DocumentOperation behaves differently when deployed

Hi,

somehow I see a pattern here. I have a DocumentOperation which works fine, when started from the IDE, but behaves differently when run as plugin. 

This might be related to: https://support.geneious.com/hc/en-us/community/posts/115001972371-Plugin-works-only-from-IDE-not-in-packaged-form-Why 

package de.mpicbg.gef;

import com.biomatters.geneious.publicapi.components.Dialogs;
import com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException;
import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument;
import com.biomatters.geneious.publicapi.plugin.*;
import jebl.util.ProgressListener;

import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;

/**
 * Created by Stephan Janosch on 17/11/17.
 */
public class GefPrimerOperation extends DocumentOperation {


 @Override
 public GeneiousActionOptions getActionOptions() {
 GeneiousActionOptions actionOptions = new GeneiousActionOptions("Create Primers around Annotation", "Generate Primers around Annotation", null, GeneiousActionOptions.Category.None);
 actionOptions.setMainMenuLocation(GeneiousActionOptions.MainMenu.Sequence);
 actionOptions.setInMainToolbar(false);

 return actionOptions;
 }

 @Override
 public String getHelp() {
 return "";
 }

 @Override
 public DocumentSelectionSignature[] getSelectionSignatures() {
 DocumentSelectionSignature sequenceSelSig = new DocumentSelectionSignature(SequenceDocument.class, 1, 100);
 return new DocumentSelectionSignature[]{sequenceSelSig};
 }


 @Override
 public void performOperation(AnnotatedPluginDocument[] annotatedDocuments, ProgressListener progressListener, Options options, SequenceSelection sequenceSelection, OperationCallback callback) throws DocumentOperationException {

 String tagType = options.getValueAsString("tagType");

 int i = 0;
 for (AnnotatedPluginDocument document : annotatedDocuments) {
 i++;
 progressListener.setProgress(i, annotatedDocuments.length);
 SequenceDocument sequenceDocument = (SequenceDocument) document.getDocument();
 //find the tag
 SequenceAnnotation tagAnnotation = null;
 for (SequenceAnnotation annotation : sequenceDocument.getSequenceAnnotations()) {
 if (tagAnnotation == null && annotation.getType().equalsIgnoreCase(tagType))
 tagAnnotation = annotation;
 else if (annotation.getType().equalsIgnoreCase(tagType))
 throw new DocumentOperationException("found more that one tag in: " + document.getName());
 }

 if (tagAnnotation == null)
 throw new DocumentOperationException("found no tag in: " + document.getName());

 String fromPosition = String.valueOf(tagAnnotation.getInterval().getMinimumIndex());
 String toPosition = String.valueOf(tagAnnotation.getInterval().getMaximumIndex());

 DocumentOperation primerOperation = PluginUtilities.getDocumentOperation("Operation_com.biomatters.plugins.primerDesign.DesignAnnotationGenerator");

 Options primerOperationOptions = primerOperation.getOptions(document);

// System.out.println(primerOperationOptions.getDescriptionAndState());
// System.out.println("Available Options: " + primerOperationOptions.getNamesAndValues(true));

 assert primerOperationOptions.setStringValue("taskOptions.chooser", "designNewOptions");
 assert primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.forwardOption", "true");
 assert primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.reverseOption", "true");
 assert primerOperationOptions.setStringValue("taskOptions.designNewOptions.oligosToPickOptions.probeOption", "false");

 assert primerOperationOptions.setStringValue("panelForRegionType.designRegionTypeOption", "genericOptionValue");
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableIncludedRegionOption", "false");

 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableTargetRegionOption", "true");
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.targetRegionFromOption", fromPosition);
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.targetRegionToOption", toPosition);

 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableProductSizeOption", "true");
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.productSizeFromOption", options.getValueAsString("productSizeFromOption"));
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.productSizeToOption", options.getValueAsString("productSizeToOption"));

 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.enableOptimalProductSizeOption", "false");
 assert primerOperationOptions.setStringValue("panelForRegionType.genericRegionOptions.numPairsOption", "1");


 try {
 callback.setSubFolder("primed sequences");
 } catch (DatabaseServiceException e) {
 e.printStackTrace();
 }
 primerOperation.performOperation(new AnnotatedPluginDocument[]{document}, ProgressListener.EMPTY, primerOperationOptions, sequenceSelection, callback);

 }

 }


 @Override
 public Options getOptions(DocumentOperationInput operationInput) throws DocumentOperationException {
 Options options = new Options(getClass());
 options.addLabel("select annotation type for tag: ");
 Options.OptionValue preselectedTag = null;
 List<String> tagTypeList = new LinkedList<String>();
 for (AnnotatedPluginDocument doc : operationInput.getInputDocumentsList()) {
 SequenceDocument sequenceDocument = null;
 if (doc.getDocument() instanceof SequenceDocument) {
 sequenceDocument = (SequenceDocument) doc.getDocument();
 }
 if (sequenceDocument == null)
 continue;
 for (SequenceAnnotation annotation : sequenceDocument.getSequenceAnnotations()) {
 String annoType = annotation.getType().toLowerCase();
 if (!tagTypeList.contains(annoType) && annoType != null && !annoType.isEmpty())
 tagTypeList.add(annoType);
 }
 }

 if (tagTypeList.isEmpty())
 throw new DocumentOperationException("no annotations found");

 final Options.OptionValue[] optionValues = new Options.OptionValue[tagTypeList.size()];
 int i = 0;
 for (String tagTypeString : tagTypeList) {
 Options.OptionValue value = new Options.OptionValue(tagTypeString, tagTypeString);
 optionValues[i] = value;
 if (tagTypeString.equalsIgnoreCase("tag"))
 preselectedTag = optionValues[i];
 i++;
 }
 options.addComboBoxOption("tagType", "select annotation type for tag", optionValues, preselectedTag);
 options.addIntegerOption("productSizeFromOption", "product size from", 1000);
 options.addIntegerOption("productSizeToOption", "product size to", 3000);

 return options;
 }
}

I checked my project settings and they fit with the setup guide.

Just for completeness I post my build file as well:

<?xml version="1.0" ?>

<project name="GefPrimerPlugin" default="distribute" basedir=".">

 <property file="plugin.properties"/>
 <property name="build" location="build"/>
 <property name="classes" location="classes"/>
 <property name="src" location="src"/>

 <path id="classpath">
 <fileset dir="../../geneiousPlugins/geneious-10.2.3-devkit/examples/GeneiousFiles/lib">
 <include name="GeneiousPublicAPI.jar"/>
 <include name="jdom.jar"/>
 <include name="jebl.jar"/>
 </fileset>
 </path>

 <target name= "distribute" depends="build">
 <copy file="${build}/${short-plugin-name}.jar" tofile="${build}/${short-plugin-name}.gplugin"/>
 <echo message="Created ${build}/${short-plugin-name}.gplugin"/>

 <!--If your plugin consists of a folder you should build it into
 a zip file with extension gplugin. See commented example below.
 Remove above line and uncomment these to use-->
 <!--
 <zip zipfile="${build}/${short-plugin-name}.gplugin">
 <fileset dir="${build}/${plugin-name}"/>
 </zip>
 -->
 </target>

 <target name="build" depends="compile">
 <jar jarfile="${build}/${short-plugin-name}.jar">
 <fileset dir="${classes}"/>
 <fileset dir="">
 <include name="plugin.properties"/>
 </fileset>
 </jar>

 <!--build example for folder type plugin. Remove above
 lines and uncomment these to use-->
 <!--
 <jar jarfile="${build}/${short-plugin-name}.jar">
 <fileset dir="${classes}"/>
 </jar>
 <mkdir dir="${build}/${plugin-name}"/>
 <copy todir="${build}/${plugin-name}">
 <fileset dir="${build}">
 <include name="ExtraFiles"/>
 <include name="ExtraFiles/*"/>
 <include name="${short-plugin-name}.jar"/>
 </fileset>
 <fileset dir="docs">
 <include name="readme.txt"/>
 </fileset>
 </copy>
 -->
 </target>

 <target name="compile" depends="prepare">
 <javac target="1.8" source="1.8" destdir="${classes}" debug="true">
 <classpath refid="classpath"/>
 <src path="${src}"/>
 </javac>
 </target>

 <target name="prepare">
 <mkdir dir="${build}"/>
 <mkdir dir="${classes}"/>
 </target>

 <target name="clean">
 <delete dir="${build}"/>
 <delete dir="${classes}"/>
 </target>
</project>

Clueless,
Stephan