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Plugin module containing SORTA (system for ontology-based re-coding and technical
annotation)
plugins.
(function ($, molgenis, w) {
"use strict";
var restApi = new molgenis.RestClient();
var nrItemsPerPage = 10;
molgenis.getTotalNumberOfItems = function (dataSetId) {
var number = 0;
var request = {
'dataSetId': dataSetId,
'query': {
'pageSize': 100000,
}
};
$.ajax({
type: 'POST',
url: molgenis.adaptContextUrl() + '/allattributes',
async: false,
data: JSON.stringify(request),
contentType: 'application/json',
success: function (data) {
number = data.searchHits.length;
}
});
return number;
};
molgenis.createMatrixForDataItems = function (options) {
var request = {
'dataSetId': options.dataSetId,
'queryString': options.queryText,
'query': {
'offset': options.page ? options.page.start : 0,
'pageSize': nrItemsPerPage,
'sort': options.sortRule
}
};
$.ajax({
type: 'POST',
url: molgenis.adaptContextUrl() + '/allattributes',
async: false,
data: JSON.stringify(request),
contentType: 'application/json',
success: function (data, textStatus, request) {
if (data.searchHits) {
var searchHits = data.searchHits;
var table = $('
').addClass('table table-bordered');
options.container.find('table').remove();
options.container.prepend(table);
var body = $('');
table.append(createTableHeader(options)).append(body);
if (options.createTableRow === undefined || options.createTableRow === null) {
options.createTableRow = createTableRow;
}
$.each(searchHits, function () {
$(options.createTableRow($(this)[0]['columnValueMap'], table)).appendTo(body);
});
initPager(options, data.totalHitCount);
} else {
molgenis.createAlert([{'message': 'There is no dataset available!'}], 'warning', $('#wizardForm'));
}
}
});
function initPager(options, totalHitCount) {
if (options.updatePager || options.container.find('#pager-' + options.dataSetId).length === 0) {
options.updatePager = false;
var tablePager = $('').attr('id', 'pager-' + options.dataSetId);
options.container.find('.pagination').parents('div:eq(1)').remove();
options.container.append(tablePager);
tablePager.pager({
'nrItems': totalHitCount,
'nrItemsPerPage': nrItemsPerPage,
'onPageChange': function (page) {
options.page = page;
molgenis.createMatrixForDataItems(options);
}
});
}
}
function createTableHeader(options) {
var headerRow = $('' + options.tableHeaders[0] + ' ').css('width', firstColumnWidth + '%').appendTo(headerRow);
if (options.sortRule) {
if (options.sortRule.orders[0].direction == 'ASC') {
$('').appendTo(firstColumn);
} else {
$('').appendTo(firstColumn);
}
} else {
$('').appendTo(firstColumn);
}
var columnWidth = (100 - firstColumnWidth) / options.tableHeaders.length;
$.each(options.tableHeaders, function (index, eachHeader) {
if (index > 0) {
$('Message : ');
items.push('Other user is currently running BiobankConnect using the same account, please be patient or login as another user! ');
$('#wizardForm').html(items.join(''));
setTimeout(function () {
molgenis.ontologyMatcherRunning(callback);
}, 5000);
} else {
var childElements = $('#wizardForm').data('childElements');
$('#wizardForm').data('childElements', null);
if (childElements !== null && childElements !== undefined) $('#wizardForm').empty().append(childElements);
$('ul.pager a').on('click', function (e) {
e.preventDefault();
if (!$(this).parent().hasClass('disabled')) {
$('#wizardForm').attr('action', $(this).attr('href')).submit();
}
return false;
});
if (callback !== undefined && callback !== null) {
callback();
}
}
}
});
};
molgenis.getFeatureFromIndex = function (feature, callback) {
$.ajax({
type: 'POST',
url: molgenis.adaptContextUrl() + '/attribute',
async: false,
data: JSON.stringify(molgenis.hrefToId(feature.href)),
contentType: 'application/json',
success: function (data, textStatus, request) {
$.each(data.searchHits, function (index, hit) {
callback(hit);
return false;
});
}
});
};
molgenis.dataItemsTypeahead = function (dataSetId, query, response, approximate) {
$.ajax({
type: 'POST',
url: molgenis.adaptContextUrl() + '/allattributes',
async: false,
data: JSON.stringify({
'dataSetId': dataSetId,
'queryString': query,
'approximate': (approximate !== undefined && approximate !== null)
}),
contentType: 'application/json',
success: function (data, textStatus, request) {
var result = [];
$.each(data.searchHits, function (index, hit) {
var value = hit.columnValueMap.name;
if ($.inArray(value, result) === -1) {
result.push(hit.columnValueMap);
}
});
response(result);
}
});
};
molgenis.ontologyTermTypeahead = function (field, query, response) {
$.ajax({
type: 'POST',
url: molgenis.adaptContextUrl() + '/ontologyterm',
async: false,
data: JSON.stringify({'queryString': query}),
contentType: 'application/json',
success: function (data, textStatus, request) {
var results = [];
var uniqueOntologyTerms = [];
$.each(data.searchHits, function (index, hit) {
var ontologyName = hit.columnValueMap.ontologyName;
var ontologyTermSynonym = hit.columnValueMap.ontologyTermSynonym;
var identifier = ontologyName === '' ? ontologyTermSynonym : ontologyName + ':' + ontologyTermSynonym;
hit.columnValueMap.identifier = identifier;
if ($.inArray(identifier, uniqueOntologyTerms) === -1) {
uniqueOntologyTerms.push(identifier);
results.push(hit.columnValueMap);
}
});
response(results);
}
});
};
molgenis.adaptContextUrl = function () {
return molgenis.getContextUrl().replace(/biobankconnect$/g, "algorithm");
};
$(function () {
var buttonGroup = $('.bwizard-buttons');
$('#wizardForm').prepend(buttonGroup);
buttonGroup.before('');
$('.wizard-page').removeClass('well');
$('div.wizard-page').css('min-height', 300);
$(document).keyup(function (e) {
if (e.which == 27) {
$('div.modal').modal('hide');
}
});
});
}($, window.top.molgenis = window.top.molgenis || {}, window.top));