Examples with AssetSpecification bio.terra.service.dataset.AssetSpecification used on opensource projects

Example 6 with AssetSpecification

use of bio.terra.service.dataset.AssetSpecification in project jade-data-repo by DataBiosphere.

the class CreateDatasetAssetStep method undoStep.

@Override
public StepResult undoStep(FlightContext context) {
    FlightMap map = context.getWorkingMap();
    if (map.get(DatasetWorkingMapKeys.ASSET_NAME_COLLISION, Boolean.class) == null) {
        Dataset dataset = getDataset(context);
        // Search the Asset list in the dataset object to see if the asset you were trying to create got created.
        AssetSpecification newAssetSpecification = getNewAssetSpec(context, dataset);
        Optional<AssetSpecification> assetSpecificationToDelete = dataset.getAssetSpecificationByName(newAssetSpecification.getName());
        // when the undoStep is run.
        if (assetSpecificationToDelete.isPresent()) {
            // If the asset is found, then you get its id and call delete.
            assetDao.delete(assetSpecificationToDelete.get().getId());
        }
    }
    // Else, if the asset is not found, then you are done. It never got created.
    return StepResult.getStepResultSuccess();
}

Example 7 with AssetSpecification

use of bio.terra.service.dataset.AssetSpecification 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));
}

Example 8 with AssetSpecification

use of bio.terra.service.dataset.AssetSpecification in project jade-data-repo by DataBiosphere.

the class BigQueryPdao method mapValuesToRows.

// compute the row ids from the input ids and validate all inputs have matches
// returns a structure with the matching row ids (suitable for calling create snapshot)
// and any mismatched input values that don't have corresponding roww.
// NOTE: In the fullness of time, we may not do this and kick the function into the UI.
// So this code assumes there is one source and one set of input values.
// The query it builds embeds data values into the query in an array. I think it will
// support about 25,000 input values. If that is not enough there is another, more
// complicated alternative:
// - create a scratch table at snapshot creation time
// - truncate before we start
// - load the values in
// - do the query
// - truncate (even tidier...)
// So if we need to make this work in the long term, we can take that approach.
@Override
public RowIdMatch mapValuesToRows(Snapshot snapshot, SnapshotSource source, List<String> inputValues) throws InterruptedException {
    // One source: grab it and navigate to the relevant parts
    BigQueryProject bigQueryProject = bigQueryProjectForSnapshot(snapshot);
    AssetSpecification asset = source.getAssetSpecification();
    Column column = asset.getRootColumn().getDatasetColumn();
    ST sqlTemplate = new ST(mapValuesToRowsTemplate);
    sqlTemplate.add("project", bigQueryProject.getProjectId());
    sqlTemplate.add("dataset", prefixName(source.getDataset().getName()));
    sqlTemplate.add("table", column.getTable().getName());
    sqlTemplate.add("column", column.getName());
    sqlTemplate.add("inputVals", inputValues);
    // Execute the query building the row id match structure that tracks the matching
    // ids and the mismatched ids
    RowIdMatch rowIdMatch = new RowIdMatch();
    String sql = sqlTemplate.render();
    logger.debug("mapValuesToRows sql: " + sql);
    TableResult result = bigQueryProject.query(sql);
    for (FieldValueList row : result.iterateAll()) {
        // Test getting these by name
        FieldValue rowId = row.get(0);
        FieldValue inputValue = row.get(1);
        if (rowId.isNull()) {
            rowIdMatch.addMismatch(inputValue.getStringValue());
            logger.debug("rowId=<NULL>" + "  inVal=" + inputValue.getStringValue());
        } else {
            rowIdMatch.addMatch(inputValue.getStringValue(), rowId.getStringValue());
            logger.debug("rowId=" + rowId.getStringValue() + "  inVal=" + inputValue.getStringValue());
        }
    }
    return rowIdMatch;
}

Example 9 with AssetSpecification

use of bio.terra.service.dataset.AssetSpecification in project jade-data-repo by DataBiosphere.

the class CreateSnapshotPrimaryDataQueryStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    // TODO: this assumes single-dataset snapshots, will need to add a loop for multiple
    // (based on the validation flight step that already occurred.)
    /*
         * get dataset and assetName
         * get asset from dataset
         * which gives the root table
         * to use in conjunction with the filtered row ids to create this snapshot
         */
    Snapshot snapshot = snapshotDao.retrieveSnapshotByName(snapshotReq.getName());
    SnapshotRequestQueryModel snapshotQuerySpec = snapshotReq.getContents().get(0).getQuerySpec();
    String snapshotAssetName = snapshotQuerySpec.getAssetName();
    String snapshotQuery = snapshotReq.getContents().get(0).getQuerySpec().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 dataset = datasetService.retrieveByName(datasetName);
    DatasetModel datasetModel = datasetService.retrieveModel(dataset);
    // get asset out of dataset
    Optional<AssetSpecification> assetSpecOp = dataset.getAssetSpecificationByName(snapshotAssetName);
    AssetSpecification assetSpec = assetSpecOp.orElseThrow(() -> new AssetNotFoundException("Expected asset specification"));
    Map<String, DatasetModel> datasetMap = Collections.singletonMap(datasetName, datasetModel);
    BigQueryVisitor bqVisitor = new BigQueryVisitor(datasetMap);
    String sqlQuery = query.translateSql(bqVisitor);
    // validate that the root table is actually a table being queried in the query -->
    // and the grammar only picks up tables names in the from clause (though there may be more than one)
    List<String> tableNames = query.getTableNames();
    String rootTablename = assetSpec.getRootTable().getTable().getName();
    if (!tableNames.contains(rootTablename)) {
        throw new InvalidQueryException("The root table of the selected asset is not present in this query");
    }
    // now using the query, get the rowIds
    // insert the rowIds into the snapshot row ids table and then kick off the rest of the relationship walking
    bigQueryPdao.queryForRowIds(assetSpec, snapshot, sqlQuery);
    return StepResult.getStepResultSuccess();
}

Example 10 with AssetSpecification

use of bio.terra.service.dataset.AssetSpecification in project jade-data-repo by DataBiosphere.

the class BigQueryPdao method createSnapshot.

@Override
public void createSnapshot(Snapshot snapshot, List<String> rowIds) throws InterruptedException {
    BigQueryProject bigQueryProject = bigQueryProjectForSnapshot(snapshot);
    String projectId = bigQueryProject.getProjectId();
    String snapshotName = snapshot.getName();
    BigQuery bigQuery = bigQueryProject.getBigQuery();
    // create snapshot BQ dataset
    snapshotCreateBQDataset(bigQueryProject, snapshot);
    // create the row id table
    bigQueryProject.createTable(snapshotName, PDAO_ROW_ID_TABLE, rowIdTableSchema());
    // populate root row ids. Must happen before the relationship walk.
    // NOTE: when we have multiple sources, we can put this into a loop
    SnapshotSource source = snapshot.getSnapshotSources().get(0);
    String datasetBqDatasetName = prefixName(source.getDataset().getName());
    AssetSpecification asset = source.getAssetSpecification();
    Table rootTable = asset.getRootTable().getTable();
    String rootTableId = rootTable.getId().toString();
    if (rowIds.size() > 0) {
        ST sqlTemplate = new ST(loadRootRowIdsTemplate);
        sqlTemplate.add("project", projectId);
        sqlTemplate.add("snapshot", snapshotName);
        sqlTemplate.add("dataset", datasetBqDatasetName);
        sqlTemplate.add("tableId", rootTableId);
        sqlTemplate.add("rowIds", rowIds);
        bigQueryProject.query(sqlTemplate.render());
    }
    ST sqlTemplate = new ST(validateRowIdsForRootTemplate);
    sqlTemplate.add("project", projectId);
    sqlTemplate.add("snapshot", snapshotName);
    sqlTemplate.add("dataset", datasetBqDatasetName);
    sqlTemplate.add("table", rootTable.getName());
    TableResult result = bigQueryProject.query(sqlTemplate.render());
    FieldValueList row = result.iterateAll().iterator().next();
    FieldValue countValue = row.get(0);
    if (countValue.getLongValue() != rowIds.size()) {
        logger.error("Invalid row ids supplied: rowIds=" + rowIds.size() + " count=" + countValue.getLongValue());
        for (String rowId : rowIds) {
            logger.error(" rowIdIn: " + rowId);
        }
        throw new PdaoException("Invalid row ids supplied");
    }
    // walk and populate relationship table row ids
    List<WalkRelationship> walkRelationships = WalkRelationship.ofAssetSpecification(asset);
    walkRelationships(datasetBqDatasetName, snapshotName, walkRelationships, rootTableId, projectId, bigQuery);
    snapshotViewCreation(datasetBqDatasetName, snapshotName, snapshot, projectId, bigQuery, bigQueryProject);
}