We are moving ourselves to 4.3.x.
The first step for me is to have a corresponding Bridge that works on 4.3.x OMERO server.
I confirmed my bridge is called from Indexer log.
But it seems like there's major change in APIs.
here's my bridge java code (which was working from 4.2.1)
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/*
* $Id$
*
* Copyright 2008 Glencoe Software, Inc. All rights reserved.
* Use is subject to license terms supplied in LICENSE.txt
*/
package edu.cmu.search.bridges;
import edu.cmu.search.bridges.ExperimentFileParser;
import edu.cmu.search.bridges.RunPython;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.Reader;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Collections;
import java.util.Iterator;
import java.util.Properties;
import java.io.*;
import org.apache.commons.io.filefilter.*;
//import omero.api.IMetadataPrx;
//import omero.api.ServiceFactoryPrx;
//import omero.api.ServiceFactory;
//import omero.api.RawFileStorePrx;
//import omero.api.RawFileStore;
//import omero.model.IObject;
import ome.model.annotations.Annotation;
import ome.model.annotations.FileAnnotation;
import ome.model.containers.Dataset;
import ome.model.containers.DatasetImageLink;
import ome.model.containers.Project;
import ome.model.containers.ProjectDatasetLink;
import ome.model.core.Image;
import ome.model.core.OriginalFile;
import ome.services.fulltext.BridgeHelper;
import ome.services.fulltext.SimpleLuceneOptions;
import org.apache.lucene.document.Document;
import org.apache.lucene.document.Field;
import org.hibernate.search.bridge.FieldBridge;
import org.hibernate.search.bridge.LuceneOptions;
/**
* Example custom {@link FieldBridge} implementation which parses all
* {@link Image} names from a {@link Project} and inserts them into the index
* for that {@link Project}.
*
* @author Josh Moore, josh at glencoesoftware.com
* @since 3.0-Beta3
*/
public class ExperimentFileBridge extends BridgeHelper {
// ExperimentFileParser exParser;
/**
* If the "value" argument is a {@link Project}, this
* {@link FieldBridge bridge} gathers all images and adds them to the index
* with a slightly reduced boost value. The field name of the image name is
* "image_name" but the values are also added to the
* {@link BridgeHelper#COMBINED} field via the
* {@link #add(Document, String, String, org.apache.lucene.document.Field.Store, org.apache.lucene.document.Field.Index, Float)}
* method.
*/
@Override
public void set(final String name, final Object value,
final Document document, final LuceneOptions _opts) {
if (value instanceof Image) {
logger().info("Scheduling all Experiment Files of " + value + " for re-indexing");
ExperimentFileParser exParser = new ExperimentFileParser();
final Image i = (Image) value;
String user = i.getDetails().getOwner().getOmeName();
String group = i.getDetails().getGroup().getName();
Long imageId = i.getId();
// this can be used later. compare the created time with the current time.
// if the difference is small, then you trigger the feature calculation
Long update = i.getDetails().getUpdateEvent().getTime().getTime();
Long creation = i.getDetails().getCreationEvent().getTime().getTime();
java.util.Date today = new java.util.Date();
Long now = today.getTime();
//RunPython rp0 = new RunPython();
//String st = rp0.testCreateUpdate(creation, update, now);
/******************* Block Start for triggering feature calculation ******************/
RunPython rp = new RunPython();
logger().info("Before Triggering Feature Calculation for " + value);
Boolean isFeatureFile = false;
for (Annotation a : i.linkedAnnotationList()) {
logger().info("Scheduling all Experiment Files of " + " for re-indexing");
logger().info("Scheduling all Experiment Files of " + a + " for re-indexing");
if (a instanceof FileAnnotation) {
FileAnnotation ann2 = (FileAnnotation) a;
String fName = ann2.getFile().getName();
String subfName = fName.substring(fName.length()-3);
if ((subfName != null)){
if (subfName.equalsIgnoreCase(".h5")){
isFeatureFile = true;
}
}
if (!isFeatureFile){
for (final DatasetImageLink dil : i.unmodifiableDatasetLinks()) {
//logger().info("WIthin Triggering Feature Calculation for " + value);
Long datasetID = dil.parent().getId();
//logger().info("WIthin Triggering Feature Calculation for " + Long.toString(datasetID));
String status = rp.runFeatCalc(Long.toString(imageId), Long.toString(datasetID), user, group);
//String status = rp.runFeatCalc(Long.toString(imageId), Long.toString(datasetID),Long.toString(creation), Long.toString(now));
logger().info("WIthin Triggering Feature Calculation STATUS: " + status);
}
}
}
}
/******************* Block Ends ******************/
/******************* Block Start for Experiment File Indexing to Lucene Index ******************/
String tagNs = null;
String tagName = null;
String subtagName = null;
String XML = null;
HashMap <String, String> map = null;
// get the annotations for the image and look for a FileAnnotation
for (Annotation a : i.linkedAnnotationList()) {
if (a instanceof FileAnnotation) {
FileAnnotation ann = (FileAnnotation) a;
tagNs = ann.getNs();
tagName = ann.getFile().getName();
subtagName = tagName.substring(tagName.length()-7);
if ((tagNs != null) && (subtagName != null)){
if (tagNs.equalsIgnoreCase("openmicroscopy.org/omero/editor/experiment") && subtagName.equalsIgnoreCase("cpe.xml")){
OriginalFile file = ann.getFile();
ome.io.nio.OriginalFilesService fileservice = (ome.io.nio.OriginalFilesService)ome.system.OmeroContext.getManagedServerContext().getBean("/OMERO/Files");
String path = fileservice.getFilesPath(file.getId());
String format = file.getMimetype();
map = exParser.parse(new File(path));
// parse the XML string
Iterator<String> iterator = map.keySet().iterator();
while (iterator.hasNext()) {
String key = (String) iterator.next();
add(document, key, map.get(key), _opts);
}
}
}
}
}
/******************* Block Ends ******************/
}
}
}
there's no compile error.
from the Indexer log, I saw the following part has been successfully went through.
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logger().info("Before Triggering Feature Calculation for " + value);
But after that, I don't see any log, meaning there might be many run time errors from the line of..
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for (Annotation a : i.linkedAnnotationList()) {
Could anyone give me the link for API documents of 4.3.x so that I can get help in order to update my code?
Best,
BK
