Convert brat ann files to WebAnno-compatible XMI

convert.groovy

/*
 * Convert brat annotations to an XMI format compatible with WebAnno.
 *
 * Using this script requires some preparation:
 * - Log in to WebAnno and create a new project 
 * - Import a simple text document into the project (the content does not matter)
 * - Create the custom layers to which you want to map your brat annotations.
 *   In this example, we assume that you want to map all brat entity/event annotations
 *   from brat to a single WebAnno span layer called "Component" and all brat relations
 *   to WebAnno relation layer called "Relation". Mind that in WebAnno presently only a
 *   single relation layer can attach to any span layer.
 *   On both layers, add a string feature called value. This will take the name of
 *   the original brat annotation.
 * - Ensure that the layer behaviors (e.g. allow cross-sentence) match the way your
 *   annotations in brat have been created. I.e. if you have any cross-sentence
 *   entities in brat, make sure that the "Component" layer allows cross-sentence
 *   annotations.
 * - Open the text document you imported before in the WebAnno annotation editor.
 * - Export the document in XMI format from the export button in the action bar.
 * - Unzip the exported file and open the typesystem.xml file for editing.
 * - Under the "types" XML element, remove all "typeDescription" elements except
 *   those describing the layers you have previously created ("webanno.custom.Component"
 *   and "webanno.custom.Relation"). Take note of the path to the typesystem.xml
 *   file as you have to pass it as the third parameter to this script.
 * - Adjust the PARAM_TYPE_MAPPINGS below according to the brat annotations you
 *   have been using. Mind that brat annotation names cannot contain underscores
 *   or dots.
 * - Ensure that you brat ".ann" files do not contain spurious trailing space
 *   characters, otherwise you might get errors such as 
 *   Illegal event annotation format [E11 subst:T41 ].
 * - Run this script with following parameters:
 *   - the path of the ".ann" file you want to convert. You can use wildcards
 *     if you want to convert multiple files.
 *   - the output directory to which the converted files are written
 *   - the path to the typesystem.xml file you have prepared before
 * - If all goes well, it will take a moment for the script to download its
 *   dependencies and then it should convert each of your ".ann" to a ".xmi"
 *   file.
 * - Log in to WebAnno and open the project you have created in the first step.
 * - Import the XMI files into this project.
 */
@Grab(group='de.tudarmstadt.ukp.dkpro.core', 
  module='de.tudarmstadt.ukp.dkpro.core.io.brat-asl', 
  version='1.9.0')
@Grab(group='de.tudarmstadt.ukp.dkpro.core', 
  module='de.tudarmstadt.ukp.dkpro.core.io.xmi-asl', 
  version='1.9.0')

import static org.apache.uima.util.CasCreationUtils.*; 
import static org.apache.uima.fit.pipeline.SimplePipeline.*;
import static org.apache.uima.fit.factory.CollectionReaderFactory.*;
import static org.apache.uima.fit.factory.AnalysisEngineFactory.*;
import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.*;

import de.tudarmstadt.ukp.dkpro.core.io.brat.*;
import de.tudarmstadt.ukp.dkpro.core.io.xmi.*;

// Load the default type system and the custom UIMA type system
// specifiction passed as the third parameter to this script.
def ts = mergeTypeSystems([
  createTypeSystemDescription(),
  createTypeSystemDescriptionFromPath(args[2])]);

// Assemble and run pipeline
runPipeline(
  createReaderDescription(BratReader, ts,
    BratReader.PARAM_SOURCE_LOCATION, args[0],
    // Specify which brat annotations map to which UIMA annotation types.
    // Mind that normally you want to map multiple brat annotations to
    // a generic annotation type.
    BratReader.PARAM_TYPE_MAPPINGS, [
        "subst -> webanno.custom.Component",
        "pron -> webanno.custom.Component",
        "ptc -> webanno.custom.Component",
        "prep -> webanno.custom.Component",
        "verb -> webanno.custom.Component",
        "konj -> webanno.custom.Component",
        "concerning -> webanno.custom.Relation",
        "location -> webanno.custom.Relation",
        "purpose -> webanno.custom.Relation"],
    // Specify which UIMA annotation types are spans. The name given after
    // the colon indicates the UIMA feature where the original brat annotation
    // name is stored.
    BratReader.PARAM_TEXT_ANNOTATION_TYPES, "webanno.custom.Component:value",
    // Specify which UIMA annotation types are relations. The name given after
    // the colon indicates the UIMA feature where the original brat annotation
    // name is stored. The source and target feature names must be Governor and
    // Dependent as this is presently hard-coded in WebAnno.
    BratReader.PARAM_RELATION_TYPES,  "webanno.custom.Relation:Governor:Dependent{A}:value"),
  createEngineDescription(XmiWriter, ts,
    XmiWriter.PARAM_TARGET_LOCATION, args[1],
    XmiWriter.PARAM_STRIP_EXTENSION, true))

@jerrychen007 I have downloaded your sample and hope to have a look at it over the weekend.

Ok, so I finally managed to have a look at this.

I could fix the exception by adding the following two lines to the .ann file:

A2	role T1 speaker
A2	role T2 speak

The BratReader right now expects that the filler of a slot feature carries an attribute called role which contains the role name.

I have opened an issue in DKPro Core for this, but I don't know when I get to fix/release it.

dkpro/dkpro-core#1489

Thank you for the information!