removed old MySQL dependencies

JaneliaSciComp · Mar 10, 2021 · a03dc89 · a03dc89
1 parent bf82ae9
commit a03dc89
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Showing 5 changed files with 2 additions and 100 deletions.
diff --git a/build.gradle b/build.gradle
@@ -7,7 +7,7 @@ allprojects {
     apply plugin: 'maven-publish'
     apply plugin: 'idea'
     group = 'org.janelia.jacs-model'
-    version = '2.41.2'
+    version = '2.42'
 }
 
 subprojects {

diff --git a/jacs-model-access/src/main/java/org/janelia/model/access/domain/dao/TmNeuronMetadataDao.java b/jacs-model-access/src/main/java/org/janelia/model/access/domain/dao/TmNeuronMetadataDao.java
@@ -20,12 +20,9 @@ public interface TmNeuronMetadataDao extends DomainObjectDao<TmNeuronMetadata> {
     List<TmNeuronMetadata> getTmNeuronMetadataByWorkspaceId(TmWorkspace workspace, String subjectKey, long offset, int length);
     Iterable<TmNeuronMetadata> streamWorkspaceNeurons(TmWorkspace workspace, String subjectKey, long offset, int length);
     List<TmNeuronMetadata> getTmNeuronMetadataByNeuronIds(TmWorkspace workspace, List<Long> neuronList);
-    List<Pair<TmNeuronMetadata, InputStream>> getTmNeuronsMetadataWithPointStreamsByWorkspaceId(
-            TmWorkspace workspace, String subjectKey, long offset, int length);
     boolean removeTmNeuron(Long neuronId, boolean isLarge, TmWorkspace workspace, String subjectKey);
     void updateNeuronStyles(BulkNeuronStyleUpdate bulkNeuronStyleUpdate, TmWorkspace workspace, String subjectKey);
     void removeEmptyNeuronsInWorkspace(TmWorkspace workspace, String subjectKey);
-    void bulkMigrateNeuronsInWorkspace(TmWorkspace workspace, Collection<TmNeuronMetadata> neurons, String subjectKey);
     void updateNeuronTagsForNeurons(TmWorkspace workspace, List<Long> neuronIds, List<String> tags, boolean tagState, String subjectKey);
     Long getNeuronCountsForWorkspace(TmWorkspace workspace, String subjectKey);
     TmNeuronMetadata saveNeuronMetadata(TmWorkspace workspace, TmNeuronMetadata neuron, String subjectKey);

diff --git a/...ess/src/main/java/org/janelia/model/access/domain/dao/mongo/TmNeuronMetadataMongoDao.java b/...ess/src/main/java/org/janelia/model/access/domain/dao/mongo/TmNeuronMetadataMongoDao.java
@@ -22,12 +22,9 @@
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
 import org.bson.conversions.Bson;
 import org.janelia.model.access.domain.DomainDAO;
 import org.janelia.model.access.domain.dao.*;
-import org.janelia.model.domain.DomainUtils;
 import org.janelia.model.domain.Reference;
 import org.janelia.model.domain.tiledMicroscope.*;
 import org.janelia.model.access.domain.TimebasedIdentifierGenerator;
@@ -357,70 +354,6 @@ public void removeEmptyNeuronsInWorkspace(TmWorkspace workspace, String subjectK
                 ));
     }
 
-    @Override
-    public void bulkMigrateNeuronsInWorkspace(TmWorkspace workspace, Collection<TmNeuronMetadata> neurons, String subjectKey) {
-        String collectionName = MongoDaoHelper.findOrCreateCappedCollection (this, mongoDatabase,
-                "tmNeuron", 20000000000L, TmNeuronMetadata.class);
-        try {
-            workspace.setNeuronCollection(collectionName);
-            workspace = domainDao.save(subjectKey, workspace);
-        } catch (Exception e) {
-            LOG.error("ERROR SAVING WORKSPACE {} - Issue with Neuron Collection Key", workspace.getId(),e);
-            throw new RuntimeException("ERROR SAVING WORKSPACE" + workspace.getId() + " - Issue with Neuron Collection Key");
-        }
-
-        MongoCollection<TmNeuronMetadata> copyLoc = getNeuronCollection(collectionName);
-        if (neurons==null || neurons.isEmpty())
-            return;
-        List<TmNeuronMetadata> neuronList = new ArrayList<>(neurons);
-        try {
-            int prevCount = 0;
-            for (int i=0; i<neuronList.size(); i=i+1000) {
-                if (neuronList.size()>(i+1000)) {
-                    copyLoc.insertMany(neuronList.subList(i, i + 1000));
-                    LOG.info("Inserted {} neurons", i+1000);
-                }
-                else {
-                    copyLoc.insertMany(neuronList.subList(i, neuronList.size()));
-                    LOG.info("Inserted {} neurons", neuronList.size());
-                }
-            }
-            LOG.info("Finished workspace {}",workspace.getId());
-        } catch (org.bson.BsonMaximumSizeExceededException e) {
-            // one or more of the documents is too big
-            // save them to gridfs and then try again
-            int count = 0;
-            List<Long> largeNeurons = new ArrayList<>();
-            List<TmNeuronMetadata> truncatedList = new ArrayList<>();
-            boolean hitFirstLarge = false;
-            for (TmNeuronMetadata neuron: neuronList) {
-                if (hitFirstLarge)
-                    truncatedList.add(neuron);
-                // remove records that were saved before batch failed
-                MongoDaoHelper.deleteMatchingRecords(copyLoc,
-                        Filters.and(MongoDaoHelper.createFilterById(neuron.getId()),
-                                permissionsHelper.createWritePermissionFilterForSubjectKey(subjectKey)));
-                boolean isLarge = checkLargeNeuron(neuron);
-                TmNeuronData pointData = neuron.getNeuronData();
-                if (isLarge) {
-                    hitFirstLarge = true;
-                    largeNeurons.add(neuron.getId());
-                    neuron.setNeuronData(null);
-                    saveLargeNeuronPointData(neuron.getId(), pointData);
-                    neuron.setLargeNeuron(isLarge);
-                }
-            }
-
-            try {
-                LOG.info("Large neurons in this batch are {}",largeNeurons);
-                if (!truncatedList.isEmpty())
-                    copyLoc.insertMany(truncatedList);
-            } catch (org.bson.BsonMaximumSizeExceededException ee) {
-                LOG.error("ERROR PROCESSING {} - Issue with Large Neurons", workspace.getId(),e);
-            }
-        }
-    }
-
     @Override
     public void updateNeuronTagsForNeurons(TmWorkspace workspace, List<Long> neuronIds, List<String> tags, boolean tagState,
                                             String subjectKey) {
@@ -459,21 +392,4 @@ public Long getNeuronCountsForWorkspace(TmWorkspace workspace, String subjectKey
     private MongoCollection<TmNeuronMetadata> getNeuronCollection(String collectionName) {
         return mongoDatabase.getCollection(collectionName, TmNeuronMetadata.class);
     }
-
-    @Override
-    public List<Pair<TmNeuronMetadata, InputStream>> getTmNeuronsMetadataWithPointStreamsByWorkspaceId(TmWorkspace workspace,
-                                                                                                       String subjectKey,
-                                                                                                       long offset, int length) {
-        workspace.setNeuronCollection("tmNeuron");
-        List<TmNeuronMetadata> workspaceNeurons = getTmNeuronMetadataByWorkspaceId(workspace,subjectKey, offset, length);
-        if (workspaceNeurons.isEmpty()) {
-            return Collections.emptyList();
-        }
-        Map<Long, TmNeuronMetadata> indexedWorkspaceNeurons = DomainUtils.getMapById(workspaceNeurons);
-        Map<Long, InputStream> neuronsPointStreams = tmNeuronBufferDao.streamNeuronPointsByWorkspaceId(indexedWorkspaceNeurons.keySet(), workspace.getId());
-
-        return workspaceNeurons.stream()
-                .map(neuron -> ImmutablePair.of(neuron, neuronsPointStreams.get(neuron.getId())))
-                .collect(Collectors.toList());
-    }
 }
diff --git a/...n/java/org/janelia/model/access/domain/dao/searchables/TmNeuronMetadataSearchableDao.java b/...n/java/org/janelia/model/access/domain/dao/searchables/TmNeuronMetadataSearchableDao.java
@@ -77,12 +77,6 @@ public void removeEmptyNeuronsInWorkspace(TmWorkspace workspace, String subjectK
         tmNeuronMetadataDao.removeEmptyNeuronsInWorkspace(workspace, subjectKey);
     }
 
-    @Override
-    public void bulkMigrateNeuronsInWorkspace(TmWorkspace workspace, Collection<TmNeuronMetadata> neurons,
-                                              String subjectKey) {
-        tmNeuronMetadataDao.bulkMigrateNeuronsInWorkspace(workspace, neurons, subjectKey);
-    }
-
     @Override
     public void updateNeuronTagsForNeurons(TmWorkspace workspace, List<Long> neuronIds, List<String> tags, boolean tagState,
                                            String subjectKey) {
@@ -109,10 +103,4 @@ public List<TmOperation> getOperations(Long workspaceId, Long neuronId, Date sta
         return tmNeuronMetadataDao.getOperations(workspaceId, neuronId, startDate, endDate);
     }
 
-    @Override
-    public List<Pair<TmNeuronMetadata, InputStream>> getTmNeuronsMetadataWithPointStreamsByWorkspaceId(TmWorkspace workspace,
-                                                                                                       String subjectKey, long offset, int length) {
-        return tmNeuronMetadataDao.getTmNeuronsMetadataWithPointStreamsByWorkspaceId(workspace, subjectKey,offset,length);
-    }
-
 }
diff --git a/jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmNeuronMetadata.java b/jacs-model-core/src/main/java/org/janelia/model/domain/tiledMicroscope/TmNeuronMetadata.java
@@ -192,6 +192,7 @@ public void initNeuronData() {
         for (Long geoId : neuronData.getGeoAnnotationMap().keySet()) {
             TmGeoAnnotation geoAnnotation = neuronData.getGeoAnnotationMap().get(geoId);
             geoAnnotation.setNeuronId(getId());
+            geoAnnotation.setModificationDate(geoAnnotation.getCreationDate());
         }
 
     }