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

Example 6 with Dataverse

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

the class CreateRoleCommandTest method testNonSuperUsersCantAddRoles.

@Test(expected = IllegalCommandException.class)
public void testNonSuperUsersCantAddRoles() throws CommandException {
    DataverseRole dvr = new DataverseRole();
    dvr.setAlias("roleTest");
    dvr.setName("Tester Role");
    dvr.addPermission(Permission.AddDataset);
    Dataverse dv = MocksFactory.makeDataverse();
    dvr.setOwner(dv);
    AuthenticatedUser normalUser = new AuthenticatedUser();
    normalUser.setSuperuser(false);
    CreateRoleCommand sut = new CreateRoleCommand(dvr, new DataverseRequest(normalUser, IpAddress.valueOf("89.17.33.33")), dv);
    engine.submit(sut);
}

Example 7 with Dataverse

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

the class CreateRoleCommandTest method testSuperUsersAddRoles.

@Test
public void testSuperUsersAddRoles() throws CommandException {
    DataverseRole dvr = new DataverseRole();
    dvr.setAlias("roleTest");
    dvr.setName("Tester Role");
    dvr.addPermission(Permission.AddDataset);
    Dataverse dv = MocksFactory.makeDataverse();
    dvr.setOwner(dv);
    AuthenticatedUser normalUser = new AuthenticatedUser();
    normalUser.setSuperuser(true);
    CreateRoleCommand sut = new CreateRoleCommand(dvr, new DataverseRequest(normalUser, IpAddress.valueOf("89.17.33.33")), dv);
    engine.submit(sut);
    assertTrue("CreateRoleCommand did not call save on the created role.", saveCalled);
}

Example 8 with Dataverse

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

the class FileAccessIO method getDatasetDirectory.

private String getDatasetDirectory() throws IOException {
    if (dvObject == null) {
        throw new IOException("No DvObject defined in the Data Access Object");
    }
    Path datasetDirectoryPath = null;
    if (dvObject instanceof Dataset) {
        datasetDirectoryPath = this.getDataset().getFileSystemDirectory();
    } else if (dvObject instanceof DataFile) {
        datasetDirectoryPath = this.getDataFile().getOwner().getFileSystemDirectory();
    } else if (dvObject instanceof Dataverse) {
        throw new IOException("FileAccessIO: Dataverses are not a supported dvObject");
    }
    if (datasetDirectoryPath == null) {
        throw new IOException("Could not determine the filesystem directory of the parent dataset.");
    }
    String datasetDirectory = datasetDirectoryPath.toString();
    if (dvObject.getStorageIdentifier() == null || dvObject.getStorageIdentifier().isEmpty()) {
        throw new IOException("Data Access: No local storage identifier defined for this datafile.");
    }
    return datasetDirectory;
}

Example 9 with Dataverse

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

the class S3AccessIO method open.

@Override
public void open(DataAccessOption... options) throws IOException {
    if (s3 == null) {
        throw new IOException("ERROR: s3 not initialised. ");
    }
    if (bucketName == null || !s3.doesBucketExist(bucketName)) {
        throw new IOException("ERROR: S3AccessIO - You must create and configure a bucket before creating datasets.");
    }
    DataAccessRequest req = this.getRequest();
    if (isWriteAccessRequested(options)) {
        isWriteAccess = true;
        isReadAccess = false;
    } else {
        isWriteAccess = false;
        isReadAccess = true;
    }
    if (dvObject instanceof DataFile) {
        String storageIdentifier = dvObject.getStorageIdentifier();
        DataFile dataFile = this.getDataFile();
        if (req != null && req.getParameter("noVarHeader") != null) {
            this.setNoVarHeader(true);
        }
        if (storageIdentifier == null || "".equals(storageIdentifier)) {
            throw new FileNotFoundException("Data Access: No local storage identifier defined for this datafile.");
        }
        if (isReadAccess) {
            key = getMainFileKey();
            S3Object s3object = s3.getObject(new GetObjectRequest(bucketName, key));
            InputStream in = s3object.getObjectContent();
            if (in == null) {
                throw new IOException("Cannot get Object" + key);
            }
            this.setInputStream(in);
            setChannel(Channels.newChannel(in));
            this.setSize(s3object.getObjectMetadata().getContentLength());
            if (dataFile.getContentType() != null && dataFile.getContentType().equals("text/tab-separated-values") && dataFile.isTabularData() && dataFile.getDataTable() != null && (!this.noVarHeader())) {
                List<DataVariable> datavariables = dataFile.getDataTable().getDataVariables();
                String varHeaderLine = generateVariableHeader(datavariables);
                this.setVarHeader(varHeaderLine);
            }
        } else if (isWriteAccess) {
            key = dataFile.getOwner().getAuthority() + "/" + this.getDataFile().getOwner().getIdentifier();
            if (storageIdentifier.startsWith(S3_IDENTIFIER_PREFIX + "://")) {
                key += "/" + storageIdentifier.substring(storageIdentifier.lastIndexOf(":") + 1);
            } else {
                key += "/" + storageIdentifier;
                dvObject.setStorageIdentifier(S3_IDENTIFIER_PREFIX + "://" + bucketName + ":" + storageIdentifier);
            }
        }
        this.setMimeType(dataFile.getContentType());
        try {
            this.setFileName(dataFile.getFileMetadata().getLabel());
        } catch (Exception ex) {
            this.setFileName("unknown");
        }
    } else if (dvObject instanceof Dataset) {
        Dataset dataset = this.getDataset();
        key = dataset.getAuthority() + "/" + dataset.getIdentifier();
        dataset.setStorageIdentifier(S3_IDENTIFIER_PREFIX + "://" + key);
    } else if (dvObject instanceof Dataverse) {
        throw new IOException("Data Access: Invalid DvObject type : Dataverse");
    } else {
        throw new IOException("Data Access: Invalid DvObject type");
    }
}

Example 10 with Dataverse

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

the class IndexServiceBean method indexDataverse.

public Future<String> indexDataverse(Dataverse dataverse) {
    logger.fine("indexDataverse called on dataverse id " + dataverse.getId() + "(" + dataverse.getAlias() + ")");
    if (dataverse.getId() == null) {
        String msg = "unable to index dataverse. id was null (alias: " + dataverse.getAlias() + ")";
        logger.info(msg);
        return new AsyncResult<>(msg);
    }
    Dataverse rootDataverse = findRootDataverseCached();
    if (rootDataverse == null) {
        String msg = "Could not find root dataverse and the root dataverse should not be indexed. Returning.";
        return new AsyncResult<>(msg);
    } else if (dataverse.getId() == rootDataverse.getId()) {
        String msg = "The root dataverse should not be indexed. Returning.";
        return new AsyncResult<>(msg);
    }
    Collection<SolrInputDocument> docs = new ArrayList<>();
    SolrInputDocument solrInputDocument = new SolrInputDocument();
    solrInputDocument.addField(SearchFields.ID, solrDocIdentifierDataverse + dataverse.getId());
    solrInputDocument.addField(SearchFields.ENTITY_ID, dataverse.getId());
    solrInputDocument.addField(SearchFields.DATAVERSE_VERSION_INDEXED_BY, systemConfig.getVersion());
    solrInputDocument.addField(SearchFields.IDENTIFIER, dataverse.getAlias());
    solrInputDocument.addField(SearchFields.TYPE, "dataverses");
    solrInputDocument.addField(SearchFields.NAME, dataverse.getName());
    solrInputDocument.addField(SearchFields.NAME_SORT, dataverse.getName());
    solrInputDocument.addField(SearchFields.DATAVERSE_NAME, dataverse.getName());
    solrInputDocument.addField(SearchFields.DATAVERSE_CATEGORY, dataverse.getIndexableCategoryName());
    if (dataverse.isReleased()) {
        solrInputDocument.addField(SearchFields.PUBLICATION_STATUS, PUBLISHED_STRING);
        solrInputDocument.addField(SearchFields.RELEASE_OR_CREATE_DATE, dataverse.getPublicationDate());
        solrInputDocument.addField(SearchFields.RELEASE_OR_CREATE_DATE_SEARCHABLE_TEXT, convertToFriendlyDate(dataverse.getPublicationDate()));
    } else {
        solrInputDocument.addField(SearchFields.PUBLICATION_STATUS, UNPUBLISHED_STRING);
        solrInputDocument.addField(SearchFields.RELEASE_OR_CREATE_DATE, dataverse.getCreateDate());
        solrInputDocument.addField(SearchFields.RELEASE_OR_CREATE_DATE_SEARCHABLE_TEXT, convertToFriendlyDate(dataverse.getCreateDate()));
    }
    /* We don't really have harvested dataverses yet; 
           (I have in fact just removed the isHarvested() method from the Dataverse object) -- L.A.
        if (dataverse.isHarvested()) {
            solrInputDocument.addField(SearchFields.IS_HARVESTED, true);
            solrInputDocument.addField(SearchFields.SOURCE, HARVESTED);
        } else { (this means that all dataverses are "local" - should this be removed? */
    solrInputDocument.addField(SearchFields.IS_HARVESTED, false);
    // rootDataverseName);
    solrInputDocument.addField(SearchFields.METADATA_SOURCE, findRootDataverseCached().getName());
    /*}*/
    addDataverseReleaseDateToSolrDoc(solrInputDocument, dataverse);
    // if (dataverse.getOwner() != null) {
    // solrInputDocument.addField(SearchFields.HOST_DATAVERSE, dataverse.getOwner().getName());
    // }
    solrInputDocument.addField(SearchFields.DESCRIPTION, StringUtil.html2text(dataverse.getDescription()));
    solrInputDocument.addField(SearchFields.DATAVERSE_DESCRIPTION, StringUtil.html2text(dataverse.getDescription()));
    // logger.info("dataverse affiliation: " + dataverse.getAffiliation());
    if (dataverse.getAffiliation() != null && !dataverse.getAffiliation().isEmpty()) {
        /**
         * @todo: stop using affiliation as category
         */
        // solrInputDocument.addField(SearchFields.CATEGORY, dataverse.getAffiliation());
        solrInputDocument.addField(SearchFields.AFFILIATION, dataverse.getAffiliation());
        solrInputDocument.addField(SearchFields.DATAVERSE_AFFILIATION, dataverse.getAffiliation());
    }
    for (ControlledVocabularyValue dataverseSubject : dataverse.getDataverseSubjects()) {
        String subject = dataverseSubject.getStrValue();
        if (!subject.equals(DatasetField.NA_VALUE)) {
            solrInputDocument.addField(SearchFields.DATAVERSE_SUBJECT, subject);
            // collapse into shared "subject" field used as a facet
            solrInputDocument.addField(SearchFields.SUBJECT, subject);
        }
    }
    // checking for NPE is important so we can create the root dataverse
    if (rootDataverse != null && !dataverse.equals(rootDataverse)) {
        // important when creating root dataverse
        if (dataverse.getOwner() != null) {
            solrInputDocument.addField(SearchFields.PARENT_ID, dataverse.getOwner().getId());
            solrInputDocument.addField(SearchFields.PARENT_NAME, dataverse.getOwner().getName());
        }
    }
    List<String> dataversePathSegmentsAccumulator = new ArrayList<>();
    List<String> dataverseSegments = findPathSegments(dataverse, dataversePathSegmentsAccumulator);
    List<String> dataversePaths = getDataversePathsFromSegments(dataverseSegments);
    if (dataversePaths.size() > 0) {
        // don't show yourself while indexing or in search results: https://redmine.hmdc.harvard.edu/issues/3613
        // logger.info(dataverse.getName() + " size " + dataversePaths.size());
        dataversePaths.remove(dataversePaths.size() - 1);
    }
    // Add paths for linking dataverses
    for (Dataverse linkingDataverse : dvLinkingService.findLinkingDataverses(dataverse.getId())) {
        List<String> linkingDataversePathSegmentsAccumulator = new ArrayList<>();
        List<String> linkingdataverseSegments = findPathSegments(linkingDataverse, linkingDataversePathSegmentsAccumulator);
        List<String> linkingDataversePaths = getDataversePathsFromSegments(linkingdataverseSegments);
        for (String dvPath : linkingDataversePaths) {
            dataversePaths.add(dvPath);
        }
    }
    solrInputDocument.addField(SearchFields.SUBTREE, dataversePaths);
    docs.add(solrInputDocument);
    String status;
    try {
        if (dataverse.getId() != null) {
            solrServer.add(docs);
        } else {
            logger.info("WARNING: indexing of a dataverse with no id attempted");
        }
    } catch (SolrServerException | IOException ex) {
        status = ex.toString();
        logger.info(status);
        return new AsyncResult<>(status);
    }
    try {
        solrServer.commit();
    } catch (SolrServerException | IOException ex) {
        status = ex.toString();
        logger.info(status);
        return new AsyncResult<>(status);
    }
    dvObjectService.updateContentIndexTime(dataverse);
    IndexResponse indexResponse = solrIndexService.indexPermissionsForOneDvObject(dataverse);
    String msg = "indexed dataverse " + dataverse.getId() + ":" + dataverse.getAlias() + ". Response from permission indexing: " + indexResponse.getMessage();
    return new AsyncResult<>(msg);
}