Difference between revisions of "Types (extension point)"

Latest revision as of 16:02, 3 June 2013

Identifier

ru.biosoft.galaxy.types

Plugin

ru.biosoft.galaxy

Since

0.9.3

Registry

FormatRegistry

[edit] Description

This extension point allows to map Galaxy data types to BioUML data types. For each Galaxy file format you should specify BioUML class and (if necessary) importer/exporter combination. If some Galaxy file format is undefined, Generic file importer and exporter are used by default.

[edit] Configuration Markup

<!ELEMENT format (exporter?,importer?)>
<!ATTLIST format
   galaxyFormat    CDATA #REQUIRED
   fileExtension   CDATA #REQUIRED
   bioumlType      CDATA #REQUIRED
>

galaxyFormat

name of the Galaxy format as it appears in Galaxy XML tool definition

fileExtension

file extension associated with this format. Usually the same as galaxyFormat.

bioumlType

fully-qualified name of BioUML Java class (must implement DataElement interface).

<!ELEMENT exporter (property*)>
<!ATTLIST exporter
   name    CDATA #REQUIRED
>

name

name of the exporter format (must be registered via ru.biosoft.access.export).

<!ELEMENT importer (property*)>
<!ATTLIST importer
   name    CDATA #REQUIRED
>

name

name of the importer format (must be registered via ru.biosoft.access.import).

<!ELEMENT property>
<!ATTLIST property
   name    CDATA #REQUIRED
   value   CDATA #REQUIRED
>

name

fully qualified name of the bean property of importer/exporter parameter to change

value

value of given property. Registry will attempt to convert it from string to the corresponding type using TextUtil.fromString method.

[edit] Example

<format galaxyFormat="tabular" fileExtension="dat" bioumlType="ru.biosoft.table.TableDataCollection">
  <exporter name="Tab-separated text (*.txt)">
    <property name="includeHeaders" value="false"/>
  </exporter>
  <importer name="Tabular (*.txt, *.xls, *.tab, etc.)">
    <property name="headerRow" value="0"/>
    <property name="dataRow" value="1"/>
    <property name="columnForID" value="Generate unique ID"/>
  </importer> 
</format>

This extension defines "tabular" Galaxy format, which maps to BioUML type TableDataCollection ( table). For exporting BioUML element to Galaxy file "Tab-separated text (*.txt)" exporter will be used with "includeHeaders" value set to false. For importing Galaxy result into BioUML "Tabular (*.txt, *.xls, *.tab, etc.)" importer will be used with some options set.