Update version of dependencies, fix build errors, address bit rot

.github/workflows/build.yml

@@ -0,0 +1,41 @@
+name: Build
+on:
+  push:
+    branches:
+      - master
+
+permissions:
+  contents: write
+  checks: write
+
+concurrency:
+    group: ${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
+
+jobs:
+  maven:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '21'
+          cache: 'maven'
+          server-id: ossrh
+          server-username: MAVEN_USERNAME
+          server-password: MAVEN_PASSWORD
+      - name: Publish snapshot
+        run: ./mvnw --batch-mode -no-transfer-progress --update-snapshots deploy -Ppackage
+        env:
+          MAVEN_USERNAME: ${{ vars.OSSRH_USERNAME }}
+          MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}
+      - name: Publish test report
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: "**/target/surefire-reports/TEST-*.xml"
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/check-pr.yaml

@@ -1,14 +1,40 @@
 name: Check PR
-on: pull_request
+on:
+    pull_request:
+      types: [opened, reopened, synchronize]
+
+permissions:
+    checks: write
+
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
 
 jobs:
   maven:
-    runs-on: ubuntu-latest
+    strategy:
+        matrix:
+          os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-java@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
+        with:
+            distribution: 'temurin'
+            java-version: '21'
+            cache: 'maven'
+      - name: Compile
+        run: ./mvnw --batch-mode --no-transfer-progress --update-snapshots -T 4 package -DskipTests=true
+      - name: Tests and additional checks
+        run: ./mvnw --batch-mode --no-transfer-progress -T 4 verify -Ppackage
+      - name: Publish test report
+        uses: mikepenz/action-junit-report@v4
+        if: (success() || failure()) && matrix.os == 'ubuntu-latest'
         with:
-          distribution: temurin
-          java-version: 11
-      - name: Run Checks
-        run: mvn --batch-mode --no-transfer-progress --update-snapshots verify
+          report_paths: "**/target/surefire-reports/TEST-*.xml"
+          job_name: "Check PR"
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.os == 'ubuntu-latest'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/spotless.yaml

@@ -0,0 +1,28 @@
+name: Format Check
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  spotless:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '21'
+      - name: spotless:check
+        run: ./mvnw spotless:check
+      - uses: mshick/add-pr-comment@v2
+        if: always()
+        with:
+          message-success: |
+            Formatting check succeeded!
+          message-failure: |
+            **This Pull Request has failed the formatting check**
+
+            Please run `mvnw spotless:apply` or `mvnw clean install -DskipTests` to fix the formatting issues.

.mvn/wrapper/maven-wrapper.properties

@@ -0,0 +1,18 @@
+# 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.
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.6/apache-maven-3.9.6-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar

.vscode/extensions.json

@@ -4,13 +4,10 @@
 	// List of extensions which should be recommended for users of this workspace.
 	"recommendations": [
 		"vscjava.vscode-java-pack",
-		"editorconfig.editorconfig",
 		"streetsidesoftware.code-spell-checker",
 		"streetsidesoftware.code-spell-checker-scientific-terms",
 		"streetsidesoftware.code-spell-checker-medical-terms",
-		"shengchen.vscode-checkstyle",
 		"sonarsource.sonarlint-vscode",
-		"redhat.fabric8-analytics"
 	],
 	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
 	"unwantedRecommendations": []

.vscode/launch.json

@@ -5,12 +5,19 @@
 {
 	"version": "0.2.0",
     "configurations": [
+        {
+            "type": "java",
+            "name": "Main",
+            "request": "launch",
+            "mainClass": "org.opencds.cqf.cql.debug.service.Main",
+            "projectName": "cql-debug-service"
+        },
         {
             "type": "java",
             "name": "Launch Main w/ Plugin",
             "request": "launch",
             "mainClass": "org.opencds.cqf.cql.ls.service.Main",
-            "projectName": "cql-ls-plugin-debug",
+            "projectName": "cql-ls-plugin-debug"
         },
         {
             "type": "java",

.vscode/settings.json

@@ -9,11 +9,6 @@
         ".idea": true,
     },
     "java.configuration.updateBuildConfiguration": "automatic",
-    "editor.formatOnSave": true,
-    "java.format.settings.url": "https://raw.githubusercontent.com/google/styleguide/gh-pages/eclipse-java-google-style.xml",
-    "editor.codeActionsOnSave": {
-        "source.organizeImports": true,
-    },
     "editor.tabSize": 4,
     "editor.insertSpaces": true,
     "editor.detectIndentation": false,
@@ -24,10 +19,8 @@
         "hamcrest",
         "opencds",
         "testng",
+        "Ucum",
         "Unregistration"
     ],
-    "formatAll.includeFileExtensions": [
-        ".java"
-    ],
     "java.compile.nullAnalysis.mode": "automatic"
 }

README.md

@@ -14,7 +14,7 @@ Build the project with:
 mvn package
 ```
 
-The language server itself is designed to be used by IDE plugins, such as the [CQL Support for VS Code]([https://atom.io/packages/language-cql](https://marketplace.visualstudio.com/items?itemName=cqframework.cql)) package.
+The language server itself is designed to be used by IDE plugins, such as the [CQL Support for VS Code](<[https://atom.io/packages/language-cql](https://marketplace.visualstudio.com/items?itemName=cqframework.cql)>) package.
 
 ## Getting Help
 
@@ -42,7 +42,7 @@ Merges to `master` trigger a deployment to the Maven Snapshots repositories. Onc
 
 ## License
 
-Copyright 2019+ Dynamic Content Group, LLC (dba Alphora)
+Copyright 2019+ Smile Digital Health
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

core/pom.xml

@@ -1,5 +1,6 @@
 <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">
+    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>
 
@@ -18,27 +19,5 @@
             <groupId>org.opencds.cqf.fhir</groupId>
             <artifactId>cqf-fhir-cr</artifactId>
         </dependency>
-
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-lang3</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-jaxb</artifactId>
-            <type>pom</type>
-        </dependency>
-
-        <dependency>
-            <groupId>com.github.ben-manes.caffeine</groupId>
-            <artifactId>caffeine</artifactId>
-            <version>3.1.1</version>
-        </dependency>
     </dependencies>
 </project>

core/src/main/java/org/opencds/cqf/cql/ls/core/ContentService.java

@@ -27,8 +27,8 @@ default InputStream read(URI root, VersionedIdentifier identifier) {
         }
 
         if (locations.size() > 1) {
-            String allLocations = String.join("%n",
-                    locations.stream().map(String::valueOf).collect(Collectors.toList()));
+            String allLocations =
+                    String.join("%n", locations.stream().map(String::valueOf).collect(Collectors.toList()));
             throw new IllegalStateException(String.format(
                     "more than one location was found for library: %s version: %s in the current workspace:%n%s",
                     identifier.getId(), identifier.getVersion(), allLocations));