kekule
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Open source JavaScript toolkit for chemoinformatics
298 lines (283 loc) • 10.4 kB
JavaScript
/**
* @fileoverview
* File to support read or write chemical data in JSON or XML format by built-in serializers.
* The JSON data serialized directly from Kekule.ChemObject is called KCJ (Kekule Chem JSON),
* while the XML data is called KCX (Kekule Chem XML).
* @author Partridge Jiang
*/
/*
* requires /lan/classes.js
* requires /lan/serializations.js
* requires /core/kekule.common.js
*/
/*
* Default options to read/write KCJ/KCX/JSON/XML format data.
* @object
*/
Kekule.globalOptions.add('IO.kekuleNative', {
prettyPrint: true
});
/**
* Reader for KCJ JSON data.
* Use KcjReader.readData() can retrieve a suitable Kekule object.
* Data fetch in should be a string or a JSON.
* @class
* @augments Kekule.IO.ChemDataReader
*/
Kekule.IO.KcjReader = Class.create(Kekule.IO.ChemDataReader,
/** @lends Kekule.IO.KcjReader# */
{
/** @private */
CLASS_NAME: 'Kekule.IO.KcjReader',
/** @private */
readData: function(/*$super, */data, dataType)
{
var dtype = dataType || Kekule.IO.ChemDataType.TEXT;
var jsonObj;
if (dtype == Kekule.IO.ChemDataType.JSON)
jsonObj = data;
if (dtype == Kekule.IO.ChemDataType.TEXT)
jsonObj = DataType.JsonUtility.parse(data);
else // can not understand data other than text or JSON
{
Kekule.error(/*Kekule.ErrorMsg.KCJ_INPUT_DATATYPE_NOT_JSON_OR_TEXT*/Kekule.$L('ErrorMsg.KCJ_INPUT_DATATYPE_NOT_JSON_OR_TEXT'));
return null;
}
return this.tryApplySuper('readData', [jsonObj, Kekule.IO.ChemDataType.JSON]) /* $super(jsonObj, Kekule.IO.ChemDataType.JSON) */;
},
/** @private */
doReadData: function(data, dataType)
{
var serializer = Class.ObjSerializerFactory.getSerializer('json');
if (!serializer)
{
Kekule.error(/*Kekule.ErrorMsg.JSON_SERIALIZER_NOT_EXISTS*/Kekule.$L('ErrorMsg.JSON_SERIALIZER_NOT_EXISTS'));
return null;
}
return serializer.load(null, data); // create new object
}
});
/**
* Writer for KCJ JSON data.
* Use KcjWriter.writeData() to save a Kekule.ChemObject.
* @class
* @augments Kekule.IO.ChemDataWriter
*/
Kekule.IO.KcjWriter = Class.create(Kekule.IO.ChemDataWriter,
/** @lends Kekule.IO.KcjWriter# */
{
/** @private */
CLASS_NAME: 'Kekule.IO.KcjWriter',
/** @private */
initialize: function(/*$super, */options)
{
this.tryApplySuper('initialize', [options]) /* $super(options) */;
var op = options || {};
this.setPrettyPrint(Kekule.ObjUtils.isUnset(op.prettyPrint)? Kekule.globalOptions.IO.kekuleNative.prettyPrint: op.prettyPrint);
},
/** @private */
initProperties: function()
{
this.defineProp('prettyPrint', {'dataType': DataType.BOOL, 'defaultValue': true});
},
/** @private */
writeData: function(/*$super, */obj, dataType, format, options)
{
var dtype = dataType || Kekule.IO.ChemDataType.TEXT;
if ((dtype != Kekule.IO.ChemDataType.JSON) && (dtype != Kekule.IO.ChemDataType.TEXT))
// can not output data other than text or JSON
{
Kekule.error(/*Kekule.ErrorMsg.KCJ_OUTPUT_DATATYPE_NOT_JSON_OR_TEXT*/Kekule.$L('ErrorMsg.KCJ_OUTPUT_DATATYPE_NOT_JSON_OR_TEXT'));
return null;
}
var result = this.tryApplySuper('writeData', [obj, Kekule.IO.ChemDataType.JSON]) /* $super(obj, Kekule.IO.ChemDataType.JSON) */;
if (dtype == Kekule.IO.ChemDataType.JSON)
return result;
if (dtype == Kekule.IO.ChemDataType.TEXT)
{
//console.log(DataType.JsonUtility.serializeToStr(result, {'prettyPrint': false}));
var prettyPrint = (options && Kekule.ObjUtils.notUnset(options.prettyPrint))? options.prettyPrint: this.getPrettyPrint();
return DataType.JsonUtility.serializeToStr(result, {'prettyPrint': prettyPrint});
}
},
/** @private */
doWriteData: function(obj, dataType, format, options)
{
var serializer = Class.ObjSerializerFactory.getSerializer('json');
if (!serializer)
{
Kekule.error(/*Kekule.ErrorMsg.JSON_SERIALIZER_NOT_EXISTS*/Kekule.$L('ErrorMsg.JSON_SERIALIZER_NOT_EXISTS'));
return null;
}
var jsonObj = {};
serializer.save(obj, jsonObj); // create new object
return jsonObj;
}
});
/**
* Reader for KCX XML data.
* Use KcxReader.readData() can retrieve a suitable Kekule object.
* Data fetch in should be a string or a XML node.
* @class
* @augments Kekule.IO.ChemDataReader
*/
Kekule.IO.KcxReader = Class.create(Kekule.IO.ChemDataReader,
/** @lends Kekule.IO.KcxReader# */
{
/** @private */
CLASS_NAME: 'Kekule.IO.KcxReader',
/** @private */
readData: function(/*$super, */data, dataType)
{
var dtype = dataType || Kekule.IO.ChemDataType.TEXT;
var srcElem;
if (dtype == Kekule.IO.ChemDataType.DOM)
srcElem = data;
if (dtype == Kekule.IO.ChemDataType.TEXT)
{
var doc = DataType.XmlUtility.parse(data);
srcElem = doc.documentElement;
}
else // can not understand data other than text or DOM
{
Kekule.error(/*Kekule.ErrorMsg.KCX_INPUT_DATATYPE_NOT_DOM_OR_TEXT*/Kekule.$L('ErrorMsg.KCX_INPUT_DATATYPE_NOT_DOM_OR_TEXT'));
return null;
}
return this.tryApplySuper('readData', [srcElem, Kekule.IO.ChemDataType.DOM]) /* $super(srcElem, Kekule.IO.ChemDataType.DOM) */;
},
/** @private */
doReadData: function(data, dataType)
{
var serializer = Class.ObjSerializerFactory.getSerializer('xml');
if (!serializer)
{
Kekule.error(/*Kekule.ErrorMsg.XML_SERIALIZER_NOT_EXISTS*/Kekule.$L('ErrorMsg.XML_SERIALIZER_NOT_EXISTS'));
return null;
}
return serializer.load(null, data); // create new object
}
});
/**
* Writer for KCX XML data.
* Use KcxWriter.writeData() to save a Kekule.ChemObject.
* @class
* @augments Kekule.IO.ChemDataWriter
*/
Kekule.IO.KcxWriter = Class.create(Kekule.IO.ChemDataWriter,
/** @lends Kekule.IO.KcxWriter# */
{
/** @private */
CLASS_NAME: 'Kekule.IO.KcxWriter',
/** @private */
initialize: function(/*$super, */options)
{
this.tryApplySuper('initialize', [options]) /* $super(options) */;
var op = options || {};
this.setPrettyPrint(Kekule.ObjUtils.isUnset(op.prettyPrint)? Kekule.globalOptions.IO.kekuleNative.prettyPrint: op.prettyPrint);
this.setRootTag(op.rootTag || 'kcx');
},
/** @private */
initProperties: function()
{
this.defineProp('prettyPrint', {'dataType': DataType.BOOL, 'defaultValue': true});
this.defineProp('rootTag', {'dataType': DataType.STRING});
},
/** @private */
writeData: function(/*$super, */obj, dataType)
{
var dtype = dataType || Kekule.IO.ChemDataType.TEXT;
if ((dtype != Kekule.IO.ChemDataType.DOM) && (dtype != Kekule.IO.ChemDataType.TEXT))
// can not output data other than DOM or text
{
Kekule.error(/*Kekule.ErrorMsg.KCX_OUTPUT_DATATYPE_NOT_DOM_OR_TEXT*/Kekule.$L('ErrorMsg.KCX_OUTPUT_DATATYPE_NOT_DOM_OR_TEXT'));
return null;
}
var result = this.tryApplySuper('writeData', [obj, Kekule.IO.ChemDataType.DOM]) /* $super(obj, Kekule.IO.ChemDataType.DOM) */;
if (dtype == Kekule.IO.ChemDataType.DOM)
return result;
if (dtype == Kekule.IO.ChemDataType.TEXT)
{
var options = {'prettyPrint': this.getPrettyPrint()};
return DataType.XmlUtility.serializeNode(result, options);
}
},
/** @private */
doWriteData: function(obj, dataType)
{
var serializer = Class.ObjSerializerFactory.getSerializer('xml');
if (!serializer)
{
Kekule.error(/*Kekule.ErrorMsg.XML_SERIALIZER_NOT_EXISTS*/Kekule.$L('ErrorMsg.XML_SERIALIZER_NOT_EXISTS'));
return null;
}
var doc = DataType.XmlUtility.newDocument(this.getRootTag());
serializer.save(obj, doc.documentElement); // create new object
return doc.documentElement;
}
});
(function(){
// extents mime type consts
Kekule.IO.MimeType.KEKULE_JSON = 'chemical/x-kekule-json';
Kekule.IO.MimeType.KEKULE_XML = 'chemical/x-kekule-xml';
Kekule.IO.DataFormat.KEKULE_JSON = 'Kekule-JSON';
Kekule.IO.DataFormat.KEKULE_XML = 'Kekule-XML';
// register chem data formats
Kekule.IO.DataFormatsManager.register('JSON', Kekule.IO.MimeType.JSON, 'json',
Kekule.IO.ChemDataType.TEXT, 'JSON format');
Kekule.IO.DataFormatsManager.register(Kekule.IO.DataFormat.KEKULE_JSON, Kekule.IO.MimeType.KEKULE_JSON, 'kcj',
Kekule.IO.ChemDataType.TEXT, 'Kekule Chemical JSON format');
Kekule.IO.DataFormatsManager.register(Kekule.IO.DataFormat.KEKULE_XML, Kekule.IO.MimeType.KEKULE_XML, 'kcx',
Kekule.IO.ChemDataType.TEXT, 'Kekule Chemical XML format');
// register ChemData reader and writer
/*
Kekule.IO.ChemDataReaderManager.register('kcj', Kekule.IO.KcjReader, {
'title': 'Kekule Chemical JSON format',
'mimeType': 'chemical/x-kekule-json',
'fileExt': 'kcj'
});
Kekule.IO.ChemDataWriterManager.register('kcj', Kekule.IO.KcjWriter,
[Kekule.ChemObject],
{
'createOptions': {'prettyPrint': true},
'title': 'Kekule Chemical JSON format',
'mimeType': 'chemical/x-kekule-json',
'fileExt': 'kcj'
});
Kekule.IO.ChemDataReaderManager.register('kcx', Kekule.IO.KcxReader, {
'title': 'Kekule Chemical XML format',
'mimeType': 'chemical/x-kekule-xml',
'fileExt': 'kcx'
});
Kekule.IO.ChemDataWriterManager.register('kcx', Kekule.IO.KcxWriter,
[Kekule.ChemObject],
{
'createOptions': {'prettyPrint': true},
'title': 'Kekule Chemical XML format',
'mimeType': 'chemical/x-kekule-xml',
'fileExt': 'kcx'
});
*/
var jsonFmtId = Kekule.IO.DataFormatsManager.findFormatId(Kekule.IO.MimeType.JSON);
var kcjFmtId = Kekule.IO.DataFormatsManager.findFormatId(Kekule.IO.MimeType.KEKULE_JSON);
var kcxFmtId = Kekule.IO.DataFormatsManager.findFormatId(Kekule.IO.MimeType.KEKULE_XML);
Kekule.IO.ChemDataReaderManager.register('json', Kekule.IO.KcjReader, jsonFmtId);
Kekule.IO.ChemDataReaderManager.register('kcj', Kekule.IO.KcjReader, kcjFmtId);
Kekule.IO.ChemDataReaderManager.register('kcx', Kekule.IO.KcxReader, kcxFmtId);
/* Avoid display two loaders
Kekule.IO.ChemDataWriterManager.register('json', Kekule.IO.KcjWriter, [Kekule.ChemObject], kcjFmtId,
{
'createOptions': {'prettyPrint': !true}
}
);
*/
Kekule.IO.ChemDataWriterManager.register('kcj', Kekule.IO.KcjWriter, [Kekule.ChemObject], kcjFmtId,
{
'createOptions': {'prettyPrint': !true}
}
);
Kekule.IO.ChemDataWriterManager.register('kcx', Kekule.IO.KcxWriter, [Kekule.ChemObject], kcxFmtId,
{
'createOptions': {'prettyPrint': true}
}
);
})();