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Add auditing of what method was used for data imports, updates, deletes
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‎luminex/src/org/labkey/luminex/LuminexRunCreator.java‎

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/*
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* Copyright (c) 2012-2018 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.labkey.luminex;
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import org.jetbrains.annotations.NotNull;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.data.Container;
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import org.labkey.api.exp.ExperimentException;
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import org.labkey.api.exp.ObjectProperty;
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import org.labkey.api.exp.OntologyManager;
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import org.labkey.api.exp.OntologyObject;
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import org.labkey.api.exp.api.ExpData;
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import org.labkey.api.exp.api.ExpExperiment;
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import org.labkey.api.exp.api.ExpRun;
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import org.labkey.api.exp.api.ExperimentService;
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import org.labkey.api.exp.property.DomainProperty;
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import org.labkey.api.query.BatchValidationException;
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import org.labkey.api.query.ValidationException;
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import org.labkey.api.security.permissions.DeletePermission;
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import org.labkey.api.assay.AssayRunUploadContext;
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import org.labkey.api.assay.DefaultAssayRunCreator;
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import org.labkey.luminex.model.Analyte;
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import java.util.List;
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import java.util.Map;
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/**
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* Saves analyte specific properties and handles re-run
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* User: jeckels
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* Date: Feb 13, 2012
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*/
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public class LuminexRunCreator extends DefaultAssayRunCreator<LuminexAssayProvider>
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{
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/** Lock object to only allow one thread to be running a Luminex transform script and importing its results at a time, issue 17424 */
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public static final Object LOCK_OBJECT = new Object();
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public LuminexRunCreator(LuminexAssayProvider provider)
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{
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super(provider);
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}
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@Override
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public ExpExperiment saveExperimentRun(AssayRunUploadContext<LuminexAssayProvider> uploadContext, @Nullable ExpExperiment batch, @NotNull ExpRun run, boolean forceSaveBatchProps) throws ExperimentException, ValidationException
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{
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// Only allow one thread to be running a Luminex transform script and importing its results at a time
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// See issue 17424
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synchronized (LOCK_OBJECT)
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{
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LuminexRunContext context = (LuminexRunContext)uploadContext;
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batch = super.saveExperimentRun(context, batch, run, forceSaveBatchProps);
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Container container = context.getContainer();
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// Save the analyte properties
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List<ExpData> outputs = run.getDataOutputs();
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for (ExpData output : outputs)
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{
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var dataId = output.getRowId();
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for (Analyte analyte : LuminexManager.get().getAnalytes(dataId))
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{
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Map<DomainProperty, String> properties = context.getAnalyteProperties(analyte.getName());
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ObjectProperty[] objProperties = new ObjectProperty[properties.size()];
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int i = 0;
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for (Map.Entry<DomainProperty, String> entry : properties.entrySet())
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{
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ObjectProperty property = new ObjectProperty(analyte.getLsid(),
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container, entry.getKey().getPropertyURI(),
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entry.getValue(), entry.getKey().getPropertyDescriptor().getPropertyType());
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objProperties[i++] = property;
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}
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removeExistingAnalyteProperties(container, analyte);
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OntologyManager.insertProperties(container, analyte.getLsid(), objProperties);
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}
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}
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}
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try
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{
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handleReRun(uploadContext, run);
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}
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catch (BatchValidationException e)
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{
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throw new ExperimentException(e);
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}
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return batch;
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}
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private void handleReRun(AssayRunUploadContext<LuminexAssayProvider> uploadContext, ExpRun run) throws ValidationException, BatchValidationException
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{
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if (uploadContext.getReRunId() != null)
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{
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ExpRun replacedRun = ExperimentService.get().getExpRun(uploadContext.getReRunId().intValue());
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if (replacedRun != null)
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{
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// Migrate the original Created and CreatedBy values from the old run to the new run
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run.setCreated(replacedRun.getCreated());
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run.setCreatedBy(replacedRun.getCreatedBy());
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run.save(uploadContext.getUser());
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if (uploadContext instanceof LuminexRunContext && ((LuminexRunContext)uploadContext).getRetainExclusions())
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LuminexManager.get().retainExclusions((LuminexRunContext)uploadContext, replacedRun, run);
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// Delete the old run, which has been replaced
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if (replacedRun.getContainer().hasPermission(uploadContext.getUser(), DeletePermission.class))
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{
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replacedRun.delete(uploadContext.getUser());
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}
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}
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}
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}
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private void removeExistingAnalyteProperties(Container container, Analyte analyte)
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{
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OntologyObject analyteObject = OntologyManager.getOntologyObject(container, analyte.getLsid());
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if (analyteObject != null)
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{
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OntologyManager.deleteProperties(container, analyteObject.getObjectId());
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}
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}
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}
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/*
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* Copyright (c) 2012-2018 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.labkey.luminex;
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import org.jetbrains.annotations.NotNull;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.audit.TransactionAuditProvider;
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import org.labkey.api.data.Container;
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import org.labkey.api.exp.ExperimentException;
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import org.labkey.api.exp.ObjectProperty;
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import org.labkey.api.exp.OntologyManager;
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import org.labkey.api.exp.OntologyObject;
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import org.labkey.api.exp.api.ExpData;
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import org.labkey.api.exp.api.ExpExperiment;
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import org.labkey.api.exp.api.ExpRun;
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import org.labkey.api.exp.api.ExperimentService;
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import org.labkey.api.exp.property.DomainProperty;
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import org.labkey.api.query.BatchValidationException;
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import org.labkey.api.query.ValidationException;
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import org.labkey.api.security.permissions.DeletePermission;
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import org.labkey.api.assay.AssayRunUploadContext;
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import org.labkey.api.assay.DefaultAssayRunCreator;
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import org.labkey.luminex.model.Analyte;
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import java.util.List;
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import java.util.Map;
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/**
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* Saves analyte specific properties and handles re-run
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* User: jeckels
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* Date: Feb 13, 2012
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*/
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public class LuminexRunCreator extends DefaultAssayRunCreator<LuminexAssayProvider>
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{
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/** Lock object to only allow one thread to be running a Luminex transform script and importing its results at a time, issue 17424 */
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public static final Object LOCK_OBJECT = new Object();
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public LuminexRunCreator(LuminexAssayProvider provider)
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{
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super(provider);
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}
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@Override
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public ExpExperiment saveExperimentRun(AssayRunUploadContext<LuminexAssayProvider> uploadContext, @Nullable ExpExperiment batch, @NotNull ExpRun run, boolean forceSaveBatchProps, @Nullable Map<TransactionAuditProvider.TransactionDetail, Object> transactionDetails) throws ExperimentException, ValidationException
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{
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// Only allow one thread to be running a Luminex transform script and importing its results at a time
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// See issue 17424
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synchronized (LOCK_OBJECT)
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{
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LuminexRunContext context = (LuminexRunContext)uploadContext;
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batch = super.saveExperimentRun(context, batch, run, forceSaveBatchProps, transactionDetails);
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Container container = context.getContainer();
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// Save the analyte properties
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List<ExpData> outputs = run.getDataOutputs();
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for (ExpData output : outputs)
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{
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var dataId = output.getRowId();
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for (Analyte analyte : LuminexManager.get().getAnalytes(dataId))
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{
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Map<DomainProperty, String> properties = context.getAnalyteProperties(analyte.getName());
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ObjectProperty[] objProperties = new ObjectProperty[properties.size()];
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int i = 0;
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for (Map.Entry<DomainProperty, String> entry : properties.entrySet())
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{
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ObjectProperty property = new ObjectProperty(analyte.getLsid(),
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container, entry.getKey().getPropertyURI(),
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entry.getValue(), entry.getKey().getPropertyDescriptor().getPropertyType());
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objProperties[i++] = property;
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}
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removeExistingAnalyteProperties(container, analyte);
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OntologyManager.insertProperties(container, analyte.getLsid(), objProperties);
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}
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}
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}
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try
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{
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handleReRun(uploadContext, run);
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}
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catch (BatchValidationException e)
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{
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throw new ExperimentException(e);
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}
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return batch;
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}
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private void handleReRun(AssayRunUploadContext<LuminexAssayProvider> uploadContext, ExpRun run) throws ValidationException, BatchValidationException
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{
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if (uploadContext.getReRunId() != null)
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{
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ExpRun replacedRun = ExperimentService.get().getExpRun(uploadContext.getReRunId().intValue());
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if (replacedRun != null)
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{
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// Migrate the original Created and CreatedBy values from the old run to the new run
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run.setCreated(replacedRun.getCreated());
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run.setCreatedBy(replacedRun.getCreatedBy());
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run.save(uploadContext.getUser());
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if (uploadContext instanceof LuminexRunContext && ((LuminexRunContext)uploadContext).getRetainExclusions())
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LuminexManager.get().retainExclusions((LuminexRunContext)uploadContext, replacedRun, run);
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// Delete the old run, which has been replaced
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if (replacedRun.getContainer().hasPermission(uploadContext.getUser(), DeletePermission.class))
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{
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replacedRun.delete(uploadContext.getUser());
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}
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}
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}
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}
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private void removeExistingAnalyteProperties(Container container, Analyte analyte)
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{
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OntologyObject analyteObject = OntologyManager.getOntologyObject(container, analyte.getLsid());
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if (analyteObject != null)
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{
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OntologyManager.deleteProperties(container, analyteObject.getObjectId());
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}
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}
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}

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