[
https://issues.apache.org/jira/browse/BEAM-11073?focusedWorklogId=504838&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-504838
]
ASF GitHub Bot logged work on BEAM-11073:
-----------------------------------------
Author: ASF GitHub Bot
Created on: 26/Oct/20 17:59
Start Date: 26/Oct/20 17:59
Worklog Time Spent: 10m
Work Description: poojavenkatram commented on a change in pull request
#13137:
URL: https://github.com/apache/beam/pull/13137#discussion_r512143891
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java
##########
@@ -0,0 +1,177 @@
+/*
+ * 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 java.io.IOException;
+import java.util.Collection;
+import java.util.Map;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+
+/**
+ * The DicomIO connectors allows Beam pipelines to make calls to the Dicom API
of the Google Cloud
+ * Healthcare API: https://cloud.google.com/healthcare/docs/how-tos#dicom-guide
+ */
+public class DicomIO {
+
+ /**
+ * This class makes a call to the retrieve metadata endpoint
+ *
(https://cloud.google.com/healthcare/docs/how-tos/dicomweb#retrieving_metadata).
It defines a function that can
+ * be used to process a Pubsub message from a DICOM store, read the DICOM
study path and get the metadata of the
+ * specified study.
+ * You can learn how to configure PubSub messages to be published when an
instance is
+ * stored by following:
https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector
+ * will output a {@link ReadDicomStudyMetadata.Result} which will contain
metadata of the study
+ * encoded as a json array.
+ */
+ public static class ReadDicomStudyMetadata
+ extends PTransform<PCollection<PubsubMessage>,
DicomIO.ReadDicomStudyMetadata.Result> {
+
+ public ReadDicomStudyMetadata() {}
+
+ /** TupleTag for the main output. */
+ public static final TupleTag<String> METADATA = new TupleTag<String>() {};
+ /** TupleTag for any error response. */
+ public static final TupleTag<String> ERROR_MESSAGE = new
TupleTag<String>() {};
+
+ public static class Result implements POutput, PInput {
+ private PCollection<String> readResponse;
+
+ private PCollection<String> failedReads;
+
+ /** Contains both the response and error outputs from the
transformation. */
+ PCollectionTuple pct;
+
+ /**
+ * Create DicomIO.ReadDicomStudyMetadata.Result form PCollectionTuple
with OUT and DEAD_LETTER
Review comment:
from instead of form and change the names here too..
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/DicomIO.java
##########
@@ -0,0 +1,177 @@
+/*
+ * 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 java.io.IOException;
+import java.util.Collection;
+import java.util.Map;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.io.gcp.pubsub.PubsubMessage;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+
+/**
+ * The DicomIO connectors allows Beam pipelines to make calls to the Dicom API
of the Google Cloud
+ * Healthcare API: https://cloud.google.com/healthcare/docs/how-tos#dicom-guide
+ */
+public class DicomIO {
+
+ /**
+ * This class makes a call to the retrieve metadata endpoint
+ *
(https://cloud.google.com/healthcare/docs/how-tos/dicomweb#retrieving_metadata).
It defines a function that can
+ * be used to process a Pubsub message from a DICOM store, read the DICOM
study path and get the metadata of the
+ * specified study.
+ * You can learn how to configure PubSub messages to be published when an
instance is
+ * stored by following:
https://cloud.google.com/healthcare/docs/how-tos/pubsub. The connector
+ * will output a {@link ReadDicomStudyMetadata.Result} which will contain
metadata of the study
+ * encoded as a json array.
+ */
+ public static class ReadDicomStudyMetadata
+ extends PTransform<PCollection<PubsubMessage>,
DicomIO.ReadDicomStudyMetadata.Result> {
+
+ public ReadDicomStudyMetadata() {}
+
+ /** TupleTag for the main output. */
+ public static final TupleTag<String> METADATA = new TupleTag<String>() {};
+ /** TupleTag for any error response. */
+ public static final TupleTag<String> ERROR_MESSAGE = new
TupleTag<String>() {};
+
+ public static class Result implements POutput, PInput {
+ private PCollection<String> readResponse;
+
+ private PCollection<String> failedReads;
+
+ /** Contains both the response and error outputs from the
transformation. */
+ PCollectionTuple pct;
+
+ /**
+ * Create DicomIO.ReadDicomStudyMetadata.Result form PCollectionTuple
with OUT and DEAD_LETTER
+ * tags.
+ *
+ * @param pct the pct
Review comment:
the PcollectionTuple which contains the response
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/HttpHealthcareApiClient.java
##########
@@ -196,6 +197,69 @@ public Empty deleteFhirStore(String name) throws
IOException {
return
client.projects().locations().datasets().fhirStores().delete(name).execute();
}
+ @Override
+ public String retrieveDicomStudyMetadata(String dicomWebPath) throws
IOException {
+ String[] webPathSplit;
+ webPathSplit = dicomWebPath.split("/dicomWeb/");
+ if (webPathSplit.length != 2) {
+ throw new IOException("Invalid Web Path");
+ }
+
+ String dicomStorePath = webPathSplit[0];
+
+ String[] searchParameters;
+ searchParameters = webPathSplit[1].split("/");
+ if (searchParameters.length < 2) {
+ throw new IOException("Invalid Web Path");
Review comment:
invalid DICOM web path
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Issue Time Tracking
-------------------
Worklog Id: (was: 504838)
Time Spent: 1h 50m (was: 1h 40m)
> GCP HCLS Api - Dicom IO Connector for Java
> ------------------------------------------
>
> Key: BEAM-11073
> URL: https://issues.apache.org/jira/browse/BEAM-11073
> Project: Beam
> Issue Type: New Feature
> Components: io-java-gcp
> Reporter: Aliraza Nagamia
> Assignee: Aliraza Nagamia
> Priority: P2
> Time Spent: 1h 50m
> Remaining Estimate: 0h
>
> We are looking to create a new Java Pipeline Connector to help facilitate
> Reading data from the Imaging API in GCP. Initially, this connector will be
> used to read study level metadata of Dicom instances.
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