use of bio.terra.model.SnapshotRequestQueryModel in project jade-data-repo by DataBiosphere.
the class SnapshotValidationTest method makeSnapshotByQueryRequest.
// Generate a valid snapshot-by-query request, we will tweak individual pieces to test validation below
public SnapshotRequestModel makeSnapshotByQueryRequest() {
SnapshotRequestQueryModel querySpec = new SnapshotRequestQueryModel().assetName("asset").query("SELECT * FROM dataset");
SnapshotRequestContentsModel snapshotRequestContentsModel = new SnapshotRequestContentsModel().datasetName("dataset").mode(SnapshotRequestContentsModel.ModeEnum.BYQUERY).querySpec(querySpec);
return new SnapshotRequestModel().contents(Collections.singletonList(snapshotRequestContentsModel));
}
use of bio.terra.model.SnapshotRequestQueryModel 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));
}
use of bio.terra.model.SnapshotRequestQueryModel 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();
}
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