Vendor the deid-redactor library (#174)

import/build.gradle

@@ -65,7 +65,7 @@ dependencies {
     compile 'com.google.guava:guava:28.1-jre'
     compile 'com.google.auth:google-auth-library-oauth2-http'
     compile "com.google.api-client:google-api-client"
-  
+
     compile "com.beust:jcommander:1.72"
     compile "org.dcm4che:dcm4che-core:5.31.2"
     compile "org.dcm4che:dcm4che-net:5.31.2"
@@ -77,7 +77,7 @@ dependencies {
     compile project(":dicom_util")
     compile project(":util")
 
-    compile "com.github.red1408:deid-redactor:233908ca"
+    compile project(":deid-redactor")
 
     compile "com.google.cloud:google-cloud-storage:1.98.0"
     compile 'com.google.cloud:google-cloud-nio:0.116.0-alpha'

settings.gradle

@@ -19,4 +19,8 @@ include ":import"
 include ":util"
 include ':dicom_util'
 include ':jai-imageio-jpeg2000'
+include ':deid-redactor'
+include ':deid-redactor-examples'
 project(':jai-imageio-jpeg2000').projectDir = new File('third_party/jai-imageio-jpeg2000')
+project(':deid-redactor').projectDir = new File('third_party/deid-redactor/lib')
+project(':deid-redactor-examples').projectDir = new File('third_party/deid-redactor/examples/tag_remover')

third_party/deid-redactor/README.md

@@ -0,0 +1,51 @@
+# DICOM Redactor Library
+
+The DICOM Redactor Library is a Java library designed to redact sensitive data contained in DICOM tags. This is an offline library which does not communicate with Google Cloud.
+
+## Getting Started
+
+### Building
+
+The DICOM redactor library can be built using [Gradle](https://gradle.org/). Please refer to these [instructions](https://gradle.org/install/) to build Gradle for your system.
+
+To build the library and examples:
+
+```shell
+cd redactor
+./gradlew build
+```
+
+### Running unit tests
+
+```shell
+cd redactor
+./gradlew test
+```
+
+## Configuration
+
+The library's redaction is primarily configured using [protobuf](https://developers.google.com/protocol-buffers/). The configuration is similar to the [DicomConfig](https://cloud.google.com/healthcare/docs/reference/rpc/google.cloud.healthcare.v1beta1/deidentify#dicomconfig) for the deidentify operation in Google's Cloud Healthcare API (although the predefined filter profiles differ).
+
+The user can configure which tags to redact/remove in one of 3 ways:
+
+1. keep_list - a list of DICOM tags to keep untouched. Other tags are removed.
+2. remove_list - a list of DICOM tags to remove. Other tags are kept untouched.
+3. filter_profile - a predefined profile that will keep and remove particular tags.
+
+See the full configuration [proto](lib/src/main/proto/DicomConfig.proto) for more info.
+
+To view the sepcific tags removed for a certain profile, see the relevant [textproto](lib/src/main/resource/chc_basic.textproto).
+
+## UID Regeneration
+
+Regardless of the configuration, several UIDs will always be regenerated: SOPInstanceUID, StudyInstanceUID, SeriesInstanceUID, and MediaStorageSOPInstanceUID.
+By default, these will be regenerated using the [UUID Derived UID](http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_B.2.html) method. Optionally, when constucting a redactor, the user can specify their own prefix to use for the regenerated UIDs.
+
+## Sample script
+
+A [command line utility](examples) for redacting tags using the library has been included. To run:
+
+```shell
+cd redactor
+./gradlew examples:tag_remover:run --args='-i in.dcm -o out.dcm -t PatientName'
+```

third_party/deid-redactor/examples/tag_remover/build.gradle

@@ -0,0 +1,46 @@
+/*
+ * Copyright 2019 Google LLC
+ *
+ * Licensed 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.
+ */
+
+plugins {
+    id 'java'
+    id 'application'
+}
+
+repositories {
+    google()
+    jcenter()
+    mavenCentral()
+    maven { url 'http://www.dcm4che.org/maven2/' }
+  }
+
+buildDir = "/tmp/gradle_build/redactor/examples"
+
+dependencies {
+  implementation project(':deid-redactor')
+  implementation 'commons-cli:commons-cli:1.4'
+
+  testImplementation 'junit:junit:4.12'
+  testImplementation 'com.google.truth:truth:0.39'
+  testImplementation 'commons-io:commons-io:2.6'
+}
+
+mainClassName = 'com.google.cloud.healthcare.deid.remover.TagRemover'
+
+jar {
+  manifest {
+    attributes 'Main-Class': mainClassName
+  }
+}

third_party/deid-redactor/examples/tag_remover/src/main/java/com/google/cloud/healthcare/deid/remover/TagRemover.java

@@ -0,0 +1,81 @@
+/*
+ * Copyright 2019 Google LLC.
+ *
+ * Licensed 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 com.google.cloud.healthcare.deid.remover;
+
+import com.google.cloud.healthcare.deid.redactor.DicomRedactor;
+import com.google.cloud.healthcare.deid.redactor.protos.DicomConfigProtos.DicomConfig;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.Arrays;
+import java.util.List;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+/**
+ * TagRemover is a command line utility that removes tags from DICOM files.
+ */
+final class TagRemover {
+
+  public static void main(String[] args) throws Exception {
+    Options options = new Options();
+    Option input = new Option("i", "input", true, "input DICOM file path");
+    input.setRequired(true);
+    options.addOption(input);
+    Option output = new Option("o", "output", true, "output DICOM file path");
+    output.setRequired(true);
+    options.addOption(output);
+    Option tags = new Option("t", "tags", true, "DICOM tags to redact");
+    tags.setRequired(true);
+    tags.setArgs(Option.UNLIMITED_VALUES);
+    options.addOption(tags);
+
+    CommandLineParser parser = new DefaultParser();
+    HelpFormatter formatter = new HelpFormatter();
+    CommandLine cmd;
+
+    try {
+      cmd = parser.parse(options, args);
+    } catch (ParseException e) {
+      System.out.println(e.getMessage());
+      formatter.printHelp("tagremove", options);
+      return;
+    }
+
+    InputStream is =
+        new BufferedInputStream(new FileInputStream(new File(cmd.getOptionValue("input"))));
+    OutputStream os =
+        new BufferedOutputStream(new FileOutputStream(new File(cmd.getOptionValue("output"))));
+
+    List<String> tagList = Arrays.asList(cmd.getOptionValues("tags"));
+    DicomConfig config = DicomConfig.newBuilder().setRemoveList(
+        DicomConfig.TagFilterList.newBuilder().addAllTags(tagList)).build();
+
+    DicomRedactor redactor = new DicomRedactor(config);
+    redactor.redact(is, os);
+  }
+
+}

third_party/deid-redactor/examples/tag_remover/src/test/java/com/google/cloud/healthcare/deid/remover/TagRemoverTest.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright 2019 Google LLC.
+ *
+ * Licensed 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 com.google.cloud.healthcare.deid.remover;
+
+import java.io.File;
+import org.apache.commons.io.FileUtils;
+import org.junit.Assert;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.junit.runner.RunWith;
+import org.junit.runners.JUnit4;
+
+/** Test basic DICOM tag removal. */
+@RunWith(JUnit4.class)
+public final class TagRemoverTest {
+  @Rule
+  public TemporaryFolder folder = new TemporaryFolder();
+  @Test
+  public void basicRedaction() throws Exception {
+    File expectedFile = new File(
+        TagRemoverTest.class.getClassLoader().getResource("basic-redacted.dcm").getFile());
+    File inFile = new File(
+        TagRemoverTest.class.getClassLoader().getResource("basic.dcm").getFile());
+    FileUtils.copyFileToDirectory(inFile, folder.getRoot());
+    String inPath = folder.getRoot() + "/basic.dcm";
+    String outPath = folder.getRoot() + "/basic-redacted.dcm";
+    String[] args = new String[]{"-i", inPath, "-o", outPath, "-t", "PatientName", "00081080"};
+    TagRemover.main(args);
+    Assert.assertTrue(FileUtils.contentEquals(expectedFile, new File(outPath)));
+  }
+}

third_party/deid-redactor/lib/build.gradle

@@ -0,0 +1,54 @@
+/*
+ * Copyright 2019 Google LLC
+ *
+ * Licensed 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.
+ */
+
+plugins {
+    id 'java-library'
+    id 'com.google.protobuf' version "0.8.13"
+    id 'maven'
+}
+
+repositories {
+    google()
+    jcenter()
+    mavenCentral()
+    maven { url 'http://www.dcm4che.org/maven2/' }
+}
+
+group = "com.google.cloud.healthcare.deid"
+archivesBaseName = "redactor"
+version = "0.1.0"
+
+buildDir = "/tmp/gradle_build/redactor"
+
+dependencies {
+    implementation "org.dcm4che:dcm4che-core:3.3.8"
+    implementation "org.dcm4che:dcm4che-imageio:3.3.8"
+
+    protobuf 'com.google.protobuf:protobuf-java:3.7.1'
+
+    api "com.google.api.grpc:proto-google-common-protos:1.16.0"
+
+    testImplementation 'junit:junit:4.12'
+    testImplementation 'com.google.truth:truth:0.39'
+    testImplementation 'commons-io:commons-io:2.6'
+}
+
+protobuf {
+  generatedFilesBaseDir = "/tmp/gradle_build/redactor/gen"
+  protoc {
+    artifact = "com.google.protobuf:protoc:3.7.1";
+  }
+}