Merge branch 'main' into refactoring/UIMA-6444-Automatically-sign-Ecl…

…ipse-plugins-during-release-builds * main: (94 commits) No issue: Remove Jira line from PR template - we do not use Jira anymore. #270 - Update dependencies #270 - Update dependencies #267 - UIMA Log4jLogger_impl not compatible with log4j 2.18.0+ No issue. Adjust jira legacy module version. [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release uimaj-3.3.1 Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #260: Issues-fixed report for GitHub and Jira Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #258: Apache UIMA Java SDK 3.3.1 release Issue #255: File handle leak accessing performanceTuning.properties Issue #252: Potential failure to look up FsGenerator3 in OSGI-like contexts Issue #225: Improve deployment in OSGi environments Issue #226: Provide SPI interfaces to locate descriptors and JCas classes Issue #226: Provide SPI interfaces to locate descriptors and JCas classes Issue #247 - RelativePathResolver should consider TCCL ... % Conflicts: % uimaj-parent/pom.xml
apache · Jan 11, 2023 · 4abc5f0 · 4abc5f0
2 parents c0a1000 + 57bc1bb
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diff --git a/.asf.yaml b/.asf.yaml
@@ -1,19 +1,55 @@
-#   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
+# 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
 #
-#   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.
+#     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.
+#
+
 github:
-  description: "UIMA Java SDK, version 3 (in main), 2 (in main-v2)"
+  description: "Apache UIMA Java SDK"
   homepage: https://uima.apache.org
+  dependabot_alerts:  true
+  dependabot_updates: false
+  notifications:
+    commits:      [email protected]
+    issues:       [email protected]
+    pullrequests: [email protected]
+    jobs:         [email protected]
+    jira_options: link label
+  labels:
+  - apache
+  - uima
+  - text-analysis
+  - java
+  features:
+    wiki: false
+    issues: true
+    projects: true
+  enabled_merge_buttons:
+    squash:  true
+    merge:   true
+    rebase:  false
+  del_branch_on_merge: true
+  protected_branches:
+    main:
+     required_status_checks:
+        strict: true
+        contexts:
+          - continuous-integration/jenkins/pr-merge
+    main-v2:
+     required_status_checks:
+        strict: true
+        contexts:
+          - continuous-integration/jenkins/pr-merge
+
+
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,5 +1,3 @@
-**JIRA Ticket:** https://issues.apache.org/jira/browse/UIMA-XXXX
-
 **What's in the PR**
 * ...
 
@@ -13,5 +11,5 @@
 * [ ] PR adds/updates documentation
 
 **Organizational**
-- [ ] PR includes new dependencies.
+- [ ] PR adds/updates dependencies.
       <sub><sup>Only dependencies under [approved licenses](http://www.apache.org/legal/resolved.html#category-a) are allowed. LICENSE and NOTICE files in the respective modules where dependencies have been added as well as in the project root have been updated.</sup></sub>
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,6 @@
 .project
 .settings
 target
-META-INF
 checkpoint_synchPoint.xml
 checkpoint_synchPoint.xml.prev
 checkpoint.dat

diff --git a/Jenkinsfile b/Jenkinsfile
@@ -18,7 +18,5 @@
 @Library('uima-build-jenkins-shared-library') _
 
 defaultPipeline {
-  // The Eclipse libraries that our plugins depend unfortunately on required Java 11
-  jdk = 'jdk_11_latest'
-  extraMavenArguments = '-Pjacoco,pmd,run-rat-report'
+  extraMavenArguments = '-Pjacoco,spotbugs,pmd,run-rat-report -Ddisable-rc-auto-staging'
 }
diff --git a/PearPackagingMavenPlugin/pom.xml b/PearPackagingMavenPlugin/pom.xml
@@ -17,7 +17,9 @@
    specific language governing permissions and limitations
    under the License.    
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
 
   <parent>
@@ -41,12 +43,20 @@
     <dependency>
       <groupId>org.apache.maven</groupId>
       <artifactId>maven-plugin-api</artifactId>
-      <version>3.1.0</version>
+      <version>${maven.version}</version>
+      <scope>provided</scope>
     </dependency>
+
     <dependency>
       <groupId>org.apache.maven.plugin-tools</groupId>
       <artifactId>maven-plugin-annotations</artifactId>
-      <version>3.2</version>
+      <scope>provided</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.apache.maven</groupId>
+      <artifactId>maven-core</artifactId>
+      <version>${maven.version}</version>
       <scope>provided</scope>
     </dependency>
 
@@ -61,13 +71,6 @@
       <artifactId>commons-io</artifactId>
       <version>2.11.0</version>
     </dependency>
-
-    <dependency>
-      <groupId>org.apache.maven</groupId>
-      <artifactId>maven-project</artifactId>
-      <version>2.0.4</version>
-    </dependency>
-
   </dependencies>
 
   <build>

diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ to your project:
 <dependency>
   <groupId>org.apache.uima</groupId>
   <artifactId>uimaj-core</artifactId>
-  <version>3.3.0</version>
+  <version>3.3.1</version>
 </dependency>
 ```
 
@@ -55,7 +55,7 @@ Apache uimaFIT is a separate dependency that you can add:
 <dependency>
   <groupId>org.apache.uima</groupId>
   <artifactId>uimafit-core</artifactId>
-  <version>3.3.0</version>
+  <version>3.3.1</version>
 </dependency>
 ```
 

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -19,15 +19,15 @@
 ***************************************************************
 -->
 
-# Apache UIMA (Unstructured Information Management Architecture) v3.3.0 Release Notes
+# Apache UIMA (Unstructured Information Management Architecture) v3.3.1 Release Notes
 
 ## Contents
 
 [What is UIMA?](#what.is.uima)  
 [Major Changes in this Release](#major.changes)  
+[List of JIRA Issues Fixed in this Release](#list.issues)  
 [How to Get Involved](#get.involved)  
 [How to Report Issues](#report.issues)  
-[List of JIRA Issues Fixed in this Release](#list.issues)  
 
 ## <a id="what.is.uima">What is UIMA?</a>
 
@@ -55,53 +55,29 @@ with some support for Perl, Python and TCL.
 
 ## <a id="major.changes">Notable changes in this release</a>
 
-* [UIMA-6418] Added support for component parameters of type "long" and "double" 
-* [UIMA-6358] Added platform-independent methods for setting the datapath in a resource manager
-* [UIMA-6374] Added an extensive CAS (de)serialization test suit
-* [UIMA-6431] Added support for using lambda functions as CAS processors
-* [UIMA-6412] Changed CPMEngine from using a thread group to using an executor service
-* [UIMA-6389] Fixed exceptions being swallowed when using Log4J2 through its SLF4J API
-* [UIMA-6386] Fixed wrong UIMA session being set on the ConfigurationManager in aggregates
-* [UIMA-6390] Fixed NPE when trying to access config names of fresh context
-* [UIMA-6378] Fixed build on Java 16
-* [UIMA-6393] Fixed circular imports in descriptors breaking the resource manager cache
-* [UIMA-6367] Fixed JCas cover annotation created in PEAR context being replaced by index operations
-* [UIMA-6388] Fixed CAS.select(null) returning all annotations instead of throwing an exception
-* [UIMA-6423] Fixed selecting a non-existing type returning all types instead of throwing an exception
-* [UIMA-6421] Fixed range check when injecting a String value into StringArray slot to throw an exception
-* [UIMA-6400] Fixed leaking ThreadLocal in UimaContextHolder
-* [UIMA-6398] Fixed memory leak in UIMA loggers and loggers using the wrong classloader for i18n messages
-* [UIMA-6413] Fixed memory leak in FSClassRegistry
-* [UIMA-6377] Fixed spurious multipleReferencesAllowed warning when serializing empty arrays
-* [UIMA-6372] Upgraded to JUnit 5
-* [UIMA-6373] Format UIMA Core Java SDK codebase
-
-### API changes
-
-#### SelectFS API with null or non-existing types
-
-When providing `null` or as a type or an non-existing type to a `select` call, then an exception is
-is thrown. Previously, all annotations were returned instead. To explicitly select any type, use
-the new `anyType()` instead of calling `type(null)`.
-
-#### ResourceManager datapath methods
-
-The methods `getDataPath()` and `setDataPath(String)` which were accepting/returning paths using 
-platform-specific path separators have been deprepcated. Instead, use the new 
-`setDataPathElements(File/String...)` and `getDataPathElements()` methods.
+This is a bug fix release.
 
-#### JUnit upgrade
+**Bugs fixed**
+* 🦟 Issue #255: File handle leak accessing performanceTuning.properties
+* 🦟 Issue #240: Helper annotation created by SelectFS should not survive
+* 🦟 Issue #238: Form 6 serializes non-reachable FSes but should not
+* 🦟 Issue #235: Misleading error message when JCas type is not registered
+* 🦟 [UIMA-6479] PearPackagingMavenPlugin has ancient JUnit dependency
+* 🦟 [UIMA-6473] CasToComparableText is broken
 
-The JUnit module has been upgraded from JUnit 4 to JUnit 5 along with the rest of the test code
-switching to JUnit 5. If you use the unit test helpers from this module, you also have to upgrade
-your tests to JUnit 5.
+**Improvements**
+* ⭐️ Issue #222: Support comparing test files irrespective of line endings
+* ⭐️ [UIMA-6480] Add tests with empty arrays to CAS de/ser-suite
 
-## <a id="list.issues">Full list of JIRA Issues affecting this Release</a>
+**Refactoring**
+* ⚙️ [UIMA-6454] Update dependencies
+* ⚙️ [UIMA-6463] Use toolchains to ensure compatibility with Java 1.8
+* ⚙️ [UIMA-6469] Cleaning up file handling code
 
-Click [issuesFixed/jira-report.hmtl](issuesFixed/jira-report.html) for the list of issues affecting
-this release.
+For a full list of issues affecting this release, please see:
 
-Please use the mailing lists ( http://uima.apache.org/mail-lists.html ) for feedback.
+* [GitHub issues](issuesFixed/github-report.html) [[online](https://github.com/apache/uima-uimaj/issues?q=milestone%3A3.3.1)]
+* [Jira issues (legacy)](issuesFixed/jira-report.html) [[online](https://issues.apache.org/jira/issues/?jql=project%20%3D%20UIMA%20AND%20fixVersion%20%3D%203.3.1SDK)]
 
 ## <a id="get.involved">How to Get Involved</a>
 
@@ -111,5 +87,5 @@ help, source code and feedback. If you are interested in contributing, please vi
 
 ## <a id="report.issues">How to Report Issues</a>
 
-The Apache UIMA project uses JIRA for issue tracking. Please report any issues you find at 
-[http://issues.apache.org/jira/browse/uima](http://issues.apache.org/jira/browse/uima).
+The Apache UIMA project uses GitHub for issue tracking. Please report any issues you find at 
+[https://github.com/apache/uima-uimaj/issues](https://github.com/apache/uima-uimaj/issues).
diff --git a/aggregate-uimaj-docbooks/pom.xml b/aggregate-uimaj-docbooks/pom.xml
@@ -68,5 +68,6 @@
     <module>../uima-docbook-tutorials-and-users-guides</module>
     <!-- Converted to Asciidoc -->
     <module>../uima-doc-v3-users-guide</module>
+    <module>../uima-doc-v3-maintainers-guide</module>
   </modules>
 </project>
diff --git a/jVinci/.gitignore b/jVinci/.gitignore
@@ -1,2 +1,3 @@
 /.apt_generated/
 /.apt_generated_tests/
+/META-INF/
diff --git a/jVinci/marker-file-identifying-osgi-bundle b/jVinci/marker-file-identifying-osgi-bundle
diff --git a/jVinci/pom.xml b/jVinci/pom.xml
@@ -17,29 +17,51 @@
    specific language governing permissions and limitations
    under the License.    
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-
-  <parent>
-    <groupId>org.apache.uima</groupId>
-    <artifactId>uimaj-parent</artifactId>
-    <version>3.4.0-SNAPSHOT</version>
-    <relativePath>../uimaj-parent/pom.xml</relativePath>
-  </parent>
-
-  <artifactId>jVinci</artifactId>
-  <packaging>jar</packaging>
-  <name>Apache UIMA Base: ${project.artifactId}: Vinci Transport Library</name>
-  <description>This is a protocol used by the base UIMA Collection processing manager for supporting
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.apache.uima</groupId>
+		<artifactId>uimaj-parent</artifactId>
+		<version>3.4.0-SNAPSHOT</version>
+		<relativePath>../uimaj-parent/pom.xml</relativePath>
+	</parent>
+
+	<artifactId>jVinci</artifactId>
+	<packaging>bundle</packaging>
+
+	<name>Apache UIMA Base: ${project.artifactId}: Vinci Transport Library</name>
+	<description>This is a protocol used by the base UIMA Collection processing manager for supporting
     networked deployment.  See UIMA-AS as a more modern alternative supporting
     more standard protocols.</description>
-  <url>${uimaWebsiteUrl}</url>
+	<url>${uimaWebsiteUrl}</url>
+
+	<properties>
+		<postNoticeText>${ibmNoticeText}</postNoticeText>
+	</properties>
 
-  <properties>
-    <postNoticeText>${ibmNoticeText}</postNoticeText>
-  </properties>
+	<build>
+		<finalName>jVinci</finalName>
 
-  <build>
-    <finalName>jVinci</finalName>
-  </build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<configuration>
+					<instructions>
+						<Bundle-RequiredExecutionEnvironment>JavaSE-1.8</Bundle-RequiredExecutionEnvironment>
+						<_dsannotations>*</_dsannotations>
+						<_metatypeannotations>*</_metatypeannotations>
+						<Export-Package>
+							org.apache.vinci.debug,
+							org.apache.vinci.transport,
+							org.apache.vinci.transport.*
+						</Export-Package>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
 </project>
diff --git a/jcasgen-maven-plugin/pom.xml b/jcasgen-maven-plugin/pom.xml
@@ -16,7 +16,9 @@
 	specific language governing permissions and limitations
 	under the License.
 -->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.apache.uima</groupId>
@@ -41,17 +43,18 @@
     <dependency>
       <groupId>org.apache.maven</groupId>
       <artifactId>maven-plugin-api</artifactId>
-      <version>3.0.3</version>
+      <version>${maven.version}</version>
+      <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.apache.maven</groupId>
       <artifactId>maven-core</artifactId>
-      <version>3.0.3</version>
+      <version>${maven.version}</version>
+      <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.apache.maven.plugin-tools</groupId>
       <artifactId>maven-plugin-annotations</artifactId>
-      <version>3.2</version>
       <scope>provided</scope>
     </dependency>
     <dependency>

diff --git a/marker-file-enabling-auto-staging b/marker-file-enabling-auto-staging
diff --git a/marker-file-enabling-tycho-release b/marker-file-enabling-tycho-release
diff --git a/marker-file-identifying-parent-pom b/marker-file-identifying-parent-pom