[
https://issues.apache.org/jira/browse/BEAM-9779?focusedWorklogId=426273&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-426273
]
ASF GitHub Bot logged work on BEAM-9779:
----------------------------------------
Author: ASF GitHub Bot
Created on: 22/Apr/20 19:30
Start Date: 22/Apr/20 19:30
Worklog Time Spent: 10m
Work Description: chamikaramj commented on a change in pull request
#11450:
URL: https://github.com/apache/beam/pull/11450#discussion_r413255742
##########
File path:
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
##########
@@ -0,0 +1,123 @@
+/*
+ * 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 static org.junit.Assert.assertEquals;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Collections;
+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.junit.After;
+import org.junit.AfterClass;
+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();
Review comment:
Seems like read and write sections are unrelated. Should these be two
different tests ?
Alternatively we can convert this to a single "write and then read pipeline"
where data needed for the read step are generated in the write step (and remove
data generation in the setUp method.
##########
File path:
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOTestUtil.java
##########
@@ -91,10 +92,13 @@ static void deleteAllHL7v2Messages(HealthcareApiClient
client, String hl7v2Store
}
/** Populate the test messages into the HL7v2 store. */
- static void writeHL7v2Messages(HealthcareApiClient client, String
hl7v2Store) throws IOException {
+ static void writeHL7v2Messages(HealthcareApiClient client, String hl7v2Store)
+ throws IOException, InterruptedException {
for (HL7v2Message msg : MESSAGES) {
client.createHL7v2Message(hl7v2Store, msg.toModel());
}
+ // [BEAM-9779] HL7v2 indexing is asyncronous. Add sleep to stabilize this
IT.
+ Sleeper.DEFAULT.sleep(5000);
Review comment:
How do we know that 5000 is enough ? If not the test will be flaky.
##########
File path:
sdks/java/io/google-cloud-platform/src/test/java/org/apache/beam/sdk/io/gcp/healthcare/HL7v2IOReadWriteIT.java
##########
@@ -0,0 +1,123 @@
+/*
+ * 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 static org.junit.Assert.assertEquals;
+
+import java.io.IOException;
+import java.security.SecureRandom;
+import java.util.Collections;
+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.junit.After;
+import org.junit.AfterClass;
+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);
Review comment:
Does the store name here uniquely identify the set of data being deleted
(just to confirm) ?
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Issue Time Tracking
-------------------
Worklog Id: (was: 426273)
Time Spent: 1h 20m (was: 1h 10m)
> HL7v2IOWriteIT is flaky
> -----------------------
>
> Key: BEAM-9779
> URL: https://issues.apache.org/jira/browse/BEAM-9779
> Project: Beam
> Issue Type: Bug
> Components: io-java-gcp
> Reporter: Jacob Ferriero
> Assignee: Jacob Ferriero
> Priority: Minor
> Time Spent: 1h 20m
> Remaining Estimate: 0h
>
> There seems to be a race condition somewhere in HL7v2IOWriteIT that causes
> flakiness.
> https://builds.apache.org/job/beam_PostCommit_Java/5947/
> https://builds.apache.org/job/beam_PostCommit_Java/5943/
> https://builds.apache.org/job/beam_PostCommit_Java/5942/
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