Java coverage fixes (#3253)

.github/workflows/coverage.yml

@@ -2,6 +2,8 @@ name: Generate API Coverage
 
 on:
   workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 0" # Run every Sunday at midnight
 
 jobs:
   generate-cpp-coverage-report:
@@ -17,18 +19,18 @@ jobs:
 
       - name: Generate C++ Coverage
         working-directory: ./cpp
-        run: ../scripts/generate-code-coverage.sh
+        run: ../scripts/generate-cpp-code-coverage.sh
 
       - name: Generate C++ Coverage Reports
         working-directory: ./cpp
         run: |
           for binary in bin/*; do
-            ../scripts/generate-code-coverage.sh "$binary"
+            ../scripts/generate-cpp-code-coverage.sh "$binary"
           done
 
           for library in lib/*; do
             if [[ $library =~ lib/lib[a-zA-Z0-9]+\.dylib ]]; then
-              ../scripts/generate-code-coverage.sh "$library"
+              ../scripts/generate-cpp-code-coverage.sh "$library"
             fi
           done
 
@@ -104,25 +106,10 @@ jobs:
         with:
           use_ccache: false
 
-      - name: Build
-        run: |
-          make -C cpp srcs
-          make -C java
-
       - name: Generate Java Coverage
         working-directory: ./java
         run: |
-          wget https://repo1.maven.org/maven2/org/jacoco/org.jacoco.cli/0.8.12/org.jacoco.cli-0.8.12-nodeps.jar
-          wget https://repo1.maven.org/maven2/org/jacoco/org.jacoco.agent/0.8.12/org.jacoco.agent-0.8.12-runtime.jar
-
-          python3 allTests.py --all --workers=4 --debug --jacoco $(pwd)/org.jacoco.agent-0.8.12-runtime.jar
-
-          args=""
-          for pkg in src/*; do
-            args="$args --classfiles $pkg/build/classes/ --sourcefiles $pkg/src/main/java/"
-          done
-
-          java -jar org.jacoco.cli-0.8.12-nodeps.jar report $(find . -name \*.jacoco.exec) $args --html coverage
+          ../scripts/generate-java-code-coverage.sh
 
       - name: Sync Documentation to S3
         working-directory: ./java/coverage

scripts/generate-java-code-coverage.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+JACOCO_VERSION=0.8.12
+
+if [ "$(basename "$(pwd)")" != "java" ]; then
+    echo "This script must be run from the 'java' directory."
+    exit 1
+fi
+
+make -C ../cpp srcs
+make
+
+if [ ! -f org.jacoco.cli-nodeps.jar ]; then
+    wget https://repo1.maven.org/maven2/org/jacoco/org.jacoco.cli/$JACOCO_VERSION/org.jacoco.cli-$JACOCO_VERSION-nodeps.jar -O org.jacoco.cli-nodeps.jar
+fi
+
+if [ ! -f org.jacoco.agent-runtime.jar ]; then
+    wget https://repo1.maven.org/maven2/org/jacoco/org.jacoco.agent/$JACOCO_VERSION/org.jacoco.agent-$JACOCO_VERSION-runtime.jar -O org.jacoco.agent-runtime.jar
+fi
+
+python3 allTests.py --all --workers=4 --debug --jacoco $(pwd)/org.jacoco.agent-runtime.jar
+
+# We don't want any coverage for generated code. We remove their class files and any inner classes.
+jacocoArgs=()
+for dir in src/*; do
+    # Skip non-directories.
+    [ -d "$dir" ] || continue
+
+    # Skip IceGridGUI
+    [ "$(basename "$dir")" == "IceGridGUI" ] && continue
+
+    jacocoArgs+=(--classfiles "$dir/build/classes/java/main")
+    jacocoArgs+=(--sourcefiles "$dir/src/main/java")
+
+    # Iterate over the generated Java files and remove the associated class and inner class files.
+    IFS=$'\n'; set -f
+    for javaFile in $(find "$dir" -name '*.java' | grep generated-src); do
+        # Remove everything up to generated-src/ from the path.
+        relativeJavaRoot=${javaFile#*generated-src/}
+        classDir="$dir/build/classes/java/main"
+        classFile=${classDir}/${relativeJavaRoot%.java}.class
+        # Remove the class file (a/b/Foo.class)
+        rm "$classFile"
+        # Remove any inner classes (a/b/Foo$*.class)
+        find "$(dirname "$classFile")" -name "$(basename -- "$classFile" ".class")\$*.class" -exec rm {} \;
+
+    done
+    unset IFS; set +f
+done
+
+IFS=$'\n'; set -f
+# shellcheck disable=SC2207
+coverageFiles=($(find . -name \*.jacoco.exec))
+unset IFS; set +f
+
+java -jar org.jacoco.cli-nodeps.jar report "${coverageFiles[@]}" "${jacocoArgs[@]}" --html coverage