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Manual
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Flattener without Graphical User Interface (GUI):
sh bin/xmlflattener -mapping mapping-file.xml; -xmlDocument your PSI1.0 XML document> -o output file; -
Flattener with GUI:
sh bin/xmlflattener-gui -
Maker without Graphical User Interface:
sh bin/xmlmaker -mapping mapping-file.xml; -o output xmlDocument; -dictionaries dictionaries; -flatfiles flat files; -
Maker without Graphical User Interface:
sh bin/xmlmaker-gui
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Flattener without Graphical User Interface (GUI):
bin/xmlflattener.bat -mapping mapping-file.xml; -xmlDocument your PSI1.0 XML document> -o output file; -
Flattener with GUI:
bin/xmlflattener-gui.bat -
Maker without Graphical User Interface:
bin/xmlmaker -mapping mapping-file.xml; -o output xmlDocument; -dictionaries dictionaries; -flatfiles flat files; -
Maker without Graphical User Interface:
bin/xmlmaker-gui.bat
XML Maker and XML Flattener are two applications that allow to convert tab delimited files to XML documents and XML documents to tab-delimited files according to an XML schema. Both application can be used either with or without graphical interface. The graphical interface allows to load an XML schema and to create a mapping between flat (tab delimited) files and XML document. Once a mapping has been created, it can be reused directly on the command line.
To create a mapping file, an XML schema should first be loaded in the GUI. A graphical tree representation of this schema is then created. On this tree it is possible first to choose the 'main node', i.e. the node that contains all information that will be displayed on a single line of the output tab-delimited file. Then it is possible to select the elements and attributes that will be exported. The application will automatically calculate the number of columns necessary according to the number of sub-elements found.
To create a mapping file, an XML schema should first be loaded in the GUI, then one (or more) flat file. A graphical tree representation of this schema is created. On this tree it is possible first to associate a node to a flat file. An element corresponding to this node will be created in the output XML document for each line of the flat file. At this point the fields of the file can be associated to the nodes of the schema. Other types of associations are possible:
- to default value: specify the value that will be always associated to this node, whatever the flat files contains
- to automatic value: a unique value will be automaticaly generated
- to dictionary: a dictionary is a tab delimited file that contains synonyms of terms. It is possible to associate a node to which has already been assigned a value (association to field, default value), to a dictionnary. When a synonym is found, it will be replace by its main value. Both applications have been develop on and required a Java 1.4 environment (or newer) (http://www.java.com/en/download/index.jsp).
-mapping mapping_file: the mapping file
-xmlDocument document.xml: the XML document to parse
-o: name of the output file
-validate (no argument): the XML document should be validated. Validation is required to retrieve automatically XML ids, used for instance in PSI-MI XML 1.0 normalized documents. Validation may be slow and it is recommended to not use when not needed (not needed for PSI unnormalized or PSI-MI 2.5). `
-mapping mapping_file: the mapping file
-o xmlDocument: name of the output XML document
-dictionaries dictionaries : names of the dictionary files in the right order, separated by comma
-flatfiles flat files : names of the flat files in the right order, separated by comma
Some files are available in the data directory. those files are relative to the Protein Standard Initiative (http://psidev.sourceforge.net/) for which this software has been created.
- mif.xsd, MIF2.5.xsd: PSI standard schema (version 1.0 and 2.5)
- flattener-mapping-psi10.xml, flattener-mapping-psi25.xml, maker-mapping-psi10.xml, maker-mapping-psi25.xml: examples of mapping files for both applications
- psimaker-template.txt: template flat file that can be used with the XML Maker application and its respective mapping files.
- psimaker-example.txt: an example (one line) of use of this template.
sh bin/xmlflattener -mapping data/flattener-mapping-psi10.xml -xmlDocument your PSI1.0 XML document; -o output file;
sh bin/xmlflattener -mapping data/flattener-mapping-psi25.xml -xmlDocument your PSI2.5 XML document; -o output file;
sh bin/xmlmaker -mapping data/maker-mapping-psi10.xml -flatfiles your flat file; -xmlDocument your PSI2.5 XML document; -o output XML document;
sh bin/xmlmaker -mapping data/maker-mapping-psi25.xml -flatfiles your flat file; -xmlDocument your PSI2.5 XML document; -o output XML document;
you can build the software using maven (http://maven.apache.org): mvn clean install appassembler:assemble assembly:assembly
The classes will be compiled into the target/classes directory, a jar file will be added to the target directory. A compressed (zip) package containing automatically generated scripts and libraries is also added to the target directory.