[GitHub] [beam] chamikaramj commented on a change in pull request #11450: [BEAM-9779] Hl7v2 io patches

[GitBox <gi...@apache.org>]

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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