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10202 extend get version files api to include total file count #10215

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merged 5 commits into from
Jan 10, 2024
Merged

10202 extend get version files api to include total file count #10215

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2b1e5dd
Extend getVersionFiles API endpoint to include the total file count
stevenwinship Jan 8, 2024
0807b1f
fix format
stevenwinship Jan 8, 2024
53e525d
fix format
stevenwinship Jan 8, 2024
622a676
updated per review comments
stevenwinship Jan 9, 2024
dfb1795
Added: minor docs formatting tweaks
GPortas Jan 9, 2024
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66 changes: 24 additions & 42 deletions src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
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Original file line number Diff line number Diff line change
@@ -1,29 +1,6 @@
package edu.harvard.iq.dataverse.api;

import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.DataFileServiceBean;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetLinkingDataverse;
import edu.harvard.iq.dataverse.DatasetLinkingServiceBean;
import edu.harvard.iq.dataverse.DatasetServiceBean;
import edu.harvard.iq.dataverse.DatasetVersionServiceBean;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseLinkingDataverse;
import edu.harvard.iq.dataverse.DataverseLinkingServiceBean;
import edu.harvard.iq.dataverse.DataverseRoleServiceBean;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.DvObjectServiceBean;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.GuestbookResponseServiceBean;
import edu.harvard.iq.dataverse.MetadataBlock;
import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
import edu.harvard.iq.dataverse.PermissionServiceBean;
import edu.harvard.iq.dataverse.RoleAssigneeServiceBean;
import edu.harvard.iq.dataverse.UserNotificationServiceBean;
import edu.harvard.iq.dataverse.UserServiceBean;
import edu.harvard.iq.dataverse.*;
import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
Expand All @@ -40,8 +17,8 @@
import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
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.locality.StorageSiteServiceBean;
import edu.harvard.iq.dataverse.metrics.MetricsServiceBean;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
Expand All @@ -51,33 +28,30 @@
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
import edu.harvard.iq.dataverse.validation.PasswordValidatorServiceBean;
import java.io.InputStream;
import java.net.URI;
import java.util.Arrays;
import java.util.Collections;
import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.logging.Level;
import java.util.logging.Logger;
import jakarta.ejb.EJB;
import jakarta.ejb.EJBException;
import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonArrayBuilder;
import jakarta.json.JsonException;
import jakarta.json.JsonObject;
import jakarta.json.JsonObjectBuilder;
import jakarta.json.JsonValue;
import jakarta.json.*;
import jakarta.json.JsonValue.ValueType;
import jakarta.persistence.EntityManager;
import jakarta.persistence.NoResultException;
import jakarta.persistence.PersistenceContext;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.ws.rs.container.ContainerRequestContext;
import jakarta.ws.rs.core.*;
import jakarta.ws.rs.core.Context;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
import jakarta.ws.rs.core.Response.ResponseBuilder;
import jakarta.ws.rs.core.Response.Status;

import java.io.InputStream;
import java.net.URI;
import java.util.Arrays;
import java.util.Collections;
import java.util.UUID;
import java.util.concurrent.Callable;
import java.util.logging.Level;
import java.util.logging.Logger;

import static org.apache.commons.lang3.StringUtils.isNumeric;

/**
Expand Down Expand Up @@ -661,7 +635,15 @@ protected Response ok( JsonArrayBuilder bld ) {
.add("data", bld).build())
.type(MediaType.APPLICATION_JSON).build();
}


protected Response ok( JsonArrayBuilder bld , long totalCount) {
return Response.ok(Json.createObjectBuilder()
.add("status", ApiConstants.STATUS_OK)
.add("total_count", totalCount)
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.add("data", bld).build())
.type(MediaType.APPLICATION_JSON).build();
}

protected Response ok( JsonArray ja ) {
return Response.ok(Json.createObjectBuilder()
.add("status", ApiConstants.STATUS_OK)
Expand Down
146 changes: 41 additions & 105 deletions src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
package edu.harvard.iq.dataverse.api;

import com.amazonaws.services.s3.model.PartETag;
import edu.harvard.iq.dataverse.*;
import edu.harvard.iq.dataverse.DatasetLock.Reason;
import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.Permission;
Expand All @@ -13,6 +15,7 @@
import edu.harvard.iq.dataverse.authorization.users.PrivateUrlUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.batch.jobs.importer.ImportMode;
import edu.harvard.iq.dataverse.dataaccess.*;
import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleUtil;
import edu.harvard.iq.dataverse.datacapturemodule.ScriptRequestResponse;
import edu.harvard.iq.dataverse.dataset.DatasetThumbnail;
Expand All @@ -23,92 +26,47 @@
import edu.harvard.iq.dataverse.datasetutility.OptionalFileParams;
import edu.harvard.iq.dataverse.engine.command.Command;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.impl.AbstractSubmitToArchiveCommand;
import edu.harvard.iq.dataverse.engine.command.impl.AddLockCommand;
import edu.harvard.iq.dataverse.engine.command.impl.AssignRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreatePrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CuratePublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeaccessionDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetLinkingDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeletePrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DestroyDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetSpecificPublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDraftDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetLatestAccessibleDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetLatestPublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetPrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ImportFromFileSystemCommand;
import edu.harvard.iq.dataverse.engine.command.impl.LinkDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListRoleAssignments;
import edu.harvard.iq.dataverse.engine.command.impl.ListVersionsCommand;
import edu.harvard.iq.dataverse.engine.command.impl.MoveDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetResult;
import edu.harvard.iq.dataverse.engine.command.impl.RemoveLockCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RequestRsyncScriptCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand;
import edu.harvard.iq.dataverse.engine.command.impl.SetDatasetCitationDateCommand;
import edu.harvard.iq.dataverse.engine.command.impl.SetCurationStatusCommand;
import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetTargetURLCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetThumbnailCommand;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.UnforcedCommandException;
import edu.harvard.iq.dataverse.engine.command.impl.*;
import edu.harvard.iq.dataverse.export.DDIExportServiceBean;
import edu.harvard.iq.dataverse.export.ExportService;
import edu.harvard.iq.dataverse.externaltools.ExternalTool;
import edu.harvard.iq.dataverse.externaltools.ExternalToolHandler;
import edu.harvard.iq.dataverse.globus.GlobusServiceBean;
import edu.harvard.iq.dataverse.globus.GlobusUtil;
import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataaccess.GlobusAccessibleStore;
import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
import edu.harvard.iq.dataverse.dataaccess.S3AccessIO;
import edu.harvard.iq.dataverse.dataaccess.StorageIO;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.UnforcedCommandException;
import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetStorageSizeCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RevokeRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDvObjectPIDMetadataCommand;
import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitations;
import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitationsServiceBean;
import edu.harvard.iq.dataverse.makedatacount.DatasetMetrics;
import edu.harvard.iq.dataverse.makedatacount.DatasetMetricsServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean;
import edu.harvard.iq.dataverse.makedatacount.*;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean.MakeDataCountEntry;
import edu.harvard.iq.dataverse.metrics.MetricsUtil;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountUtil;
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.ArchiverUtil;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.EjbUtil;
import edu.harvard.iq.dataverse.util.FileUtil;
import edu.harvard.iq.dataverse.util.MarkupChecker;
import edu.harvard.iq.dataverse.util.SystemConfig;
import edu.harvard.iq.dataverse.util.URLTokenUtil;
import edu.harvard.iq.dataverse.util.*;
import edu.harvard.iq.dataverse.util.bagit.OREMap;
import edu.harvard.iq.dataverse.util.json.JSONLDUtil;
import edu.harvard.iq.dataverse.util.json.JsonLDTerm;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.util.SignpostingResources;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import static edu.harvard.iq.dataverse.api.ApiConstants.*;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
import edu.harvard.iq.dataverse.util.json.*;
import edu.harvard.iq.dataverse.workflow.Workflow;
import edu.harvard.iq.dataverse.workflow.WorkflowContext;
import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
import edu.harvard.iq.dataverse.workflow.WorkflowContext.TriggerType;
import edu.harvard.iq.dataverse.globus.GlobusServiceBean;
import edu.harvard.iq.dataverse.globus.GlobusUtil;
import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
import jakarta.ejb.EJB;
import jakarta.ejb.EJBException;
import jakarta.inject.Inject;
import jakarta.json.*;
import jakarta.json.stream.JsonParsingException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import jakarta.ws.rs.*;
import jakarta.ws.rs.container.ContainerRequestContext;
import jakarta.ws.rs.core.*;
import jakarta.ws.rs.core.Response.Status;
import org.apache.commons.lang3.StringUtils;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;

import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
Expand All @@ -117,45 +75,21 @@
import java.text.SimpleDateFormat;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.util.*;
import java.util.concurrent.*;
import java.util.function.Predicate;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.Map.Entry;
import java.util.concurrent.ExecutionException;
import java.util.function.Predicate;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import jakarta.ejb.EJB;
import jakarta.ejb.EJBException;
import jakarta.inject.Inject;
import jakarta.json.*;
import jakarta.json.stream.JsonParsingException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import jakarta.ws.rs.BadRequestException;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.DELETE;
import jakarta.ws.rs.DefaultValue;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.NotAcceptableException;
import jakarta.ws.rs.POST;
import jakarta.ws.rs.PUT;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.PathParam;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.QueryParam;
import jakarta.ws.rs.container.ContainerRequestContext;
import jakarta.ws.rs.core.*;
import jakarta.ws.rs.core.Response.Status;

import static edu.harvard.iq.dataverse.api.ApiConstants.*;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
import org.apache.commons.lang3.StringUtils;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;
import com.amazonaws.services.s3.model.PartETag;
import edu.harvard.iq.dataverse.settings.JvmSettings;

@Path("datasets")
public class Datasets extends AbstractApiBean {
Expand Down Expand Up @@ -546,7 +480,9 @@ public Response getVersionFiles(@Context ContainerRequestContext crc,
} catch (IllegalArgumentException e) {
return badRequest(BundleUtil.getStringFromBundle("datasets.api.version.files.invalid.access.status", List.of(accessStatus)));
}
return ok(jsonFileMetadatas(datasetVersionFilesServiceBean.getFileMetadatas(datasetVersion, limit, offset, fileSearchCriteria, fileOrderCriteria)));
// TODO: should we count the total every time or only when offset = 0?
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return ok(jsonFileMetadatas(datasetVersionFilesServiceBean.getFileMetadatas(datasetVersion, limit, offset, fileSearchCriteria, fileOrderCriteria)),
datasetVersionFilesServiceBean.getFileMetadataCount(datasetVersion, fileSearchCriteria));
}, getRequestUser(crc));
}

Expand Down
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