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Faster combined query for retrieving datasets via API #9684

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merged 16 commits into from
May 24, 2024
Merged

Faster combined query for retrieving datasets via API #9684

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2968ba2
combined query for retrieving datasets with API
ErykKul Jun 28, 2023
c8a1352
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul Jun 28, 2023
cdc3e3d
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul Jun 29, 2023
6083ead
better error handling - should fix failed integration test
ErykKul Jun 29, 2023
8e75241
find deep in file listing
ErykKul Jul 4, 2023
ca5b28c
Merge branch 'develop' into 9683_get_dataset_api_in_single_query
ErykKul Sep 1, 2023
2f98f23
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul Sep 6, 2023
53d0d85
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul Sep 19, 2023
9599f44
merged develop branch
ErykKul Apr 17, 2024
773e2e2
fixed error type: badRequest -> notFound
ErykKul Apr 17, 2024
6d0a1ba
if global Id not found, try alt global Id
ErykKul Apr 19, 2024
f558e33
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul Apr 22, 2024
60c53af
find deep disabled for the files API
ErykKul Apr 22, 2024
1eea73c
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul May 2, 2024
3b97add
removed newline
ErykKul May 6, 2024
fb4eb8b
Merge branch 'IQSS:develop' into 9683_get_dataset_api_in_single_query
ErykKul May 24, 2024
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3 changes: 2 additions & 1 deletion src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,8 @@ public Dataset findDeep(Object pk) {
.setHint("eclipselink.left-join-fetch", "o.files.dataFileTags")
.setHint("eclipselink.left-join-fetch", "o.files.fileMetadatas")
.setHint("eclipselink.left-join-fetch", "o.files.fileMetadatas.fileCategories")
//.setHint("eclipselink.left-join-fetch", "o.files.guestbookResponses")
.setHint("eclipselink.left-join-fetch", "o.files.fileMetadatas.varGroups")
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Is this part of the optimization here? I would guess this isn't often accessed, so I'm not sure how much of a performance help it would be.

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I had seen in in the query log even when it was not used. For large datasets it does make a difference (one query less for each file).

//.setHint("eclipselink.left-join-fetch", "o.files.guestbookResponses
.setHint("eclipselink.left-join-fetch", "o.files.embargo")
.setHint("eclipselink.left-join-fetch", "o.files.fileAccessRequests")
.setHint("eclipselink.left-join-fetch", "o.files.owner")
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39 changes: 29 additions & 10 deletions src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
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Expand Up @@ -17,6 +17,7 @@
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.DvObjectServiceBean;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.GuestbookResponseServiceBean;
import edu.harvard.iq.dataverse.MetadataBlock;
import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
Expand All @@ -41,6 +42,7 @@
import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean;
import edu.harvard.iq.dataverse.license.LicenseServiceBean;
import edu.harvard.iq.dataverse.metrics.MetricsServiceBean;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
import edu.harvard.iq.dataverse.locality.StorageSiteServiceBean;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
Expand Down Expand Up @@ -390,31 +392,48 @@ protected DataverseLinkingDataverse findDataverseLinkingDataverseOrDie(String da
}

protected Dataset findDatasetOrDie(String id) throws WrappedResponse {
return findDatasetOrDie(id, false);
}

protected Dataset findDatasetOrDie(String id, boolean deep) throws WrappedResponse {
Long datasetId;
Dataset dataset;
if (id.equals(PERSISTENT_ID_KEY)) {
String persistentId = getRequestParameter(PERSISTENT_ID_KEY.substring(1));
if (persistentId == null) {
throw new WrappedResponse(
badRequest(BundleUtil.getStringFromBundle("find.dataset.error.dataset_id_is_null", Collections.singletonList(PERSISTENT_ID_KEY.substring(1)))));
}
dataset = datasetSvc.findByGlobalId(persistentId);
if (dataset == null) {
throw new WrappedResponse(notFound(BundleUtil.getStringFromBundle("find.dataset.error.dataset.not.found.persistentId", Collections.singletonList(persistentId))));
GlobalId globalId;
try {
globalId = PidUtil.parseAsGlobalID(persistentId);
} catch (IllegalArgumentException e) {
throw new WrappedResponse(
badRequest(BundleUtil.getStringFromBundle("find.dataset.error.dataset.not.found.bad.id", Collections.singletonList(persistentId))));
}
datasetId = dvObjSvc.findIdByGlobalId(globalId, DvObject.DType.Dataset);
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if (datasetId == null) {
throw new WrappedResponse(
badRequest(BundleUtil.getStringFromBundle("find.dataset.error.dataset_id_is_null", Collections.singletonList(PERSISTENT_ID_KEY.substring(1)))));
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}
return dataset;

} else {
try {
dataset = datasetSvc.find(Long.parseLong(id));
if (dataset == null) {
throw new WrappedResponse(notFound(BundleUtil.getStringFromBundle("find.dataset.error.dataset.not.found.id", Collections.singletonList(id))));
}
return dataset;
datasetId = Long.parseLong(id);
} catch (NumberFormatException nfe) {
throw new WrappedResponse(
badRequest(BundleUtil.getStringFromBundle("find.dataset.error.dataset.not.found.bad.id", Collections.singletonList(id))));
}
}

if (deep) {
dataset = datasetSvc.findDeep(datasetId);
} else {
dataset = datasetSvc.find(datasetId);
}
if (dataset == null) {
throw new WrappedResponse(notFound(BundleUtil.getStringFromBundle("find.dataset.error.dataset.not.found.id", Collections.singletonList(id))));
}
return dataset;
}

protected DataFile findDataFileOrDie(String id) throws WrappedResponse {
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
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Expand Up @@ -252,7 +252,7 @@ public interface DsVersionHandler<T> {
@Path("{id}")
public Response getDataset(@Context ContainerRequestContext crc, @PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) {
return response( req -> {
final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id)));
final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id, true)));
final DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(req, retrieved));
final JsonObjectBuilder jsonbuilder = json(retrieved);
//Report MDC if this is a released version (could be draft if user has access, or user may not have access at all and is not getting metadata beyond the minimum)
Expand Down Expand Up @@ -490,7 +490,7 @@ public Response getVersion(@Context ContainerRequestContext crc, @PathParam("id"
@Path("{id}/versions/{versionId}/files")
public Response getVersionFiles(@Context ContainerRequestContext crc, @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
return response( req -> ok( jsonFileMetadatas(
getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas())), getRequestUser(crc));
getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId, true), uriInfo, headers).getFileMetadatas())), getRequestUser(crc));
}

@GET
Expand Down
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