Examples with Dataset edu.harvard.iq.dataverse.Dataset used on opensource projects

Example 26 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class Datasets method createAssignment.

/**
 * @todo Make this real. Currently only used for API testing. Copied from
 * the equivalent API endpoint for dataverses and simplified with values
 * hard coded.
 */
@POST
@Path("{identifier}/assignments")
public Response createAssignment(String userOrGroup, @PathParam("identifier") String id, @QueryParam("key") String apiKey) {
    boolean apiTestingOnly = true;
    if (apiTestingOnly) {
        return error(Response.Status.FORBIDDEN, "This is only for API tests.");
    }
    try {
        Dataset dataset = findDatasetOrDie(id);
        RoleAssignee assignee = findAssignee(userOrGroup);
        if (assignee == null) {
            return error(Response.Status.BAD_REQUEST, "Assignee not found");
        }
        DataverseRole theRole = rolesSvc.findBuiltinRoleByAlias("admin");
        String privateUrlToken = null;
        return ok(json(execCommand(new AssignRoleCommand(assignee, theRole, dataset, createDataverseRequest(findUserOrDie()), privateUrlToken))));
    } catch (WrappedResponse ex) {
        logger.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage());
        return ex.getResponse();
    }
}

Example 27 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class Datasets method returnToAuthor.

@POST
@Path("{id}/returnToAuthor")
public Response returnToAuthor(@PathParam("id") String idSupplied, String jsonBody) {
    if (jsonBody == null || jsonBody.isEmpty()) {
        return error(Response.Status.BAD_REQUEST, "You must supply JSON to this API endpoint and it must contain a reason for returning the dataset.");
    }
    StringReader rdr = new StringReader(jsonBody);
    JsonObject json = Json.createReader(rdr).readObject();
    try {
        Dataset dataset = findDatasetOrDie(idSupplied);
        String reasonForReturn = null;
        reasonForReturn = json.getString("reasonForReturn");
        // TODO: Once we add a box for the curator to type into, pass the reason for return to the ReturnDatasetToAuthorCommand and delete this check and call to setReturnReason on the API side.
        if (reasonForReturn == null || reasonForReturn.isEmpty()) {
            return error(Response.Status.BAD_REQUEST, "You must enter a reason for returning a dataset to the author(s).");
        }
        AuthenticatedUser authenticatedUser = findAuthenticatedUserOrDie();
        Dataset updatedDataset = execCommand(new ReturnDatasetToAuthorCommand(createDataverseRequest(authenticatedUser), dataset, reasonForReturn));
        boolean inReview = updatedDataset.isLockedFor(DatasetLock.Reason.InReview);
        JsonObjectBuilder result = Json.createObjectBuilder();
        result.add("inReview", inReview);
        result.add("message", "Dataset id " + updatedDataset.getId() + " has been sent back to the author(s).");
        return ok(result);
    } catch (WrappedResponse wr) {
        return wr.getResponse();
    }
}

Example 28 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class Datasets method submitForReview.

@POST
@Path("{id}/submitForReview")
public Response submitForReview(@PathParam("id") String idSupplied) {
    try {
        Dataset updatedDataset = execCommand(new SubmitDatasetForReviewCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(idSupplied)));
        JsonObjectBuilder result = Json.createObjectBuilder();
        boolean inReview = updatedDataset.isLockedFor(DatasetLock.Reason.InReview);
        result.add("inReview", inReview);
        result.add("message", "Dataset id " + updatedDataset.getId() + " has been submitted for review.");
        return ok(result);
    } catch (WrappedResponse wr) {
        return wr.getResponse();
    }
}

Example 29 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class WorldMapRelatedData method getWorldMapDatafileInfo.

/**
 * Retrieve FileMetadata for Use by WorldMap.
 *  This includes information about the DataFile, Dataset, DatasetVersion, and Dataverse
 *
 * @param jsonTokenData
 * @param request
 * @return
 */
@POST
// + "{worldmap_token}")
@Path(GET_WORLDMAP_DATAFILE_API_PATH_FRAGMENT)
public Response getWorldMapDatafileInfo(String jsonTokenData, @Context HttpServletRequest request) {
    // , @PathParam("worldmap_token") String worldmapTokenParam) {
    if (true) {
    // return okResponse("Currently deactivated");
    // return okResponse("remote server: " + request.getRemoteAddr());
    }
    logger.info("API call: getWorldMapDatafileInfo");
    // ----------------------------------
    // Auth check: Parse the json message and check for a valid GEOCONNECT_TOKEN_KEY and GEOCONNECT_TOKEN_VALUE
    // -- For testing, the GEOCONNECT_TOKEN_VALUE will be dynamic, found in the db
    // ----------------------------------
    logger.info("(1) jsonTokenData: " + jsonTokenData);
    // Parse JSON
    JsonObject jsonTokenInfo;
    try (StringReader rdr = new StringReader(jsonTokenData)) {
        jsonTokenInfo = Json.createReader(rdr).readObject();
    } catch (JsonParsingException jpe) {
        logger.log(Level.SEVERE, "Json: " + jsonTokenData);
        return error(Response.Status.BAD_REQUEST, "Error parsing Json: " + jpe.getMessage());
    }
    logger.info("(1a) jsonTokenInfo: " + jsonTokenInfo);
    // Retrieve token string
    String worldmapTokenParam = this.retrieveTokenValueFromJson(jsonTokenInfo);
    logger.info("(1b) token from JSON: " + worldmapTokenParam);
    if (worldmapTokenParam == null) {
        return error(Response.Status.BAD_REQUEST, "Token not found in JSON request.");
    }
    // Retrieve WorldMapToken and make sure it is valid
    // 
    WorldMapToken wmToken = tokenServiceBean.retrieveAndRefreshValidToken(worldmapTokenParam);
    logger.info("(2) token retrieved from db: " + wmToken);
    if (wmToken == null) {
        return error(Response.Status.UNAUTHORIZED, "No access. Invalid token.");
    }
    // Make sure the token's User still has permissions to access the file
    // 
    logger.info("(3) check permissions");
    if (!(tokenServiceBean.canTokenUserEditFile(wmToken))) {
        tokenServiceBean.expireToken(wmToken);
        return error(Response.Status.UNAUTHORIZED, "No access. Invalid token.");
    }
    // (1) Retrieve token connected data: DataverseUser, DataFile
    // 
    // Make sure token user and file are still available
    // 
    AuthenticatedUser dvUser = wmToken.getDataverseUser();
    if (dvUser == null) {
        return error(Response.Status.NOT_FOUND, "DataverseUser not found for token");
    }
    DataFile dfile = wmToken.getDatafile();
    if (dfile == null) {
        return error(Response.Status.NOT_FOUND, "DataFile not found for token");
    }
    // (1a) Retrieve FileMetadata
    FileMetadata dfile_meta = dfile.getFileMetadata();
    if (dfile_meta == null) {
        return error(Response.Status.NOT_FOUND, "FileMetadata not found");
    }
    // (2) Now get the dataset and the latest DatasetVersion
    Dataset dset = dfile.getOwner();
    if (dset == null) {
        return error(Response.Status.NOT_FOUND, "Owning Dataset for this DataFile not found");
    }
    // (2a) latest DatasetVersion
    // !! How do you check if the lastest version has this specific file?
    // 
    DatasetVersion dset_version = dset.getLatestVersion();
    if (dset_version == null) {
        return error(Response.Status.NOT_FOUND, "Latest DatasetVersion for this DataFile not found");
    }
    // (3) get Dataverse
    Dataverse dverse = dset.getOwner();
    if (dverse == null) {
        return error(Response.Status.NOT_FOUND, "Dataverse for this DataFile's Dataset not found");
    }
    // (4) Roll it all up in a JSON response
    final JsonObjectBuilder jsonData = Json.createObjectBuilder();
    // ------------------------------------
    if (dfile.isShapefileType()) {
        jsonData.add("mapping_type", "shapefile");
    } else if (dfile.isTabularData()) {
        jsonData.add("mapping_type", "tabular");
    } else {
        logger.log(Level.SEVERE, "This was neither a Shapefile nor a Tabular data file.  DataFile id: " + dfile.getId());
        return error(Response.Status.BAD_REQUEST, "Sorry! This file does not have mapping data. Please contact the Dataverse administrator. DataFile id: " + dfile.getId());
    }
    // ------------------------------------
    // DataverseUser Info
    // ------------------------------------
    jsonData.add("dv_user_id", dvUser.getId());
    jsonData.add("dv_username", dvUser.getUserIdentifier());
    jsonData.add("dv_user_email", dvUser.getEmail());
    // ------------------------------------
    // Dataverse URLs to this server
    // ------------------------------------
    String serverName = systemConfig.getDataverseSiteUrl();
    jsonData.add("return_to_dataverse_url", dset_version.getReturnToFilePageURL(serverName, dset, dfile));
    jsonData.add("datafile_download_url", dfile.getMapItFileDownloadURL(serverName));
    // ------------------------------------
    // Dataverse
    // ------------------------------------
    // jsonData.add("dataverse_installation_name", "Harvard Dataverse"); // todo / fix
    // is this enough to distinguish a dataverse installation?
    jsonData.add("dataverse_installation_name", systemConfig.getDataverseSiteUrl());
    jsonData.add("dataverse_id", dverse.getId());
    jsonData.add("dataverse_name", dverse.getName());
    String dataverseDesc = dverse.getDescription();
    if (dataverseDesc == null || dataverseDesc.equalsIgnoreCase("")) {
        dataverseDesc = "";
    }
    jsonData.add("dataverse_description", dataverseDesc);
    // ------------------------------------
    // Dataset Info
    // ------------------------------------
    jsonData.add("dataset_id", dset.getId());
    // ------------------------------------
    // DatasetVersion Info
    // ------------------------------------
    // database id
    jsonData.add("dataset_version_id", dset_version.getId());
    // major/minor version number, e.g. 3.1
    jsonData.add("dataset_semantic_version", dset_version.getSemanticVersion());
    jsonData.add("dataset_name", dset_version.getTitle());
    jsonData.add("dataset_citation", dset_version.getCitation(true));
    // Need to fix to/do
    jsonData.add("dataset_description", "");
    jsonData.add("dataset_is_public", dset_version.isReleased());
    // ------------------------------------
    // DataFile/FileMetaData Info
    // ------------------------------------
    jsonData.add("datafile_id", dfile.getId());
    jsonData.add("datafile_label", dfile_meta.getLabel());
    // jsonData.add("filename", dfile_meta.getLabel());
    jsonData.add("datafile_expected_md5_checksum", dfile.getChecksumValue());
    Long fsize = dfile.getFilesize();
    if (fsize == null) {
        fsize = new Long(-1);
    }
    jsonData.add("datafile_filesize", fsize);
    jsonData.add("datafile_content_type", dfile.getContentType());
    jsonData.add("datafile_create_datetime", dfile.getCreateDate().toString());
    // restriction status of the DataFile
    jsonData.add("datafile_is_restricted", dfile.isRestricted());
    return ok(jsonData);
}

Example 30 with Dataset

use of edu.harvard.iq.dataverse.Dataset in project dataverse by IQSS.

the class CollectionListManagerImpl method listCollectionContents.

@Override
public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, SwordConfiguration swordConfiguration) throws SwordServerException, SwordAuthException, SwordError {
    AuthenticatedUser user = swordAuth.auth(authCredentials);
    DataverseRequest dvReq = new DataverseRequest(user, request);
    urlManager.processUrl(iri.toString());
    String dvAlias = urlManager.getTargetIdentifier();
    if (urlManager.getTargetType().equals("dataverse") && dvAlias != null) {
        Dataverse dv = dataverseService.findByAlias(dvAlias);
        if (dv != null) {
            /**
             * We'll say having AddDataset is enough to use this API
             * endpoint, which means you are a Contributor to that
             * dataverse. If we let just anyone call this endpoint, they
             * will be able to see if the supplied dataverse is published or
             * not.
             */
            if (!permissionService.requestOn(dvReq, dv).has(Permission.AddDataset)) {
                throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "user " + user.getDisplayInfo().getTitle() + " is not authorized to list datasets in dataverse " + dv.getAlias());
            }
            Abdera abdera = new Abdera();
            Feed feed = abdera.newFeed();
            feed.setTitle(dv.getName());
            String baseUrl = urlManager.getHostnamePlusBaseUrlPath(iri.toString());
            List<Dataset> datasets = datasetService.findByOwnerId(dv.getId());
            for (Dataset dataset : datasets) {
                /**
                 * @todo Will this be performant enough with production
                 * data, say in the root dataverse? Remove this todo if
                 * there are no complaints. :)
                 */
                if (!permissionService.isUserAllowedOn(user, new UpdateDatasetCommand(dataset, dvReq), dataset)) {
                    continue;
                }
                String editUri = baseUrl + "/edit/study/" + dataset.getGlobalId();
                String editMediaUri = baseUrl + "/edit-media/study/" + dataset.getGlobalId();
                Entry entry = feed.addEntry();
                entry.setId(editUri);
                entry.setTitle(datasetService.getTitleFromLatestVersion(dataset.getId()));
                entry.setBaseUri(new IRI(editUri));
                entry.addLink(editMediaUri, "edit-media");
                feed.addEntry(entry);
            }
            Boolean dvHasBeenReleased = dv.isReleased();
            feed.addSimpleExtension(new QName(UriRegistry.SWORD_STATE, "dataverseHasBeenReleased"), dvHasBeenReleased.toString());
            return feed;
        } else {
            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
        }
    } else {
        throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't determine target type or identifer from URL: " + iri);
    }
}