Examples with SnapshotRequestRowIdModel bio.terra.model.SnapshotRequestRowIdModel used on opensource projects

Example 1 with SnapshotRequestRowIdModel

use of bio.terra.model.SnapshotRequestRowIdModel in project jade-data-repo by DataBiosphere.

the class CreateSnapshotPrimaryDataRowIdsStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    // TODO: this assumes single-dataset snapshots, will need to add a loop for multiple
    SnapshotRequestContentsModel contentsModel = snapshotReq.getContents().get(0);
    Snapshot snapshot = snapshotDao.retrieveSnapshotByName(snapshotReq.getName());
    SnapshotSource source = snapshot.getSnapshotSources().get(0);
    SnapshotRequestRowIdModel rowIdModel = contentsModel.getRowIdSpec();
    // for each table, make sure all of the row ids match
    for (SnapshotRequestRowIdTableModel table : rowIdModel.getTables()) {
        List<String> rowIds = table.getRowIds();
        if (!rowIds.isEmpty()) {
            RowIdMatch rowIdMatch = bigQueryPdao.matchRowIds(snapshot, source, table.getTableName(), rowIds);
            if (!rowIdMatch.getUnmatchedInputValues().isEmpty()) {
                String unmatchedValues = String.join("', '", rowIdMatch.getUnmatchedInputValues());
                String message = String.format("Mismatched row ids: '%s'", unmatchedValues);
                FlightUtils.setErrorResponse(context, message, HttpStatus.BAD_REQUEST);
                return new StepResult(StepStatus.STEP_RESULT_FAILURE_FATAL, new MismatchedValueException(message));
            }
        }
    }
    bigQueryPdao.createSnapshotWithProvidedIds(snapshot, contentsModel);
    return StepResult.getStepResultSuccess();
}

Example 2 with SnapshotRequestRowIdModel

use of bio.terra.model.SnapshotRequestRowIdModel in project jade-data-repo by DataBiosphere.

the class SnapshotValidationTest method testSnapshotRowIdsEmptyColumns.

@Test
public void testSnapshotRowIdsEmptyColumns() throws Exception {
    SnapshotRequestRowIdModel rowIdSpec = snapshotByRowIdsRequestModel.getContents().get(0).getRowIdSpec();
    rowIdSpec.getTables().get(0).setColumns(Collections.emptyList());
    expectBadSnapshotCreateRequest(snapshotByRowIdsRequestModel);
}

Example 3 with SnapshotRequestRowIdModel

use of bio.terra.model.SnapshotRequestRowIdModel in project jade-data-repo by DataBiosphere.

the class SnapshotValidationTest method makeSnapshotRowIdsRequest.

// Generate a valid snapshot-by-rowId request, we will tweak individual pieces to test validation below
public SnapshotRequestModel makeSnapshotRowIdsRequest() {
    SnapshotRequestRowIdTableModel snapshotRequestTableModel = new SnapshotRequestRowIdTableModel().tableName("snapshot").columns(Arrays.asList("col1", "col2", "col3")).rowIds(Arrays.asList("row1", "row2", "row3"));
    SnapshotRequestRowIdModel rowIdSpec = new SnapshotRequestRowIdModel().tables(Collections.singletonList(snapshotRequestTableModel));
    SnapshotRequestContentsModel snapshotRequestContentsModel = new SnapshotRequestContentsModel().datasetName("dataset").mode(SnapshotRequestContentsModel.ModeEnum.BYROWID).rowIdSpec(rowIdSpec);
    return new SnapshotRequestModel().contents(Collections.singletonList(snapshotRequestContentsModel));
}

Example 4 with SnapshotRequestRowIdModel

use of bio.terra.model.SnapshotRequestRowIdModel in project jade-data-repo by DataBiosphere.

the class SnapshotService method conjureSnapshotTablesFromRowIds.

private void conjureSnapshotTablesFromRowIds(SnapshotRequestRowIdModel requestRowIdModel, Snapshot snapshot, SnapshotSource snapshotSource) {
    // TODO this will need to be changed when we have more than one dataset per snapshot (>1 contentsModel)
    List<SnapshotTable> tableList = new ArrayList<>();
    snapshot.snapshotTables(tableList);
    List<SnapshotMapTable> mapTableList = new ArrayList<>();
    snapshotSource.snapshotMapTables(mapTableList);
    Dataset dataset = snapshotSource.getDataset();
    // create a lookup from tableName -> table spec from the request
    Map<String, SnapshotRequestRowIdTableModel> requestTableLookup = requestRowIdModel.getTables().stream().collect(Collectors.toMap(SnapshotRequestRowIdTableModel::getTableName, Function.identity()));
    // for each dataset table specified in the request, create a table in the snapshot with the same name
    for (DatasetTable datasetTable : dataset.getTables()) {
        if (!requestTableLookup.containsKey(datasetTable.getName())) {
            // only capture the dataset tables in the request model
            continue;
        }
        List<Column> columnList = new ArrayList<>();
        SnapshotTable snapshotTable = new SnapshotTable().name(datasetTable.getName()).columns(columnList);
        tableList.add(snapshotTable);
        List<SnapshotMapColumn> mapColumnList = new ArrayList<>();
        mapTableList.add(new SnapshotMapTable().fromTable(datasetTable).toTable(snapshotTable).snapshotMapColumns(mapColumnList));
        // for each dataset column specified in the request, create a column in the snapshot with the same name
        Set<String> requestColumns = new HashSet<>(requestTableLookup.get(datasetTable.getName()).getColumns());
        datasetTable.getColumns().stream().filter(c -> requestColumns.contains(c.getName())).forEach(datasetColumn -> {
            Column snapshotColumn = new Column().name(datasetColumn.getName());
            SnapshotMapColumn snapshotMapColumn = new SnapshotMapColumn().fromColumn(datasetColumn).toColumn(snapshotColumn);
            columnList.add(snapshotColumn);
            mapColumnList.add(snapshotMapColumn);
        });
    }
}

Example 5 with SnapshotRequestRowIdModel

use of bio.terra.model.SnapshotRequestRowIdModel in project jade-data-repo by DataBiosphere.

the class SnapshotService method makeSnapshotFromSnapshotRequest.

/**
 * Make a Snapshot structure with all of its parts from an incoming snapshot request.
 * Note that the structure does not have UUIDs or created dates filled in. Those are
 * updated by the DAO when it stores the snapshot in the repository metadata.
 *
 * @param snapshotRequestModel
 * @return Snapshot
 */
public Snapshot makeSnapshotFromSnapshotRequest(SnapshotRequestModel snapshotRequestModel) {
    // Make this early so we can hook up back links to it
    Snapshot snapshot = new Snapshot();
    List<SnapshotRequestContentsModel> requestContentsList = snapshotRequestModel.getContents();
    // TODO: for MVM we only allow one source list
    if (requestContentsList.size() > 1) {
        throw new ValidationException("Only a single snapshot contents entry is currently allowed.");
    }
    SnapshotRequestContentsModel requestContents = requestContentsList.get(0);
    Dataset dataset = datasetService.retrieveByName(requestContents.getDatasetName());
    SnapshotSource snapshotSource = new SnapshotSource().snapshot(snapshot).dataset(dataset);
    switch(snapshotRequestModel.getContents().get(0).getMode()) {
        case BYASSET:
            // TODO: When we implement explicit definition of snapshot tables, we will handle that here.
            // For now, we generate the snapshot tables directly from the asset tables of the one source
            // allowed in a snapshot.
            AssetSpecification assetSpecification = getAssetSpecificationFromRequest(requestContents);
            snapshotSource.assetSpecification(assetSpecification);
            conjureSnapshotTablesFromAsset(snapshotSource.getAssetSpecification(), snapshot, snapshotSource);
            break;
        case BYFULLVIEW:
            conjureSnapshotTablesFromDatasetTables(snapshot, snapshotSource);
            break;
        case BYQUERY:
            SnapshotRequestQueryModel queryModel = requestContents.getQuerySpec();
            String assetName = queryModel.getAssetName();
            String snapshotQuery = queryModel.getQuery();
            Query query = Query.parse(snapshotQuery);
            List<String> datasetNames = query.getDatasetNames();
            // TODO this makes the assumption that there is only one dataset
            // (based on the validation flight step that already occurred.)
            // This will change when more than 1 dataset is allowed
            String datasetName = datasetNames.get(0);
            Dataset queryDataset = datasetService.retrieveByName(datasetName);
            AssetSpecification queryAssetSpecification = queryDataset.getAssetSpecificationByName(assetName).orElseThrow(() -> new AssetNotFoundException("This dataset does not have an asset specification with name: " + assetName));
            snapshotSource.assetSpecification(queryAssetSpecification);
            // TODO this is wrong? why dont we just pass the assetSpecification?
            conjureSnapshotTablesFromAsset(snapshotSource.getAssetSpecification(), snapshot, snapshotSource);
            break;
        case BYROWID:
            SnapshotRequestRowIdModel requestRowIdModel = requestContents.getRowIdSpec();
            conjureSnapshotTablesFromRowIds(requestRowIdModel, snapshot, snapshotSource);
            break;
        default:
            throw new InvalidSnapshotException("Snapshot does not have required mode information");
    }
    return snapshot.name(snapshotRequestModel.getName()).description(snapshotRequestModel.getDescription()).snapshotSources(Collections.singletonList(snapshotSource)).profileId(UUID.fromString(snapshotRequestModel.getProfileId())).relationships(createSnapshotRelationships(dataset.getRelationships(), snapshotSource));
}