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(function ($, molgenis) {
"use strict";
/**
* Generate an algorithm based on category selections
*
* @param mappedCategoryIds
* a list of category identifiers
* @param attribute
* the source attribute
* @param defaultValue
* The value used as a default value
* @param nullValue
* The value used for missing
*/
function generateAlgorithm(mappedCategoryIds, attribute, defaultValue, nullValue) {
var algorithm;
if (nullValue !== undefined) {
algorithm = "$('" + attribute + "').map(" + JSON.stringify(mappedCategoryIds) + ", " + JSON.stringify(defaultValue) + ", " + JSON.stringify(nullValue)
+ ").value();";
} else if (defaultValue !== undefined) {
algorithm = "$('" + attribute + "').map(" + JSON.stringify(mappedCategoryIds) + ", " + JSON.stringify(defaultValue) + ").value();";
} else {
algorithm = "$('" + attribute + "').map(" + JSON.stringify(mappedCategoryIds) + ").value();";
}
return algorithm;
}
/**
* Searches the source attributes in an algorithm string.
*
* @param algorithm
* the algorithm string to search
*/
function getSourceAttrs(algorithm) {
var regex = /\$\(['"]([^\$\(\)]+)['"]\)/g, match, result = [];
while ((match = regex.exec(algorithm))) {
if (match) {
result.push(match[1]);
}
}
return result;
}
var timeoutId, isValidating;
/**
* Validate algorithm on source entities, render UI component that displays
* the number of total/success/errors and corresponding error messages.
* Stops after a max. number of validation errors.
*/
function validateAttrMapping(algorithm) {
var validationDelay = 2000;
var validationBatchSize = 500;
var validationMaxErrors = 100;
isValidating = false;
if (timeoutId) {
clearTimeout(timeoutId);
}
$('#mapping-validation-container').html('Pending ...');
$('#validation-error-messages-table-body').empty();
timeoutId = setTimeout(
function () {
isValidating = true;
var request = {
targetEntityName: $('#target').val(),
sourceEntityName: $('#source').val(),
targetAttributeName: $('#targetAttribute').val(),
algorithm: algorithm,
depth: parseInt($('#depth').val(), 10)
};
var items = [];
items.push(' ');
items.push('Total: ? ');
items.push('Success: 0 ');
items
.push('Errors: 0 ');
items.push('(Validation aborted, encountered too many errors)');
$('#mapping-validation-container').html(items.join(''));
validateAttrMappingRec(request, 0, validationBatchSize, 0, 0, validationMaxErrors);
}, validationDelay);
}
function validateAttrMappingRec(request, offset, num, nrSuccess, nrErrors, validationMaxErrors) {
$.ajax({
type: 'POST',
url: molgenis.getContextUrl() + '/validateAttrMapping',
data: JSON.stringify(_.extend({}, request, {
offset: offset,
num: num
})),
showSpinner: false,
contentType: 'application/json'
}).done(function (data) {
nrSuccess += data.nrSuccess;
nrErrors += data.nrErrors;
if (offset + num >= data.total || nrErrors >= validationMaxErrors) {
$('#validation-spinner').hide();
}
$('#validation-total').html(data.total);
$('#validation-success').html(nrSuccess);
$('#validation-errors').html(nrErrors);
if (nrErrors > 0) {
_.each(data.errorMessages, function (message, id) {
$('#validation-error-messages-table-body').append('
' + id + '
' + message + '
');
});
}
if (nrErrors >= validationMaxErrors) {
$('#max-errors-msg').removeClass('hidden');
return;
}
if (offset + num < data.total) {
if (isValidating) {
validateAttrMappingRec(request, offset + num, num, nrSuccess, nrErrors, validationMaxErrors);
} else {
$('#mapping-validation-container').html('Pending ...');
}
}
});
}
/**
* Load result table from view-attribute-mapping-feedback.ftl
*
* @param algorithm
* the algorithm that is send to the server to apply over the
* submitted source values
*/
function loadAlgorithmResult(algorithm) {
$("#result-table-container").load("attributemappingfeedback #algorithm-result-feedback-container", {
mappingProjectId: $('#mappingProjectId').val(),
target: $('#target').val(),
source: $('#source').val(),
targetAttribute: $('#targetAttribute').val(),
algorithm: algorithm
}, function () {
$('.show-error-message').on('click', function () {
$('#algorithm-error-message-container').html($(this).data('message'));
});
});
}
/**
* Load mapping table from view-advanced-mapping-editor.ftl
*
* @param algorithm
* The algorithm to set presets when opening the editor a second
* time
*/
function loadMappingEditor(algorithm) {
if (algorithm) {
$("#advanced-mapping-table").load("advancedmappingeditor #advanced-mapping-editor", {
mappingProjectId: $('#mappingProjectId').val(),
target: $('#target').val(),
source: $('#source').val(),
targetAttribute: $('#targetAttribute').val(),
sourceAttribute: getSourceAttrs(algorithm)[0],
depth: parseInt($('#depth').val(), 10),
algorithm: algorithm
});
}
}
/**
* Selects the attributes mentioned in the algorithm
*
* @param algorithm
* the algorithm string
*/
function checkSelectedAttributes(algorithm) {
var sourceAttrs = getSourceAttrs(algorithm);
$('input:checkbox').each(function (index, value) {
var name = $(this).data('attribute-name'), inArray = $.inArray(name, sourceAttrs);
$(this).prop('checked', inArray >= 0);
});
}
/**
* Move suggested attributes to the top of the attribute table
*/
function createAttributeTable(explainedAttributes, resultTable, dataExplorerUri) {
//Remove the existing content of the result table
resultTable.empty();
//Add the header to the result table
resultTable.append('
Select
Attribute label
Name
');
if (explainedAttributes != null) {
var tbody = $('').appendTo(resultTable);
var counter = 0;
$.each(explainedAttributes, function (index, explainedAttribute) {
var attribute = explainedAttribute.attribute;
var explainedQueryStrings = explainedAttribute.explainedQueryStrings;
var row = $('
');
row.append(attributeInfo.join('')).appendTo(tbody);
if (counter < 10) {
if (explainedQueryStrings.length > 0) {
var matchedWords = [];
var attributeInfoElement = $(row).find('td.source-attribute-information');
var attributeLabel = attribute.label;
//Create a detailed explanation popover to show how the attributes get matched
createPopoverExplanation(row, attributeInfoElement, attributeLabel, explainedQueryStrings);
//Collect all matched words from all explanations
$.each(explainedQueryStrings, function (index, explainedQueryString) {
var matchedWordsFromOneExplanation = extendPartialWord(attributeLabel, explainedQueryString.matchedWords.split(' '));
$.each(matchedWordsFromOneExplanation, function (index, element) {
matchedWords.push(element);
});
});
//Connect matched words and highlight them together
$.each(connectNeighboredWords(attributeLabel, matchedWords), function (index, word) {
$(attributeInfoElement).highlight(word);
});
}
}
counter++;
});
checkSelectedAttributes(getAceEditor().getSession().getValue());
}
updateSearchResultMessage();
bindTableCheckBoxesEvents();
}
function updateSearchResultMessage() {
//Update the search result message above the table
var numberOfVisibleAttributes = $('#attribute-mapping-table>tbody tr:visible').length;
var totalNumberOfAttributes = $('#sourceAttributeSize').val();
$('#attribute-search-result-message').empty().append(numberOfVisibleAttributes + ' attributes have been found out of ' + totalNumberOfAttributes);
// hide/show the header of the table depending on whether or not there are any visiable attributes
if (numberOfVisibleAttributes == 0) {
$('#attribute-mapping-table>thead tr').hide();
} else {
$('#attribute-mapping-table>thead tr').show();
}
}
function getAceEditor() {
var $textarea = $("#ace-editor-text-area");
if (!$textarea.data('ace')) {
// create ace editor
$textarea.ace({
options: {
enableBasicAutocompletion: true
},
readOnly: $textarea.data('readonly') === true,
theme: 'eclipse',
mode: 'javascript',
showGutter: true,
highlightActiveLine: true
});
}
return $textarea.data('ace').editor;
}
function bindTableCheckBoxesEvents() {
// on load use algorithm to set selected attributes and editor value
var editor = getAceEditor();
checkSelectedAttributes(editor.getSession().getValue());
$('#attribute-mapping-table :checkbox').on('change', function () {
var selectedAttributes = [];
$('#attribute-mapping-table :checkbox:checked').each(function () {
selectedAttributes.push($(this).data('attribute-name'));
});
var algorithm = editor.getSession().getValue();
var generateAlgorithmRequest = {
'targetEntityTypeId': $('[name="target"]').val(),
'sourceEntityTypeId': $('[name="source"]').val(),
'targetAttributeName': $('[name="targetAttribute"]').val(),
'sourceAttributes': selectedAttributes
};
$.ajax({
type: 'POST',
url: molgenis.getContextUrl() + '/attributemapping/algorithm',
data: JSON.stringify(generateAlgorithmRequest),
contentType: 'application/json',
success: function (generatedAlgorithm) {
// If the generated algorithm is empty
if (selectedAttributes.length === 0) {
$('#result-container').css('display', 'none');
$('.nav-tabs a[href=\\#script]').tab('show');
$('#map-tab').hide();
} else {
// on selection of an attribute, show all fields
$('#result-container').css('display', 'inline');
}
// generate result table
editor.getSession().setValue(generatedAlgorithm);
loadAlgorithmResult(generatedAlgorithm);
// generate mapping editor if target attribute is an xref or
// categorical
var targetAttributeDataType = $('input[name="targetAttributeType"]').val();
if (targetAttributeDataType === 'xref' || targetAttributeDataType === 'categorical') {
loadMappingEditor(generatedAlgorithm);
$('#map-tab').show();
}
}
});
});
}
/**
* Create a boostrap popover message to show the explanation
*/
function createPopoverExplanation(row, attributeInfoElement, attributeLabel, explainedQueryStrings) {
if (explainedQueryStrings.length > 0) {
var message = '', matchedWords, queryString, score;
$.each(explainedQueryStrings, function (index, explainedQueryString) {
matchedWords = extendPartialWord(attributeLabel, explainedQueryString.matchedWords.split(' '));
queryString = explainedQueryString.queryString;
score = explainedQueryString.score;
message += 'The query ' + queryString + ' derived from ' + explainedQueryString.tagName;
message += ' is matched to the label on words ' + matchedWords.join(' ').toLowerCase() + ' with ' + score + '%
';
});
var option = {
'title': 'Explanation',
'content': message,
'html': true,
'placement': 'top',
'container': row,
'trigger': 'hover'
};
$(attributeInfoElement).popover(option);
}
}
/**
* connect the matched words that are neighbors in order to highlight them together
* TODO : move these string operation related methods to the server
*/
function connectNeighboredWords(attributeLabel, matchedWords) {
var connectedPhrases = [], connectedPhrase, potentialConnectedPhrase, orderedMatchedWords;
if (attributeLabel && matchedWords && matchedWords.length > 0) {
attributeLabel = attributeLabel.toUpperCase();
//Order the matched words
orderedMatchedWords = orderMatchedWords(attributeLabel, matchedWords);
if (orderedMatchedWords.length > 0) {
//Algorithm to connect the words that are sitting next each other
connectedPhrase = orderedMatchedWords[0];
for (var i = 1; i < orderedMatchedWords.length; i++) {
//Try to connect the next matched words with previous one
potentialConnectedPhrase = connectedPhrase + ' ' + orderedMatchedWords[i];
//See if the connected phrase can be found in the label string
if (attributeLabel.indexOf(potentialConnectedPhrase) !== -1) {
connectedPhrase = connectedPhrase + ' ' + orderedMatchedWords[i];
} else {
connectedPhrases.push(connectedPhrase.trim());
connectedPhrase = orderedMatchedWords[i];
}
}
//Push the leftover phrase to the list
if (connectedPhrase.length > 0) {
connectedPhrases.push(connectedPhrase);
}
}
}
return connectedPhrases;
}
/**
* Order the matched the words according to the order of words in the attribute label
*/
function orderMatchedWords(attributeLabel, matchedWords) {
var hash = {}, orderedMatchedWords = [], wordIndices = [];
$.each(matchedWords, function (index, matchedWord) {
var index = attributeLabel.indexOf(matchedWord);
hash[index] = matchedWord;
wordIndices.push(index);
});
wordIndices.sort(function (a, b) {
return a - b;
});
$.each(wordIndices, function (i, wordIndex) {
if (hash[wordIndex]) {
orderedMatchedWords.push(hash[wordIndex]);
}
});
return orderedMatchedWords;
}
/**
* Explain API provides stemmed words, this method finds the 'original' word in the attribute label based the stemmed word.
*/
function extendPartialWord(attributeLabel, partialWords) {
var completeWords = [];
if (attributeLabel && partialWords && partialWords.length > 0) {
$.each(partialWords, function (index, partialWord) {
if (partialWord.length > 2) {
attributeLabel = attributeLabel.toUpperCase();
partialWord = partialWord.toUpperCase();
var startIndex = attributeLabel.indexOf(partialWord);
while (startIndex == -1 && partialWord.length > 0) {
partialWord = partialWord.substring(0, partialWord.length - 1);
startIndex = attributeLabel.indexOf(partialWord);
}
if (startIndex != -1) {
var endIndex = startIndex + partialWord.length;
while (attributeLabel.length > endIndex && attributeLabel.charAt(endIndex).match(/[A-Z0-9]/i)) {
endIndex++;
}
completeWords.push(attributeLabel.substring(startIndex, endIndex));
} else {
completeWords.push(partialWord)
}
}
});
}
return completeWords;
}
//A helper function to perform post-redirect action
function redirect(method, url, data) {
showSpinner();
var form = '';
if (data) {
$.each(data, function (key, value) {
form += '';
});
}
$('').appendTo('body').submit();
}
function saveAttributeMapping(algorithm, algorithmState) {
$.post(molgenis.getContextUrl() + "/saveattributemapping", {
mappingProjectId: $('#mappingProjectId').val(),
target: $('#target').val(),
source: $('#source').val(),
targetAttribute: $('#targetAttribute').val(),
algorithm: algorithm,
algorithmState: algorithmState
},
function (data) {
$('#algorithmState').empty().html(algorithmState);
molgenis.createAlert([{message: 'This attribute mapping is saved with the state ' + algorithmState}], 'success');
dislpayFindFirstNotCuratedAttributeMappingButton();
}
).fail(function () {
$('.alerts').empty();
molgenis.createAlert([{message: 'Error trying to save the attribuet mapping'}], 'error');
});
}
/**
* The button only appears when there is a attribute to curate that has no status Discuss or Curated
* find first not curated attribute mapping (Not curated and not to be discussed)
* If the data is unknown or similar to the displaed attribute mapping the the button will not be shown
*/
function dislpayFindFirstNotCuratedAttributeMappingButton() {
$.post(molgenis.getContextUrl() + "/firstattributemapping", {
mappingProjectId: $('#mappingProjectId').val(),
target: $('#target').val(),
'skipAlgorithmStates': ['DISCUSS', 'CURATED']
}, function (data) {
$('#find-first-to-curate-attribute-btn').remove();
if (data.length !== 0 && ($('#targetAttribute').val() !== data.targetAttribute || $('#source').val() !== data.source)) {
$('#attribute-mapping-toolbar').append($(''));
$('#find-first-to-curate-attribute-btn').on('click', function () {
redirect('get', molgenis.getContextUrl() + '/attributeMapping', data);
});
}
});
}
/**
* When the save buttons: 'save curated' and 'save to discuss' are clicked the algorithm must be filled in.
*/
function disableEnableSaveButtons(algorithm) {
if (null != algorithm && algorithm.length > 0) {
$('#save-mapping-btn').prop('disabled', false);
$('#save-discuss-mapping-btn').prop('disabled', false);
} else {
$('#save-mapping-btn').prop('disabled', true);
$('#save-discuss-mapping-btn').prop('disabled', true);
}
}
/**
* Get the relevant attributes
*
* searchTerms
* if empty uses tags
* if not empty uses key words
*/
function findRelevantAttributes(requestBody, resultTable, dataExplorerUri) {
requestBody["searchTerms"] = $('#attribute-search-field').val();
$.ajax({
type: 'POST',
url: molgenis.getContextUrl() + '/attributeMapping/semanticsearch',
data: JSON.stringify(requestBody),
contentType: 'application/json',
success: function (relevantAttributes) {
createAttributeTable(relevantAttributes, resultTable, dataExplorerUri);
}
});
}
$(function () {
// Initialize all variables
var aceEditor, algorithm, requestBody = {
'mappingProjectId': $('[name="mappingProjectId"]').val(),
'target': $('[name="target"]').val(),
'source': $('[name="source"]').val(),
'targetAttribute': $('[name="targetAttribute"]').val(),
'searchTerms': ""
}, explainedAttributes, attributes = [];
$('#validate-algorithm-btn').on('click', function () {
var algorithm = $("#ace-editor-text-area").data('ace').editor.getSession().getValue();
// check attributes if manually added
checkSelectedAttributes(algorithm);
// update save buttons visibility
disableEnableSaveButtons(algorithm);
// validate mapping
validateAttrMapping(algorithm);
// preview mapping results
loadAlgorithmResult(algorithm);
// Show the result container
$('#result-container').css('display', 'inline');
});
// tooltip placement
$("[rel=tooltip]").tooltip({
placement: 'right'
});
$('.ontologytag-tooltip').css({'cursor': 'pointer'}).popover({
'html': true,
'placement': 'right',
'trigger': 'hover'
});
findRelevantAttributes(requestBody, $('#attribute-mapping-table'), $('#dataExplorerUri').val());
aceEditor = getAceEditor();
algorithm = aceEditor.getSession().getValue();
// if there is an algorithm present on load, show the result table
if (algorithm.trim()) {
loadAlgorithmResult(algorithm);
} else {
// if no algorithm is present hide the result container
$('#result-container').css('display', 'none');
}
// save button for saving generated mapping
$('#save-mapping-btn').on('click', function () {
saveAttributeMapping(aceEditor.getSession().getValue(), "CURATED")
});
// save button for discuss status generated mapping
$('#save-discuss-mapping-btn').on('click', function () {
saveAttributeMapping(aceEditor.getSession().getValue(), "DISCUSS")
});
// Update save buttons visibility
disableEnableSaveButtons(algorithm);
// Display next button
dislpayFindFirstNotCuratedAttributeMappingButton();
$('#js-function-modal-btn').on('click', function () {
$('#js-function-modal').modal('show');
});
// Using the semantic search functionality from the server
$('#attribute-search-field-button').on('click', function (e) {
findRelevantAttributes(requestBody, $('#attribute-mapping-table'), $('#dataExplorerUri').val());
});
// Bind keydown and keyup event to the textField to prevend the form from being submitted
$('#attribute-search-field').keydown(function (event) {
if (event.keyCode === 13) {
event.preventDefault();
$('#attribute-search-field-button').trigger('click');
return false;
}
}).keyup(function () {
if ($(this).val() === '') {
$('#attribute-search-field-button').trigger('click');
}
});
// when the map tab is selected, load its contents
// loading on page load will fail because bootstrap tab blocks it
$('a[href=\\#map]').on('shown.bs.tab', function () {
loadMappingEditor(aceEditor.getSession().getValue());
});
$('a[href=\\#script]').on('shown.bs.tab', function () {
// when users switch back to the script tab, the value in the editor is not updated
// until the editor is clicked. A workaround is to move the page by calling the method to
// flush the changes.
aceEditor.scrollPageDown();
});
$('#advanced-mapping-table').on('change', function () {
var mappedCategoryIds = {}, defaultValue = undefined, nullValue = undefined, key, val;
// for each source xref value, check which target xref value
// was chosen
$('#advanced-mapping-table > tbody > tr').each(function () {
key = $(this).attr('id');
val = $(this).find('option:selected').val();
if (key === 'nullValue') {
if (val !== 'use-default-option') {
if (val === 'use-null-value') {
nullValue = null;
} else {
nullValue = val;
}
}
} else {
if (val !== 'use-default-option') {
if (val === 'use-null-value') {
mappedCategoryIds[$(this).attr('id')] = null;
} else {
mappedCategoryIds[$(this).attr('id')] = val;
}
}
}
});
if (nullValue !== undefined) {
defaultValue = null;
}
if ($('#default-value').is(":visible")) {
defaultValue = $('#default-value').find('option:selected').val();
if (defaultValue === 'use-null-value') {
defaultValue = null;
}
}
var categoricalAlgorithm = generateAlgorithm(mappedCategoryIds, $('input[name="sourceAttribute"]').val(), defaultValue, nullValue);
getAceEditor().setValue(categoricalAlgorithm);
loadAlgorithmResult(categoricalAlgorithm);
});
});
}($, window.top.molgenis = window.top.molgenis || {}));
');
items.push('Total: ? ');
items.push('Success: 0 ');
items
.push('Errors: 0 ');
items.push('(Validation aborted, encountered too many errors)');
$('#mapping-validation-container').html(items.join(''));
validateAttrMappingRec(request, 0, validationBatchSize, 0, 0, validationMaxErrors);
}, validationDelay);
}
function validateAttrMappingRec(request, offset, num, nrSuccess, nrErrors, validationMaxErrors) {
$.ajax({
type: 'POST',
url: molgenis.getContextUrl() + '/validateAttrMapping',
data: JSON.stringify(_.extend({}, request, {
offset: offset,
num: num
})),
showSpinner: false,
contentType: 'application/json'
}).done(function (data) {
nrSuccess += data.nrSuccess;
nrErrors += data.nrErrors;
if (offset + num >= data.total || nrErrors >= validationMaxErrors) {
$('#validation-spinner').hide();
}
$('#validation-total').html(data.total);
$('#validation-success').html(nrSuccess);
$('#validation-errors').html(nrErrors);
if (nrErrors > 0) {
_.each(data.errorMessages, function (message, id) {
$('#validation-error-messages-table-body').append('