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morpheus.js
Commit c2db34e2 authored by Joshua Gould's avatar Joshua Gould
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quote terms

parent 7a4eca6e
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Showing with 81 additions and 71 deletions
src/matrix/metadata_util.js
View file @ c2db34e2
morpheus.MetadataUtil = function() {
morpheus.MetadataUtil = function () {
};
morpheus.MetadataUtil.renameFields = function(dataset, options) {
_.each(options.rows, function(item) {
morpheus.MetadataUtil.renameFields = function (dataset, options) {
_.each(options.rows, function (item) {
if (item.renameTo) {
var v = dataset.getRowMetadata().getByName(item.field);
if (v) {
......@@ -10,7 +10,7 @@ morpheus.MetadataUtil.renameFields = function(dataset, options) {
}
}
});
_.each(options.columns, function(item) {
_.each(options.columns, function (item) {
if (item.renameTo) {
var v = dataset.getColumnMetadata().getByName(item.field);
if (v) {
......@@ -29,15 +29,15 @@ morpheus.MetadataUtil.renameFields = function(dataset, options) {
* Whether to search columns
* @param options.defaultMatchMode
* 'exact' or 'contains'
*
*
*/
morpheus.MetadataUtil.search = function(options) {
morpheus.MetadataUtil.search = function (options) {
var model = options.model;
var text = options.text;
var isColumns = options.isColumns;
text = $.trim(text);
if (text === '') {
return null;
return null;
}
var tokens = morpheus.Util.getAutocompleteTokens(text);
if (tokens.length == 0) {
......@@ -47,9 +47,9 @@ morpheus.MetadataUtil.search = function(options) {
var fieldNames = morpheus.MetadataUtil.getMetadataNames(model);
fieldNames.push(indexField);
var predicates = morpheus.Util.createSearchPredicates({
tokens : tokens,
fields : fieldNames,
defaultMatchMode : options.defaultMatchMode
tokens: tokens,
fields: fieldNames,
defaultMatchMode: options.defaultMatchMode
});
var vectors = [];
var nameToVector = new morpheus.Map();
......@@ -57,9 +57,9 @@ morpheus.MetadataUtil.search = function(options) {
var v = model.get(j);
var dataType = morpheus.VectorUtil.getDataType(v);
var wrapper = {
vector : v,
dataType : dataType,
isArray : dataType.indexOf('[') === 0
vector: v,
dataType: dataType,
isArray: dataType.indexOf('[') === 0
};
nameToVector.set(v.getName(), wrapper);
vectors.push(wrapper);
......@@ -135,18 +135,18 @@ morpheus.MetadataUtil.search = function(options) {
return indices;
};
morpheus.MetadataUtil.shallowCopy = function(model) {
morpheus.MetadataUtil.shallowCopy = function (model) {
var copy = new morpheus.MetadataModel(model.getItemCount());
for (var i = 0; i < model.getMetadataCount(); i++) {
var v = model.get(i);
// copy properties b/c they can be modified via ui
var newVector = new morpheus.VectorAdapter(v);
newVector.properties = new morpheus.Map();
newVector.getProperties = function() {
newVector.getProperties = function () {
return this.properties;
};
v.getProperties().forEach(function(val, key) {
v.getProperties().forEach(function (val, key) {
if (!morpheus.VectorKeys.COPY_IGNORE.has(key)) {
newVector.properties.set(key, val);
}
......@@ -157,14 +157,14 @@ morpheus.MetadataUtil.shallowCopy = function(model) {
}
return copy;
};
morpheus.MetadataUtil.autocomplete = function(model) {
return function(tokens, cb) {
morpheus.MetadataUtil.autocomplete = function (model) {
return function (tokens, cb) {
// check for term:searchText
var matches = [];
var regex = null;
var searchModel = model;
var token = tokens != null && tokens.length > 0 ? tokens[tokens.selectionStartIndex]
: '';
: '';
token = $.trim(token);
try {
if (token !== '') {
......@@ -174,17 +174,17 @@ morpheus.MetadataUtil.autocomplete = function(model) {
if (token.charCodeAt(semi - 1) !== 92) { // \:
var possibleField = $.trim(token.substring(0, semi));
if (possibleField.length > 0
&& possibleField[0] === '"'
&& possibleField[token.length - 1] === '"') {
&& possibleField[0] === '"'
&& possibleField[token.length - 1] === '"') {
possibleField = possibleField.substring(1,
possibleField.length - 1);
possibleField.length - 1);
}
var index = morpheus.MetadataUtil.indexOf(searchModel,
possibleField);
possibleField);
if (index !== -1) {
token = $.trim(token.substring(semi + 1));
searchModel = new morpheus.MetadataModelColumnView(
model, [ index ]);
model, [index]);
}
}
......@@ -219,8 +219,8 @@ morpheus.MetadataUtil.autocomplete = function(model) {
if (val != null) {
if (isArray[j]) {
for (var k = 0; k < val.length; k++) {
var id = new morpheus.Identifier([ val[k],
v.getName() ]);
var id = new morpheus.Identifier([val[k],
v.getName()]);
if (!set.has(id) && regex.test(val[k])) {
set.add(id);
if (set.size() === max) {
......@@ -229,8 +229,8 @@ morpheus.MetadataUtil.autocomplete = function(model) {
}
}
} else {
var id = new morpheus.Identifier([ val,
v.getName() ]);
var id = new morpheus.Identifier([val,
v.getName()]);
if (!set.has(id) && regex.test(val)) {
set.add(id);
if (set.size() === max) {
......@@ -243,16 +243,24 @@ morpheus.MetadataUtil.autocomplete = function(model) {
}
}
set.forEach(function(id) {
set.forEach(function (id) {
var array = id.getArray();
var field = array[1];
var val = array[0];
var quotedField = field;
if (quotedField.indexOf(' ') !== -1) {
quotedField = '"' + quotedField + '"';
}
var quotedValue = val;
if (quotedValue.indexOf(' ') !== -1) {
quotedValue = '"' + quotedValue + '"';
}
matches.push({
value : field + ':' + val,
label : '<span style="font-weight:300;">' + field
+ ':</span>'
+ '<span style="font-weight:900;">' + val
+ '</span>'
value: quotedField + ':' + quotedValue,
label: '<span style="font-weight:300;">' + field
+ ':</span>'
+ '<span style="font-weight:900;">' + val
+ '</span>'
});
});
......@@ -269,13 +277,17 @@ morpheus.MetadataUtil.autocomplete = function(model) {
var dataType = morpheus.VectorUtil.getDataType(v);
var field = v.getName();
if (dataType === 'number' || dataType === 'string'
|| dataType === '[string]') {
|| dataType === '[string]') {
if (regex.test(field)) {
var quotedField = field;
if (quotedField.indexOf(' ') !== -1) {
quotedField = '"' + quotedField + '"';
}
matches.push({
value : field + ':',
label : '<span style="font-weight:300;">' + field
+ ':</span>',
show : true
value: quotedField + ':',
label: '<span style="font-weight:300;">' + field
+ ':</span>',
show: true
});
}
}
......@@ -284,31 +296,31 @@ morpheus.MetadataUtil.autocomplete = function(model) {
};
};
morpheus.MetadataUtil.getMetadataNames = function(metadataModel) {
morpheus.MetadataUtil.getMetadataNames = function (metadataModel) {
var names = [];
for (var i = 0, count = metadataModel.getMetadataCount(); i < count; i++) {
names.push(metadataModel.get(i).getName(i));
}
names.sort(function(a, b) {
names.sort(function (a, b) {
a = a.toLowerCase();
b = b.toLowerCase();
return (a < b ? -1 : (a === b ? 0 : 1));
});
return names;
};
morpheus.MetadataUtil.getVectors = function(metadataModel, names) {
morpheus.MetadataUtil.getVectors = function (metadataModel, names) {
var vectors = [];
names.forEach(function(name) {
names.forEach(function (name) {
var v = metadataModel.getByName(name);
if (!v) {
throw name + ' not found. Available fields are '
+ morpheus.MetadataUtil.getMetadataNames(metadataModel);
+ morpheus.MetadataUtil.getMetadataNames(metadataModel);
}
vectors.push(v);
});
return vectors;
};
morpheus.MetadataUtil.indexOf = function(metadataModel, name) {
morpheus.MetadataUtil.indexOf = function (metadataModel, name) {
for (var i = 0, length = metadataModel.getMetadataCount(); i < length; i++) {
if (name === metadataModel.get(i).getName()) {
return i;
......@@ -317,38 +329,38 @@ morpheus.MetadataUtil.indexOf = function(metadataModel, name) {
return -1;
};
morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS = [ 'target', 'moa' ];
morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS = ['target', 'moa'];
morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS = new morpheus.Set();
[ 'pr_analyte_id', 'pr_gene_title', 'pr_gene_id', 'pr_analyte_num',
'pr_bset_id', 'pr_lua_id', 'pr_pool_id', 'pr_is_bing', 'pr_is_inf',
'pr_is_lmark', 'qc_slope', 'qc_f_logp', 'qc_iqr', 'bead_batch',
'bead_revision', 'bead_set', 'det_mode', 'det_plate', 'det_well',
'mfc_plate_dim', 'mfc_plate_id', 'mfc_plate_name', 'mfc_plate_quad',
'mfc_plate_well', 'pert_dose_unit', 'pert_id_vendor', 'pert_mfc_desc',
'pert_mfc_id', 'pert_time', 'pert_time_unit', 'pert_univ_id',
'pert_vehicle', 'pool_id', 'rna_plate', 'rna_well', 'count_mean',
'count_cv', 'provenance_code' ].forEach(function(name) {
['pr_analyte_id', 'pr_gene_title', 'pr_gene_id', 'pr_analyte_num',
'pr_bset_id', 'pr_lua_id', 'pr_pool_id', 'pr_is_bing', 'pr_is_inf',
'pr_is_lmark', 'qc_slope', 'qc_f_logp', 'qc_iqr', 'bead_batch',
'bead_revision', 'bead_set', 'det_mode', 'det_plate', 'det_well',
'mfc_plate_dim', 'mfc_plate_id', 'mfc_plate_name', 'mfc_plate_quad',
'mfc_plate_well', 'pert_dose_unit', 'pert_id_vendor', 'pert_mfc_desc',
'pert_mfc_id', 'pert_time', 'pert_time_unit', 'pert_univ_id',
'pert_vehicle', 'pool_id', 'rna_plate', 'rna_well', 'count_mean',
'count_cv', 'provenance_code'].forEach(function (name) {
morpheus.MetadataUtil.DEFAULT_HIDDEN_FIELDS.add(name);
});
morpheus.MetadataUtil.maybeConvertStrings = function(metadata,
metadataStartIndex) {
morpheus.MetadataUtil.maybeConvertStrings = function (metadata,
metadataStartIndex) {
for (var i = metadataStartIndex, count = metadata.getMetadataCount(); i < count; i++) {
morpheus.VectorUtil.maybeConvertStringToNumber(metadata.get(i));
}
morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS.forEach(function(field) {
morpheus.MetadataUtil.DEFAULT_STRING_ARRAY_FIELDS.forEach(function (field) {
if (metadata.getByName(field)) {
morpheus.VectorUtil.maybeConvertToStringArray(metadata
.getByName(field), ',');
.getByName(field), ',');
}
});
};
morpheus.MetadataUtil.copy = function(src, dest) {
morpheus.MetadataUtil.copy = function (src, dest) {
if (src.getItemCount() != dest.getItemCount()) {
throw 'Item count not equal in source and destination. '
+ src.getItemCount() + ' != ' + dest.getItemCount();
+ src.getItemCount() + ' != ' + dest.getItemCount();
}
var itemCount = src.getItemCount();
var metadataColumns = src.getMetadataCount();
......@@ -363,21 +375,21 @@ morpheus.MetadataUtil.copy = function(src, dest) {
}
}
};
morpheus.MetadataUtil.addVectorIfNotExists = function(metadataModel, name) {
morpheus.MetadataUtil.addVectorIfNotExists = function (metadataModel, name) {
var v = metadataModel.getByName(name);
if (!v) {
v = metadataModel.add(name);
}
return v;
};
morpheus.MetadataUtil.getMatchingIndices = function(metadataModel, tokens) {
morpheus.MetadataUtil.getMatchingIndices = function (metadataModel, tokens) {
var indices = {};
for (var itemIndex = 0, nitems = metadataModel.getItemCount(); itemIndex < nitems; itemIndex++) {
var matches = false;
for (var metadataIndex = 0, metadataCount = metadataModel
.getMetadataCount(); metadataIndex < metadataCount && !matches; metadataIndex++) {
.getMetadataCount(); metadataIndex < metadataCount && !matches; metadataIndex++) {
var vector = metadataModel.get(metadataModel
.getColumnName(metadataIndex));
.getColumnName(metadataIndex));
var value = vector.getValue(itemIndex);
for (var i = 0, length = tokens.length; i < length; i++) {
if (tokens[i] == value) {
......@@ -391,4 +403,4 @@ morpheus.MetadataUtil.getMatchingIndices = function(metadataModel, tokens) {
}
}
return indices;
};
\ No newline at end of file
};
src/util/util.js
View file @ c2db34e2
......@@ -493,12 +493,8 @@ morpheus.Util.autosuggest = function (options) {
trim: false,
selectionStart: options.$el[0].selectionStart
});
// quote value if needed
var value = (ui.item.value[0] !== '"'
&& ui.item.value.indexOf(' ') > 0 ? ('"'
+ ui.item.value + '"')
: ui.item.value);
var value = ui.item.value;
var show = ui.item.show; // || (ui.item.space
// &&
// options.suggestWhenEmpty);
......@@ -598,6 +594,7 @@ morpheus.Util.getAutocompleteTokens = function (text, options) {
if (i === options.selectionStart - 1) {
currentToken.inSelectionStart = true;
}
}
tokens.push({
......@@ -1054,6 +1051,7 @@ morpheus.Util.createSearchPredicates = function (options) {
possibleToken = '"' + possibleToken;
}
if (!validateFieldNames
|| availableFields.indexOf(possibleField) !== -1) {
token = possibleToken;
......
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