chamikaramj commented on a change in pull request #11450:
URL: https://github.com/apache/beam/pull/11450#discussion_r415909848
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
##########
@@ -127,6 +114,7 @@ public ListMessagesResponse makeHL7v2ListRequest(
.messages()
.list(hl7v2Store)
.set("view", "full")
+ .setPageSize(1000)
Review comment:
This is a pretty large sleep for a single test. Java post commit test
suite is run pretty regularly with limited Jenkins resources so I suggest
adding a separate test suite for HI7v2 tests and removing this and any other
tests that need large sleeps from general Java post-commit test suite.
##########
File path:
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
##########
@@ -0,0 +1,129 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE;
+import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.MESSAGES;
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.deleteAllHL7v2Messages;
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.writeHL7v2Messages;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Collections;
+import java.util.concurrent.TimeoutException;
+import org.apache.beam.sdk.extensions.gcp.options.GcpOptions;
+import
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.ListHL7v2MessageIDs;
+import org.apache.beam.sdk.testing.PAssert;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.transforms.Count;
Review comment:
Can we please defer adding these new tests till we are sure that the
changes to fix flakyness actually fix the immediate issue. Also can you please
send additional changes that are not related to BEAM
https://issues.apache.org/jira/browse/BEAM-9779 as a separate PR and mention
the correct JIRA.
##########
File path:
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
##########
@@ -0,0 +1,129 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.HEALTHCARE_DATASET_TEMPLATE;
+import static org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.MESSAGES;
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.deleteAllHL7v2Messages;
+import static
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.writeHL7v2Messages;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Collections;
+import java.util.concurrent.TimeoutException;
+import org.apache.beam.sdk.extensions.gcp.options.GcpOptions;
+import
org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOTestUtil.ListHL7v2MessageIDs;
+import org.apache.beam.sdk.testing.PAssert;
+import org.apache.beam.sdk.testing.TestPipeline;
+import org.apache.beam.sdk.transforms.Count;
+import org.apache.beam.sdk.values.PCollection;
+import org.joda.time.Duration;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+
+/**
+ * This should catch that we read {@link HL7v2Message} with schematized data
but do not fail inserts
+ * with schematized data which should be output only.
+ */
+@RunWith(JUnit4.class)
+public class HL7v2IOReadWriteIT {
+
+ private transient HealthcareApiClient client;
+ private static String healthcareDataset;
+ private static final String BASE =
+ "hl7v2_store_rw_it_" + System.currentTimeMillis() + "_" + (new
SecureRandom().nextInt(32));
+ private static final String INPUT_HL7V2_STORE_NAME = BASE + "INPUT";
+ private static final String OUTPUT_HL7V2_STORE_NAME = BASE + "OUTPUT";
+
+ @Rule public transient TestPipeline pipeline = TestPipeline.create();
+
+ @BeforeClass
+ public static void createHL7v2tores() throws IOException {
+ String project =
TestPipeline.testingPipelineOptions().as(GcpOptions.class).getProject();
+ healthcareDataset = String.format(HEALTHCARE_DATASET_TEMPLATE, project);
+ HealthcareApiClient client = new HttpHealthcareApiClient();
+ client.createHL7v2Store(healthcareDataset, INPUT_HL7V2_STORE_NAME);
+ client.createHL7v2Store(healthcareDataset, OUTPUT_HL7V2_STORE_NAME);
+ }
+
+ @AfterClass
+ public static void deleteHL7v2tores() throws IOException {
+ HealthcareApiClient client = new HttpHealthcareApiClient();
+ client.deleteHL7v2Store(healthcareDataset + "/hl7V2Stores/" +
INPUT_HL7V2_STORE_NAME);
+ client.deleteHL7v2Store(healthcareDataset + "/hl7V2Stores/" +
OUTPUT_HL7V2_STORE_NAME);
+ }
+
+ @Before
+ public void setup() throws Exception {
+ if (client == null) {
+ client = new HttpHealthcareApiClient();
+ }
+
+ // Create HL7 messages and write them to HL7v2 Store.
+ writeHL7v2Messages(this.client, healthcareDataset + "/hl7V2Stores/" +
INPUT_HL7V2_STORE_NAME);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ deleteAllHL7v2Messages(client, healthcareDataset + "/hl7V2Stores/" +
OUTPUT_HL7V2_STORE_NAME);
+ }
+
+ @Test
+ public void testHL7v2IOE2E() throws Exception {
+ HL7v2IO.Read.Result readResult =
+ pipeline
+ .apply(
+ new ListHL7v2MessageIDs(
+ Collections.singletonList(
+ healthcareDataset + "/hl7V2Stores/" +
INPUT_HL7V2_STORE_NAME)))
+ .apply(HL7v2IO.getAll());
+
+ PCollection<Long> numReadMessages =
+ readResult.getMessages().setCoder(new
HL7v2MessageCoder()).apply(Count.globally());
+ PAssert.thatSingleton(numReadMessages).isEqualTo((long) MESSAGES.size());
+ PAssert.that(readResult.getFailedReads()).empty();
+
+ HL7v2IO.Write.Result writeResult =
+ readResult
+ .getMessages()
+ .apply(
+ HL7v2IO.ingestMessages(
+ healthcareDataset + "/hl7V2Stores/" +
OUTPUT_HL7V2_STORE_NAME));
+
+ PAssert.that(writeResult.getFailedInsertsWithErr()).empty();
+
+ pipeline.run().waitUntilFinish();
+
+ try {
+ HL7v2IOTestUtil.waitForHL7v2Indexing(
+ client,
+ healthcareDataset + "/hl7V2Stores/" + OUTPUT_HL7V2_STORE_NAME,
+ MESSAGES.size(),
+ Duration.standardMinutes(10));
Review comment:
Ditto. I suggest moving tests that require a large sleep to a new test
suite.
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