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hapi-fhir
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Fix vulnerability warning on maven plugin (#2621) 

* Fix vulnerability warning on maven plugin

* Compile fixes

* Fix bootstrap dep

* Test fix

* Fix tests

* FIx deps
This commit is contained in:
James Agnew 2021-05-02 12:14:32 -04:00 committed by GitHub
parent 970a9884f0
commit 0cea403800
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
16 changed files with 213 additions and 73 deletions
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6
.lgtm.yml Normal file
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@ -0,0 +1,6 @@
# Don't run the tests when doing LGTM analysis
extraction:
java:
index:
build_command: mvn clean install -DskipTests

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/changes.yaml
View File

@ -15,13 +15,15 @@
<li>Gson (JPA): 2.8.5 -> 2.8.6</li>
<li>Caffeine (JPA): 2.7.0 -> 3.0.1</li>
<li>Hibernate (JPA): 5.4.26.Final -> 5.4.30.Final</li>
<li>Hibernate Search (JPA): 6.0.0.Final -> 6.0.2.Final</li>
<li>Hibernate Search (JPA): 6.0.0.Final -> 6.0.3.Final</li>
<li>Spring (JPA): 5.3.3 -> 5.3.6</li>
<li>Spring Batch (JPA): 4.2.3.RELEASE -> 4.3.2</li>
<li>Spring Data (JPA): 2.4.2 -> 2.4.7</li>
<li>Spring Data (JPA): 2.4.2 -> 2.5.0</li>
<li>Commons DBCP2 (JPA): 2.7.0 -> 2.8.0</li>
<li>ElasticSearch Client (JPA): 7.10.2 -> 7.12.1</li>
<li>Thymeleaf (Testpage Overlay): 3.0.11.RELEASE -> 3.0.12.RELEASE</li>
<li>JAnsi (CLI): 2.1.1 -> 2.3.2</li>
<li>JArchivelib (CLI): 1.0.0 -> 1.1.0</li>
</ul>
"

4
hapi-fhir-jpaserver-base/pom.xml
View File

@ -353,6 +353,10 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
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@ -1298,6 +1298,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public Pageable first() {
return null;
}
@Override
public Pageable withPage(int theI) {
return null;
}
};
return page;

25
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java
View File

@ -391,6 +391,11 @@ public class GiantTransactionPerfTest {
throw new UnsupportedOperationException();
}
@Override
public void deleteAllById(Iterable<? extends Long> ids) {
}
@Override
public void deleteAll(Iterable<? extends ResourceHistoryTable> entities) {
throw new UnsupportedOperationException();
@ -432,11 +437,26 @@ public class GiantTransactionPerfTest {
throw new UnsupportedOperationException();
}
@Override
public <S extends ResourceHistoryTable> List<S> saveAllAndFlush(Iterable<S> entities) {
throw new UnsupportedOperationException();
}
@Override
public void deleteInBatch(Iterable<ResourceHistoryTable> entities) {
throw new UnsupportedOperationException();
}
@Override
public void deleteAllInBatch(Iterable<ResourceHistoryTable> entities) {
throw new UnsupportedOperationException();
}
@Override
public void deleteAllByIdInBatch(Iterable<Long> ids) {
throw new UnsupportedOperationException();
}
@Override
public void deleteAllInBatch() {
throw new UnsupportedOperationException();
@ -447,6 +467,11 @@ public class GiantTransactionPerfTest {
throw new UnsupportedOperationException();
}
@Override
public ResourceHistoryTable getById(Long theLong) {
throw new UnsupportedOperationException();
}
@Override
public <S extends ResourceHistoryTable> Optional<S> findOne(Example<S> example) {
return Optional.empty();

20
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/dstu3/listener/ElmCacheResourceChangeListener.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.cql.dstu3.listener;
/*-
* #%L
* HAPI FHIR JPA Server - Clinical Quality Language
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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.
* #L%
*/
import java.util.Collection;
import java.util.List;
import java.util.Map;

20
hapi-fhir-jpaserver-cql/src/main/java/ca/uhn/fhir/cql/r4/listener/ElmCacheResourceChangeListener.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.cql.r4.listener;
/*-
* #%L
* HAPI FHIR JPA Server - Clinical Quality Language
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* 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.
* #L%
*/
import java.util.Collection;
import java.util.List;
import java.util.Map;

5
hapi-fhir-structures-r4/pom.xml
View File

@ -139,19 +139,16 @@
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.4</version>
<artifactId>poi-ooxml-schemas</artifactId>
<optional>true</optional>
</dependency>
<dependency>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -113,13 +113,11 @@
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>

4
hapi-fhir-testpage-overlay/src/main/webapp/WEB-INF/templates/tmpl-head.html
View File

@ -11,11 +11,11 @@
<!-- JQuery and Bootstrap -->
<script th:src="@{/resources/jquery/dist/jquery.js}"></script>
<link rel="stylesheet" th:href="@{/resources/bootstrap/dist/css/bootstrap.css}" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.2.1/css/bootstrap.min.css"/>
<link rel="stylesheet" th:href="@{/resources/bootstrap/dist/css/bootstrap.css}"/>
<link rel="stylesheet" media="screen" th:href="@{/resources/font-awesome/css/fontawesome.min.css}" />
<script th:src="@{/resources/font-awesome/js/all.min.js}" data-auto-replace-svg="nest"></script>
<link rel="stylesheet" media="screen" th:href="@{/resources/awesome-bootstrap-checkbox/awesome-bootstrap-checkbox.css}" />
<script th:src="@{/resources/bootstrap/dist/js/bootstrap.min.js}" src="https://maxcdn.bootstrapcdn.com/bootstrap/4.2.1/js/bootstrap.min.js"></script>
<script th:src="@{/resources/bootstrap/dist/js/bootstrap.min.js}"></script>
<!--<script th:src="@{/resources/bootstrap/js/tab.js}"></script>-->

15
hapi-tinder-plugin/pom.xml
View File

@ -36,7 +36,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>2.2</version>
<version>5.3.0</version>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
@ -47,7 +47,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
<version>3.3.0</version>
<version>5.3.0</version>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
@ -97,7 +97,7 @@
<dependency>
<artifactId>commons-lang</artifactId>
<groupId>commons-lang</groupId>
<version>2.5</version>
<version>2.6</version>
</dependency>
<dependency>
@ -188,7 +188,7 @@
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.10.8</version>
<version>1.10.10</version>
</dependency>
<!-- This is just used for -->
@ -199,15 +199,10 @@
<scope>test</scope>
</dependency>
<!--
Android includes an old version of commons-codec, so
we compile against the old version to make sure we can compile
against it
-->
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.1</version>
<version>1.15</version>
</dependency>

57
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderJpaRestServerMojo.java
View File

@ -1,20 +1,35 @@
package ca.uhn.fhir.tinder;
import java.io.*;
import java.util.*;
import org.apache.commons.lang.WordUtils;
import org.apache.maven.model.Resource;
import org.apache.maven.plugin.*;
import org.apache.maven.plugins.annotations.*;
import org.apache.maven.plugins.annotations.Mojo;
import org.apache.maven.project.MavenProject;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.tinder.parser.*;
import ca.uhn.fhir.tinder.parser.BaseStructureSpreadsheetParser;
import ca.uhn.fhir.tinder.parser.ResourceGeneratorUsingModel;
import ca.uhn.fhir.tinder.parser.ResourceGeneratorUsingSpreadsheet;
import org.apache.commons.lang.WordUtils;
import org.apache.maven.model.Resource;
import org.apache.maven.plugin.AbstractMojo;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.plugin.MojoFailureException;
import org.apache.maven.plugins.annotations.Component;
import org.apache.maven.plugins.annotations.LifecyclePhase;
import org.apache.maven.plugins.annotations.Mojo;
import org.apache.maven.plugins.annotations.Parameter;
import org.apache.maven.project.MavenProject;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
import org.apache.velocity.runtime.RuntimeConstants;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import java.util.TreeSet;
@Mojo(name = "generate-jparest-server", defaultPhase = LifecyclePhase.GENERATE_SOURCES)
public class TinderJpaRestServerMojo extends AbstractMojo {
@ -74,7 +89,7 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
if (baseResourceNames == null || baseResourceNames.isEmpty()) {
baseResourceNames = new ArrayList<>();
ourLog.info("No resource names supplied, going to use all resources from version: {}",fhirContext.getVersion().getVersion());
ourLog.info("No resource names supplied, going to use all resources from version: {}", fhirContext.getVersion().getVersion());
Properties p = new Properties();
try {
@ -83,10 +98,10 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
throw new MojoFailureException("Failed to load version property file", e);
}
ourLog.debug("Property file contains: {}",p);
ourLog.debug("Property file contains: {}", p);
TreeSet<String> keys = new TreeSet<>();
for(Object next : p.keySet()) {
for (Object next : p.keySet()) {
keys.add((String) next);
}
for (String next : keys) {
@ -126,7 +141,7 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
gen.setFilenameSuffix("ResourceProvider");
gen.setTemplate("/vm/jpa_resource_provider.vm");
gen.writeAll(packageDirectoryBase, null,packageBase);
gen.writeAll(packageDirectoryBase, null, packageBase);
// gen.setFilenameSuffix("ResourceTable");
// gen.setTemplate("/vm/jpa_resource_table.vm");
@ -154,14 +169,14 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
String capitalize = WordUtils.capitalize(version);
if ("Dstu".equals(capitalize)) {
capitalize="Dstu1";
capitalize = "Dstu1";
}
ctx.put("versionCapitalized", capitalize);
VelocityEngine v = new VelocityEngine();
v.setProperty("resource.loader", "cp");
v.setProperty("cp.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.references.strict", Boolean.TRUE);
v.setProperty(RuntimeConstants.RESOURCE_LOADERS, "cp");
v.setProperty("resource.loader.cp.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.strict_mode.enable", Boolean.TRUE);
/*

13
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderResourceGeneratorMojo.java
View File

@ -11,8 +11,13 @@ import org.apache.maven.plugins.annotations.Mojo;
import org.apache.maven.plugins.annotations.Parameter;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
import org.apache.velocity.runtime.RuntimeConstants;
import java.io.*;
import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
@Mojo(name = "generate-resource", defaultPhase = LifecyclePhase.GENERATE_RESOURCES)
public class TinderResourceGeneratorMojo extends AbstractGeneratorMojo {
@ -45,9 +50,9 @@ public class TinderResourceGeneratorMojo extends AbstractGeneratorMojo {
ctx.put("versionCapitalized", configuration.getVersionCapitalized());
VelocityEngine v = new VelocityEngine();
v.setProperty("resource.loader", "cp");
v.setProperty("cp.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.references.strict", Boolean.TRUE);
v.setProperty(RuntimeConstants.RESOURCE_LOADERS, "cp");
v.setProperty("resource.loader.cp.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.strict_mode.enable", Boolean.TRUE);
InputStream templateIs = ResourceGeneratorUsingSpreadsheet.class.getResourceAsStream(templateName);
InputStreamReader templateReader = new InputStreamReader(templateIs);

4
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/VelocityHelper.java
View File

@ -74,8 +74,8 @@ public class VelocityHelper {
result.setProperty(RuntimeConstants.FILE_RESOURCE_LOADER_PATH, path);
}
} else {
result.setProperty("resource.loader", "cp");
result.setProperty("cp.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
result.setProperty(RuntimeConstants.RESOURCE_LOADERS, "cp");
result.setProperty("resource.loader.cp.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
}
}

37
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/parser/BaseStructureParser.java
View File

@ -12,7 +12,14 @@ import ca.uhn.fhir.tinder.TinderResourceGeneratorMojo;
import ca.uhn.fhir.tinder.TinderStructuresMojo;
import ca.uhn.fhir.tinder.ValueSetGenerator;
import ca.uhn.fhir.tinder.VelocityHelper;
import ca.uhn.fhir.tinder.model.*;
import ca.uhn.fhir.tinder.model.BaseElement;
import ca.uhn.fhir.tinder.model.BaseRootType;
import ca.uhn.fhir.tinder.model.Child;
import ca.uhn.fhir.tinder.model.Composite;
import ca.uhn.fhir.tinder.model.Extension;
import ca.uhn.fhir.tinder.model.Resource;
import ca.uhn.fhir.tinder.model.ResourceBlock;
import ca.uhn.fhir.tinder.model.SimpleChild;
import ca.uhn.fhir.tinder.model.SimpleSetter.Parameter;
import com.google.common.base.Charsets;
import org.apache.commons.io.FileUtils;
@ -23,14 +30,30 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.maven.plugin.MojoFailureException;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
import org.apache.velocity.runtime.RuntimeConstants;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import java.io.*;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.lang.annotation.Annotation;
import java.lang.reflect.Constructor;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import static org.apache.commons.lang.StringUtils.defaultString;
import static org.apache.commons.lang.StringUtils.isNotBlank;
@ -311,7 +334,7 @@ public abstract class BaseStructureParser {
return myTemplateFile;
}
public void setTemplateFile (File theTemplateFile) {
public void setTemplateFile(File theTemplateFile) {
myTemplateFile = theTemplateFile;
}
@ -674,9 +697,9 @@ public abstract class BaseStructureParser {
ctx.put("versionCapitalized", capitalize);
VelocityEngine v = new VelocityEngine();
v.setProperty("resource.loader", "cp");
v.setProperty("cp.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.references.strict", Boolean.TRUE);
v.setProperty(RuntimeConstants.RESOURCE_LOADERS, "cp");
v.setProperty("resource.loader.cp.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");
v.setProperty("runtime.strict_mode.enable", Boolean.TRUE);
InputStream templateIs = ResourceGeneratorUsingSpreadsheet.class.getResourceAsStream("/vm/fhirversion_properties.vm");
InputStreamReader templateReader = new InputStreamReader(templateIs);

33
pom.xml
View File

@ -789,7 +789,7 @@
<flexmark_version>0.50.40</flexmark_version>
<flyway_version>6.5.4</flyway_version>
<hibernate_version>5.4.30.Final</hibernate_version>
<hibernate_search_version>6.0.2.Final</hibernate_search_version>
<hibernate_search_version>6.0.3.Final</hibernate_search_version>
<!-- Update lucene version when you update hibernate-search version -->
<lucene_version>8.7.0</lucene_version>
<hamcrest_version>2.2</hamcrest_version>
@ -811,7 +811,7 @@
<log4j_to_slf4j_version>2.11.1</log4j_to_slf4j_version>
<spring_version>5.3.6</spring_version>
<!-- FYI: Spring Data JPA 2.1.9 causes test failures due to unexpected cascading deletes -->
<spring_data_version>2.4.7</spring_data_version>
<spring_data_version>2.5.0</spring_data_version>
<spring_batch_version>4.3.2</spring_batch_version>
<spring_boot_version>2.4.4</spring_boot_version>
<spring_retry_version>1.2.2.RELEASE</spring_retry_version>
@ -1157,7 +1157,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>8.0.20</version>
<version>8.0.24</version>
</dependency>
<dependency>
<groupId>net.sourceforge.htmlunit</groupId>
@ -1329,6 +1329,21 @@
<artifactId>maven-plugin-annotations</artifactId>
<version>3.6.0</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.1.2</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.1.2</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>4.1.2</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
@ -1547,6 +1562,10 @@
</exclusions>
</dependency>
<dependency>
<!--
Be careful bumping this, you need to match the maximum version supported by Hibernate Search.
See: https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#getting-started-compatibility
-->
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>7.10.2</version>
@ -1620,7 +1639,7 @@
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.2.19</version>
<version>42.2.20</version>
</dependency>
<dependency>
<groupId>org.quartz-scheduler</groupId>
@ -1751,6 +1770,12 @@
<groupId>org.webjars</groupId>
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
<version>4.17.47</version>
<exclusions>
<exclusion>
<groupId>*</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.webjars</groupId>