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24 changes: 24 additions & 0 deletions
24
src/main/java/life/qbic/registration/openbis/OpenBisSearch.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| package life.qbic.registration.openbis; | ||
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| import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable; | ||
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| /** | ||
| * Interface that allows for searching openbis infrastructure | ||
| */ | ||
| public interface OpenBisSearch { | ||
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| /** | ||
| * Searches for a sample with the measurement code in openbis. Assumes that there is one sample and only one; Fails otherwise. | ||
| * @param measurementId the identifier of the measurement | ||
| * @return the existing measurement | ||
| */ | ||
| ISampleImmutable getMeasurementSample(String measurementId); | ||
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| /** | ||
| * Checks for datasets attached to a measurement sample | ||
| * @param measurementSample | ||
| * @return true if a dataset is contained in the measurement; false otherwise. | ||
| */ | ||
| boolean doesMeasurementHaveData(ISampleImmutable measurementSample); | ||
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| } |
69 changes: 69 additions & 0 deletions
69
src/main/java/life/qbic/registration/openbis/OpenBisSearchImpl.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,69 @@ | ||
| package life.qbic.registration.openbis; | ||
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| import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable; | ||
| import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable; | ||
| import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService; | ||
| import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria; | ||
| import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause; | ||
| import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute; | ||
| import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria; | ||
| import java.util.List; | ||
| import life.qbic.registration.openbis.exceptions.fail.ToManyMeasurementsException; | ||
| import life.qbic.registration.openbis.exceptions.retry.NoMeasurementsFoundException; | ||
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| /** | ||
| * Implements the Openbis access | ||
| */ | ||
| public class OpenBisSearchImpl implements OpenBisSearch { | ||
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| private final ISearchService searchService; | ||
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| public OpenBisSearchImpl(ISearchService searchService) { | ||
| this.searchService = searchService; | ||
| } | ||
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| @Override | ||
| public ISampleImmutable getMeasurementSample(String measurementId) { | ||
| return findMeasurementSample(measurementId, searchService); | ||
| } | ||
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| private static ISampleImmutable findMeasurementSample(String measurementId, | ||
| ISearchService searchService) { | ||
| SearchCriteria measurementSearchCriteria = new SearchCriteria(); | ||
| measurementSearchCriteria.addMatchClause( | ||
| MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, measurementId)); | ||
| List<ISampleImmutable> immutableSamples = searchService.searchForSamples( | ||
| measurementSearchCriteria); | ||
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| if (immutableSamples.isEmpty()) { | ||
| //measurement not found | ||
| throw new NoMeasurementsFoundException("Measurement '" + measurementId + "' not found"); | ||
| } | ||
| if (immutableSamples.size() > 1) { | ||
| throw new ToManyMeasurementsException( | ||
| "Multiple measurement with id '" + measurementId + "' found"); | ||
| } | ||
| return immutableSamples.get(0); | ||
| } | ||
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| @Override | ||
| public boolean doesMeasurementHaveData(ISampleImmutable sample) { | ||
| return doesMeasurementHaveData(sample, searchService); | ||
| } | ||
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| private static boolean doesMeasurementHaveData(ISampleImmutable sample, | ||
| ISearchService searchService) { | ||
| SearchCriteria parentSampleSearchCriteria = new SearchCriteria(); | ||
| parentSampleSearchCriteria.addMatchClause( | ||
| MatchClause.createAttributeMatch(MatchClauseAttribute.PERM_ID, sample.getPermId())); | ||
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| SearchCriteria dataSetSearchCriteria = new SearchCriteria(); | ||
| dataSetSearchCriteria.addSubCriteria( | ||
| SearchSubCriteria.createDataSetContainerCriteria(parentSampleSearchCriteria)); | ||
| List<IDataSetImmutable> existingDataSets = searchService.searchForDataSets( | ||
| dataSetSearchCriteria); | ||
| return !existingDataSets.isEmpty(); | ||
| } | ||
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| } |
28 changes: 28 additions & 0 deletions
28
src/test/java/life/qbic/registration/openbis/ProvenanceParserTest.groovy
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| @@ -0,0 +1,28 @@ | ||
| package life.qbic.registration.openbis | ||
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| import spock.lang.Specification | ||
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| /** | ||
| * TODO! | ||
| * <b>short description</b> | ||
| * | ||
| * <p>detailed description</p> | ||
| * | ||
| * @since <version tag> | ||
| */ | ||
| class ProvenanceParserTest extends Specification { | ||
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| final File validFile = new File(ProvenanceParserTest.class.getClassLoader().getResource("valid-provenance.json").toURI()); | ||
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| def "parsing just works"() { | ||
| when: | ||
| var resultingProvenanceObject = new ProvenanceParser().parseProvenanceJson(validFile) | ||
| then: | ||
| resultingProvenanceObject.measurementId() == "NGSQTEST001AE-1234512312" | ||
| resultingProvenanceObject.origin() == "/Users/myuser/registration" | ||
| resultingProvenanceObject.datasetFiles() == ["file1.fastq.gz", "file2.fastq.gz"] | ||
| resultingProvenanceObject.user() == "/Users/myuser" | ||
| resultingProvenanceObject.taskId() == "ce36775e-0d06-471e-baa7-1e3b63de871f" | ||
| resultingProvenanceObject.history() == ["/some/dir", "/some/other/dir"] | ||
| } | ||
| } |
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|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| { | ||
| "origin": "/Users/myuser/registration", | ||
| "user": "/Users/myuser", | ||
| "measurementId": "NGSQTEST001AE-1234512312", | ||
| "datasetFiles" : [ | ||
| "file1.fastq.gz", | ||
| "file2.fastq.gz" | ||
| ], | ||
| "taskId": "ce36775e-0d06-471e-baa7-1e3b63de871f", | ||
| "history": [ | ||
| "/some/dir", | ||
| "/some/other/dir" | ||
| ] | ||
| } |