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Links to DB search and ID'd item in normalization
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@spyysalo
spyysalo committed Apr 24, 2012
1 parent 321cfb8 commit fe18bb3
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Showing 4 changed files with 93 additions and 24 deletions.
108 changes: 89 additions & 19 deletions client/src/annotator_ui.js
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,10 @@ var AnnotatorUI = (function($, window, undefined) {
// for double-click selection simulation hack
var lastDoubleClickedChunkId = null;

// for normalization: URLs bases by norm DB name
var normDbUrlByDbName = {};
var normDbUrlBaseByDbName = {};

that.user = null;
var svgElement = $(svg._svg);
var svgId = svgElement.parent().attr('id');
Expand Down Expand Up @@ -425,21 +429,24 @@ var AnnotatorUI = (function($, window, undefined) {
// fill normalizations (if any)
if (!reselectedSpan) {
// clear first
var $normid = $('#span_norm_id');
var $normtxt = $('#span_norm_txt');
$normid.val('');
$normid.removeClass('valid_value').removeClass('invalid_value');
$normtxt.val('');
clearNormalizationUI();

var $normId = $('#span_norm_id');
var $normText = $('#span_norm_txt');

// fill if found (NOTE: only shows last on multiple)
$.each(span ? span.normalizations : [], function(normNo, norm) {
// stored as array (sorry)
var refdb = norm[0], refid = norm[1], reftext = norm[2];
$normid.val(refid);
$normtxt.val(reftext);
$normId.val(refid);
$normText.val(reftext);
// just assume the ID is valid (TODO: check)
$normid.addClass('valid_value')
$normId.addClass('valid_value')
});

// update links
updateNormalizationRefLink();
updateNormalizationDbLink();
}

var showAttributesFor = function(attrTypes, type) {
Expand Down Expand Up @@ -618,9 +625,7 @@ var AnnotatorUI = (function($, window, undefined) {
$('#clear_notes_button').click(clearSpanNotes);

var clearSpanNorm = function(evt) {
$('#span_norm_id').val('');
$('#span_norm_id').removeClass('valid_value').removeClass('invalid_value');
$('#span_norm_txt').val('');
clearNormalizationUI();
}
$('#clear_norm_button').button();
$('#clear_norm_button').click(clearSpanNorm);
Expand All @@ -645,6 +650,14 @@ var AnnotatorUI = (function($, window, undefined) {
$('#span_norm_txt').val(response.value);
}

// on any change to the normalization DB, clear everything and
// update link
var spanNormDbUpdate = function(evt) {
clearNormalizationUI();
updateNormalizationDbLink();
}
$('#span_norm_db').change(spanNormDbUpdate);

// on any change to the normalization ID, update the text of the
// reference
var oldSpanNormIdValue = '';
Expand All @@ -653,9 +666,8 @@ var AnnotatorUI = (function($, window, undefined) {
var db = $('#span_norm_db').val();
if (key != oldSpanNormIdValue) {
if (key.match(/^\s*$/)) {
// don't query empties, just clear style and ref
$(this).removeClass('valid_value').removeClass('invalid_value');
$('#span_norm_txt').val('');
// don't query empties, just clear instead
clearNormalizationUI();
} else {
dispatcher.post('ajax', [ {
action: 'normGetName',
Expand Down Expand Up @@ -1427,9 +1439,12 @@ var AnnotatorUI = (function($, window, undefined) {
// fill in new
html = [];
$.each(norm_resources, function(normNo, norm) {
var norm_name = norm[0], norm_url = norm[1], norm_url_base = norm[2];
html.push('<option value="'+Util.escapeHTML(norm_name)+'">'+
Util.escapeHTML(norm_name)+'</option>');
var normName = norm[0], normUrl = norm[1], normUrlBase = norm[2];
html.push('<option value="'+Util.escapeHTML(normName)+'">'+
Util.escapeHTML(normName)+'</option>');
// remember the urls for updates
normDbUrlByDbName[normName] = normUrl;
normDbUrlBaseByDbName[normName] = normUrlBase;
});
$norm_select.html(html.join(''));
// if we have nothing, just hide the whole thing
Expand All @@ -1440,6 +1455,61 @@ var AnnotatorUI = (function($, window, undefined) {
}
}

// updates the reference link in the normalization UI according
// to the current value of the normalization DB and ID.
var updateNormalizationRefLink = function() {
var $normId = $('#span_norm_id');
var $normLink = $('#span_norm_ref_link');
var normId = $normId.val();
if (!normId || normId.match(/^\s*$/)) {
$normLink.hide();
} else {
var $normDb = $('#span_norm_db');
var normDb = $normDb.val();
var base = normDbUrlBaseByDbName[normDb];
// assume hidden unless everything goes through
$normLink.hide();
if (!base) {
dispatcher.post('messages', [[['No base URL for '+normDb, 'error']]]);
} else if (base.indexOf('%s') == -1) {
dispatcher.post('messages', [[['Base URL "'+base+'" for '+normDb+' does not contain "%s"', 'error']]]);
} else {
// TODO: protect against strange chars in ID
link = base.replace('%s', normId);
$normLink.attr('href', link);
$normLink.show();
}
}
}

// updates the DB search link in the normalization UI according
// to the current value of the normalization DB.
var updateNormalizationDbLink = function() {
var $dbLink = $('#span_norm_db_link');
var $normDb = $('#span_norm_db');
var normDb = $normDb.val();
var link = normDbUrlByDbName[normDb];
if (!link || link.match(/^\s*$/)) {
dispatcher.post('messages', [[['No URL for '+normDb, 'error']]]);
$dbLink.hide();
} else {
// TODO: protect against weirdness in DB link
$dbLink.attr('href', link);
$dbLink.show();
}
}

// resets all normalization-related UI elements to a blank
// state
var clearNormalizationUI = function() {
var $normId = $('#span_norm_id');
var $normText = $('#span_norm_txt');
$normId.val('');
$normId.removeClass('valid_value').removeClass('invalid_value');
$normText.val('');
updateNormalizationRefLink();
}

var spanAndAttributeTypesLoaded = function(_spanTypes,
_entityAttributeTypes,
_eventAttributeTypes,
Expand Down Expand Up @@ -1642,10 +1712,10 @@ var AnnotatorUI = (function($, window, undefined) {
var normalizations = [];
var normDb = $('#span_norm_db').val();
var normId = $('#span_norm_id').val();
var normTxt = $('#span_norm_txt').val();
var normText = $('#span_norm_txt').val();
// empty ID -> no normalization
if (!normId.match(/^\s*$/)) {
normalizations.push([normDb, normId, normTxt]);
normalizations.push([normDb, normId, normText]);
}
spanOptions.normalizations = $.toJSON(normalizations);

Expand Down
9 changes: 4 additions & 5 deletions index.xhtml
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Original file line number Diff line number Diff line change
Expand Up @@ -566,16 +566,15 @@
<fieldset id="norm_fieldset">
<legend>Normalization</legend>
<div id="norm_container">
<select id="span_norm_db">
<option value="UniProt">UniProt</option>
<option value="FMA">FMA</option>
</select>
<select id="span_norm_db"/>
<a id="span_norm_db_link" target="brat_linked" href="#" title="Search DB"><img src="static/img/Fugue-shadowless-magnifier.png" style="vertical-align: middle"/></a>
<span class="span_norm_label">ID:</span>
<input id="span_norm_id" class="span_norm_id_input"
style="width:20%"/>
<span class="span_norm_label">Ref:</span>
<input id="span_norm_txt" class="span_norm_txt_input"
readonly="readonly" style="width:50%"/>
readonly="readonly" style="width:45%"/>
<a id="span_norm_ref_link" target="brat_linked" href="#" title="See in DB"><img src="static/img/Fugue-shadowless-external.png" style="vertical-align: middle"/></a>
<input id="clear_norm_button" type="button"
value="&#x2715;" title="Clear normalization"/>
</div>
Expand Down
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