Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance.
Project price only 1 $
You can buy this project and download/modify it how often you want.
io.hyperfoil.tools.horreum.svc.RunServiceImpl Maven / Gradle / Ivy
package io.hyperfoil.tools.horreum.svc;
import static com.fasterxml.jackson.databind.node.JsonNodeFactory.instance;
import static io.hyperfoil.tools.horreum.entity.data.SchemaDAO.*;
import java.io.IOException;
import java.time.Instant;
import java.util.*;
import java.util.function.BiConsumer;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
import jakarta.annotation.security.PermitAll;
import jakarta.annotation.security.RolesAllowed;
import jakarta.enterprise.context.ApplicationScoped;
import jakarta.inject.Inject;
import jakarta.persistence.*;
import jakarta.persistence.TransactionRequiredException;
import jakarta.transaction.*;
import jakarta.ws.rs.WebApplicationException;
import jakarta.ws.rs.core.HttpHeaders;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hibernate.Session;
import org.hibernate.query.NativeQuery;
import org.hibernate.type.StandardBasicTypes;
import org.jboss.logging.Logger;
import org.jboss.resteasy.reactive.multipart.FileUpload;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import com.fasterxml.jackson.databind.node.TextNode;
import io.hyperfoil.tools.horreum.api.SortDirection;
import io.hyperfoil.tools.horreum.api.data.*;
import io.hyperfoil.tools.horreum.api.data.Access;
import io.hyperfoil.tools.horreum.api.services.RunService;
import io.hyperfoil.tools.horreum.api.services.SchemaService;
import io.hyperfoil.tools.horreum.bus.AsyncEventChannels;
import io.hyperfoil.tools.horreum.datastore.BackendResolver;
import io.hyperfoil.tools.horreum.datastore.Datastore;
import io.hyperfoil.tools.horreum.datastore.DatastoreResponse;
import io.hyperfoil.tools.horreum.entity.PersistentLogDAO;
import io.hyperfoil.tools.horreum.entity.alerting.DataPointDAO;
import io.hyperfoil.tools.horreum.entity.alerting.TransformationLogDAO;
import io.hyperfoil.tools.horreum.entity.data.*;
import io.hyperfoil.tools.horreum.hibernate.JsonBinaryType;
import io.hyperfoil.tools.horreum.hibernate.JsonbSetType;
import io.hyperfoil.tools.horreum.mapper.DatasetMapper;
import io.hyperfoil.tools.horreum.mapper.RunMapper;
import io.hyperfoil.tools.horreum.server.RoleManager;
import io.hyperfoil.tools.horreum.server.WithRoles;
import io.hyperfoil.tools.horreum.server.WithToken;
import io.quarkus.narayana.jta.runtime.TransactionConfiguration;
import io.quarkus.runtime.Startup;
import io.quarkus.security.identity.SecurityIdentity;
@ApplicationScoped
@Startup
public class RunServiceImpl implements RunService {
private static final Logger log = Logger.getLogger(RunServiceImpl.class);
//@formatter:off
private static final String FIND_AUTOCOMPLETE = """
SELECT * FROM (
SELECT DISTINCT jsonb_object_keys(q) AS key
FROM run, jsonb_path_query(run.data, ? ::jsonpath) q
WHERE jsonb_typeof(q) = 'object') AS keys
WHERE keys.key LIKE CONCAT(?, '%');
""";
protected static final String FIND_RUNS_WITH_URI = """
SELECT id, testid
FROM run
WHERE NOT trashed
AND (data->>'$schema' = ?1
OR (CASE
WHEN jsonb_typeof(data) = 'object' THEN ?1 IN (SELECT values.value->>'$schema' FROM jsonb_each(data) as values)
WHEN jsonb_typeof(data) = 'array' THEN ?1 IN (SELECT jsonb_array_elements(data)->>'$schema')
ELSE false
END)
OR (metadata IS NOT NULL AND ?1 IN (SELECT jsonb_array_elements(metadata)->>'$schema'))
)
""";
//@formatter:on
private static final String[] CONDITION_SELECT_TERMINAL = { "==", "!=", "<>", "<", "<=", ">", ">=", " " };
private static final String UPDATE_TOKEN = "UPDATE run SET token = ? WHERE id = ?";
private static final String CHANGE_ACCESS = "UPDATE run SET owner = ?, access = ? WHERE id = ?";
private static final String SCHEMA_USAGE = "COALESCE(jsonb_agg(jsonb_build_object(" +
"'id', schema.id, 'uri', rs.uri, 'name', schema.name, 'source', rs.source, " +
"'type', rs.type, 'key', rs.key, 'hasJsonSchema', schema.schema IS NOT NULL)), '[]')";
@Inject
EntityManager em;
@Inject
SecurityIdentity identity;
@Inject
RoleManager roleManager;
@Inject
TransactionManager tm;
@Inject
SqlServiceImpl sqlService;
@Inject
TestServiceImpl testService;
@Inject
ObjectMapper mapper;
@Inject
ServiceMediator mediator;
@Inject
BackendResolver backendResolver;
@Inject
Session session;
@Transactional
@WithRoles(extras = Roles.HORREUM_SYSTEM)
void onTestDeleted(int testId) {
log.debugf("Trashing runs for test (%d)", testId);
ScrollableResults results = session.createNativeQuery("SELECT id FROM run WHERE testid = ?1", Integer.class)
.setParameter(1, testId)
.setReadOnly(true)
.setFetchSize(100)
.scroll(ScrollMode.FORWARD_ONLY);
while (results.next()) {
int id = results.get();
trashDueToTestDeleted(id);
}
}
// plain trash does not have the right privileges and @RolesAllowed would cause ContextNotActiveException
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional
void trashDueToTestDeleted(int id) {
trashInternal(id, true);
}
// We cannot run this without a transaction (to avoid timeout) because we have not request going on
// and EM has to bind its lifecycle either to current request or transaction.
@Transactional(Transactional.TxType.REQUIRES_NEW)
@TransactionConfiguration(timeout = 3600) // 1 hour, this may run a long time
@WithRoles(extras = Roles.HORREUM_SYSTEM)
void onNewOrUpdatedSchema(int schemaId) {
SchemaDAO schema = SchemaDAO.findById(schemaId);
if (schema == null) {
log.errorf("Cannot process schema add/update: cannot load schema %d", schemaId);
return;
}
processNewOrUpdatedSchema(schema);
}
@Transactional
void processNewOrUpdatedSchema(SchemaDAO schema) {
// we don't have to care about races with new runs
findRunsWithUri(schema.uri, (runId, testId) -> {
log.debugf("Recalculate Datasets for run %d - schema %d (%s) changed", runId, schema.id, schema.uri);
onNewOrUpdatedSchemaForRun(runId, schema.id);
});
}
void findRunsWithUri(String uri, BiConsumer consumer) {
ScrollableResults results = session.createNativeQuery(FIND_RUNS_WITH_URI, Tuple.class).setParameter(1, uri)
.setTupleTransformer((tuple, aliases) -> {
RunFromUri r = new RunFromUri();
r.id = (int) tuple[0];
r.testId = (int) tuple[1];
return r;
})
.setFetchSize(100)
.scroll(ScrollMode.FORWARD_ONLY);
while (results.next()) {
RunFromUri r = results.get();
consumer.accept(r.id, r.testId);
}
}
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional
void onNewOrUpdatedSchemaForRun(int runId, int schemaId) {
em.createNativeQuery("SELECT update_run_schemas(?1)::text").setParameter(1, runId).getSingleResult();
//clear validation error tables by schemaId
em.createNativeQuery("DELETE FROM dataset_validationerrors WHERE schema_id = ?1")
.setParameter(1, schemaId).executeUpdate();
em.createNativeQuery("DELETE FROM run_validationerrors WHERE schema_id = ?1")
.setParameter(1, schemaId).executeUpdate();
Util.registerTxSynchronization(tm, txStatus -> mediator.queueRunRecalculation(runId));
// transform(runId, true);
}
@PermitAll
@WithRoles
@WithToken
@Override
public RunExtended getRun(int id, String token) {
RunExtended runExtended = null;
String extendedData = (String) Util.runQuery(em, "SELECT (to_jsonb(run) || jsonb_build_object(" +
"'schemas', (SELECT " + SCHEMA_USAGE
+ " FROM run_schemas rs JOIN schema ON rs.schemaid = schema.id WHERE runid = run.id), " +
"'testname', (SELECT name FROM test WHERE test.id = run.testid), " +
"'datasets', (SELECT jsonb_agg(id ORDER BY id) FROM dataset WHERE runid = run.id), " +
"'validationErrors', (SELECT jsonb_agg(jsonb_build_object('schemaId', schema_id, 'error', error)) FROM run_validationerrors WHERE run_id = ?1)"
+
"))::text FROM run WHERE id = ?1", id);
try {
runExtended = mapper.readValue(extendedData, RunExtended.class);
} catch (JsonProcessingException e) {
throw ServiceException.serverError("Could not retrieve extended run");
}
return runExtended;
}
@WithRoles
@Override
public RunSummary getRunSummary(int id, String token) {
try {
Query query = em.createNativeQuery("SELECT run.id, run.start, run.stop, run.testid, " +
"run.owner, run.access, run.token, run.trashed, run.description, run.metadata IS NOT NULL as has_metadata, "
+
"(SELECT name FROM test WHERE test.id = run.testid) as testname, " +
"(SELECT " + SCHEMA_USAGE
+ " FROM run_schemas rs JOIN schema ON schema.id = rs.schemaid WHERE rs.runid = run.id) as schemas, " +
"(SELECT json_agg(id ORDER BY id) FROM dataset WHERE runid = run.id) as datasets, " +
"(SELECT jsonb_agg(jsonb_build_object('schemaId', schema_id, 'error', error)) AS errors FROM run_validationerrors WHERE run_id = ?1 GROUP BY run_id) AS validationErrors "
+
"FROM run where id = ?1").setParameter(1, id);
initTypes(query);
return createSummary((Object[]) query.getSingleResult());
} catch (NoResultException e) {
throw ServiceException.notFound("Run " + id + " not found");
}
}
@PermitAll
@WithRoles
@WithToken
@Override
public Object getData(int id, String token, String schemaUri) {
if (schemaUri == null || schemaUri.isEmpty()) {
return Util.runQuery(em, "SELECT data#>>'{}' from run where id = ?", id);
} else {
String sqlQuery = "SELECT (CASE " +
"WHEN rs.type = 0 THEN run.data " +
"WHEN rs.type = 1 THEN run.data->rs.key " +
"ELSE run.data->(rs.key::integer) " +
"END)#>>'{}' FROM run JOIN run_schemas rs ON rs.runid = run.id WHERE id = ?1 AND rs.source = 0 AND rs.uri = ?2";
return Util.runQuery(em, sqlQuery, id, schemaUri);
}
}
//this is nearly identical to TestServiceImpl.labelValues (except the return object)
//this reads from the dataset table but provides data specific to the run...
@Override
public List labelValues(int runId, String filter, String sort, String direction, int limit, int page,
List include, List exclude, boolean multiFilter) {
List rtrn = new ArrayList<>();
Run run = getRun(runId, null);
if (run == null) {
throw ServiceException.serverError("Cannot find run " + runId);
}
Object filterObject = Util.getFilterObject(filter);
TestServiceImpl.FilterDef filterDef = TestServiceImpl.getFilterDef(filter, null, null, multiFilter,
(str) -> labelValues(runId, str, sort, direction, limit, page, include, exclude, false), em);
String filterSql = filterDef.sql();
if (filterDef.filterObject() != null) {
filterObject = filterDef.filterObject();
}
if (filterSql.isBlank() && filter != null && !filter.isBlank()) {
//TODO there was an error with the filter, do we return that info to the user?
}
String orderSql = "";
String orderDirection = direction.equalsIgnoreCase("ascending") ? "ASC" : "DESC";
if (!sort.isBlank()) {
Util.CheckResult jsonpathResult = Util.castCheck(sort, "jsonpath", em);
if (jsonpathResult.ok()) {
orderSql = "order by jsonb_path_query(combined.values,CAST( :orderBy as jsonpath)) " + orderDirection
+ ", combined.datasetId DESC";
} else {
orderSql = "order by combined.datasetId DESC";
}
}
String includeExcludeSql = "";
List mutableInclude = new ArrayList<>(include);
if (include != null && !include.isEmpty()) {
if (exclude != null && !exclude.isEmpty()) {
mutableInclude.removeAll(exclude);
}
if (!mutableInclude.isEmpty()) {
includeExcludeSql = " AND label.name in :include";
}
}
//includeExcludeSql is empty if include did not contain entries after exclude removal
if (includeExcludeSql.isEmpty() && exclude != null && !exclude.isEmpty()) {
includeExcludeSql = " AND label.name NOT in :exclude";
}
String sql = """
WITH
combined as (
SELECT DISTINCT COALESCE(jsonb_object_agg(label.name, lv.value) FILTER (WHERE label.name IS NOT NULL INCLUDE_EXCLUDE_PLACEHOLDER), '{}'::jsonb) AS values, dataset.id AS datasetId, dataset.start AS start, dataset.stop AS stop
FROM dataset
LEFT JOIN label_values lv ON dataset.id = lv.dataset_id
LEFT JOIN label ON label.id = lv.label_id
WHERE runId = :runId
GROUP BY dataset.id
) select * from combined FILTER_PLACEHOLDER ORDER_PLACEHOLDER limit :limit offset :offset
"""
.replace("FILTER_PLACEHOLDER", filterSql)
.replace("INCLUDE_EXCLUDE_PLACEHOLDER", includeExcludeSql)
.replace("ORDER_PLACEHOLDER", orderSql);
NativeQuery query = ((NativeQuery) em.createNativeQuery(sql))
.setParameter("runId", runId);
if (!filterSql.isEmpty()) {
if (filterSql.contains(TestServiceImpl.LABEL_VALUES_FILTER_CONTAINS_JSON)) {
query.setParameter("filter", filterObject, JsonBinaryType.INSTANCE);
} else if (filterSql.contains(TestServiceImpl.LABEL_VALUES_FILTER_MATCHES_NOT_NULL)) {
query.setParameter("filter", filter);
}
}
if (!filterDef.multis().isEmpty() && filterDef.filterObject() != null) {
ObjectNode fullFilterObject = (ObjectNode) Util.getFilterObject(filter);
for (int i = 0; i < filterDef.multis().size(); i++) {
String key = filterDef.multis().get(i);
ArrayNode value = (ArrayNode) fullFilterObject.get(key);
query.setParameter("key" + i, "$." + key);
query.setParameter("value" + i, value, JsonbSetType.INSTANCE);
}
}
if (includeExcludeSql.contains(":include")) {
query.setParameter("include", mutableInclude);
} else if (includeExcludeSql.contains(":exclude")) {
query.setParameter("exclude", exclude);
}
if (orderSql.contains(":orderBy")) {
query.setParameter("orderBy", sort);
}
query
.setParameter("limit", limit)
.setParameter("offset", limit * Math.max(0, page))
.unwrap(NativeQuery.class)
.addScalar("values", JsonBinaryType.INSTANCE)
.addScalar("datasetId", Integer.class)
.addScalar("start", StandardBasicTypes.INSTANT)
.addScalar("stop", StandardBasicTypes.INSTANT);
//casting because type inference cannot detect there will be two scalars in the result
//TODO replace this with strictly typed entries
((List) query.getResultList()).forEach(objects -> {
JsonNode node = (JsonNode) objects[0];
Integer datasetId = Integer.parseInt(objects[1] == null ? "-1" : objects[1].toString());
Instant start = (Instant) objects[2];
Instant stop = (Instant) objects[3];
if (node.isObject()) {
rtrn.add(new ExportedLabelValues(
LabelValueMap.fromObjectNode((ObjectNode) node),
runId,
datasetId,
start,
stop));
} else {
//TODO alert that something is wrong in the db response
}
});
return rtrn;
}
@PermitAll
@WithRoles
@WithToken
@Override
public JsonNode getMetadata(int id, String token, String schemaUri) {
String result;
if (schemaUri == null || schemaUri.isEmpty()) {
result = (String) Util.runQuery(em, "SELECT coalesce((metadata#>>'{}')::jsonb, '{}'::jsonb) from run where id = ?",
id);
} else {
String sqlQuery = "SELECT run.metadata->(rs.key::integer)#>>'{}' FROM run " +
"JOIN run_schemas rs ON rs.runid = run.id WHERE id = ?1 AND rs.source = 1 AND rs.uri = ?2";
result = (String) Util.runQuery(em, sqlQuery, id, schemaUri);
}
try {
return Util.OBJECT_MAPPER.readTree(result);
} catch (JsonProcessingException e) {
throw ServiceException.serverError(e.getMessage());
}
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
public String resetToken(int id) {
return updateToken(id, Tokens.generateToken());
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
public String dropToken(int id) {
return updateToken(id, null);
}
private String updateToken(int id, String token) {
Query query = em.createNativeQuery(UPDATE_TOKEN);
query.setParameter(1, token);
query.setParameter(2, id);
if (query.executeUpdate() != 1) {
throw ServiceException.serverError("Token reset failed (missing permissions?)");
} else {
return token;
}
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
// TODO: it would be nicer to use @FormParams but fetchival on client side doesn't support that
public void updateAccess(int id, String owner, Access access) {
Query query = em.createNativeQuery(CHANGE_ACCESS);
query.setParameter(1, owner);
query.setParameter(2, access.ordinal());
query.setParameter(3, id);
if (query.executeUpdate() != 1) {
throw ServiceException.serverError("Access change failed (missing permissions?)");
}
}
@PermitAll // all because of possible token-based upload
@WithRoles
@WithToken
@Transactional
@Override
public Response add(String testNameOrId, String owner, Access access, String token, Run run) {
if (owner != null) {
run.owner = owner;
}
if (access != null) {
run.access = access;
}
log.debugf("About to add new run to test %s using owner", testNameOrId, owner);
if (testNameOrId == null || testNameOrId.isEmpty()) {
if (run.testid == null || run.testid == 0) {
return Response.status(Response.Status.BAD_REQUEST).entity("No test name or id provided").build();
} else
testNameOrId = run.testid.toString();
}
TestDAO test = testService.ensureTestExists(testNameOrId, token);
run.testid = test.id;
Integer runId = addAuthenticated(RunMapper.to(run), test);
return Response.status(Response.Status.OK).entity(String.valueOf(runId)).header(HttpHeaders.LOCATION, "/run/" + runId)
.build();
}
@Override
public Response addRunFromData(String start, String stop, String test,
String owner, Access access, String token,
String schemaUri, String description,
String data) {
return addRunFromData(start, stop, test, owner, access, token, schemaUri, description, data, null);
}
@Override
public Response addRunFromData(String start, String stop, String test, String owner, Access access, String token,
String schemaUri, String description, FileUpload data, FileUpload metadata) {
if (data == null) {
log.debugf("Failed to upload for test %s with description %s because of missing data.", test, description);
throw ServiceException.badRequest("No data!");
} else if (!MediaType.APPLICATION_JSON.equals(data.contentType())) {
log.debugf("Failed to upload for test %s with description %s because of wrong data content type: %s.", test,
description, data.contentType());
throw ServiceException
.badRequest("Part 'data' must use content-type: application/json, currently: " + data.contentType());
}
if (metadata != null && !MediaType.APPLICATION_JSON.equals(metadata.contentType())) {
log.debugf("Failed to upload for test %s with description %s because of wrong metadata content type: %s.", test,
description, metadata.contentType());
throw ServiceException.badRequest(
"Part 'metadata' must use content-type: application/json, currently: " + metadata.contentType());
}
JsonNode dataNode;
JsonNode metadataNode = null;
try {
dataNode = Util.OBJECT_MAPPER.readTree(data.uploadedFile().toFile());
if (metadata != null) {
metadataNode = Util.OBJECT_MAPPER.readTree(metadata.uploadedFile().toFile());
if (metadataNode.isArray()) {
for (JsonNode item : metadataNode) {
if (!item.isObject()) {
log.debugf(
"Failed to upload for test %s with description %s because of wrong item in metadata: %s.",
test, description, item);
throw ServiceException.badRequest("One of metadata elements is not an object!");
} else if (!item.has("$schema")) {
log.debugf(
"Failed to upload for test %s with description %s because of missing schema in metadata: %s.",
test, description, item);
throw ServiceException.badRequest("One of metadata elements is missing a schema!");
}
}
} else if (metadataNode.isObject()) {
if (!metadataNode.has("$schema")) {
log.debugf("Failed to upload for test %s with description %s because of missing schema in metadata.",
test, description);
throw ServiceException.badRequest("Metadata is missing schema!");
}
metadataNode = instance.arrayNode().add(metadataNode);
}
}
} catch (IOException e) {
log.error("Failed to read data/metadata from upload file", e);
throw ServiceException.badRequest("Provided data/metadata can't be read (JSON encoding problem?)");
}
return addRunFromData(start, stop, test, owner, access, token, schemaUri, description, dataNode.toString(),
metadataNode);
}
@PermitAll // all because of possible token-based upload
@Transactional
@WithRoles
@WithToken
Response addRunFromData(String start, String stop, String test,
String owner, Access access, String token,
String schemaUri, String description,
String stringData, JsonNode metadata) {
if (stringData == null) {
log.debugf("Failed to upload for test %s with description %s because of missing data.", test, description);
throw ServiceException.badRequest("No data!");
}
JsonNode data = null;
try {
data = Util.OBJECT_MAPPER.readValue(stringData, JsonNode.class);
} catch (JsonProcessingException e) {
throw ServiceException.badRequest("Could not map incoming data to JsonNode: " + e.getMessage());
}
Object foundTest = findIfNotSet(test, data);
String testNameOrId = foundTest == null ? null : foundTest.toString().trim();
if (testNameOrId == null || testNameOrId.isEmpty()) {
log.debugf("Failed to upload for test %s with description %s as the test cannot be identified.", test, description);
throw ServiceException.badRequest("Cannot identify test name.");
}
TestDAO testEntity = testService.ensureTestExists(testNameOrId, token);
Datastore datastore = backendResolver.getBackend(testEntity.backendConfig.type);
DatastoreResponse response = datastore.handleRun(data, metadata, testEntity.backendConfig,
Optional.ofNullable(schemaUri), mapper);
List runIds = new ArrayList<>();
String responseString;
if (datastore.uploadType() == Datastore.UploadType.MUILTI
&& response.payload instanceof ArrayNode) {
//if we return more than 10 results, offload to async queue to process - this might take a LOOONG time
if (response.payload.size() > 10) {
response.payload.forEach(jsonNode -> {
mediator.queueRunUpload(start, stop, test, owner, access, token, schemaUri, description, null, jsonNode,
testEntity);
});
} else { //process synchronously
response.payload.forEach(jsonNode -> {
runIds.add(getPersistRun(start, stop, test, owner, access, token, schemaUri, description, metadata,
jsonNode, testEntity));
});
}
} else {
runIds.add(getPersistRun(start, stop, test, owner, access, token, schemaUri, description, metadata,
response.payload, testEntity));
}
if (runIds.size() > 0) {
return Response.status(Response.Status.OK)
.entity(String.valueOf(runIds.stream().map(val -> Integer.toString(val)).collect(Collectors.joining(", "))))
.build();
} else {
return Response.status(Response.Status.ACCEPTED).entity("More than 10 runs uploaded, processing asynchronously")
.build();
}
}
@Transactional
void persistRun(ServiceMediator.RunUpload runUpload) {
runUpload.roles.add("horreum.system");
roleManager.setRoles(runUpload.roles.stream().collect(Collectors.joining(",")));
TestDAO testEntity = TestDAO.findById(runUpload.testId);
if (testEntity == null) {
log.errorf("Could not find Test (%d) for Run Upload", runUpload.testId);
return;
}
try {
Integer runID = getPersistRun(runUpload.start, runUpload.stop, runUpload.test,
runUpload.owner, runUpload.access, runUpload.token, runUpload.schemaUri,
runUpload.description, runUpload.metaData, runUpload.payload, testEntity);
if (runID == null) {
log.errorf("Could not persist Run for Test: %d", testEntity.name);
}
} catch (ServiceException serviceException) {
log.errorf("Could not persist Run for Test: %d", testEntity.name, serviceException);
}
}
private Integer getPersistRun(String start, String stop, String test, String owner, Access access, String token,
String schemaUri, String description, JsonNode metadata, JsonNode data, TestDAO testEntity) {
Object foundStart = findIfNotSet(start, data);
Object foundStop = findIfNotSet(stop, data);
Object foundDescription = findIfNotSet(description, data);
Instant startInstant = Util.toInstant(foundStart);
Instant stopInstant = Util.toInstant(foundStop);
if (startInstant == null) {
log.debugf("Failed to upload for test %s with description %s; cannot parse start time %s (%s)", test, description,
foundStart, start);
throw ServiceException.badRequest("Cannot parse start time from " + foundStart + " (" + start + ")");
} else if (stopInstant == null) {
log.debugf("Failed to upload for test %s with description %s; cannot parse start time %s (%s)", test, description,
foundStop, stop);
throw ServiceException.badRequest("Cannot parse stop time from " + foundStop + " (" + stop + ")");
}
if (schemaUri != null && !schemaUri.isEmpty()) {
if (data.isObject()) {
((ObjectNode) data).put("$schema", schemaUri);
} else if (data.isArray()) {
data.forEach(node -> {
if (node.isObject() && !node.hasNonNull("$schema")) {
((ObjectNode) node).put("$schema", schemaUri);
}
});
}
}
log.debugf("Creating new run for test %s(%d) with description %s", testEntity.name, testEntity.id, foundDescription);
RunDAO run = new RunDAO();
run.testid = testEntity.id;
run.start = startInstant;
run.stop = stopInstant;
run.description = foundDescription != null ? foundDescription.toString() : null;
run.data = data;
run.metadata = metadata;
run.owner = owner;
run.access = access;
// Some triggered functions in the database need to be able to read the just-inserted run
// otherwise RLS policies will fail. That's why we reuse the token for the test and later wipe it out.
run.token = token;
Integer runId = addAuthenticated(run, testEntity);
if (token != null) {
// TODO: remove the token
}
return runId;
}
private Object findIfNotSet(String value, JsonNode data) {
if (value != null && !value.isEmpty()) {
if (value.startsWith("$.")) {
return Util.findJsonPath(data, value);
} else {
return value;
}
} else {
return null;
}
}
@WithRoles(extras = Roles.HORREUM_SYSTEM)
private Integer addAuthenticated(RunDAO run, TestDAO test) {
// Id will be always generated anew
run.id = null;
//if run.metadata is null on the client, it will be converted to a NullNode, not null...
if (run.metadata != null && run.metadata.isNull())
run.metadata = null;
if (run.owner == null) {
List uploaders = identity.getRoles().stream().filter(role -> role.endsWith("-uploader"))
.collect(Collectors.toList());
if (uploaders.size() != 1) {
log.debugf("Failed to upload for test %s: no owner, available uploaders: %s", test.name, uploaders);
throw ServiceException.badRequest(
"Missing owner and cannot select single default owners; this user has these uploader roles: "
+ uploaders);
}
String uploader = uploaders.get(0);
run.owner = uploader.substring(0, uploader.length() - 9) + "-team";
} else if (!Objects.equals(test.owner, run.owner) && !identity.getRoles().contains(run.owner)) {
log.debugf("Failed to upload for test %s: requested owner %s, available roles: %s", test.name, run.owner,
identity.getRoles());
throw ServiceException.badRequest("This user does not have permissions to upload run for owner=" + run.owner);
}
if (run.access == null) {
run.access = Access.PRIVATE;
}
log.debugf("Uploading with owner=%s and access=%s", run.owner, run.access);
try {
if (run.id == null) {
em.persist(run);
} else {
trashConnectedDatasets(run.id, run.testid);
em.merge(run);
}
em.flush();
} catch (Exception e) {
log.error("Failed to persist run.", e);
throw ServiceException.serverError("Failed to persist run");
}
log.debugf("Upload flushed, run ID %d", run.id);
mediator.newRun(RunMapper.from(run));
transform(run.id, false);
if (mediator.testMode())
Util.registerTxSynchronization(tm,
txStatus -> mediator.publishEvent(AsyncEventChannels.RUN_NEW, test.id, RunMapper.from(run)));
return run.id;
}
@PermitAll
@WithRoles
@WithToken
@Override
public List autocomplete(String query) {
if (query == null || query.isEmpty()) {
return null;
}
String jsonpath = query.trim();
String incomplete = "";
if (jsonpath.endsWith(".")) {
jsonpath = jsonpath.substring(0, jsonpath.length() - 1);
} else {
int lastDot = jsonpath.lastIndexOf('.');
if (lastDot > 0) {
incomplete = jsonpath.substring(lastDot + 1);
jsonpath = jsonpath.substring(0, lastDot);
} else {
incomplete = jsonpath;
jsonpath = "$.**";
}
}
int conditionIndex = jsonpath.indexOf('@');
if (conditionIndex >= 0) {
int conditionSelectEnd = jsonpath.length();
for (String terminal : CONDITION_SELECT_TERMINAL) {
int ti = jsonpath.indexOf(terminal, conditionIndex + 1);
if (ti >= 0) {
conditionSelectEnd = Math.min(conditionSelectEnd, ti);
}
}
String conditionSelect = jsonpath.substring(conditionIndex + 1, conditionSelectEnd);
int queryIndex = jsonpath.indexOf('?');
if (queryIndex < 0) {
// This is a shortcut query '@.foo...'
jsonpath = "$.**" + conditionSelect;
} else if (queryIndex > conditionIndex) {
// Too complex query with multiple conditions
return Collections.emptyList();
} else {
while (queryIndex > 0 && Character.isWhitespace(jsonpath.charAt(queryIndex - 1))) {
--queryIndex;
}
jsonpath = jsonpath.substring(0, queryIndex) + conditionSelect;
}
}
if (!jsonpath.startsWith("$")) {
jsonpath = "$.**." + jsonpath;
}
try {
NativeQuery findAutocomplete = session.createNativeQuery(FIND_AUTOCOMPLETE, String.class);
findAutocomplete.setParameter(1, jsonpath);
findAutocomplete.setParameter(2, incomplete);
List results = findAutocomplete.getResultList();
return results.stream().map(option -> option.matches("^[a-zA-Z0-9_-]*$") ? option : "\"" + option + "\"")
.collect(Collectors.toList());
} catch (PersistenceException e) {
throw ServiceException.badRequest("Failed processing query '" + query + "':\n" + e.getLocalizedMessage());
}
}
@PermitAll
@WithRoles
@WithToken
@Override
public RunsSummary listAllRuns(String query, boolean matchAll, String roles, boolean trashed,
Integer limit, Integer page, String sort, SortDirection direction) {
StringBuilder sql = new StringBuilder("SELECT run.id, run.start, run.stop, run.testId, ")
.append("run.owner, run.access, run.token, run.trashed, run.description, ")
.append("run.metadata IS NOT NULL AS has_metadata, test.name AS testname, ")
.append("'[]'::jsonb AS schemas, '[]'::jsonb AS datasets, '[]'::jsonb AS validationErrors ")
.append("FROM run JOIN test ON test.id = run.testId WHERE ");
String[] queryParts;
boolean whereStarted = false;
if (query == null || query.isEmpty()) {
queryParts = new String[0];
} else {
query = query.trim();
if (query.startsWith("$") || query.startsWith("@")) {
queryParts = new String[] { query };
} else {
queryParts = query.split("([ \t\n,]+)|\\bOR\\b");
}
sql.append("(");
for (int i = 0; i < queryParts.length; ++i) {
if (i != 0) {
sql.append(matchAll ? " AND " : " OR ");
}
sql.append("jsonb_path_exists(data, ?").append(i + 1).append(" ::jsonpath)");
if (queryParts[i].startsWith("$")) {
// no change
} else if (queryParts[i].startsWith("@")) {
queryParts[i] = "$.** ? (" + queryParts[i] + ")";
} else {
queryParts[i] = "$.**." + queryParts[i];
}
}
sql.append(")");
whereStarted = true;
}
whereStarted = Roles.addRolesSql(identity, "run", sql, roles, queryParts.length + 1, whereStarted ? " AND" : null)
|| whereStarted;
if (!trashed) {
if (whereStarted) {
sql.append(" AND ");
}
sql.append(" trashed = false ");
}
Util.addPaging(sql, limit, page, sort, direction);
NativeQuery sqlQuery = session.createNativeQuery(sql.toString(), Object[].class);
for (int i = 0; i < queryParts.length; ++i) {
sqlQuery.setParameter(i + 1, queryParts[i]);
}
Roles.addRolesParam(identity, sqlQuery, queryParts.length + 1, roles);
try {
List runs = sqlQuery.getResultList();
RunsSummary summary = new RunsSummary();
// TODO: total does not consider the query but evaluating all the expressions would be expensive
summary.total = trashed ? RunDAO.count() : RunDAO.count("trashed = false");
summary.runs = runs.stream().map(this::createSummary).collect(Collectors.toList());
return summary;
} catch (PersistenceException pe) {
// In case of an error PostgreSQL won't let us execute another query in the same transaction
try {
Transaction old = tm.suspend();
try {
for (String jsonpath : queryParts) {
JsonpathValidation result = sqlService.testJsonPathInternal(jsonpath);
if (!result.valid) {
throw new WebApplicationException(Response.status(400).entity(result).build());
}
}
} finally {
tm.resume(old);
}
} catch (InvalidTransactionException | SystemException e) {
// ignore
}
throw new WebApplicationException(pe, 500);
}
}
private void initTypes(Query query) {
query.unwrap(NativeQuery.class)
.addScalar("id", StandardBasicTypes.INTEGER)
.addScalar("start", StandardBasicTypes.INSTANT)
.addScalar("stop", StandardBasicTypes.INSTANT)
.addScalar("testid", StandardBasicTypes.INTEGER)
.addScalar("owner", StandardBasicTypes.TEXT)
.addScalar("access", StandardBasicTypes.INTEGER)
.addScalar("token", StandardBasicTypes.TEXT)
.addScalar("trashed", StandardBasicTypes.BOOLEAN)
.addScalar("description", StandardBasicTypes.TEXT)
.addScalar("has_metadata", StandardBasicTypes.BOOLEAN)
.addScalar("testname", StandardBasicTypes.TEXT)
.addScalar("schemas", JsonBinaryType.INSTANCE)
.addScalar("datasets", JsonBinaryType.INSTANCE)
.addScalar("validationErrors", JsonBinaryType.INSTANCE);
}
private RunSummary createSummary(Object[] row) {
RunSummary run = new RunSummary();
run.id = (int) row[0];
if (row[1] != null)
run.start = ((Instant) row[1]);
if (row[2] != null)
run.stop = ((Instant) row[2]);
run.testid = (int) row[3];
run.owner = (String) row[4];
run.access = Access.fromInt((int) row[5]);
run.token = (String) row[6];
run.trashed = (boolean) row[7];
run.description = (String) row[8];
run.hasMetadata = (boolean) row[9];
run.testname = (String) row[10];
//if we send over an empty JsonNode object it will be a NullNode, that can be cast to a string
if (row[11] != null && !(row[11] instanceof String)) {
run.schemas = Util.OBJECT_MAPPER.convertValue(row[11], new TypeReference>() {
});
}
//if we send over an empty JsonNode object it will be a NullNode, that can be cast to a string
if (row[12] != null && !(row[12] instanceof String)) {
try {
run.datasets = Util.OBJECT_MAPPER.treeToValue(((ArrayNode) row[12]), Integer[].class);
} catch (JsonProcessingException e) {
log.warnf("Could not map datasets to array");
}
}
//if we send over an empty JsonNode object it will be a NullNode, that can be cast to a string
if (row[13] != null && !(row[13] instanceof String)) {
try {
run.validationErrors = Util.OBJECT_MAPPER.treeToValue(((ArrayNode) row[13]), ValidationError[].class);
} catch (JsonProcessingException e) {
log.warnf("Could not map validation errors to array");
}
}
return run;
}
@PermitAll
@WithRoles
@WithToken
@Override
public RunCount runCount(int testId) {
RunCount counts = new RunCount();
counts.total = RunDAO.count("testid = ?1", testId);
counts.active = RunDAO.count("testid = ?1 AND trashed = false", testId);
counts.trashed = counts.total - counts.active;
return counts;
}
@PermitAll
@WithRoles
@WithToken
@Override
public RunsSummary listTestRuns(int testId, boolean trashed,
Integer limit, Integer page, String sort, SortDirection direction) {
StringBuilder sql = new StringBuilder("WITH schema_agg AS (")
.append(" SELECT " + SCHEMA_USAGE + " AS schemas, rs.runid ")
.append(" FROM run_schemas rs JOIN schema ON schema.id = rs.schemaid WHERE rs.testid = ?1 GROUP BY rs.runid")
.append("), dataset_agg AS (")
.append(" SELECT runid, jsonb_agg(id ORDER BY id) as datasets FROM dataset WHERE testid = ?1 GROUP BY runid")
.append("), validation AS (")
.append(" SELECT run_id, jsonb_agg(jsonb_build_object('schemaId', schema_id, 'error', error)) AS errors FROM run_validationerrors GROUP BY run_id")
.append(") SELECT run.id, run.start, run.stop, run.testid, run.owner, run.access, run.token, run.trashed, run.description, ")
.append("run.metadata IS NOT NULL AS has_metadata, test.name AS testname, ")
.append("schema_agg.schemas AS schemas, ")
.append("COALESCE(dataset_agg.datasets, '[]') AS datasets, ")
.append("COALESCE(validation.errors, '[]') AS validationErrors FROM run ")
.append("LEFT JOIN schema_agg ON schema_agg.runid = run.id ")
.append("LEFT JOIN dataset_agg ON dataset_agg.runid = run.id ")
.append("LEFT JOIN validation ON validation.run_id = run.id ")
.append("JOIN test ON test.id = run.testid ")
.append("WHERE run.testid = ?1 ");
if (!trashed) {
sql.append(" AND NOT run.trashed ");
}
Util.addOrderBy(sql, sort, direction);
Util.addLimitOffset(sql, limit, page);
TestDAO test = TestDAO.find("id", testId).firstResult();
if (test == null) {
throw ServiceException.notFound("Cannot find test ID " + testId);
}
NativeQuery query = session.createNativeQuery(sql.toString(), Object[].class);
query.setParameter(1, testId);
initTypes(query);
List resultList = query.getResultList();
RunsSummary summary = new RunsSummary();
summary.total = trashed ? RunDAO.count("testid = ?1", testId) : RunDAO.count("testid = ?1 AND trashed = false", testId);
summary.runs = resultList.stream().map(this::createSummary).collect(Collectors.toList());
return summary;
}
@PermitAll
@WithRoles
@WithToken
@Override
public RunsSummary listBySchema(String uri, Integer limit, Integer page, String sort, SortDirection direction) {
if (uri == null || uri.isEmpty()) {
throw ServiceException.badRequest("No `uri` query parameter given.");
}
StringBuilder sql = new StringBuilder("SELECT run.id, run.start, run.stop, run.testId, ")
.append("run.owner, run.access, run.token, run.trashed, run.description, ")
.append("run.metadata IS NOT NULL AS has_metadata, test.name AS testname, ")
.append("'[]'::jsonb AS schemas, '[]'::jsonb AS datasets, '[]'::jsonb AS validationErrors ")
.append("FROM run_schemas rs JOIN run ON rs.runid = run.id JOIN test ON rs.testid = test.id ")
.append("WHERE uri = ? AND NOT run.trashed");
Util.addPaging(sql, limit, page, sort, direction);
NativeQuery query = session.createNativeQuery(sql.toString(), Object[].class);
query.setParameter(1, uri);
initTypes(query);
List runs = query.getResultList();
RunsSummary summary = new RunsSummary();
summary.runs = runs.stream().map(this::createSummary).collect(Collectors.toList());
summary.total = SchemaDAO.count("uri", uri);
return summary;
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
public void trash(int id, Boolean isTrashed) {
trashInternal(id, isTrashed == null || isTrashed);
}
private void trashInternal(int id, boolean trashed) {
RunDAO run = RunDAO.findById(id);
if (run == null) {
throw ServiceException.notFound("Run not found: " + id);
}
if (run.trashed == trashed)
throw ServiceException.badRequest("The run " + id + " has already been trashed, not possible to trash it again.");
if (trashed) {
trashConnectedDatasets(run.id, run.testid);
run.trashed = trashed;
run.persist();
if (mediator.testMode())
Util.registerTxSynchronization(tm,
txStatus -> mediator.publishEvent(AsyncEventChannels.RUN_TRASHED, run.testid, id));
}
// if the run was trashed because of a deleted test we need to ensure that the test actually exist
// before we try to recalculate the dataset
else {
if (TestDAO.findById(run.testid) != null) {
run.trashed = trashed;
run.persistAndFlush();
transform(id, true);
} else
throw ServiceException.badRequest("Not possible to un-trash a run that's not referenced to a Test");
}
}
private void trashConnectedDatasets(int runId, int testId) {
//Make sure to remove run_schemas as we've trashed the run
em.createNativeQuery("DELETE FROM run_schemas WHERE runid = ?1").setParameter(1, runId).executeUpdate();
List datasets = DatasetDAO.list("run.id", runId);
log.debugf("Trashing run %d (test %d, %d datasets)", runId, testId, datasets.size());
for (var dataset : datasets) {
mediator.propagatedDatasetDelete(dataset.id);
}
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
public void updateDescription(int id, String description) {
// FIXME: fetchival stringifies the body into JSON string :-/
RunDAO run = RunDAO.findById(id);
if (run == null) {
throw ServiceException.notFound("Run not found: " + id);
}
run.description = description;
run.persistAndFlush();
}
@RolesAllowed(Roles.TESTER)
@WithRoles
@Transactional
@Override
public Map updateSchema(int id, String path, String schemaUri) {
// FIXME: fetchival stringifies the body into JSON string :-/
RunDAO run = RunDAO.findById(id);
if (run == null) {
throw ServiceException.notFound("Run not found: " + id);
}
String uri = Util.destringify(schemaUri);
Optional schemaOptional = SchemaDAO.find("uri", uri).firstResultOptional();
if (schemaOptional.isEmpty()) {
throw ServiceException.notFound("Schema not found: " + uri);
}
// Triggering dirty property on Run
JsonNode updated = run.data.deepCopy();
JsonNode item;
if (updated.isObject()) {
item = path == null ? updated : updated.path(path);
} else if (updated.isArray()) {
if (path == null) {
throw ServiceException.badRequest("Cannot update root schema in an array.");
}
item = updated.get(Integer.parseInt(path));
} else {
throw ServiceException.serverError("Cannot update run data with path " + path);
}
if (item.isObject()) {
if (uri != null && !uri.isEmpty()) {
((ObjectNode) item).set("$schema", new TextNode(uri));
} else {
((ObjectNode) item).remove("$schema");
}
} else {
throw ServiceException.badRequest(
"Cannot update schema at " + (path == null ? "" : path) + " as the target is not an object");
}
run.data = updated;
trashConnectedDatasets(run.id, run.testid);
run.persist();
onNewOrUpdatedSchemaForRun(run.id, schemaOptional.get().id);
Map schemas = session
.createNativeQuery("SELECT schemaid AS key, uri AS value FROM run_schemas WHERE runid = ? ORDER BY schemaid",
Tuple.class)
.setParameter(1, run.id)
.getResultStream()
.distinct()
.collect(
Collectors.toMap(
tuple -> ((Integer) tuple.get("key")).intValue(),
tuple -> ((String) tuple.get("value"))));
em.flush();
return schemas;
}
@WithRoles
@Transactional
@Override
public List recalculateDatasets(int runId) {
transform(runId, true);
return session.createNativeQuery("SELECT id FROM dataset WHERE runid = ? ORDER BY ordinal", Integer.class)
.setParameter(1, runId).getResultList();
}
@RolesAllowed(Roles.ADMIN)
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional
@Override
public void recalculateAll(String fromStr, String toStr) {
Instant from = Util.toInstant(fromStr);
Instant to = Util.toInstant(toStr);
if (from == null || to == null) {
throw ServiceException.badRequest("Time range is required");
} else if (to.isBefore(from)) {
throw ServiceException.badRequest("Time range is invalid (from > to)");
}
long deleted = em.createNativeQuery(
"DELETE FROM dataset USING run WHERE run.id = dataset.runid AND run.trashed AND run.start BETWEEN ?1 AND ?2")
.setParameter(1, from).setParameter(2, to).executeUpdate();
if (deleted > 0) {
log.debugf("Deleted %d datasets for trashed runs between %s and %s", deleted, from, to);
}
ScrollableResults results = session
.createNativeQuery("SELECT id, testid FROM run WHERE start BETWEEN ?1 AND ?2 AND NOT trashed ORDER BY start",
Recalculate.class)
.setParameter(1, from).setParameter(2, to)
.setTupleTransformer((tuples, aliases) -> {
Recalculate r = new Recalculate();
r.runId = (int) tuples[0];
r.testId = (int) tuples[1];
return r;
})
.setReadOnly(true).setFetchSize(100)
.scroll(ScrollMode.FORWARD_ONLY);
while (results.next()) {
Recalculate r = results.get();
log.debugf("Recalculate Datasets for run %d - forcing recalculation of all between %s and %s", r.runId, from, to);
// transform will add proper roles anyway
// messageBus.executeForTest(r.testId, () -> datasetService.withRecalculationLock(() -> transform(r.runId, true)));
Util.registerTxSynchronization(tm, txStatus -> mediator.queueRunRecalculation(r.runId));
}
}
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional
int transform(int runId, boolean isRecalculation) {
if (runId < 1) {
log.errorf("Transformation parameters error: run %s", runId);
return 0;
}
log.debugf("Transforming run ID %d, recalculation? %s", runId, Boolean.toString(isRecalculation));
// We need to make sure all old datasets are gone before creating new; otherwise we could
// break the runid,ordinal uniqueness constraint
for (DatasetDAO old : DatasetDAO. list("run.id", runId)) {
for (DataPointDAO dp : DataPointDAO. list("dataset.id", old.getInfo().id)) {
dp.delete();
}
mediator.propagatedDatasetDelete(old.id);
}
RunDAO run = RunDAO.findById(runId);
if (run == null) {
log.errorf("Cannot load run ID %d for transformation", runId);
return 0;
}
int ordinal = 0;
Map transformerResults = new TreeMap<>();
// naked nodes (those produced by implicit identity transformers) are all added to each dataset
List nakedNodes = new ArrayList<>();
List relevantSchemas = unchecked(em.createNamedQuery(QUERY_TRANSFORMER_TARGETS)
.setParameter(1, run.id)
.unwrap(NativeQuery.class)
.addScalar("type", StandardBasicTypes.INTEGER)
.addScalar("key", StandardBasicTypes.TEXT)
.addScalar("transformer_id", StandardBasicTypes.INTEGER)
.addScalar("uri", StandardBasicTypes.TEXT)
.addScalar("source", StandardBasicTypes.INTEGER)
.getResultList());
int schemasAndTransformers = relevantSchemas.size();
for (Object[] relevantSchema : relevantSchemas) {
int type = (int) relevantSchema[0];
String key = (String) relevantSchema[1];
Integer transformerId = (Integer) relevantSchema[2];
String uri = (String) relevantSchema[3];
Integer source = (Integer) relevantSchema[4];
TransformerDAO t;
if (transformerId != null) {
t = TransformerDAO.findById(transformerId);
if (t == null) {
log.errorf("Missing transformer with ID %d", transformerId);
}
} else {
t = null;
}
if (t != null) {
JsonNode root = JsonNodeFactory.instance.objectNode();
JsonNode result;
if (t.extractors != null && !t.extractors.isEmpty()) {
List extractedData;
try {
if (type == SchemaDAO.TYPE_1ST_LEVEL) {
// note: metadata always follow the 2nd level format
extractedData = unchecked(em.createNamedQuery(QUERY_1ST_LEVEL_BY_RUNID_TRANSFORMERID_SCHEMA_ID)
.setParameter(1, run.id).setParameter(2, transformerId)
.unwrap(NativeQuery.class)
.addScalar("name", StandardBasicTypes.TEXT)
.addScalar("value", JsonBinaryType.INSTANCE)
.getResultList());
} else {
extractedData = unchecked(em.createNamedQuery(QUERY_2ND_LEVEL_BY_RUNID_TRANSFORMERID_SCHEMA_ID)
.setParameter(1, run.id).setParameter(2, transformerId)
.setParameter(3, type == SchemaDAO.TYPE_2ND_LEVEL ? key : Integer.parseInt(key))
.setParameter(4, source)
.unwrap(NativeQuery.class)
.addScalar("name", StandardBasicTypes.TEXT)
.addScalar("value", JsonBinaryType.INSTANCE)
.getResultList());
}
} catch (PersistenceException e) {
logMessage(run, PersistentLogDAO.ERROR,
"Failed to extract data (JSONPath expression error?): " + Util.explainCauses(e));
findFailingExtractor(runId);
extractedData = Collections.emptyList();
}
addExtracted((ObjectNode) root, extractedData);
}
// In Horreum it's customary that when a single extractor is used we pass the result directly to the function
// without wrapping it in an extra object.
if (t.extractors.size() == 1) {
if (root.size() != 1) {
// missing results should be null nodes
log.errorf("Unexpected result for single extractor: %s", root.toPrettyString());
} else {
root = root.iterator().next();
}
}
logMessage(run, PersistentLogDAO.DEBUG,
"Run transformer %s/%s with input: %s , function: %s ",
uri, t.name, limitLength(root.toPrettyString()), t.function);
if (t.function != null && !t.function.isBlank()) {
result = Util.evaluateOnce(t.function, root, Util::convertToJson,
(code, e) -> logMessage(run, PersistentLogDAO.ERROR,
"Evaluation of transformer %s/%s failed: '%s' Code: %s ", uri, t.name,
e.getMessage(), code),
output -> logMessage(run, PersistentLogDAO.DEBUG,
"Output while running transformer %s/%s: %s ", uri, t.name, output));
if (result == null) {
// this happens upon error
result = JsonNodeFactory.instance.nullNode();
}
} else {
result = root;
}
if (t.targetSchemaUri != null) {
if (result.isObject()) {
putIfAbsent(run, t.targetSchemaUri, (ObjectNode) result);
} else if (result.isArray()) {
ArrayNode array = (ArrayNode) result;
for (JsonNode node : array) {
if (node.isObject()) {
putIfAbsent(run, t.targetSchemaUri, (ObjectNode) node);
}
}
} else {
result = instance.objectNode()
.put("$schema", t.targetSchemaUri).set("value", result);
}
} else if (!result.isContainerNode() || (result.isObject() && !result.has("$schema")) ||
(result.isArray()
&& StreamSupport.stream(result.spliterator(), false).anyMatch(item -> !item.has("$schema")))) {
logMessage(run, PersistentLogDAO.WARN, "Dataset will contain element without a schema.");
}
JsonNode existing = transformerResults.get(transformerId);
if (existing == null) {
transformerResults.put(transformerId, result);
} else if (existing.isArray()) {
if (result.isArray()) {
((ArrayNode) existing).addAll((ArrayNode) result);
} else {
((ArrayNode) existing).add(result);
}
} else {
if (result.isArray()) {
((ArrayNode) result).insert(0, existing);
transformerResults.put(transformerId, result);
} else {
transformerResults.put(transformerId, instance.arrayNode().add(existing).add(result));
}
}
} else {
JsonNode node;
JsonNode sourceNode = source == 0 ? run.data : run.metadata;
switch (type) {
case SchemaDAO.TYPE_1ST_LEVEL:
node = sourceNode;
break;
case SchemaDAO.TYPE_2ND_LEVEL:
node = sourceNode.path(key);
break;
case SchemaDAO.TYPE_ARRAY_ELEMENT:
node = sourceNode.path(Integer.parseInt(key));
break;
default:
throw new IllegalStateException("Unknown type " + type);
}
nakedNodes.add(node);
logMessage(run, PersistentLogDAO.DEBUG,
"This test (%d) does not use any transformer for schema %s (key %s), passing as-is.", run.testid, uri,
key);
}
}
if (schemasAndTransformers > 0) {
int max = transformerResults.values().stream().filter(JsonNode::isArray).mapToInt(JsonNode::size).max().orElse(1);
for (int position = 0; position < max; position += 1) {
ArrayNode all = instance.arrayNode(max + nakedNodes.size());
for (var entry : transformerResults.entrySet()) {
JsonNode node = entry.getValue();
if (node.isObject()) {
all.add(node);
} else if (node.isArray()) {
if (position < node.size()) {
all.add(node.get(position));
} else {
String message = String.format(
"Transformer %d produced an array of %d elements but other transformer " +
"produced %d elements; dataset %d/%d might be missing some data.",
entry.getKey(), node.size(), max, run.id, ordinal);
logMessage(run, PersistentLogDAO.WARN, "%s", message);
log.warnf(message);
}
} else {
logMessage(run, PersistentLogDAO.WARN, "Unexpected result provided by one of the transformers: %s",
node);
log.warnf("Unexpected result provided by one of the transformers: %s", node);
}
}
nakedNodes.forEach(all::add);
createDataset(new DatasetDAO(run, ordinal++, run.description, all), isRecalculation);
}
mediator.validateRun(run.id);
return ordinal;
} else {
logMessage(run, PersistentLogDAO.INFO, "No applicable schema, dataset will be empty.");
createDataset(new DatasetDAO(
run, 0, "Empty Dataset for run data without any schema.",
instance.arrayNode()), isRecalculation);
mediator.validateRun(run.id);
return 1;
}
}
private String limitLength(String str) {
return str.length() > 1024 ? str.substring(0, 1024) + "...(truncated)" : str;
}
private void createDataset(DatasetDAO ds, boolean isRecalculation) {
try {
ds.persistAndFlush();
mediator.newDataset(new Dataset.EventNew(DatasetMapper.from(ds), isRecalculation));
mediator.validateDataset(ds.id);
if (mediator.testMode())
Util.registerTxSynchronization(tm, txStatus -> mediator.publishEvent(AsyncEventChannels.DATASET_NEW, ds.testid,
new Dataset.EventNew(DatasetMapper.from(ds), isRecalculation)));
} catch (TransactionRequiredException tre) {
log.error(
"Failed attempt to persist and send Dataset event during inactive Transaction. Likely due to prior error.",
tre);
}
}
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional(Transactional.TxType.REQUIRES_NEW)
protected void logMessage(RunDAO run, int level, String format, Object... args) {
String msg = args.length > 0 ? String.format(format, args) : format;
new TransformationLogDAO(em.getReference(TestDAO.class, run.testid), run, level, msg).persist();
}
@WithRoles(extras = Roles.HORREUM_SYSTEM)
@Transactional(Transactional.TxType.REQUIRES_NEW)
protected void findFailingExtractor(int runId) {
List extractors = session.createNativeQuery(
"SELECT rs.uri, rs.type, rs.key, t.name, te.name AS extractor_name, te.jsonpath FROM run_schemas rs " +
"JOIN transformer t ON t.schema_id = rs.schemaid AND t.id IN (SELECT transformer_id FROM test_transformers WHERE test_id = rs.testid) "
+
"JOIN transformer_extractors te ON te.transformer_id = t.id " +
"WHERE rs.runid = ?1",
Object[].class).setParameter(1, runId).getResultList();
for (Object[] row : extractors) {
try {
int type = (int) row[1];
// actual result of query is ignored
if (type == SchemaDAO.TYPE_1ST_LEVEL) {
em.createNativeQuery(
"SELECT jsonb_path_query_first(data, (?1)::jsonpath)#>>'{}' FROM dataset WHERE id = ?2")
.setParameter(1, row[5]).setParameter(2, runId).getSingleResult();
} else {
em.createNativeQuery(
"SELECT jsonb_path_query_first(data -> (?1), (?2)::jsonpath)#>>'{}' FROM dataset WHERE id = ?3")
.setParameter(1, type == SchemaDAO.TYPE_2ND_LEVEL ? row[2] : Integer.parseInt((String) row[2]))
.setParameter(2, row[5])
.setParameter(3, runId).getSingleResult();
}
} catch (PersistenceException e) {
logMessage(em.getReference(RunDAO.class, runId), PersistentLogDAO.ERROR,
"There seems to be an error in schema %s transformer %s, extractor %s, JSONPath expression %s: %s",
row[0], row[3], row[4], row[5], Util.explainCauses(e));
return;
}
}
logMessage(em.getReference(RunDAO.class, runId), PersistentLogDAO.DEBUG,
"We thought there's an error in one of the JSONPaths but independent validation did not find any problems.");
}
@SuppressWarnings("unchecked")
private List unchecked(@SuppressWarnings("rawtypes") List list) {
return (List) list;
}
private void addExtracted(ObjectNode root, List resultSet) {
for (Object[] labelValue : resultSet) {
String name = (String) labelValue[0];
JsonNode value = (JsonNode) labelValue[1];
root.set(name, value);
}
}
private void putIfAbsent(RunDAO run, String uri, ObjectNode node) {
if (uri != null && !uri.isBlank() && node != null) {
if (node.path("$schema").isMissingNode()) {
node.put("$schema", uri);
} else {
logMessage(run, PersistentLogDAO.DEBUG, "$schema present (%s), not overriding with %s",
node.path("$schema").asText(), uri);
}
}
}
class Recalculate {
private int runId;
private int testId;
}
class RunFromUri {
private int id;
private int testId;
}
}
