taxons.join('+OR+');
var taxonFq = '';
if (document.getElementById("taxon_all").value === 'All') { taxonFq = ''; }
else { taxonFq = 'taxon_label:"' + document.getElementById("taxon_all").value + '"'; }
var datatypeValue = 'biggo';
var sUrl = cgiUrl + "?action=autocompleteXHR&datatype=" + datatypeValue + "&taxonFq=" + taxonFq + "&field=Gene&"; // for biggo
var oDS = new YAHOO.util.XHRDataSource(sUrl); // Use an XHRDataSource
oDS.responseType = YAHOO.util.XHRDataSource.TYPE_TEXT; // Set the responseType
oDS.responseSchema = { // Define the schema of the delimited results
recordDelim: "\n",
fieldDelim: "\t"
};
oDS.maxCacheEntries = 5; // Enable caching
var forcedOrFree = "forced";
var inputElement = document.getElementById('input_'+field);
var containerElement = document.getElementById(forcedOrFree + field + "Container");
var forcedOAC = new YAHOO.widget.AutoComplete(inputElement, containerElement, oDS);
forcedOAC.queryQuestionMark = false; // don't add a ? to the sUrl query since it's been built with some other values
forcedOAC.queryDelay = 0.1; // add a delay to wait for user to stop typing
forcedOAC.maxResultsDisplayed = 500;
forcedOAC.forceSelection = true;
forcedOAC.generateRequest = function(sQuery) { return "userValue=" + sQuery ; }; // instead of sending 'query' to form, use 'userValue'
forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelect);
return {
oDS: oDS,
forcedOAC: forcedOAC
}
}();
} // else if (whichPage === 'pickOneGeneBiggoPage')
else if (whichPage === 'pickTwoGenesBiggoPage') {
var autocompleteFieldsArray = ['One', 'Two'];
for (var j = 0; j < autocompleteFieldsArray.length; j++) { // for each field to autocomplete
var fieldCount = autocompleteFieldsArray[j];
var field = 'Gene' + fieldCount;
settingAutocompleteListeners = function() {
// to select from checkboxes instead of drop down
// var taxons = [];
// var arrCheckbox = document.getElementsByClassName("taxon" + fieldCount);
// for (var i = 0; arrCheckbox[i]; i++) {
// if (arrCheckbox[i].checked) {
// taxons.push('taxon_label:"'+ arrCheckbox[i].value + '"'); } }
// var taxonFq = taxons.join('+OR+');
var taxonFq = '';
if (document.getElementById("taxon" + fieldCount).value === 'All') { taxonFq = ''; }
else { taxonFq = 'taxon_label:"' + document.getElementById("taxon" + fieldCount).value + '"'; }
var datatypeValue = 'biggo';
var sUrl = cgiUrl + "?action=autocompleteXHR&datatype=" + datatypeValue + "&taxonFq=" + taxonFq + "&field=Gene&"; // for biggo
var oDS = new YAHOO.util.XHRDataSource(sUrl); // Use an XHRDataSource
oDS.responseType = YAHOO.util.XHRDataSource.TYPE_TEXT; // Set the responseType
oDS.responseSchema = { // Define the schema of the delimited results
recordDelim: "\n",
fieldDelim: "\t"
};
oDS.maxCacheEntries = 5; // Enable caching
var forcedOrFree = "forced";
var inputElement = document.getElementById('input_'+field);
var containerElement = document.getElementById(forcedOrFree + field + "Container");
var forcedOAC = new YAHOO.widget.AutoComplete(inputElement, containerElement, oDS);
forcedOAC.queryQuestionMark = false; // don't add a ? to the sUrl query since it's been built with some other values
forcedOAC.queryDelay = 0.1; // add a delay to wait for user to stop typing
forcedOAC.maxResultsDisplayed = 500;
forcedOAC.forceSelection = true;
forcedOAC.generateRequest = function(sQuery) { return "userValue=" + sQuery ; }; // instead of sending 'query' to form, use 'userValue'
forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelect);
return {
oDS: oDS,
forcedOAC: forcedOAC
}
}();
} // for (var j = 0; j < autocompleteFieldsArray.length; j++) // for each field to autocomplete
} // else if (whichPage === 'pickTwoGenesBiggoPage')
else if (whichPage === 'pickTwoGenesPage') {
var autocompleteFieldsArray = ['One', 'Two'];
for (var j = 0; j < autocompleteFieldsArray.length; j++) { // for each field to autocomplete
var fieldCount = autocompleteFieldsArray[j];
var field = 'Gene' + fieldCount;
settingAutocompleteListeners = function() {
var taxons = [];
var arrCheckbox = document.getElementsByClassName("taxon" + fieldCount);
for (var i = 0; arrCheckbox[i]; i++) {
if (arrCheckbox[i].checked) {
taxons.push('taxon_label:"'+ arrCheckbox[i].value + '"');
}
} // for (i = arrCheckbox.length - 1; i > -1; i--)
var taxonFq = taxons.join('+OR+');
// alert(taxonFq);
var datatypeValue = 'phenotype';
var radioDatatypeElements = document.getElementsByName("radio_datatype");
for (var i = 0, length = radioDatatypeElements.length; i < length; i++) {
if (radioDatatypeElements[i].checked) {
datatypeValue = radioDatatypeElements[i].value; } }
// var sUrl = cgiUrl + "?action=autocompleteXHR&datatype=" + datatypeValue + "&taxonFq=" + taxonFq + "&field=Gene&";
// var sUrl = cgiUrl + "?action=autocompleteTazendraXHR&objectType=gene&"; // to try to get from tazendra OA through cgi
// var sUrl = "https://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/datatype_objects.cgi?action=autocompleteXHR&objectType=gene&"; // to try to get from tazendra OA
var sUrl = "https://caltech-curation.textpressolab.com/pub/cgi-bin/forms/datatype_objects.cgi?action=autocompleteXHR&objectType=gene&"; // to try to get from tazendra OA
var oDS = new YAHOO.util.XHRDataSource(sUrl); // Use an XHRDataSource
oDS.responseType = YAHOO.util.XHRDataSource.TYPE_TEXT; // Set the responseType
oDS.responseSchema = { // Define the schema of the delimited results
recordDelim: "\n",
fieldDelim: "\t"
};
oDS.maxCacheEntries = 5; // Enable caching
var forcedOrFree = "forced";
var inputElement = document.getElementById('input_'+field);
var containerElement = document.getElementById(forcedOrFree + field + "Container");
var forcedOAC = new YAHOO.widget.AutoComplete(inputElement, containerElement, oDS);
forcedOAC.queryQuestionMark = false; // don't add a ? to the sUrl query since it's been built with some other values
forcedOAC.queryDelay = 0.1; // add a delay to wait for user to stop typing
forcedOAC.maxResultsDisplayed = 500;
forcedOAC.forceSelection = true;
forcedOAC.generateRequest = function(sQuery) { return "userValue=" + sQuery ; }; // instead of sending 'query' to form, use 'userValue'
forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelect);
// if (fieldCount === 'One') {
// forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelectOne); }
// else if (fieldCount === 'Two') {
// forcedOAC.itemSelectEvent.subscribe(onAutocompleteItemSelectTwo); }
return {
oDS: oDS,
forcedOAC: forcedOAC
}
}();
} // for (var j = 0; j < autocompleteFieldsArray.length; j++) // for each field to autocomplete
} // else if (whichPage === 'pickTwoGenesPage')
// from http://stackoverflow.com/questions/1909441/jquery-keyup-delay
var delay = (function(){ // delay executing a function until user has stopped typing for a timeout amount
var timer = 0;
return function(callback, ms){
clearTimeout (timer);
timer = setTimeout(callback, ms);
};
})();
} // function setAutocompleteListeners()
function radioDatatypeClick(whichPage) {
if (whichPage === 'TwoGenes') {
validateGeneDatatype('GeneOne');
validateGeneDatatype('GeneTwo'); }
console.log('clicked radio');
} // function radioDatatypeClick('whichPage')
function onAutocompleteItemSelect(oSelf , elItem) { // if an item is highlighted from arrows or mouseover, populate obo
var match = elItem[0]._sName.match(/input_(.*)/); // get the key and value
var field = match[1];
console.log('field: ' + field);
if (field === 'Gene') {
var value = elItem[1].innerHTML; // get the selected value
var datatypeValue = 'phenotype';
var radioDatatypeElements = document.getElementsByName("radio_datatype");
for (var i = 0, length = radioDatatypeElements.length; i < length; i++) {
if (radioDatatypeElements[i].checked) {
datatypeValue = radioDatatypeElements[i].value; } }
var url = 'soba.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=' + datatypeValue + '&autocompleteValue=' + value;
// window.location = url; // uncomment to load graph automatically
}
else if (field === 'GeneOne') {
validateGeneDatatype('GeneOne');
document.getElementById('controlsOne').style.display = 'none';
document.getElementById('controlsTwo').style.display = ''; }
else if (field === 'GeneTwo') {
console.log('genetwo');
validateGeneDatatype('GeneTwo');
// to automaticaly load graph on selection of gene two
// var geneOneValue = document.getElementById('input_GeneOne').value;
// var url = 'soba.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=' + datatypeValue + '&geneOneValue=' + geneOneValue + '&autocompleteValue=' + value;
// console.log('genetwo: ' + url);
// window.location = url; // uncomment to load graph automatically
}
} // function onAutocompleteItemSelect(oSelf , elItem)
function validateGeneDatatype(whichGene) {
let datatypeValue = getSelectedDatatype();
let elMatch = document.getElementById('input_'+whichGene).value.match(/\( (.*?) \)/);
if (elMatch !== null) {
let geneId = 'WB:' + elMatch[1];
console.log('geneId: ' + geneId + ' datatype: ' + datatypeValue);
asyncCheckGeneDatatype(whichGene, geneId, datatypeValue); }
} // function validateGeneDatatype(whichGene)
function getSelectedDatatype() {
let datatypeValue = 'phenotype';
var radioDatatypeElements = document.getElementsByName("radio_datatype");
for (var i = 0, length = radioDatatypeElements.length; i < length; i++) {
if (radioDatatypeElements[i].checked) {
datatypeValue = radioDatatypeElements[i].value; } }
return datatypeValue;
} // function getSelectedDatatype()
function asyncCheckGeneDatatype(whichGene, geneId, datatypeValue) {
var callbacks = {
success : function (o) { // Successful XHR response handler
if (o.responseText !== undefined) {
if (o.responseText === 'no data') {
document.getElementById('message'+whichGene).style.color = 'red';
document.getElementById('message'+whichGene).innerHTML = o.responseText; }
else if (o.responseText === 'has data') {
document.getElementById('message'+whichGene).style.color = 'green';
document.getElementById('message'+whichGene).innerHTML = o.responseText; }
else {
document.getElementById('message'+whichGene).style.color = 'orange';
document.getElementById('message'+whichGene).innerHTML = 'unexpected response'; }
// console.log('SUCCESS!');
} }, };
// value = convertDisplayToUrlFormat(value); // convert <newValue> to URL format by escaping characters
// var sUrl = cgiUrl + "?action=asyncTermInfo&field="+field+"&termid="+value;
// let sUrl = 'http://wobr2.caltech.edu:8080/solr/' + datatypeValue + '/select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22' + geneId + '%22'; // CORS does not allow this nor localhost:8080
let sUrl = 'soba.cgi?action=validateGeneDatatype&datatype=' + datatypeValue + '&gene=' + geneId;
console.log('send ' + sUrl);
YAHOO.util.Connect.asyncRequest('GET', sUrl, callbacks); // Make the call to the server for term info data
} // function function asyncTermInfo(field, value)
// http://wobr2.caltech.edu:8080/solr/phenotype/select?qt=standard&indent=on&wt=json&version=2.2&rows=100000&fl=regulates_closure,id,annotation_class&q=document_category:annotation&fq=-qualifier:%22not%22&fq=bioentity:%22WB:WBGene00003009%22
// function asyncWbdescription(wbgene) {
// var callbacks = {
// success : function (o) { // Successful XHR response handler
// if (o.responseText !== undefined) {
// // document.getElementById('wbDescription').innerHTML = o.responseText + "<br/> ";
// var jsonData = [];
// try { jsonData = YAHOO.lang.JSON.parse(o.responseText); } // Use the JSON Utility to parse the data returned from the server
// catch (x) { alert("JSON Parse failed!"); return; }
// var one = jsonData.shift();
// var two = jsonData.shift();
// var three = jsonData.shift();
// var four = jsonData.shift();
// var five = jsonData.shift();
// document.getElementById('wbDescription').value = two;
// document.getElementById('wbDescriptionDiv').innerHTML = two;
// document.getElementById('concisedescription').innerHTML = two;
// document.getElementById('wbDescriptionGuide').value = three;
// document.getElementById('wbDescriptionGuideSpan').innerHTML = three;
// if (four !== 'noperson') {
// document.getElementById('contributedBy').value = four;
// document.getElementById('contributedByDiv').innerHTML = four;
// document.getElementById('contributedByGuideSpan').innerHTML = five;
// } else {
// document.getElementById('contributedBy').value = '';
// document.getElementById('contributedByDiv').innerHTML = '';
// document.getElementById('contributedByGuideSpan').innerHTML = '';
// }
//
// } }, };
// wbgene = convertDisplayToUrlFormat(wbgene); // convert <newValue> to URL format by escaping characters
// var sUrl = cgiUrl + "?action=asyncWbdescription&wbgene=" + wbgene + "&";
// // alert(sUrl);
// YAHOO.util.Connect.asyncRequest('GET', sUrl, callbacks); // Make the call to the server for term info data
// } // function function asyncWbdescription(field, value)
//
//
// function onAutocompleteItemHighlight(sType, aArgs) { // if an item is highlighted from arrows or mouseover, populate obo
// // var value = elItem[1].innerHTML;
// // document.getElementById('wbDescription').innerHTML = value;
// var match = aArgs[0]._sName.match(/input_(.*)/); // get the key and value
// var field = match[1];
// var myAC = aArgs[0]; // reference back to the AC instance
// var elLI = aArgs[1]; // reference to the selected LI element
// if (field === 'person') {
// document.getElementById('term_info').parentNode.style.display = '';
// if (elLI.innerHTML.match(/\( (.*?) \)/) ) { // match wb id in span and parenthesis
// match = myAC._sName.match(/input_(.*)/);
// var field = match[1];
// var elMatch = elLI.innerHTML.match(/\( (.*?) \)/);
// var wbid = elMatch[1];
// document.getElementById('termid_person').value = wbid;
// asyncTermInfo(field, wbid);
// }
// }
// } // function onAutocompleteItemHighlight(oSelf , elItem)
//
// function asyncTermInfo(field, value) {
// var callbacks = {
// success : function (o) { // Successful XHR response handler
// if (o.responseText !== undefined) { document.getElementById('term_info').innerHTML = o.responseText + "<br/> "; } }, };
// value = convertDisplayToUrlFormat(value); // convert <newValue> to URL format by escaping characters
// var sUrl = cgiUrl + "?action=asyncTermInfo&field="+field+"&termid="+value;
// YAHOO.util.Connect.asyncRequest('GET', sUrl, callbacks); // Make the call to the server for term info data
// } // function function asyncTermInfo(field, value)
//
//
//
// function convertDisplayToUrlFormat(value) {
// if (value !== undefined) { // if there is a display value replace stuff
// if (value.match(/\n/)) { value = value.replace(/\n/g, " "); } // replace linebreaks with <space>
// if (value.match(/\+/)) { value = value.replace(/\+/g, "%2B"); } // replace + with escaped +
// if (value.match(/\#/)) { value = value.replace(/\#/g, "%23"); } // replace # with escaped #
// }
// return value; // return value in format for URL
// } // function convertDisplayToUrlFormat(value)