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Dataverses.java
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Dataverses.java
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package edu.harvard.iq.dataverse.api;
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseFacet;
import edu.harvard.iq.dataverse.DataverseContact;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.MetadataBlock;
import edu.harvard.iq.dataverse.RoleAssignment;
import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
import edu.harvard.iq.dataverse.api.dto.ExplicitGroupDTO;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
import edu.harvard.iq.dataverse.api.dto.RoleDTO;
import edu.harvard.iq.dataverse.api.imports.ImportException;
import edu.harvard.iq.dataverse.api.imports.ImportServiceBean;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.RoleAssignee;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroup;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupProvider;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.impl.AddRoleAssigneesToExplicitGroupCommand;
import edu.harvard.iq.dataverse.engine.command.impl.AssignRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateExplicitGroupCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateNewDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDataverseLinkingDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteExplicitGroupCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDataverseStorageSizeCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetExplicitGroupCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ImportDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.LinkDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListDataverseContentCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListExplicitGroupsCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListFacetsCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListMetadataBlocksCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListRoleAssignments;
import edu.harvard.iq.dataverse.engine.command.impl.ListRolesCommand;
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.MoveDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RemoveRoleAssigneesFromExplicitGroupCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RevokeRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseDefaultContributorRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseMetadataBlocksCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateExplicitGroupCommand;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.StringUtil;
import static edu.harvard.iq.dataverse.util.StringUtil.nonEmpty;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.brief;
import java.io.StringReader;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.TreeSet;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.ejb.EJB;
import javax.ejb.EJBException;
import javax.ejb.Stateless;
import javax.json.Json;
import javax.json.JsonArrayBuilder;
import javax.json.JsonNumber;
import javax.json.JsonObject;
import javax.json.JsonObjectBuilder;
import javax.json.JsonString;
import javax.json.JsonValue;
import javax.json.JsonValue.ValueType;
import javax.json.stream.JsonParsingException;
import javax.validation.ConstraintViolation;
import javax.validation.ConstraintViolationException;
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.GET;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.Response.Status;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import java.text.MessageFormat;
import java.util.Arrays;
import java.util.Date;
import java.util.Optional;
import javax.xml.stream.XMLStreamException;
/**
* A REST API for dataverses.
*
* @author michael
*/
@Stateless
@Path("dataverses")
public class Dataverses extends AbstractApiBean {
private static final Logger logger = Logger.getLogger(Dataverses.class.getCanonicalName());
@EJB
ExplicitGroupServiceBean explicitGroupSvc;
@EJB
ImportServiceBean importService;
@EJB
SettingsServiceBean settingsService;
@POST
public Response addRoot(String body) {
logger.info("Creating root dataverse");
return addDataverse(body, "");
}
@POST
@Path("{identifier}")
public Response addDataverse(String body, @PathParam("identifier") String parentIdtf) {
Dataverse d;
JsonObject dvJson;
try (StringReader rdr = new StringReader(body)) {
dvJson = Json.createReader(rdr).readObject();
d = jsonParser().parseDataverse(dvJson);
} catch (JsonParsingException jpe) {
logger.log(Level.SEVERE, "Json: {0}", body);
return error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage());
} catch (JsonParseException ex) {
logger.log(Level.SEVERE, "Error parsing dataverse from json: " + ex.getMessage(), ex);
return error(Response.Status.BAD_REQUEST,
"Error parsing the POSTed json into a dataverse: " + ex.getMessage());
}
try {
if (!parentIdtf.isEmpty()) {
Dataverse owner = findDataverseOrDie(parentIdtf);
d.setOwner(owner);
}
// set the dataverse - contact relationship in the contacts
for (DataverseContact dc : d.getDataverseContacts()) {
dc.setDataverse(d);
}
AuthenticatedUser u = findAuthenticatedUserOrDie();
d = execCommand(new CreateDataverseCommand(d, createDataverseRequest(u), null, null));
return created("/dataverses/" + d.getAlias(), json(d));
} catch (WrappedResponse ww) {
Throwable cause = ww.getCause();
StringBuilder sb = new StringBuilder();
if (cause == null) {
return ww.refineResponse("cause was null!");
}
while (cause.getCause() != null) {
cause = cause.getCause();
if (cause instanceof ConstraintViolationException) {
ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ")
.append(violation.getPropertyPath()).append(" at ")
.append(violation.getLeafBean()).append(" - ")
.append(violation.getMessage());
}
}
}
String error = sb.toString();
if (!error.isEmpty()) {
logger.log(Level.INFO, error);
return ww.refineResponse(error);
}
return ww.getResponse();
} catch (EJBException ex) {
Throwable cause = ex;
StringBuilder sb = new StringBuilder();
sb.append("Error creating dataverse.");
while (cause.getCause() != null) {
cause = cause.getCause();
if (cause instanceof ConstraintViolationException) {
ConstraintViolationException constraintViolationException = (ConstraintViolationException) cause;
for (ConstraintViolation<?> violation : constraintViolationException.getConstraintViolations()) {
sb.append(" Invalid value: <<<").append(violation.getInvalidValue()).append(">>> for ")
.append(violation.getPropertyPath()).append(" at ")
.append(violation.getLeafBean()).append(" - ")
.append(violation.getMessage());
}
}
}
logger.log(Level.SEVERE, sb.toString());
return error(Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + sb.toString());
} catch (Exception ex) {
logger.log(Level.SEVERE, "Error creating dataverse", ex);
return error(Response.Status.INTERNAL_SERVER_ERROR, "Error creating dataverse: " + ex.getMessage());
}
}
@POST
@Path("{identifier}/datasets")
public Response createDataset(String jsonBody, @PathParam("identifier") String parentIdtf) {
try {
User u = findUserOrDie();
Dataverse owner = findDataverseOrDie(parentIdtf);
Dataset ds = parseDataset(jsonBody);
ds.setOwner(owner);
if (ds.getVersions().isEmpty()) {
return badRequest("Please provide initial version in the dataset json");
}
if (!ds.getFiles().isEmpty() && !u.isSuperuser()){
return badRequest("Only a superuser may add files via this api");
}
// clean possible version metadata
DatasetVersion version = ds.getVersions().get(0);
version.setMinorVersionNumber(null);
version.setVersionNumber(null);
version.setVersionState(DatasetVersion.VersionState.DRAFT);
ds.setAuthority(null);
ds.setIdentifier(null);
ds.setProtocol(null);
ds.setGlobalIdCreateTime(null);
Dataset managedDs = execCommand(new CreateNewDatasetCommand(ds, createDataverseRequest(u)));
return created("/datasets/" + managedDs.getId(),
Json.createObjectBuilder()
.add("id", managedDs.getId())
.add("persistentId", managedDs.getGlobalIdString())
);
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
@POST
@Path("{identifier}/datasets/:import")
public Response importDataset(String jsonBody, @PathParam("identifier") String parentIdtf, @QueryParam("pid") String pidParam, @QueryParam("release") String releaseParam) {
try {
User u = findUserOrDie();
if (!u.isSuperuser()) {
return error(Status.FORBIDDEN, "Not a superuser");
}
Dataverse owner = findDataverseOrDie(parentIdtf);
Dataset ds = parseDataset(jsonBody);
ds.setOwner(owner);
if (ds.getVersions().isEmpty()) {
return badRequest("Supplied json must contain a single dataset version.");
}
DatasetVersion version = ds.getVersions().get(0);
if (version.getVersionState() == null) {
version.setVersionState(DatasetVersion.VersionState.DRAFT);
}
if (nonEmpty(pidParam)) {
if (!GlobalId.verifyImportCharacters(pidParam)) {
return badRequest("PID parameter contains characters that are not allowed by the Dataverse application. On import, the PID must only contain characters specified in this regex: " + BundleUtil.getStringFromBundle("pid.allowedCharacters"));
}
Optional<GlobalId> maybePid = GlobalId.parse(pidParam);
if (maybePid.isPresent()) {
ds.setGlobalId(maybePid.get());
} else {
// unparsable PID passed. Terminate.
return badRequest("Cannot parse the PID parameter '" + pidParam + "'. Make sure it is in valid form - see Dataverse Native API documentation.");
}
}
if (ds.getIdentifier() == null) {
return badRequest("Please provide a persistent identifier, either by including it in the JSON, or by using the pid query parameter.");
}
boolean shouldRelease = StringUtil.isTrue(releaseParam);
DataverseRequest request = createDataverseRequest(u);
if (shouldRelease) {
DatasetVersion latestVersion = ds.getLatestVersion();
latestVersion.setVersionState(DatasetVersion.VersionState.RELEASED);
latestVersion.setVersionNumber(1l);
latestVersion.setMinorVersionNumber(0l);
if (latestVersion.getCreateTime() != null) {
latestVersion.setCreateTime(new Date());
}
if (latestVersion.getLastUpdateTime() != null) {
latestVersion.setLastUpdateTime(new Date());
}
}
Dataset managedDs = execCommand(new ImportDatasetCommand(ds, request));
JsonObjectBuilder responseBld = Json.createObjectBuilder()
.add("id", managedDs.getId())
.add("persistentId", managedDs.getGlobalIdString());
if (shouldRelease) {
PublishDatasetResult res = execCommand(new PublishDatasetCommand(managedDs, request, false, shouldRelease));
responseBld.add("releaseCompleted", res.isCompleted());
}
return created("/datasets/" + managedDs.getId(), responseBld);
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
// TODO decide if I merge importddi with import just below (xml and json on same api, instead of 2 api)
@POST
@Path("{identifier}/datasets/:importddi")
public Response importDatasetDdi(String xml, @PathParam("identifier") String parentIdtf, @QueryParam("pid") String pidParam, @QueryParam("release") String releaseParam) {
try {
User u = findUserOrDie();
if (!u.isSuperuser()) {
return error(Status.FORBIDDEN, "Not a superuser");
}
Dataverse owner = findDataverseOrDie(parentIdtf);
Dataset ds = null;
try {
ds = jsonParser().parseDataset(importService.ddiToJson(xml));
} catch (JsonParseException jpe) {
return badRequest("Error parsing data as Json: "+jpe.getMessage());
} catch (ImportException e) {
return badRequest("Invalid DOI found in the XML: "+e.getMessage());
} catch (XMLStreamException e) {
return badRequest("Invalid file content: "+e.getMessage());
}
ds.setOwner(owner);
if (nonEmpty(pidParam)) {
if (!GlobalId.verifyImportCharacters(pidParam)) {
return badRequest("PID parameter contains characters that are not allowed by the Dataverse application. On import, the PID must only contain characters specified in this regex: " + BundleUtil.getStringFromBundle("pid.allowedCharacters"));
}
Optional<GlobalId> maybePid = GlobalId.parse(pidParam);
if (maybePid.isPresent()) {
ds.setGlobalId(maybePid.get());
} else {
// unparsable PID passed. Terminate.
return badRequest("Cannot parse the PID parameter '" + pidParam + "'. Make sure it is in valid form - see Dataverse Native API documentation.");
}
}
boolean shouldRelease = StringUtil.isTrue(releaseParam);
DataverseRequest request = createDataverseRequest(u);
Dataset managedDs = null;
if (nonEmpty(pidParam)) {
managedDs = execCommand(new ImportDatasetCommand(ds, request));
}
else {
managedDs = execCommand(new CreateNewDatasetCommand(ds, request));
}
JsonObjectBuilder responseBld = Json.createObjectBuilder()
.add("id", managedDs.getId())
.add("persistentId", managedDs.getGlobalIdString());
if (shouldRelease) {
DatasetVersion latestVersion = ds.getLatestVersion();
latestVersion.setVersionState(DatasetVersion.VersionState.RELEASED);
latestVersion.setVersionNumber(1l);
latestVersion.setMinorVersionNumber(0l);
if (latestVersion.getCreateTime() != null) {
latestVersion.setCreateTime(new Date());
}
if (latestVersion.getLastUpdateTime() != null) {
latestVersion.setLastUpdateTime(new Date());
}
PublishDatasetResult res = execCommand(new PublishDatasetCommand(managedDs, request, false, shouldRelease));
responseBld.add("releaseCompleted", res.isCompleted());
}
return created("/datasets/" + managedDs.getId(), responseBld);
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
private Dataset parseDataset(String datasetJson) throws WrappedResponse {
try (StringReader rdr = new StringReader(datasetJson)) {
return jsonParser().parseDataset(Json.createReader(rdr).readObject());
} catch (JsonParsingException | JsonParseException jpe) {
logger.log(Level.SEVERE, "Error parsing dataset json. Json: {0}", datasetJson);
throw new WrappedResponse(error(Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage()));
}
}
@GET
@Path("{identifier}")
public Response viewDataverse(@PathParam("identifier") String idtf) {
return response(req -> ok(
json(execCommand(new GetDataverseCommand(req, findDataverseOrDie(idtf))),
settingsService.isTrueForKey(SettingsServiceBean.Key.ExcludeEmailFromExport, false)
)));
}
@DELETE
@Path("{identifier}")
public Response deleteDataverse(@PathParam("identifier") String idtf) {
return response(req -> {
execCommand(new DeleteDataverseCommand(req, findDataverseOrDie(idtf)));
return ok("Dataverse " + idtf + " deleted");
});
}
@DELETE
@Path("{linkingDataverseId}/deleteLink/{linkedDataverseId}")
public Response deleteDataverseLinkingDataverse(@PathParam("linkingDataverseId") String linkingDataverseId, @PathParam("linkedDataverseId") String linkedDataverseId) {
boolean index = true;
return response(req -> {
execCommand(new DeleteDataverseLinkingDataverseCommand(req, findDataverseOrDie(linkingDataverseId), findDataverseLinkingDataverseOrDie(linkingDataverseId, linkedDataverseId), index));
return ok("Link from Dataverse " + linkingDataverseId + " to linked Dataverse " + linkedDataverseId + " deleted");
});
}
@GET
@Path("{identifier}/metadatablocks")
public Response listMetadataBlocks(@PathParam("identifier") String dvIdtf) {
try {
JsonArrayBuilder arr = Json.createArrayBuilder();
final List<MetadataBlock> blocks = execCommand(new ListMetadataBlocksCommand(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf)));
for (MetadataBlock mdb : blocks) {
arr.add(brief.json(mdb));
}
return ok(arr);
} catch (WrappedResponse we) {
return we.getResponse();
}
}
@POST
@Path("{identifier}/metadatablocks")
@Produces(MediaType.APPLICATION_JSON)
public Response setMetadataBlocks(@PathParam("identifier") String dvIdtf, String blockIds) {
List<MetadataBlock> blocks = new LinkedList<>();
try {
for (JsonValue blockId : Util.asJsonArray(blockIds).getValuesAs(JsonValue.class)) {
MetadataBlock blk = (blockId.getValueType() == ValueType.NUMBER)
? findMetadataBlock(((JsonNumber) blockId).longValue())
: findMetadataBlock(((JsonString) blockId).getString());
if (blk == null) {
return error(Response.Status.BAD_REQUEST, "Can't find metadata block '" + blockId + "'");
}
blocks.add(blk);
}
} catch (Exception e) {
return error(Response.Status.BAD_REQUEST, e.getMessage());
}
try {
execCommand(new UpdateDataverseMetadataBlocksCommand.SetBlocks(createDataverseRequest(findUserOrDie()), findDataverseOrDie(dvIdtf), blocks));
return ok("Metadata blocks of dataverse " + dvIdtf + " updated.");
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
@GET
@Path("{identifier}/metadatablocks/:isRoot")
public Response getMetadataRoot_legacy(@PathParam("identifier") String dvIdtf) {
return getMetadataRoot(dvIdtf);
}
@GET
@Path("{identifier}/metadatablocks/isRoot")
@Produces(MediaType.APPLICATION_JSON)
public Response getMetadataRoot(@PathParam("identifier") String dvIdtf) {
return response(req -> {
final Dataverse dataverse = findDataverseOrDie(dvIdtf);
if (permissionSvc.request(req)
.on(dataverse)
.has(Permission.EditDataverse)) {
return ok(dataverse.isMetadataBlockRoot());
} else {
return error(Status.FORBIDDEN, "Not authorized");
}
});
}
@POST
@Path("{identifier}/metadatablocks/:isRoot")
@Produces(MediaType.APPLICATION_JSON)
@Consumes(MediaType.WILDCARD)
public Response setMetadataRoot_legacy(@PathParam("identifier") String dvIdtf, String body) {
return setMetadataRoot(dvIdtf, body);
}
@PUT
@Path("{identifier}/metadatablocks/isRoot")
@Produces(MediaType.APPLICATION_JSON)
@Consumes(MediaType.WILDCARD)
public Response setMetadataRoot(@PathParam("identifier") String dvIdtf, String body) {
return response(req -> {
final boolean root = parseBooleanOrDie(body);
final Dataverse dataverse = findDataverseOrDie(dvIdtf);
execCommand(new UpdateDataverseMetadataBlocksCommand.SetRoot(req, dataverse, root));
return ok("Dataverse " + dataverse.getName() + " is now a metadata " + (root ? "" : "non-") + "root");
});
}
@GET
@Path("{identifier}/facets/")
/**
* return list of facets for the dataverse with alias `dvIdtf`
*/
public Response listFacets(@PathParam("identifier") String dvIdtf) {
try {
User u = findUserOrDie();
DataverseRequest r = createDataverseRequest(u);
Dataverse dataverse = findDataverseOrDie(dvIdtf);
JsonArrayBuilder fs = Json.createArrayBuilder();
for (DataverseFacet f : execCommand(new ListFacetsCommand(r, dataverse))) {
fs.add(f.getDatasetFieldType().getName());
}
return ok(fs);
} catch (WrappedResponse e) {
return e.getResponse();
}
}
@POST
@Path("{identifier}/facets")
@Produces(MediaType.APPLICATION_JSON)
/**
* (not publicly documented) API endpoint for assigning facets to a
* dataverse. `curl -X POST -H "X-Dataverse-key: $ADMIN_KEY"
* http://localhost:8088/api/dataverses/$dv/facets --upload-file foo.json`;
* where foo.json contains a list of datasetField names, works as expected
* (judging by the UI). This triggers a 500 when '-d @foo.json' is used.
*/
public Response setFacets(@PathParam("identifier") String dvIdtf, String facetIds) {
List<DatasetFieldType> facets = new LinkedList<>();
for (JsonString facetId : Util.asJsonArray(facetIds).getValuesAs(JsonString.class)) {
DatasetFieldType dsfType = findDatasetFieldType(facetId.getString());
if (dsfType == null) {
return error(Response.Status.BAD_REQUEST, "Can't find dataset field type '" + facetId + "'");
} else if (!dsfType.isFacetable()) {
return error(Response.Status.BAD_REQUEST, "Dataset field type '" + facetId + "' is not facetable");
}
facets.add(dsfType);
}
try {
Dataverse dataverse = findDataverseOrDie(dvIdtf);
// by passing null for Featured Dataverses and DataverseFieldTypeInputLevel, those are not changed
execCommand(new UpdateDataverseCommand(dataverse, facets, null, createDataverseRequest(findUserOrDie()), null));
return ok("Facets of dataverse " + dvIdtf + " updated.");
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
// FIXME: This listContent method is way too optimistic, always returning "ok" and never "error".
// TODO: Investigate why there was a change in the timeframe of when pull request #4350 was merged
// (2438-4295-dois-for-files branch) such that a contributor API token no longer allows this method
// to be called without a PermissionException being thrown.
@GET
@Path("{identifier}/contents")
public Response listContent(@PathParam("identifier") String dvIdtf) throws WrappedResponse {
DvObject.Visitor<JsonObjectBuilder> ser = new DvObject.Visitor<JsonObjectBuilder>() {
@Override
public JsonObjectBuilder visit(Dataverse dv) {
return Json.createObjectBuilder().add("type", "dataverse")
.add("id", dv.getId())
.add("title", dv.getName());
}
@Override
public JsonObjectBuilder visit(Dataset ds) {
return json(ds).add("type", "dataset");
}
@Override
public JsonObjectBuilder visit(DataFile df) {
throw new UnsupportedOperationException("Files don't live directly in Dataverses");
}
};
return response(req -> ok(
execCommand(new ListDataverseContentCommand(req, findDataverseOrDie(dvIdtf)))
.stream()
.map(dvo -> (JsonObjectBuilder) dvo.accept(ser))
.collect(toJsonArray())
));
}
@GET
@Path("{identifier}/storagesize")
public Response getStorageSize(@PathParam("identifier") String dvIdtf, @QueryParam("includeCached") boolean includeCached) throws WrappedResponse {
return response(req -> ok(MessageFormat.format(BundleUtil.getStringFromBundle("dataverse.datasize"),
execCommand(new GetDataverseStorageSizeCommand(req, findDataverseOrDie(dvIdtf), includeCached)))));
}
@GET
@Path("{identifier}/roles")
public Response listRoles(@PathParam("identifier") String dvIdtf) {
return response(req -> ok(
execCommand(new ListRolesCommand(req, findDataverseOrDie(dvIdtf)))
.stream().map(r -> json(r))
.collect(toJsonArray())
));
}
@POST
@Path("{identifier}/roles")
public Response createRole(RoleDTO roleDto, @PathParam("identifier") String dvIdtf) {
return response(req -> ok(json(execCommand(new CreateRoleCommand(roleDto.asRole(), req, findDataverseOrDie(dvIdtf))))));
}
@GET
@Path("{identifier}/assignments")
public Response listAssignments(@PathParam("identifier") String dvIdtf) {
return response(req -> ok(
execCommand(new ListRoleAssignments(req, findDataverseOrDie(dvIdtf)))
.stream()
.map(a -> json(a))
.collect(toJsonArray())
));
}
/**
* This code for setting a dataverse logo via API was started when initially
* investigating https://github.com/IQSS/dataverse/issues/3559 but it isn't
* finished so it's commented out. See also * "No functionality should be
* GUI-only. Make all functionality reachable via the API" at
* https://github.com/IQSS/dataverse/issues/3440
*/
// File tempDir;
//
// private void createTempDir(Dataverse editDv) {
// try {
// File tempRoot = java.nio.file.Files.createDirectories(Paths.get("../docroot/logos/temp")).toFile();
// tempDir = java.nio.file.Files.createTempDirectory(tempRoot.toPath(), editDv.getId().toString()).toFile();
// } catch (IOException e) {
// throw new RuntimeException("Error creating temp directory", e); // improve error handling
// }
// }
//
// private DataverseTheme initDataverseTheme(Dataverse editDv) {
// DataverseTheme dvt = new DataverseTheme();
// dvt.setLinkColor(DEFAULT_LINK_COLOR);
// dvt.setLogoBackgroundColor(DEFAULT_LOGO_BACKGROUND_COLOR);
// dvt.setBackgroundColor(DEFAULT_BACKGROUND_COLOR);
// dvt.setTextColor(DEFAULT_TEXT_COLOR);
// dvt.setDataverse(editDv);
// return dvt;
// }
//
// @PUT
// @Path("{identifier}/logo")
// @Consumes(MediaType.MULTIPART_FORM_DATA)
// public Response setDataverseLogo(@PathParam("identifier") String dvIdtf,
// @FormDataParam("file") InputStream fileInputStream,
// @FormDataParam("file") FormDataContentDisposition contentDispositionHeader,
// @QueryParam("key") String apiKey) {
// boolean disabled = true;
// if (disabled) {
// return error(Status.FORBIDDEN, "Setting the dataverse logo via API needs more work.");
// }
// try {
// final DataverseRequest req = createDataverseRequest(findUserOrDie());
// final Dataverse editDv = findDataverseOrDie(dvIdtf);
//
// logger.finer("entering fileUpload");
// if (tempDir == null) {
// createTempDir(editDv);
// logger.finer("created tempDir");
// }
// File uploadedFile;
// try {
// String fileName = contentDispositionHeader.getFileName();
//
// uploadedFile = new File(tempDir, fileName);
// if (!uploadedFile.exists()) {
// uploadedFile.createNewFile();
// }
// logger.finer("created file");
// File file = null;
// file = FileUtil.inputStreamToFile(fileInputStream);
// if (file.length() > systemConfig.getUploadLogoSizeLimit()) {
// return error(Response.Status.BAD_REQUEST, "File is larger than maximum size: " + systemConfig.getUploadLogoSizeLimit() + ".");
// }
// java.nio.file.Files.copy(fileInputStream, uploadedFile.toPath(), StandardCopyOption.REPLACE_EXISTING);
// logger.finer("copied inputstream to file");
// editDv.setDataverseTheme(initDataverseTheme(editDv));
// editDv.getDataverseTheme().setLogo(fileName);
//
// } catch (IOException e) {
// logger.finer("caught IOException");
// logger.throwing("ThemeWidgetFragment", "handleImageFileUpload", e);
// throw new RuntimeException("Error uploading logo file", e); // improve error handling
// }
// // If needed, set the default values for the logo
// if (editDv.getDataverseTheme().getLogoFormat() == null) {
// editDv.getDataverseTheme().setLogoFormat(DataverseTheme.ImageFormat.SQUARE);
// }
// logger.finer("end handelImageFileUpload");
// UpdateDataverseThemeCommand cmd = new UpdateDataverseThemeCommand(editDv, uploadedFile, req);
// Dataverse saved = execCommand(cmd);
//
// /**
// * @todo delete the temp file:
// * docroot/logos/temp/1148114212463761832421/cc0.png
// */
// return ok("logo uploaded: " + saved.getDataverseTheme().getLogo());
// } catch (WrappedResponse ex) {
// return error(Status.BAD_REQUEST, "problem uploading logo: " + ex);
// }
// }
@POST
@Path("{identifier}/assignments")
public Response createAssignment(RoleAssignmentDTO ra, @PathParam("identifier") String dvIdtf, @QueryParam("key") String apiKey) {
try {
final DataverseRequest req = createDataverseRequest(findUserOrDie());
final Dataverse dataverse = findDataverseOrDie(dvIdtf);
RoleAssignee assignee = findAssignee(ra.getAssignee());
if (assignee == null) {
return error(Status.BAD_REQUEST, "Assignee not found");
}
DataverseRole theRole;
Dataverse dv = dataverse;
theRole = null;
while ((theRole == null) && (dv != null)) {
for (DataverseRole aRole : rolesSvc.availableRoles(dv.getId())) {
if (aRole.getAlias().equals(ra.getRole())) {
theRole = aRole;
break;
}
}
dv = dv.getOwner();
}
if (theRole == null) {
return error(Status.BAD_REQUEST, "Can't find role named '" + ra.getRole() + "' in dataverse " + dataverse);
}
String privateUrlToken = null;
return ok(json(execCommand(new AssignRoleCommand(assignee, theRole, dataverse, req, privateUrlToken))));
} catch (WrappedResponse ex) {
logger.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage());
return ex.getResponse();
}
}
@DELETE
@Path("{identifier}/assignments/{id}")
public Response deleteAssignment(@PathParam("id") long assignmentId, @PathParam("identifier") String dvIdtf) {
RoleAssignment ra = em.find(RoleAssignment.class, assignmentId);
if (ra != null) {
try {
findDataverseOrDie(dvIdtf);
execCommand(new RevokeRoleCommand(ra, createDataverseRequest(findUserOrDie())));
return ok("Role " + ra.getRole().getName()
+ " revoked for assignee " + ra.getAssigneeIdentifier()
+ " in " + ra.getDefinitionPoint().accept(DvObject.NamePrinter));
} catch (WrappedResponse ex) {
return ex.getResponse();
}
} else {
return error(Status.NOT_FOUND, "Role assignment " + assignmentId + " not found");
}
}
@POST
@Path("{identifier}/actions/:publish")
public Response publishDataverse(@PathParam("identifier") String dvIdtf) {
try {
Dataverse dv = findDataverseOrDie(dvIdtf);
return ok(json(execCommand(new PublishDataverseCommand(createDataverseRequest(findAuthenticatedUserOrDie()), dv))));
} catch (WrappedResponse wr) {
return wr.getResponse();
}
}
@POST
@Path("{identifier}/groups/")
public Response createExplicitGroup(ExplicitGroupDTO dto, @PathParam("identifier") String dvIdtf) {
return response(req -> {
ExplicitGroupProvider prv = explicitGroupSvc.getProvider();
ExplicitGroup newGroup = dto.apply(prv.makeGroup());
newGroup = execCommand(new CreateExplicitGroupCommand(req, findDataverseOrDie(dvIdtf), newGroup));
String groupUri = String.format("%s/groups/%s", dvIdtf, newGroup.getGroupAliasInOwner());
return created(groupUri, json(newGroup));
});
}
@GET
@Path("{identifier}/groups/")
public Response listGroups(@PathParam("identifier") String dvIdtf, @QueryParam("key") String apiKey) {
return response(req -> ok(
execCommand(new ListExplicitGroupsCommand(req, findDataverseOrDie(dvIdtf)))
.stream().map(eg -> json(eg))
.collect(toJsonArray())
));
}
@GET
@Path("{identifier}/groups/{aliasInOwner}")
public Response getGroupByOwnerAndAliasInOwner(@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner) {
return response(req -> ok(json(findExplicitGroupOrDie(findDataverseOrDie(dvIdtf),
req,
grpAliasInOwner))));
}
@PUT
@Path("{identifier}/groups/{aliasInOwner}")
public Response updateGroup(ExplicitGroupDTO groupDto,
@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner) {
return response(req -> ok(json(execCommand(
new UpdateExplicitGroupCommand(req,
groupDto.apply(findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner)))))));
}
@PUT
@Path("{identifier}/defaultContributorRole/{roleAlias}")
public Response updateDefaultContributorRole(
@PathParam("identifier") String dvIdtf,
@PathParam("roleAlias") String roleAlias) {
DataverseRole defaultRole;
if (roleAlias.equals(DataverseRole.NONE)) {
defaultRole = null;
} else {
try {
Dataverse dv = findDataverseOrDie(dvIdtf);
defaultRole = rolesSvc.findCustomRoleByAliasAndOwner(roleAlias, dv.getId());
} catch (Exception nre) {
List<String> args = Arrays.asList(roleAlias);
String retStringError = BundleUtil.getStringFromBundle("dataverses.api.update.default.contributor.role.failure.role.not.found", args);
return error(Status.NOT_FOUND, retStringError);
}
if (!defaultRole.doesDvObjectClassHavePermissionForObject(Dataset.class)) {
List<String> args = Arrays.asList(roleAlias);
String retStringError = BundleUtil.getStringFromBundle("dataverses.api.update.default.contributor.role.failure.role.does.not.have.dataset.permissions", args);
return error(Status.BAD_REQUEST, retStringError);
}
}
try {
Dataverse dv = findDataverseOrDie(dvIdtf);
String defaultRoleName = defaultRole == null ? BundleUtil.getStringFromBundle("permission.default.contributor.role.none.name") : defaultRole.getName();
return response(req -> {
execCommand(new UpdateDataverseDefaultContributorRoleCommand(defaultRole, req, dv));
List<String> args = Arrays.asList(dv.getDisplayName(), defaultRoleName);
String retString = BundleUtil.getStringFromBundle("dataverses.api.update.default.contributor.role.success", args);
return ok(retString);
});
} catch (WrappedResponse wr) {
return wr.getResponse();
}
}
@DELETE
@Path("{identifier}/groups/{aliasInOwner}")
public Response deleteGroup(@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner) {
return response(req -> {
execCommand(new DeleteExplicitGroupCommand(req,
findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner)));
return ok("Group " + dvIdtf + "/" + grpAliasInOwner + " deleted");
});
}
@POST
@Path("{identifier}/groups/{aliasInOwner}/roleAssignees")
@Consumes("application/json")
public Response addRoleAssingees(List<String> roleAssingeeIdentifiers,
@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner) {
return response(req -> ok(
json(
execCommand(
new AddRoleAssigneesToExplicitGroupCommand(req,
findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner),
new TreeSet<>(roleAssingeeIdentifiers))))));
}
@PUT
@Path("{identifier}/groups/{aliasInOwner}/roleAssignees/{roleAssigneeIdentifier: .*}")
public Response addRoleAssingee(@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner,
@PathParam("roleAssigneeIdentifier") String roleAssigneeIdentifier) {
return addRoleAssingees(Collections.singletonList(roleAssigneeIdentifier), dvIdtf, grpAliasInOwner);
}
@DELETE
@Path("{identifier}/groups/{aliasInOwner}/roleAssignees/{roleAssigneeIdentifier: .*}")
public Response deleteRoleAssingee(@PathParam("identifier") String dvIdtf,
@PathParam("aliasInOwner") String grpAliasInOwner,
@PathParam("roleAssigneeIdentifier") String roleAssigneeIdentifier) {
return response(req -> ok(json(execCommand(
new RemoveRoleAssigneesFromExplicitGroupCommand(req,
findExplicitGroupOrDie(findDataverseOrDie(dvIdtf), req, grpAliasInOwner),
Collections.singleton(roleAssigneeIdentifier))))));
}
private ExplicitGroup findExplicitGroupOrDie(DvObject dv, DataverseRequest req, String groupIdtf) throws WrappedResponse {
ExplicitGroup eg = execCommand(new GetExplicitGroupCommand(req, dv, groupIdtf));
if (eg == null) {
throw new WrappedResponse(notFound("Can't find " + groupIdtf + " in dataverse " + dv.getId()));
}
return eg;
}
@GET
@Path("{identifier}/links")
public Response listLinks(@PathParam("identifier") String dvIdtf) {
try {
User u = findUserOrDie();
Dataverse dv = findDataverseOrDie(dvIdtf);
if (!u.isSuperuser()) {
return error(Status.FORBIDDEN, "Not a superuser");
}
List<Dataverse> dvsThisDvHasLinkedToList = dataverseSvc.findDataversesThisIdHasLinkedTo(dv.getId());
JsonArrayBuilder dvsThisDvHasLinkedToBuilder = Json.createArrayBuilder();
for (Dataverse dataverse : dvsThisDvHasLinkedToList) {
dvsThisDvHasLinkedToBuilder.add(dataverse.getAlias());
}
List<Dataverse> dvsThatLinkToThisDvList = dataverseSvc.findDataversesThatLinkToThisDvId(dv.getId());
JsonArrayBuilder dvsThatLinkToThisDvBuilder = Json.createArrayBuilder();
for (Dataverse dataverse : dvsThatLinkToThisDvList) {
dvsThatLinkToThisDvBuilder.add(dataverse.getAlias());
}
List<Dataset> datasetsThisDvHasLinkedToList = dataverseSvc.findDatasetsThisIdHasLinkedTo(dv.getId());
JsonArrayBuilder datasetsThisDvHasLinkedToBuilder = Json.createArrayBuilder();
for (Dataset dataset : datasetsThisDvHasLinkedToList) {
datasetsThisDvHasLinkedToBuilder.add(dataset.getLatestVersion().getTitle());
}
JsonObjectBuilder response = Json.createObjectBuilder();
response.add("dataverses that the " + dv.getAlias() + " dataverse has linked to", dvsThisDvHasLinkedToBuilder);
response.add("dataverses that link to the " + dv.getAlias(), dvsThatLinkToThisDvBuilder);
response.add("datasets that the " + dv.getAlias() + " has linked to", datasetsThisDvHasLinkedToBuilder);
return ok(response);
} catch (WrappedResponse wr) {
return wr.getResponse();
}
}
@POST
@Path("{id}/move/{targetDataverseAlias}")
public Response moveDataverse(@PathParam("id") String id, @PathParam("targetDataverseAlias") String targetDataverseAlias, @QueryParam("forceMove") Boolean force) {
try {
User u = findUserOrDie();
Dataverse dv = findDataverseOrDie(id);
Dataverse target = findDataverseOrDie(targetDataverseAlias);
if (target == null) {
return error(Response.Status.BAD_REQUEST, "Target Dataverse not found.");
}
execCommand(new MoveDataverseCommand(
createDataverseRequest(u), dv, target, force
));
return ok("Dataverse moved successfully");
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}