Merge branch 'release/3.6.x' into release/4.0.x

* release/3.6.x: (805 commits) Issue #421: Apache UIMA Java SDK 3.6.0 Issue #409: Update dependencies Issue #417: BOM should not inherit build setup from parent POM Issue #417: BOM should not inherit build setup from parent POM Issue #409: Update dependencies Issue #393: Include uimaFIT artifacts in binary distribution Issue #409: Update dependencies Issue #409: Update dependencies Issue #407: Clean up PearPackagingMavenPlugin Issue #385: Allow import of type systems published through SPI Issue #385: Allow import of type systems published through SPI No issue: Fix some typos Issue #404: Remove toolchains Issue #404: Remove toolchains No issue. Fix typo and add parent back to BOM Issue #402: Provide bnd plugin to generate package imports based on imports in UIMA descriptors Issue #402: Provide bnd plugin to generate package imports based on imports in UIMA descriptors Issue #385: Allow import of type systems published through SPI Issue #385: Allow import of type systems published through SPI Issue #398: Mark Maven plugins as thread-safe ... % Conflicts: % PearPackagingMavenPlugin/pom.xml % aggregate-uimaj-eclipse-plugins/pom.xml % aggregate-uimaj/pom.xml % jVinci/pom.xml % jcasgen-maven-plugin/pom.xml % pom.xml % uimaj-adapter-vinci/pom.xml % uimaj-bom/pom.xml % uimaj-bootstrap/pom.xml % uimaj-component-test-util/pom.xml % uimaj-core/pom.xml % uimaj-cpe/pom.xml % uimaj-document-annotation/pom.xml % uimaj-documentation/pom.xml % uimaj-eclipse-feature-runtime/pom.xml % uimaj-eclipse-feature-tools/pom.xml % uimaj-eclipse-maven-p2-site/pom.xml % uimaj-eclipse-update-site/pom.xml % uimaj-ep-cas-editor-ide/pom.xml % uimaj-ep-cas-editor/pom.xml % uimaj-ep-configurator/pom.xml % uimaj-ep-debug/pom.xml % uimaj-ep-jcasgen/pom.xml % uimaj-ep-launcher/pom.xml % uimaj-ep-pear-packager/pom.xml % uimaj-ep-runtime/pom.xml % uimaj-examples/pom.xml % uimaj-json/pom.xml % uimaj-parent/pom.xml % uimaj-test-util/pom.xml % uimaj-tools/pom.xml % uimaj-v3migration-jcas/pom.xml
apache · Nov 21, 2024 · 0246160 · 0246160
2 parents e4b5bdb + a6477bb
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diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,79 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main", "main-v2", "rel/*" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main", "main-v2", "rel/*" ]
+  schedule:
+    - cron: '30 20 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        os: [ubuntu-latest]
+        jdk: [17]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.head_ref || github.ref }}
+
+    - name: Set up JDK ${{ matrix.jdk }}
+      uses: actions/setup-java@v4
+      with:
+        java-version: ${{ matrix.jdk }}
+        distribution: 'temurin'
+        cache: maven
+
+    - name: Set up Maven
+      uses: stCarolas/setup-maven@v5
+      with:
+        maven-version: 3.9.8
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    - name: Set up cache date
+      run: echo "CACHE_DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+    - name: Build with Maven
+      run: mvn --no-transfer-progress -B -DskipTests clean verify --file pom.xml
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/.gitignore b/.gitignore
@@ -12,3 +12,4 @@ issuesFixed
 .idea
 *.iml
 .tycho-consumer-pom.xml
+dependency-reduced-pom.xml
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,40 @@
+# How to contribute to Apache UIMA Java SDK
+
+Thank you for your intention to contribute to the Apache UIMA Java SDK project. 
+As an open-source community, we highly appreciate external contributions to our project.
+
+To make the process smooth for the project *committers* (those who review and accept changes) and *contributors* (those who propose new changes via pull requests), there are a few rules to follow.
+
+## Contribution Guidelines
+
+Please check out the [How to get involved](https://uima.apache.org/get-involved.html) to understand how contributions are made. 
+A detailed list of coding standards can be found at [Apache UIMA Code Conventions](https://uima.apache.org/codeConventions.html) which also contains a list of coding guidelines that you should follow.
+For pull requests, there is a [check list](PULL_REQUEST_TEMPLATE.md) with criteria for acceptable contributions.
+
+## Preparing a Pull Request (PR)
+
+In order to contribute to the  project, you need to create a **pull request**. 
+This section briefly guides you through the best way of doing this:
+
+* Before creating a pull request, create an issue in the issue tracker of the project to which
+  you wish to contribute
+* Fork the project on GitHub
+* Create a branch based on the branch to which you wish to contribute. Normally, you should create
+  this branch from the **main** branch of the respective project. In the case you want to fix
+  a bug in the latest released version, you should consider to branch off the latest maintenance
+  branch (e.g. **2.4.x**). If you are not sure, ask via the issue you have just created. Do **not**
+  make changes directly to the master or maintenance branches in your fork. The name of the branch
+  should be e.g. `feature/UIMA-[ISSUE-NUMBER]-[SHORT-ISSUE-DESCRIPTION]` or `bugfix/UIMA-[ISSUE-NUMBER]-[SHORT-ISSUE-DESCRIPTION]`.
+* Now you make changes to your branch. When committing to your branch, use the format shown below
+  for your commit messages.
+```
+[UIMA-<ISSUE-NUMBER>] <ISSUE TITLE>
+<EMPTY LINE>
+- <CHANGE 1>
+- <CHANGE 2>
+- ...
+```
+* You can create the pull request any time after your first commit. I.e. you do not have to wait
+  until you are completely finished with your implementation. Creating a pull request early 
+  tells other developers that you are actively working on an issue and facilitates asking questions
+  about and discussing implementation details.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -19,4 +19,5 @@
 
 defaultPipeline {
   // extraMavenArguments = '-Pjacoco,spotbugs,pmd'
+  extraMavenArguments = '-Ddisable-rc-auto-staging'
 }
diff --git a/NOTICE.md b/NOTICE.md
@@ -33,4 +33,24 @@ from the source code management (SCM) system project uses.
 
 The class org.apache.uima.internal.util.WeakIdentityMap<K, V> was copied from
 the Apache Lucene project which in turn derived it from the Apache CXF project 
-and is Apache License 2.0.
+and is Apache License 2.0.
+
+# Apache UIMA uimaFIT
+Copyright 2013-2020 The Apache Software Foundation
+
+Copyright 2009-2012 Regents of the University of Colorado.
+All rights reserved.
+
+Copyright 2009-2012 Ubiquitous Knowledge Processing (UKP) Lab.
+Technische Universität Darmstadt.
+All rights reserved.
+
+
+# AnnotationLiteral.java
+
+Licensed under the Apache License, Version 2.0.
+File was copied from the javax.enterprise cdi-api version 1.0.
+
+JBoss, Home of Professional Open Source
+Copyright 2008, Red Hat Middleware LLC, and individual contributors
+by the @authors tag.
diff --git a/PearPackagingMavenPlugin/marker-file-enabling-dependency-check b/PearPackagingMavenPlugin/marker-file-enabling-dependency-check
@@ -0,0 +1 @@
+Enables the "dependency-check" profile
diff --git a/PearPackagingMavenPlugin/marker-file-maven-plugin-module b/PearPackagingMavenPlugin/marker-file-maven-plugin-module
@@ -0,0 +1 @@
+Enables the "maven-plugin-module" profile
diff --git a/PearPackagingMavenPlugin/pom.xml b/PearPackagingMavenPlugin/pom.xml
@@ -17,19 +17,21 @@
    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>
     <groupId>org.apache.uima</groupId>
-    <artifactId>uimaj-parent</artifactId>
+    <artifactId>uimaj-parent-internal</artifactId>
     <version>4.0.0-SNAPSHOT</version>
-    <relativePath>../uimaj-parent/pom.xml</relativePath>
+    <relativePath>../uimaj-parent-internal/pom.xml</relativePath>
   </parent>
 
   <artifactId>PearPackagingMavenPlugin</artifactId>
   <packaging>maven-plugin</packaging>
-  <name>Apache UIMA Maven: ${project.artifactId}</name>
+  <name>Apache UIMA Tools: ${project.artifactId}</name>
   <description>This is a maven plugin that produces a pear artifact.</description>
   <url>${uimaWebsiteUrl}</url>
 
@@ -38,33 +40,29 @@
   </properties>
 
   <dependencies>
-    <dependency>
-      <groupId>org.apache.maven</groupId>
-      <artifactId>maven-plugin-api</artifactId>
-      <scope>provided</scope>
-    </dependency>
-
-    <dependency>
-      <groupId>org.apache.maven.plugin-tools</groupId>
-      <artifactId>maven-plugin-annotations</artifactId>
-      <scope>provided</scope>
-    </dependency>
-
-    <dependency>
-      <groupId>org.apache.maven</groupId>
-      <artifactId>maven-core</artifactId>
-      <scope>provided</scope>
-    </dependency>
-
     <dependency>
       <groupId>org.apache.uima</groupId>
       <artifactId>uimaj-core</artifactId>
-      <version>${project.parent.version}</version>
+      <version>${project.version}</version>
     </dependency>
 
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>
     </dependency>
   </dependencies>
+
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-plugin-plugin</artifactId>
+          <configuration>
+            <goalPrefix>pear</goalPrefix>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
 </project>
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,3 +12,4 @@ issuesFixed @@
     .idea
     *.iml
     .tycho-consumer-pom.xml
+    dependency-reduced-pom.xml