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Provided means to set DB taxonomy thru back-office
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| var taxonCellIndex = null; | ||
|
|
||
| function getNcbiTaxonDetails(ncbiTaxonId, retrying) | ||
| { | ||
| var failed = false, result = $.ajax({ | ||
| async:false, | ||
| type:"GET", | ||
| url:"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&retmode=json&id=" + ncbiTaxonId, | ||
| error:function(xhr, ajaxOptions, thrownError) { | ||
| failed = true; | ||
| } | ||
| }); | ||
|
|
||
| if (!failed) | ||
| return result['responseJSON']['result'][ncbiTaxonId]; | ||
|
|
||
| if (retrying) | ||
| return null; | ||
|
|
||
| console.log("Retrying to fetch taxon from ID " + ncbiTaxonId); | ||
| return getNcbiTaxonDetails(ncbiTaxonId, true); | ||
| } | ||
|
|
||
| function grabNcbiTaxon(inputObj, taxonId) | ||
| { | ||
| if (taxonId == null) | ||
| return false; | ||
|
|
||
| if (taxonId == "" || isNaN(taxonId)) { | ||
| $(inputObj).removeAttr('data-id'); | ||
| $(inputObj).removeAttr('data-species'); | ||
| if (typeof setDirty != 'undefined' && $(inputObj).val() != taxonId) | ||
| setDirty($(inputObj).closest("tr").attr("id").substring(4), true); | ||
| $(inputObj).val(taxonId).attr('title', taxonId + '\n(Click to change selection)'); | ||
| return; | ||
| } | ||
|
|
||
| try { | ||
| var taxonDetails = getNcbiTaxonDetails(taxonId), taxonName = taxonDetails['scientificname'], genus = taxonDetails['genus'], species = taxonDetails['species']; | ||
| if (taxonName != null && taxonName != '') | ||
| $(inputObj).attr('data-id', taxonId); | ||
| if (species != null && species != '') | ||
| $(inputObj).attr('data-species', genus + " " + species); | ||
|
|
||
| if (typeof setDirty != 'undefined' && $(inputObj).val() != taxonId) | ||
| setDirty($(inputObj).closest("tr").attr("id").substring(4), true); | ||
| $(inputObj).val(taxonName).attr('title', taxonName + '\n(Click to change selection)'); | ||
| } | ||
| catch(error) { | ||
| alert("Unable to fetch NCBI taxon info for ID " + taxonId); | ||
| } | ||
| } | ||
|
|
||
| function customizeModuleList() { | ||
| let cell = $("#moduleTable thead th").filter(function() { | ||
| return $(this).text().trim() === "Category"; | ||
| }); | ||
|
|
||
| if (cell.length == 0) | ||
| return; | ||
|
|
||
| cell.text("Taxon"); | ||
| taxonCellIndex = cell.index() + 1; | ||
|
|
||
| $("#moduleTable tbody tr td:nth-child(" + taxonCellIndex + ")").each(function() { | ||
| updateTaxonCell(this); | ||
| }) | ||
| if ($("#moduleTable tbody tr td:nth-child(" + taxonCellIndex + ") input").length > 0) | ||
| cell.append('<span style="font-weight:normal; margin-left:50px; color:black;">Find NCBI IDs <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi" target="_blank"><img id="igvTooltip" style="cursor:pointer; cursor:hand;" src="../images/magnifier.gif" title="Click to find out taxon id. Specifying an id is preferred because it avoids typos."></a></span>'); | ||
| } | ||
|
|
||
| function updateTaxonCell(taxonCell) { | ||
| let idTaxonSpecies = $(taxonCell).text().split(":"), inputVal = idTaxonSpecies.length < 3 ? idTaxonSpecies[0] : (idTaxonSpecies[1] != '' ? idTaxonSpecies[1]: idTaxonSpecies[2]); | ||
| if (isAdmin || permissions.has($(taxonCell).parent().attr("id").substring(4) + "$" + supervisorRole)) { | ||
| $(taxonCell).html("<input type='text' readonly='true' value=\"" + inputVal + "\" data-id='" + idTaxonSpecies[0] + "' title='" + inputVal + "\n(Click to change selection)' />"); | ||
| $(taxonCell).find("input").css("width", "200px").css("font-style", "italic").css("text-align", "center").css("border", "none").css("background-color", "inherit !important").css("cursor", "pointer").on("click", function() { | ||
| grabNcbiTaxon($(this).get(), prompt("Please specify NCBI taxon, preferrably by ID\n(enter blank string to clear out)")); | ||
| }); | ||
| } | ||
| else | ||
| $(taxonCell).html("<i>" + inputVal + "</i>").css("background-color", "lightgrey"); | ||
| } | ||
|
|
||
| saveChanges = function(moduleName) { // override default function so we can account for the taxon field | ||
| let itemRow = $("#row_" + moduleName); | ||
| let setToPublic = itemRow.find(".flagCol1").prop("checked"); | ||
| let setToHidden = itemRow.find(".flagCol2").prop("checked"); | ||
| var taxonDetailsFieldContents = new Array(); | ||
| let taxonInput = itemRow.find("td:nth-child(" + taxonCellIndex + ") input"); | ||
| if (taxonInput.attr('data-id') != "") | ||
| { | ||
| taxonDetailsFieldContents.push(taxonInput.attr('data-id')); | ||
| taxonDetailsFieldContents.push(taxonInput.val() == taxonInput.attr('data-species') ? "" : taxonInput.val()); | ||
| taxonDetailsFieldContents.push(taxonInput.attr('data-species')); | ||
| } | ||
| $.getJSON(moduleDetailsURL, { module:moduleName,public:setToPublic,hidden:setToHidden,category:taxonDetailsFieldContents.join(":") }, function(updated){ | ||
| if (!updated) | ||
| alert("Unable to apply changes for " + moduleName); | ||
| else | ||
| { | ||
| moduleData[moduleName][modulePublicFieldName] = setToPublic; | ||
| moduleData[moduleName][moduleHiddenFieldName] = setToHidden; | ||
| setDirty(moduleName, false); | ||
| } | ||
| }).error(function(xhr) { handleError(xhr); }); | ||
| } | ||
|
|
||
| resetFlags = function(moduleName) { // override default function so we can account for the taxon field | ||
| let itemRow = $("#row_" + moduleName); | ||
| itemRow.find(".flagCol1").prop("checked", moduleData[moduleName][modulePublicFieldName]); | ||
| itemRow.find(".flagCol2").prop("checked", moduleData[moduleName][moduleHiddenFieldName]); | ||
| let taxonCell = itemRow.find("td:nth-child(" + taxonCellIndex + ")"); | ||
| taxonCell.text(moduleData[moduleName]["category"]); | ||
| updateTaxonCell(taxonCell.get()); | ||
| setDirty(moduleName, false); | ||
| } |