Examples with DatasetDTO org.broadinstitute.consent.http.models.dto.DatasetDTO used on opensource projects

Example 1 with DatasetDTO

use of org.broadinstitute.consent.http.models.dto.DatasetDTO in project consent by DataBiosphere.

the class DacWithDatasetsReducer method accumulate.

@Override
public void accumulate(Map<Integer, Dac> container, RowView rowView) {
    try {
        Dac dac = container.computeIfAbsent(rowView.getColumn("dac_id", Integer.class), id -> rowView.getRow(Dac.class));
        if (Objects.nonNull(rowView.getColumn("datasetid", Integer.class))) {
            DatasetDTO dto = rowView.getRow(DatasetDTO.class);
            try {
                if (Objects.nonNull(rowView.getColumn("dataset_alias", String.class))) {
                    String dsAlias = rowView.getColumn("dataset_alias", String.class);
                    try {
                        dto.setAlias(Integer.parseInt(dsAlias));
                    } catch (Exception e) {
                        logger.error("Exception parsing dataset alias: " + dsAlias, e);
                    }
                }
                if (Objects.nonNull(rowView.getColumn("dataset_create_date", Date.class))) {
                    Date createDate = rowView.getColumn("dataset_create_date", Date.class);
                    dto.setCreateDate(createDate);
                }
                if (Objects.nonNull(rowView.getColumn("dataset_update_date", Timestamp.class))) {
                    Timestamp updateDate = rowView.getColumn("dataset_update_date", Timestamp.class);
                    dto.setUpdateDate(updateDate);
                }
            } catch (Exception e) {
            // no values for these columns
            }
            if (Objects.nonNull(rowView.getColumn("consent_data_use", String.class))) {
                String duStr = rowView.getColumn("consent_data_use", String.class);
                Optional<DataUse> du = DataUse.parseDataUse(duStr);
                du.ifPresent(dto::setDataUse);
            }
            if (Objects.nonNull(dto)) {
                dac.addDatasetDTO(dto);
            }
        }
    } catch (MappingException e) {
        logger.warn(e.getMessage());
    }
}

Example 2 with DatasetDTO

use of org.broadinstitute.consent.http.models.dto.DatasetDTO in project consent by DataBiosphere.

the class DataSetPropertiesMapper method map.

public DatasetDTO map(ResultSet r, StatementContext ctx) throws SQLException {
    DatasetDTO dataSetDTO;
    Integer dataSetId = r.getInt("dataSetId");
    String consentId = r.getString("consentId");
    Integer alias = r.getInt("alias");
    if (!dataSets.containsKey(dataSetId)) {
        dataSetDTO = new DatasetDTO(new ArrayList<>());
        if (hasColumn(r, "dac_id")) {
            int dacId = r.getInt("dac_id");
            if (dacId > 0) {
                dataSetDTO.setDacId(dacId);
            }
        }
        dataSetDTO.setConsentId(consentId);
        dataSetDTO.setAlias(alias);
        dataSetDTO.setDataSetId(dataSetId);
        dataSetDTO.setActive(r.getBoolean("active"));
        dataSetDTO.setTranslatedUseRestriction(r.getString("translatedUseRestriction"));
        if (hasColumn(r, "datause")) {
            dataSetDTO.setDataUse(DataUse.parseDataUse(r.getString("datause")).orElse(null));
        }
        if (hasColumn(r, "createdate")) {
            dataSetDTO.setCreateDate(r.getDate("createdate"));
        }
        if (hasColumn(r, "create_user_id")) {
            int userId = r.getInt("create_user_id");
            if (userId > 0) {
                dataSetDTO.setCreateUserId(userId);
            }
        }
        if (hasColumn(r, "update_date")) {
            dataSetDTO.setUpdateDate(r.getTimestamp("update_date"));
        }
        if (hasColumn(r, "update_user_id")) {
            int userId = r.getInt("update_user_id");
            if (userId > 0) {
                dataSetDTO.setUpdateUserId(userId);
            }
        }
        DataSetPropertyDTO property = new DataSetPropertyDTO("Dataset Name", r.getString("name"));
        dataSetDTO.addProperty(property);
        property = new DataSetPropertyDTO(r.getString(PROPERTY_KEY), r.getString(PROPERTY_PROPERTYVALUE));
        if (property.getPropertyName() != null) {
            dataSetDTO.addProperty(property);
        }
        dataSetDTO.setNeedsApproval(r.getBoolean("needs_approval"));
        dataSetDTO.setObjectId(r.getString("objectId"));
        dataSets.put(dataSetId, dataSetDTO);
    } else {
        dataSetDTO = dataSets.get(dataSetId);
        DataSetPropertyDTO property = new DataSetPropertyDTO(r.getString(PROPERTY_KEY), r.getString(PROPERTY_PROPERTYVALUE));
        if (property.getPropertyName() != null) {
            dataSetDTO.addProperty(property);
        }
    }
    return dataSetDTO;
}

Example 3 with DatasetDTO

use of org.broadinstitute.consent.http.models.dto.DatasetDTO in project consent by DataBiosphere.

the class DatasetResourceTest method testDescribeDataSetSuccess.

@Test
public void testDescribeDataSetSuccess() {
    DatasetDTO testDTO = createMockDatasetDTO();
    when(datasetService.getDatasetDTO(any())).thenReturn(testDTO);
    initResource();
    Response response = resource.describeDataSet(1);
    assertEquals(200, response.getStatus());
}

Example 4 with DatasetDTO

use of org.broadinstitute.consent.http.models.dto.DatasetDTO in project consent by DataBiosphere.

the class DatasetResourceTest method testCreateDatasetSuccess.

@Test
public void testCreateDatasetSuccess() throws Exception {
    DatasetDTO result = createMockDatasetDTO();
    Consent consent = new Consent();
    String json = createPropertiesJson("Dataset Name", "test");
    when(datasetService.getDatasetByName("test")).thenReturn(null);
    when(datasetService.createDatasetWithConsent(any(), any(), anyInt())).thenReturn(result);
    when(datasetService.createConsentForDataset(any())).thenReturn(consent);
    when(datasetService.getDatasetDTO(any())).thenReturn(result);
    when(authUser.getGoogleUser()).thenReturn(googleUser);
    when(googleUser.getEmail()).thenReturn("email@email.com");
    when(userService.findUserByEmail(any())).thenReturn(dacUser);
    when(dacUser.getDacUserId()).thenReturn(1);
    when(uriInfo.getRequestUriBuilder()).thenReturn(uriBuilder);
    when(uriBuilder.replacePath(anyString())).thenReturn(uriBuilder);
    when(uriBuilder.build(anyString())).thenReturn(new URI("/api/dataset/1"));
    initResource();
    Response response = resource.createDataset(authUser, uriInfo, json);
    assertEquals(201, response.getStatus());
    assertEquals(result, response.getEntity());
}

Example 5 with DatasetDTO

use of org.broadinstitute.consent.http.models.dto.DatasetDTO in project consent by DataBiosphere.

the class DatasetResource method downloadDataSets.

@POST
@Path("/download")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
@PermitAll
public Response downloadDataSets(List<Integer> idList) {
    try {
        String msg = "GETing DataSets to download";
        logger().debug(msg);
        JSONObject json = new JSONObject();
        Collection<Dictionary> headers = datasetService.describeDictionaryByReceiveOrder();
        StringBuilder sb = new StringBuilder();
        String TSV_DELIMITER = "\t";
        for (Dictionary header : headers) {
            if (sb.length() > 0)
                sb.append(TSV_DELIMITER);
            sb.append(header.getKey());
        }
        sb.append(END_OF_LINE);
        if (CollectionUtils.isEmpty(idList)) {
            json.put("datasets", sb.toString());
            return Response.ok(json.toString(), MediaType.APPLICATION_JSON).build();
        }
        Collection<DatasetDTO> rows = datasetService.describeDataSetsByReceiveOrder(idList);
        for (DatasetDTO row : rows) {
            StringBuilder sbr = new StringBuilder();
            DataSetPropertyDTO property = new DataSetPropertyDTO("Consent ID", row.getConsentId());
            List<DataSetPropertyDTO> props = row.getProperties();
            props.add(property);
            for (DataSetPropertyDTO prop : props) {
                if (sbr.length() > 0)
                    sbr.append(TSV_DELIMITER);
                sbr.append(prop.getPropertyValue());
            }
            sbr.append(END_OF_LINE);
            sb.append(sbr);
        }
        String tsv = sb.toString();
        json.put("datasets", tsv);
        return Response.ok(json.toString(), MediaType.APPLICATION_JSON).build();
    } catch (Exception e) {
        return createExceptionResponse(e);
    }
}