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remove the provenance file from the dataset #4

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merged 3 commits into from
Jun 3, 2024
Merged

remove the provenance file from the dataset #4

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aa79280
remove the provenance file from the dataset
KochTobi Jun 3, 2024
62ed696
make code better
KochTobi Jun 3, 2024
9b3a246
remove recovery
KochTobi Jun 3, 2024
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23 changes: 21 additions & 2 deletions src/main/java/life/qbic/registration/openbis/OpenBisDropboxETL.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import life.qbic.registration.openbis.exceptions.fail.MeasurementHasDataException;
import life.qbic.registration.openbis.exceptions.fail.UnknownSampleTypeException;
import life.qbic.registration.openbis.types.QDatasetType;
Expand Down Expand Up @@ -50,8 +52,9 @@ public boolean shouldRetryProcessing(DataSetRegistrationContext context, Excepti

@Override
public void process(IDataSetRegistrationTransactionV2 transaction) {
File provenanceFile = new File(transaction.getIncoming(), PROVENANCE_FILE_NAME);
DataSetProvenance dataSetProvenance = ProvenanceParser.parseProvenanceJson(
new File(transaction.getIncoming(), PROVENANCE_FILE_NAME));
provenanceFile);

String measurementId = dataSetProvenance.measurementId();

Expand All @@ -68,8 +71,24 @@ public void process(IDataSetRegistrationTransactionV2 transaction) {
newDataSet.setPropertyValue(QPropertyType.Q_TASK_ID.getOpenBisPropertyName(), dataSetProvenance.taskId());
QDatasetType qDatasetType = getDatasetType(measurementSample);
newDataSet.setDataSetType(qDatasetType.name());
moveFiles(transaction, newDataSet, provenanceFile);

transaction.moveFile(transaction.getIncoming().getAbsolutePath(), newDataSet);
}

private void moveFiles(IDataSetRegistrationTransactionV2 transactionV2, IDataSet dataSet, File provenanceFile) {

try {
var buffer = Files.readAllBytes(provenanceFile.toPath().toAbsolutePath());
Files.delete(provenanceFile.toPath());
try {
transactionV2.moveFile(transactionV2.getIncoming().getAbsolutePath(), dataSet);
} catch (Exception e) {
Files.write(provenanceFile.toPath().toAbsolutePath(), buffer);
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I'm like 99% sure openBIS will automatically recover deleted files (I think it stores a copy of the original folder) on failure, so I advise against writing anything after an exception the ETL service - I'm not sure how this will influence the behaviour

throw new RuntimeException(e);
}
} catch (IOException e) {
throw new RuntimeException(e);
}
}

private static QDatasetType getDatasetType(ISampleImmutable measurementSample) {
Expand Down