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

Example 36 with Dataverse

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

the class Access method dvCardImage.

@Path("dvCardImage/{dataverseId}")
@GET
@Produces({ "image/png" })
public InputStream dvCardImage(@PathParam("dataverseId") Long dataverseId, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/
{
    logger.fine("entering dvCardImage");
    Dataverse dataverse = dataverseService.find(dataverseId);
    if (dataverse == null) {
        logger.warning("Preview: Version service could not locate a DatasetVersion object for id " + dataverseId + "!");
        return null;
    }
    String imageThumbFileName = null;
    if (dataverse.getDataverseTheme() != null && dataverse.getDataverseTheme().getLogo() != null && !dataverse.getDataverseTheme().getLogo().equals("")) {
        File dataverseLogoFile = getLogo(dataverse);
        if (dataverseLogoFile != null) {
            logger.fine("dvCardImage: logo file found");
            String logoThumbNailPath = null;
            InputStream in = null;
            try {
                if (dataverseLogoFile.exists()) {
                    logoThumbNailPath = ImageThumbConverter.generateImageThumbnailFromFile(dataverseLogoFile.getAbsolutePath(), 48);
                    if (logoThumbNailPath != null) {
                        in = new FileInputStream(logoThumbNailPath);
                    }
                }
            } catch (Exception ex) {
                in = null;
            }
            if (in != null) {
                logger.fine("dvCardImage: successfully obtained thumbnail for dataverse logo.");
                return in;
            }
        }
    }
    /*
        StorageIO thumbnailDataAccess = null; 
        
        if (!dataverse.isHarvested()) {
            for (Dataset dataset : datasetService.findPublishedByOwnerId(dataverseId)) {
                logger.info("dvCardImage: checking dataset "+dataset.getGlobalId());
                if (dataset != null) {
                    DatasetVersion releasedVersion = dataset.getReleasedVersion();
                    logger.info("dvCardImage: obtained released version "+releasedVersion.getTitle());
                    thumbnailDataAccess = getThumbnailForDatasetVersion(releasedVersion); 
                    if (thumbnailDataAccess != null) {
                        logger.info("dvCardImage: obtained thumbnail for the version.");
                        break;
                    }
                }
            }
        }
        
        if (thumbnailDataAccess != null && thumbnailDataAccess.getInputStream() != null) {
            return thumbnailDataAccess.getInputStream();
        }
        */
    return null;
}

Example 37 with Dataverse

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

the class JsonParser method parseDataverse.

public Dataverse parseDataverse(JsonObject jobj) throws JsonParseException {
    Dataverse dv = new Dataverse();
    /**
     * @todo Instead of this getMandatoryString method we should run the
     * String through ConstraintValidator. See EMailValidatorTest and
     * EMailValidator for examples. That way we can check not only if it's
     * required or not but other bean validation rules such as "must match
     * this regex".
     */
    dv.setAlias(getMandatoryString(jobj, "alias"));
    dv.setName(getMandatoryString(jobj, "name"));
    dv.setDescription(jobj.getString("description", null));
    dv.setPermissionRoot(jobj.getBoolean("permissionRoot", false));
    dv.setFacetRoot(jobj.getBoolean("facetRoot", false));
    dv.setAffiliation(jobj.getString("affiliation", null));
    if (jobj.containsKey("dataverseContacts")) {
        JsonArray dvContacts = jobj.getJsonArray("dataverseContacts");
        int i = 0;
        List<DataverseContact> dvContactList = new LinkedList<>();
        for (JsonValue jsv : dvContacts) {
            DataverseContact dvc = new DataverseContact(dv);
            dvc.setContactEmail(getMandatoryString((JsonObject) jsv, "contactEmail"));
            dvc.setDisplayOrder(i++);
            dvContactList.add(dvc);
        }
        dv.setDataverseContacts(dvContactList);
    }
    if (jobj.containsKey("theme")) {
        DataverseTheme theme = parseDataverseTheme(jobj.getJsonObject("theme"));
        dv.setDataverseTheme(theme);
        theme.setDataverse(dv);
    }
    // default
    dv.setDataverseType(Dataverse.DataverseType.UNCATEGORIZED);
    if (jobj.containsKey("dataverseType")) {
        for (Dataverse.DataverseType dvtype : Dataverse.DataverseType.values()) {
            if (dvtype.name().equals(jobj.getString("dataverseType"))) {
                dv.setDataverseType(dvtype);
            }
        }
    }
    return dv;
}

Example 38 with Dataverse

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

the class JsonPrinter method getRootDataverseNameforCitation.

private static String getRootDataverseNameforCitation(Dataset dataset) {
    Dataverse root = dataset.getOwner();
    while (root.getOwner() != null) {
        root = root.getOwner();
    }
    String rootDataverseName = root.getName();
    if (!StringUtil.isEmpty(rootDataverseName)) {
        return rootDataverseName;
    } else {
        return "";
    }
}

Example 39 with Dataverse

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

the class SolrIndexServiceBean method indexPermissionsOnSelfAndChildren.

/**
 * We use the database to determine direct children since there is no
 * inheritance
 */
public IndexResponse indexPermissionsOnSelfAndChildren(DvObject definitionPoint) {
    List<DvObject> dvObjectsToReindexPermissionsFor = new ArrayList<>();
    List<DataFile> filesToReindexAsBatch = new ArrayList<>();
    // so don't create a Solr "permission" doc either.
    if (definitionPoint.isInstanceofDataverse()) {
        Dataverse selfDataverse = (Dataverse) definitionPoint;
        if (!selfDataverse.equals(dataverseService.findRootDataverse())) {
            dvObjectsToReindexPermissionsFor.add(definitionPoint);
        }
        List<Dataset> directChildDatasetsOfDvDefPoint = datasetService.findByOwnerId(selfDataverse.getId());
        for (Dataset dataset : directChildDatasetsOfDvDefPoint) {
            dvObjectsToReindexPermissionsFor.add(dataset);
            for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
                filesToReindexAsBatch.add(datafile);
            }
        }
    } else if (definitionPoint.isInstanceofDataset()) {
        // index the dataset itself
        indexPermissionsForOneDvObject(definitionPoint);
        dvObjectsToReindexPermissionsFor.add(definitionPoint);
        // index files
        Dataset dataset = (Dataset) definitionPoint;
        for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
            filesToReindexAsBatch.add(datafile);
        }
    } else {
        dvObjectsToReindexPermissionsFor.add(definitionPoint);
    }
    /**
     * @todo Error handling? What to do with response?
     *
     * @todo Should update timestamps, probably, even thought these are
     * files, see https://github.com/IQSS/dataverse/issues/2421
     */
    String response = reindexFilesInBatches(filesToReindexAsBatch);
    List<String> updatePermissionTimeSuccessStatus = new ArrayList<>();
    for (DvObject dvObject : dvObjectsToReindexPermissionsFor) {
        /**
         * @todo do something with this response
         */
        IndexResponse indexResponse = indexPermissionsForOneDvObject(dvObject);
        DvObject managedDefinitionPoint = dvObjectService.updatePermissionIndexTime(definitionPoint);
        boolean updatePermissionTimeSuccessful = false;
        if (managedDefinitionPoint != null) {
            updatePermissionTimeSuccessful = true;
        }
        updatePermissionTimeSuccessStatus.add(dvObject + ":" + updatePermissionTimeSuccessful);
    }
    return new IndexResponse("Number of dvObject permissions indexed for " + definitionPoint + " (updatePermissionTimeSuccessful:" + updatePermissionTimeSuccessStatus + "): " + dvObjectsToReindexPermissionsFor.size());
}

Example 40 with Dataverse

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

the class IndexAllServiceBean method indexAllOrSubset.

public Future<String> indexAllOrSubset(long numPartitions, long partitionId, boolean skipIndexed) {
    long indexAllTimeBegin = System.currentTimeMillis();
    String status;
    String resultOfClearingIndexTimes;
    /**
     * @todo Should we allow sysadmins to request that the Solr index and
     * related timestamps in the database be cleared as part of "index all"?
     * If so, we can make this boolean a parameter that's passed into this
     * method. A method to do this clearing has been added as a separate API
     * endpoint.
     */
    boolean clearSolrAndTimestamps = false;
    /**
     * We only allow clearing of Solr and database index timestamps if we
     * are operating on the entire index ("index all") and if we are not
     * running in "continue" mode.
     */
    if (numPartitions == 1 && !skipIndexed && clearSolrAndTimestamps) {
        logger.info("attempting to delete all Solr documents before a complete re-index");
        try {
            JsonObject response = solrIndexService.deleteAllFromSolrAndResetIndexTimes().build();
            String message = response.getString(SolrIndexServiceBean.messageString);
            int numRowsCleared = response.getInt(SolrIndexServiceBean.numRowsClearedByClearAllIndexTimes);
            resultOfClearingIndexTimes = message + " Database rows from which index timestamps were cleared: " + numRowsCleared;
        } catch (SolrServerException | IOException ex) {
            resultOfClearingIndexTimes = "Solr index and database timestamps were not cleared: " + ex;
        }
    } else {
        resultOfClearingIndexTimes = "Solr index was not cleared before indexing.";
    }
    // List<Dataverse> dataverses = dataverseService.findAllOrSubset(numPartitions, partitionId, skipIndexed);
    // Note: no support for "partitions" in this experimental branch.
    // The method below returns the ids of all the unindexed dataverses.
    List<Long> dataverseIds = dataverseIds = dataverseService.findDataverseIdsForIndexing(skipIndexed);
    int dataverseIndexCount = 0;
    int dataverseFailureCount = 0;
    // for (Dataverse dataverse : dataverses) {
    for (Long id : dataverseIds) {
        try {
            dataverseIndexCount++;
            Dataverse dataverse = dataverseService.find(id);
            logger.info("indexing dataverse " + dataverseIndexCount + " of " + dataverseIds.size() + " (id=" + id + ", persistentId=" + dataverse.getAlias() + ")");
            Future<String> result = indexService.indexDataverseInNewTransaction(dataverse);
            dataverse = null;
        } catch (Exception e) {
            // We want to keep running even after an exception so throw some more info into the log
            dataverseFailureCount++;
            logger.info("FAILURE indexing dataverse " + dataverseIndexCount + " of " + dataverseIds.size() + " (id=" + id + ") Exception info: " + e.getMessage());
        }
    }
    int datasetIndexCount = 0;
    int datasetFailureCount = 0;
    List<Long> datasetIds = datasetService.findAllOrSubset(numPartitions, partitionId, skipIndexed);
    for (Long id : datasetIds) {
        try {
            datasetIndexCount++;
            logger.info("indexing dataset " + datasetIndexCount + " of " + datasetIds.size() + " (id=" + id + ")");
            Future<String> result = indexService.indexDatasetInNewTransaction(id);
        } catch (Exception e) {
            // We want to keep running even after an exception so throw some more info into the log
            datasetFailureCount++;
            logger.info("FAILURE indexing dataset " + datasetIndexCount + " of " + datasetIds.size() + " (id=" + id + ") Exception info: " + e.getMessage());
        }
    }
    logger.info("done iterating through all datasets");
    long indexAllTimeEnd = System.currentTimeMillis();
    String timeElapsed = "index all took " + (indexAllTimeEnd - indexAllTimeBegin) + " milliseconds";
    logger.info(timeElapsed);
    if (datasetFailureCount + dataverseFailureCount > 0) {
        String failureMessage = "There were index failures. " + dataverseFailureCount + " dataverse(s) and " + datasetFailureCount + " dataset(s) failed to index. Please check the log for more information.";
        logger.info(failureMessage);
    }
    status = dataverseIndexCount + " dataverses and " + datasetIndexCount + " datasets indexed. " + timeElapsed + ". " + resultOfClearingIndexTimes + "\n";
    logger.info(status);
    return new AsyncResult<>(status);
}