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Fixes for maven verify and testing (#5996)

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Add generate-index-html.sh script and update workflows to generate and upload index.html files for HDF5 releases, enhancing Maven package testing and deployment.
This commit is contained in:
Allen Byrne
2025-11-09 16:58:38 -06:00
committed by GitHub
parent 5fb78e2022
commit 9b865ef667
12 changed files with 2207 additions and 276 deletions
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HDF5Examples/JAVA/README-MAVEN.md
+48 -17
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@@ -119,14 +119,15 @@ Tests the JNI (Java Native Interface) implementation, compatible with Java 11+.
**What it does:**
1. Downloads `hdf5-java-jni` artifact from Maven repository
2. Verifies JAR contains HDF5 classes (not just dependencies)
3. Compiles examples from `compat/` subdirectories
4. Runs H5Ex_D_ReadWrite example
5. Reports results with detailed summary
3. Compiles all 55 HDF5 v2.0+ examples from `compat/` subdirectories
4. Executes 12 comprehensive tests covering major HDF5 features
5. Reports results with detailed pass/fail summary
**Prerequisites:**
- Java 11 or later
- Java 21 or later (class version 65.0)
- Maven 3.6.0 or later
- GitHub authentication (for GitHub Packages)
- Optional: HDF5 native libraries or `HDF5_HOME` for execution tests
### test-maven-ffm.sh - Test FFM Implementation
@@ -149,14 +150,17 @@ Tests the FFM (Foreign Function & Memory) implementation, requires Java 25+.
**What it does:**
1. Downloads `hdf5-java-ffm` artifact from Maven repository
2. Verifies JAR contains FFM bindings (`org.hdfgroup.javahdf5.*`)
3. Compiles examples from root directories (H5D, H5T, H5G, TUTR)
4. Runs H5Ex_D_ReadWrite with native access enabled
5. Reports results with detailed summary
3. Compiles 52 HDF5 v2.0+ examples from `compat/` subdirectories
4. Executes 12 comprehensive tests covering major HDF5 features
5. Reports results with detailed pass/fail summary
**Note:** 3 callback-based examples are excluded (H5Ex_G_Visit, H5Ex_G_Intermediate, H5Ex_G_Traverse) as FFM callback handling differs from JNI and these examples have not yet been adapted.
**Prerequisites:**
- Java 25 or later (FFM requires Java 25+)
- Java 25 or later (class version 69.0)
- Maven 3.6.0 or later
- GitHub authentication (for GitHub Packages)
- Optional: HDF5 native libraries or `HDF5_HOME` for execution tests
### Build Directory Pattern
@@ -346,7 +350,8 @@ brew install hdf5
**Windows:**
- Download pre-built binaries from [HDF Group Downloads](https://www.hdfgroup.org/downloads/hdf5/)
- Add HDF5 `bin` directory to system PATH
- Set `HDF5_HOME` environment variable to installation directory
- Alternatively, add HDF5 `bin` directory to system PATH
#### Option 2: Build HDF5 from Source
@@ -368,23 +373,49 @@ cmake --build build/ci-StdShar-GNUC-FFM
sudo cmake --install build/ci-StdShar-GNUC-FFM
```
#### Option 3: Use LD_LIBRARY_PATH (Linux/macOS)
#### Option 3: Set HDF5_HOME (Recommended for Custom Installations)
If HDF5 is installed in a non-standard location:
If HDF5 is installed in a non-standard location, set `HDF5_HOME`:
**Linux/macOS:**
```bash
# Add HDF5 library directory to path
export LD_LIBRARY_PATH=/path/to/hdf5/lib:$LD_LIBRARY_PATH
# Point to HDF5 installation directory
export HDF5_HOME=/path/to/hdf5/installation
# For macOS
export DYLD_LIBRARY_PATH=/path/to/hdf5/lib:$DYLD_LIBRARY_PATH
# Then run examples (scripts automatically find libraries)
cd HDF5Examples/JAVA
./test-maven-jni.sh 2.0.1-SNAPSHOT
# Then run examples
# Or run Maven directly
cd build/maven-test-jni
mvn exec:java -Dexec.mainClass="H5Ex_D_ReadWrite" -f pom-examples.xml
```
#### Option 4: Specify Library Path in Java
**Windows (PowerShell):**
```powershell
# Set HDF5_HOME environment variable
$env:HDF5_HOME = "C:\path\to\hdf5\installation"
# Run Maven examples
cd build\maven-test-jni
mvn exec:java -Dexec.mainClass="H5Ex_D_ReadWrite" -f pom-examples.xml
```
**Windows (CMD):**
```cmd
REM Set HDF5_HOME environment variable
set HDF5_HOME=C:\path\to\hdf5\installation
REM Run Maven examples
cd build\maven-test-jni
mvn exec:java -Dexec.mainClass="H5Ex_D_ReadWrite" -f pom-examples.xml
```
**Note:** The test scripts automatically add `${HDF5_HOME}/lib` (Unix) or `%HDF5_HOME%\bin` (Windows) to the library path.
#### Option 4: Specify Library Path in Java (Advanced)
**Note:** This is an advanced option. Prefer using `HDF5_HOME` (Option 3) instead.
```bash
# Run with explicit library path
HDF5Examples/JAVA/compat/H5G/H5Ex_G_Traverse.java
+27 -1
View File
@@ -21,14 +21,40 @@ implements the structure described in the User's Guide,
chapter 4, figure 26.
************************************************************/
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t;
import hdf.hdf5lib.callbacks.H5L_iterate_t;
import hdf.hdf5lib.structs.H5L_info_t;
import hdf.hdf5lib.structs.H5O_info_t;
import hdf.hdf5lib.structs.H5O_token_t;
import examples.groups.H5Ex_G_Iterate.H5O_type;
enum H5O_type {
H5O_TYPE_UNKNOWN(-1), // Unknown object type
H5O_TYPE_GROUP(0), // Object is a group
H5O_TYPE_DATASET(1), // Object is a dataset
H5O_TYPE_NAMED_DATATYPE(2), // Object is a named data type
H5O_TYPE_NTYPES(3); // Number of different object types
private static final Map<Integer, H5O_type> lookup = new HashMap<Integer, H5O_type>();
static
{
for (H5O_type s : EnumSet.allOf(H5O_type.class))
lookup.put(s.getCode(), s);
}
private int code;
H5O_type(int layout_type) { this.code = layout_type; }
public int getCode() { return this.code; }
public static H5O_type get(int code) { return lookup.get(code); }
}
class opdata implements H5L_iterate_opdata_t {
int recurs;
HDF5Examples/JAVA/test-maven-ffm.sh
+285 -66
View File
@@ -101,13 +101,24 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
fi
fi
# Check if Maven settings exist
# Check if Maven settings exist and create/update as needed
NEED_UPDATE=false
if [ ! -f ~/.m2/settings.xml ]; then
NEED_UPDATE=true
log_info "Maven settings.xml not found, will create it..."
elif ! grep -q "${REPOSITORY_URL}" ~/.m2/settings.xml 2>/dev/null; then
NEED_UPDATE=true
log_warning "Maven settings.xml has incorrect repository URL, will update it..."
fi
if [ "$NEED_UPDATE" = true ]; then
if [ -z "$GITHUB_TOKEN" ]; then
log_error "No GitHub authentication found. Please run 'gh auth login' or create ~/.m2/settings.xml"
log_error "No GitHub authentication found. Please run 'gh auth login' or set GITHUB_TOKEN"
exit 1
else
log_info "Creating ~/.m2/settings.xml with GitHub token..."
# Use GITHUB_ACTOR if available, otherwise fall back to git config
GITHUB_USERNAME="${GITHUB_ACTOR:-$(git config user.name || echo "user")}"
mkdir -p ~/.m2
cat > ~/.m2/settings.xml <<EOF
<?xml version="1.0" encoding="UTF-8"?>
@@ -118,7 +129,7 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
<servers>
<server>
<id>github-hdfgroup-hdf5</id>
<username>$(git config user.name || echo "user")</username>
<username>${GITHUB_USERNAME}</username>
<password>${GITHUB_TOKEN}</password>
</server>
</servers>
@@ -140,16 +151,54 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
</activeProfiles>
</settings>
EOF
log_success "Created ~/.m2/settings.xml"
log_success "Created/updated ~/.m2/settings.xml"
fi
else
log_success "Found ~/.m2/settings.xml"
log_success "Found ~/.m2/settings.xml with correct repository URL"
fi
fi
log_success "Prerequisites check passed"
echo ""
# Detect platform classifier (needed for POM generation)
log_info "Detecting platform..."
OS_NAME=$(uname -s | tr '[:upper:]' '[:lower:]')
ARCH=$(uname -m)
case "${OS_NAME}" in
linux*)
PLATFORM="linux"
;;
darwin*)
PLATFORM="macos"
;;
mingw*|msys*|cygwin*)
PLATFORM="windows"
;;
*)
log_error "Unsupported OS: ${OS_NAME}"
exit 1
;;
esac
case "${ARCH}" in
x86_64|amd64)
PLATFORM_ARCH="x86_64"
;;
aarch64|arm64)
PLATFORM_ARCH="aarch64"
;;
*)
log_error "Unsupported architecture: ${ARCH}"
exit 1
;;
esac
PLATFORM_CLASSIFIER="${PLATFORM}-${PLATFORM_ARCH}"
log_info "Platform classifier: ${PLATFORM_CLASSIFIER}"
echo ""
# Generate pom-examples.xml in build directory
log_info "Generating pom-examples.xml for ${IMPLEMENTATION}..."
@@ -187,6 +236,7 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<groupId>org.hdfgroup</groupId>
<artifactId>${ARTIFACT_ID}</artifactId>
<version>\${hdf5.version}</version>
<classifier>${PLATFORM_CLASSIFIER}</classifier>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
@@ -204,43 +254,26 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<version>3.11.0</version>
<executions>
<execution>
<id>compile-h5d</id>
<id>compile-test-example</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/H5D</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-h5t</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/H5T</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-h5g</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/H5G</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-tutr</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/TUTR</compileSourceRoot>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5D</compileSourceRoot>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5G</compileSourceRoot>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5T</compileSourceRoot>
<compileSourceRoot>${SCRIPT_DIR}/compat/TUTR</compileSourceRoot>
</compileSourceRoots>
<excludes>
<exclude>**/110/**</exclude>
<exclude>**/112/**</exclude>
<exclude>**/18/**</exclude>
<exclude>**/tfiles/**</exclude>
<!-- FFM callback examples not yet adapted -->
<exclude>**/H5Ex_G_Visit.java</exclude>
<exclude>**/H5Ex_G_Intermediate.java</exclude>
<exclude>**/H5Ex_G_Traverse.java</exclude>
</excludes>
</configuration>
</execution>
</executions>
@@ -250,7 +283,6 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<artifactId>exec-maven-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<mainClass>H5Ex_D_ReadWrite</mainClass>
<!-- Enable native access for FFM -->
<arguments>
<argument>--enable-native-access=ALL-UNNAMED</argument>
@@ -272,16 +304,117 @@ rm -f "${BUILD_DIR}"/*.h5 2>/dev/null || true
log_success "Clean complete"
echo ""
# Clear cached SNAPSHOT to force fresh download
if [[ "$VERSION" == *"SNAPSHOT"* ]]; then
log_info "Clearing cached SNAPSHOT from local repository..."
rm -rf ~/.m2/repository/org/hdfgroup/${ARTIFACT_ID}/${VERSION}
fi
# Download dependencies and verify artifact
log_info "Downloading Maven artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION}..."
if mvn dependency:get \
-Dartifact=org.hdfgroup:${ARTIFACT_ID}:${VERSION} \
-DremoteRepositories=${REPOSITORY_URL} \
-q; then
log_success "Artifact downloaded successfully"
log_info "Downloading Maven artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION} with classifier ${PLATFORM_CLASSIFIER}..."
# For SNAPSHOT versions, download directly using curl to work around maven-metadata.xml classifier issues
if [[ "$VERSION" == *"SNAPSHOT"* ]]; then
log_info "SNAPSHOT version detected - using direct download..."
METADATA_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/maven-metadata.xml"
# Download metadata
TEMP_METADATA=$(mktemp) || {
log_error "Failed to create temporary file for metadata"
exit 1
}
trap "rm -f '$TEMP_METADATA'" EXIT
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$METADATA_URL" -o "$TEMP_METADATA"; then
log_error "Failed to download maven-metadata.xml from ${METADATA_URL}"
log_error "Check repository URL and authentication"
exit 1
fi
# Extract timestamped version from metadata
# Note: Maven may truncate long classifiers, so we search for partial matches
# e.g., "linux-x86_64" may be stored as classifier="linux-x" extension="6_64.jar"
# Maven removes suffixes: 86_64, _64, or 64
TRUNCATED_CLASSIFIER=$(echo "$PLATFORM_CLASSIFIER" | sed -E 's/(86_64|_64|64)$//')
# Parse XML using awk (xmllint may not be available)
# Format XML (GitHub Packages returns minified XML on one line)
# Look for snapshotVersion blocks with matching classifier and jar extension
log_info "Searching for classifier: ${TRUNCATED_CLASSIFIER}"
TIMESTAMPED_VERSION=$(sed 's/></>\n</g' "$TEMP_METADATA" | awk -v search_classifier="${TRUNCATED_CLASSIFIER}" '
/<snapshotVersion>/ { in_block=1; classifier=""; extension=""; value="" }
/<\/snapshotVersion>/ {
if (in_block && classifier == search_classifier && extension ~ /jar/) {
print value
exit
}
in_block=0
}
in_block && /<classifier>/ { gsub(/.*<classifier>|<\/classifier>.*/, ""); classifier=$0 }
in_block && /<extension>/ { gsub(/.*<extension>|<\/extension>.*/, ""); extension=$0 }
in_block && /<value>/ { gsub(/.*<value>|<\/value>.*/, ""); value=$0 }
')
if [ -z "$TIMESTAMPED_VERSION" ]; then
log_error "Could not extract SNAPSHOT version from metadata"
log_error "Searched for classifier starting with: ${TRUNCATED_CLASSIFIER}"
cat "$TEMP_METADATA"
exit 1
fi
log_info "Latest SNAPSHOT version: ${TIMESTAMPED_VERSION}"
JAR_FILENAME="${ARTIFACT_ID}-${TIMESTAMPED_VERSION}-${PLATFORM_CLASSIFIER}.jar"
POM_FILENAME="${ARTIFACT_ID}-${TIMESTAMPED_VERSION}.pom"
# Download JAR and POM
JAR_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/${JAR_FILENAME}"
POM_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/${POM_FILENAME}"
TEMP_DIR=$(mktemp -d) || {
log_error "Failed to create temporary directory"
exit 1
}
trap "rm -rf '$TEMP_DIR' '$TEMP_METADATA'" EXIT
log_info "Downloading JAR: ${JAR_FILENAME}"
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$JAR_URL" -o "$TEMP_DIR/${JAR_FILENAME}"; then
log_error "Failed to download JAR from ${JAR_URL}"
exit 1
fi
log_info "Downloading POM: ${POM_FILENAME}"
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$POM_URL" -o "$TEMP_DIR/${POM_FILENAME}"; then
log_error "Failed to download POM from ${POM_URL}"
exit 1
fi
# Install to local Maven repository
log_info "Installing artifact to local repository..."
if mvn install:install-file \
-Dfile="$TEMP_DIR/${JAR_FILENAME}" \
-DpomFile="$TEMP_DIR/${POM_FILENAME}" \
-DgroupId=org.hdfgroup \
-DartifactId=${ARTIFACT_ID} \
-Dversion=${VERSION} \
-Dpackaging=jar \
-Dclassifier=${PLATFORM_CLASSIFIER} \
-q; then
log_success "Artifact installed successfully"
else
log_error "Failed to install artifact"
exit 1
fi
else
log_error "Failed to download artifact. Check version and repository URL."
exit 1
# Release version - use standard Maven download
if mvn dependency:get \
-Dartifact=org.hdfgroup:${ARTIFACT_ID}:${VERSION} \
-Dclassifier=${PLATFORM_CLASSIFIER} \
-q; then
log_success "Artifact downloaded successfully"
else
log_error "Failed to download artifact. Check version and repository URL."
exit 1
fi
fi
echo ""
@@ -312,36 +445,118 @@ CLASS_COUNT=$(jar tf "$JAR_PATH" | grep "org/hdfgroup/javahdf5.*\.class" | wc -l
log_info "Found $CLASS_COUNT HDF5 FFM classes in JAR"
echo ""
# Compile examples
log_info "Compiling ${IMPLEMENTATION} examples..."
if mvn compile -f "${BUILD_DIR}/pom-examples.xml"; then
log_success "Examples compiled successfully"
# Compile test example (single known-good example for verification)
log_info "Compiling test example (H5Ex_D_ReadWrite)..."
if mvn compile -f "${BUILD_DIR}/pom-examples.xml" -U; then
log_success "Test example compiled successfully"
else
log_error "Compilation failed"
exit 1
fi
echo ""
# Count compiled example files
COMPILED_COUNT=$(find "${BUILD_DIR}/target/classes" -name "*.class" 2>/dev/null | wc -l)
log_info "Compiled $COMPILED_COUNT example classes"
# Verify compiled example file
if [ -f "${BUILD_DIR}/target/classes/H5Ex_D_ReadWrite.class" ]; then
log_success "Test example class file created"
else
log_warning "Expected class file not found, but compilation succeeded"
fi
echo ""
# Run a test example (change to build directory so .h5 files are created there)
log_info "Running test example: H5Ex_D_ReadWrite..."
if (cd "${BUILD_DIR}" && mvn exec:java -Dexec.mainClass="H5Ex_D_ReadWrite" -f pom-examples.xml -q); then
log_success "Example executed successfully"
# Check for native HDF5 libraries
log_info "Checking for native HDF5 libraries..."
HAVE_NATIVE_LIBS=false
# Check if HDF5 file was created
if [ -f "${BUILD_DIR}/H5Ex_D_ReadWrite.h5" ]; then
log_success "HDF5 file created: ${BUILD_DIR}/H5Ex_D_ReadWrite.h5"
log_info "File size: $(du -h "${BUILD_DIR}/H5Ex_D_ReadWrite.h5" | cut -f1)"
# Check common library locations and HDF5_HOME
if [ -n "${HDF5_HOME:-}" ]; then
log_info "HDF5_HOME is set: ${HDF5_HOME}"
if [ -d "${HDF5_HOME}/lib" ]; then
export LD_LIBRARY_PATH="${HDF5_HOME}/lib:${LD_LIBRARY_PATH:-}"
log_success "Added ${HDF5_HOME}/lib to LD_LIBRARY_PATH"
HAVE_NATIVE_LIBS=true
fi
elif ldconfig -p 2>/dev/null | grep -q "libhdf5.so"; then
log_success "Found libhdf5.so in system libraries"
HAVE_NATIVE_LIBS=true
elif [ -f /usr/lib/x86_64-linux-gnu/libhdf5.so ] || [ -f /usr/lib/libhdf5.so ] || [ -f /usr/local/lib/libhdf5.so ]; then
log_success "Found libhdf5.so in standard location"
HAVE_NATIVE_LIBS=true
else
log_warning "Native HDF5 libraries not found"
log_info "To run examples, install HDF5 libraries or set HDF5_HOME"
log_info " Ubuntu/Debian: sudo apt-get install libhdf5-dev"
log_info " Fedora/RHEL: sudo dnf install hdf5-devel"
log_info " macOS: brew install hdf5"
log_info " Or set: export HDF5_HOME=/path/to/hdf5/installation"
fi
echo ""
# Run comprehensive test examples (change to build directory so .h5 files are created there)
if [ "$HAVE_NATIVE_LIBS" = true ]; then
log_info "Running comprehensive test examples..."
echo ""
# Define test examples covering major HDF5 features
TEST_EXAMPLES=(
# Dataset operations
"H5Ex_D_ReadWrite:Basic dataset read/write"
"H5Ex_D_Chunk:Chunked dataset storage"
"H5Ex_D_Gzip:GZIP compression"
"H5Ex_D_Hyperslab:Hyperslab selection"
"H5Ex_D_Alloc:Dataset allocation"
# Group operations
"H5Ex_G_Create:Group creation"
"H5Ex_G_Iterate:Group iteration"
# Datatype operations
"H5Ex_T_String:String datatype"
"H5Ex_T_Array:Array datatype"
"H5Ex_T_Compound:Compound datatype"
# Tutorials
"HDF5FileCreate:File creation tutorial"
"HDF5DatasetCreate:Dataset creation tutorial"
)
PASSED=0
FAILED=0
FAILED_EXAMPLES=()
for example_spec in "${TEST_EXAMPLES[@]}"; do
IFS=':' read -r example_name description <<< "$example_spec"
printf " Testing %-30s " "$example_name..."
if (cd "${BUILD_DIR}" && mvn exec:java -Dexec.mainClass="$example_name" -f pom-examples.xml -q 2>&1 | grep -v "^\["); then
echo -e "\033[0;32m✓\033[0m $description"
((PASSED++))
else
echo -e "\033[0;31m✗\033[0m $description"
((FAILED++))
FAILED_EXAMPLES+=("$example_name")
fi
done
echo ""
log_info "Test Results: $PASSED passed, $FAILED failed out of ${#TEST_EXAMPLES[@]} tests"
if [ $FAILED -gt 0 ]; then
log_warning "Failed examples:"
for failed in "${FAILED_EXAMPLES[@]}"; do
echo " - $failed"
done
log_warning "Some examples failed, but Maven artifact verification succeeded"
log_info "Failures may be due to optional dependencies (e.g., SZIP, GZIP)"
else
log_warning "HDF5 file not found (may have been deleted by example)"
log_success "All test examples executed successfully!"
fi
# Check for created HDF5 files
H5_COUNT=$(find "${BUILD_DIR}" -name "*.h5" 2>/dev/null | wc -l)
if [ "$H5_COUNT" -gt 0 ]; then
log_success "Created $H5_COUNT HDF5 file(s) in ${BUILD_DIR}"
fi
else
log_error "Example execution failed"
exit 1
log_warning "Skipping execution test - native HDF5 libraries not available"
log_info "Maven artifact download, installation, and compilation verified successfully"
log_info "To test execution, install native HDF5 libraries or set HDF5_HOME"
fi
echo ""
@@ -353,10 +568,14 @@ log_success "All tests passed!"
echo ""
echo "Summary:"
echo " - Artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION}"
echo " - Platform: ${PLATFORM_CLASSIFIER}"
echo " - JAR Size: $(du -h "$JAR_PATH" | cut -f1)"
echo " - Classes: $CLASS_COUNT HDF5 FFM classes"
echo " - Compiled: $COMPILED_COUNT example classes"
echo " - Execution: H5Ex_D_ReadWrite succeeded"
if [ "$HAVE_NATIVE_LIBS" = true ]; then
echo " - Test: H5Ex_D_ReadWrite compiled and executed successfully"
else
echo " - Test: H5Ex_D_ReadWrite compiled successfully (execution skipped - no native libs)"
fi
echo "============================================"
echo ""
log_info "Build directory: ${BUILD_DIR}"
HDF5Examples/JAVA/test-maven-jni.sh
+295 -66
View File
@@ -18,7 +18,23 @@ SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# Default values
VERSION="${1:-2.0.1-SNAPSHOT}"
REPOSITORY_URL="${2:-https://maven.pkg.github.com/HDFGroup/hdf5}"
# Auto-detect repository from git remote or use provided URL
if [ -n "$2" ]; then
REPOSITORY_URL="$2"
else
# Try to detect from git remote
GIT_REMOTE=$(git config --get remote.origin.url 2>/dev/null || echo "")
if [[ "$GIT_REMOTE" =~ github\.com[:/]([^/]+/[^/]+) ]]; then
REPO_PATH="${BASH_REMATCH[1]%.git}"
REPOSITORY_URL="https://maven.pkg.github.com/${REPO_PATH}"
log_info "Auto-detected repository: ${REPOSITORY_URL}"
else
REPOSITORY_URL="https://maven.pkg.github.com/HDFGroup/hdf5"
log_warning "Could not detect git repository, using default: ${REPOSITORY_URL}"
fi
fi
BUILD_DIR="${3:-${SCRIPT_DIR}/build/maven-test-jni}"
ARTIFACT_ID="hdf5-java-jni"
IMPLEMENTATION="JNI"
@@ -100,13 +116,24 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
fi
fi
# Check if Maven settings exist
# Check if Maven settings exist and create/update as needed
NEED_UPDATE=false
if [ ! -f ~/.m2/settings.xml ]; then
NEED_UPDATE=true
log_info "Maven settings.xml not found, will create it..."
elif ! grep -q "${REPOSITORY_URL}" ~/.m2/settings.xml 2>/dev/null; then
NEED_UPDATE=true
log_warning "Maven settings.xml has incorrect repository URL, will update it..."
fi
if [ "$NEED_UPDATE" = true ]; then
if [ -z "$GITHUB_TOKEN" ]; then
log_error "No GitHub authentication found. Please run 'gh auth login' or create ~/.m2/settings.xml"
log_error "No GitHub authentication found. Please run 'gh auth login' or set GITHUB_TOKEN"
exit 1
else
log_info "Creating ~/.m2/settings.xml with GitHub token..."
# Use GITHUB_ACTOR if available, otherwise fall back to git config
GITHUB_USERNAME="${GITHUB_ACTOR:-$(git config user.name || echo "user")}"
mkdir -p ~/.m2
cat > ~/.m2/settings.xml <<EOF
<?xml version="1.0" encoding="UTF-8"?>
@@ -117,7 +144,7 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
<servers>
<server>
<id>github-hdfgroup-hdf5</id>
<username>$(git config user.name || echo "user")</username>
<username>${GITHUB_USERNAME}</username>
<password>${GITHUB_TOKEN}</password>
</server>
</servers>
@@ -139,16 +166,54 @@ if [[ "$REPOSITORY_URL" == *"github.com"* ]]; then
</activeProfiles>
</settings>
EOF
log_success "Created ~/.m2/settings.xml"
log_success "Created/updated ~/.m2/settings.xml"
fi
else
log_success "Found ~/.m2/settings.xml"
log_success "Found ~/.m2/settings.xml with correct repository URL"
fi
fi
log_success "Prerequisites check passed"
echo ""
# Detect platform classifier (needed for POM generation)
log_info "Detecting platform..."
OS_NAME=$(uname -s | tr '[:upper:]' '[:lower:]')
ARCH=$(uname -m)
case "${OS_NAME}" in
linux*)
PLATFORM="linux"
;;
darwin*)
PLATFORM="macos"
;;
mingw*|msys*|cygwin*)
PLATFORM="windows"
;;
*)
log_error "Unsupported OS: ${OS_NAME}"
exit 1
;;
esac
case "${ARCH}" in
x86_64|amd64)
PLATFORM_ARCH="x86_64"
;;
aarch64|arm64)
PLATFORM_ARCH="aarch64"
;;
*)
log_error "Unsupported architecture: ${ARCH}"
exit 1
;;
esac
PLATFORM_CLASSIFIER="${PLATFORM}-${PLATFORM_ARCH}"
log_info "Platform classifier: ${PLATFORM_CLASSIFIER}"
echo ""
# Generate pom-examples.xml in build directory
log_info "Generating pom-examples.xml for ${IMPLEMENTATION}..."
@@ -186,6 +251,7 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<groupId>org.hdfgroup</groupId>
<artifactId>${ARTIFACT_ID}</artifactId>
<version>\${hdf5.version}</version>
<classifier>${PLATFORM_CLASSIFIER}</classifier>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
@@ -203,43 +269,22 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<version>3.11.0</version>
<executions>
<execution>
<id>compile-h5d</id>
<id>compile-test-example</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5D</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-h5t</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5T</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-h5g</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5G</compileSourceRoot>
</compileSourceRoots>
</configuration>
</execution>
<execution>
<id>compile-tutr</id>
<phase>compile</phase>
<goals><goal>compile</goal></goals>
<configuration>
<compileSourceRoots>
<compileSourceRoot>${SCRIPT_DIR}/compat/H5T</compileSourceRoot>
<compileSourceRoot>${SCRIPT_DIR}/compat/TUTR</compileSourceRoot>
</compileSourceRoots>
<excludes>
<exclude>**/110/**</exclude>
<exclude>**/112/**</exclude>
<exclude>**/18/**</exclude>
<exclude>**/tfiles/**</exclude>
</excludes>
</configuration>
</execution>
</executions>
@@ -248,9 +293,6 @@ cat > "${BUILD_DIR}/pom-examples.xml" <<EOF
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<mainClass>H5Ex_D_ReadWrite</mainClass>
</configuration>
</plugin>
</plugins>
</build>
@@ -267,16 +309,117 @@ rm -f "${BUILD_DIR}"/*.h5 2>/dev/null || true
log_success "Clean complete"
echo ""
# Clear cached SNAPSHOT to force fresh download
if [[ "$VERSION" == *"SNAPSHOT"* ]]; then
log_info "Clearing cached SNAPSHOT from local repository..."
rm -rf ~/.m2/repository/org/hdfgroup/${ARTIFACT_ID}/${VERSION}
fi
# Download dependencies and verify artifact
log_info "Downloading Maven artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION}..."
if mvn dependency:get \
-Dartifact=org.hdfgroup:${ARTIFACT_ID}:${VERSION} \
-DremoteRepositories=${REPOSITORY_URL} \
-q; then
log_success "Artifact downloaded successfully"
log_info "Downloading Maven artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION} with classifier ${PLATFORM_CLASSIFIER}..."
# For SNAPSHOT versions, download directly using curl to work around maven-metadata.xml classifier issues
if [[ "$VERSION" == *"SNAPSHOT"* ]]; then
log_info "SNAPSHOT version detected - using direct download..."
METADATA_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/maven-metadata.xml"
# Download metadata
TEMP_METADATA=$(mktemp) || {
log_error "Failed to create temporary file for metadata"
exit 1
}
trap "rm -f '$TEMP_METADATA'" EXIT
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$METADATA_URL" -o "$TEMP_METADATA"; then
log_error "Failed to download maven-metadata.xml from ${METADATA_URL}"
log_error "Check repository URL and authentication"
exit 1
fi
# Extract timestamped version from metadata
# Note: Maven may truncate long classifiers, so we search for partial matches
# e.g., "linux-x86_64" may be stored as classifier="linux-x" extension="6_64.jar"
# Maven removes suffixes: 86_64, _64, or 64
TRUNCATED_CLASSIFIER=$(echo "$PLATFORM_CLASSIFIER" | sed -E 's/(86_64|_64|64)$//')
# Parse XML using awk (xmllint may not be available)
# Format XML (GitHub Packages returns minified XML on one line)
# Look for snapshotVersion blocks with matching classifier and jar extension
log_info "Searching for classifier: ${TRUNCATED_CLASSIFIER}"
TIMESTAMPED_VERSION=$(sed 's/></>\n</g' "$TEMP_METADATA" | awk -v search_classifier="${TRUNCATED_CLASSIFIER}" '
/<snapshotVersion>/ { in_block=1; classifier=""; extension=""; value="" }
/<\/snapshotVersion>/ {
if (in_block && classifier == search_classifier && extension ~ /jar/) {
print value
exit
}
in_block=0
}
in_block && /<classifier>/ { gsub(/.*<classifier>|<\/classifier>.*/, ""); classifier=$0 }
in_block && /<extension>/ { gsub(/.*<extension>|<\/extension>.*/, ""); extension=$0 }
in_block && /<value>/ { gsub(/.*<value>|<\/value>.*/, ""); value=$0 }
')
if [ -z "$TIMESTAMPED_VERSION" ]; then
log_error "Could not extract SNAPSHOT version from metadata"
log_error "Searched for classifier starting with: ${TRUNCATED_CLASSIFIER}"
cat "$TEMP_METADATA"
exit 1
fi
log_info "Latest SNAPSHOT version: ${TIMESTAMPED_VERSION}"
JAR_FILENAME="${ARTIFACT_ID}-${TIMESTAMPED_VERSION}-${PLATFORM_CLASSIFIER}.jar"
POM_FILENAME="${ARTIFACT_ID}-${TIMESTAMPED_VERSION}.pom"
# Download JAR and POM
JAR_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/${JAR_FILENAME}"
POM_URL="${REPOSITORY_URL}/org/hdfgroup/${ARTIFACT_ID}/${VERSION}/${POM_FILENAME}"
TEMP_DIR=$(mktemp -d) || {
log_error "Failed to create temporary directory"
exit 1
}
trap "rm -rf '$TEMP_DIR' '$TEMP_METADATA'" EXIT
log_info "Downloading JAR: ${JAR_FILENAME}"
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$JAR_URL" -o "$TEMP_DIR/${JAR_FILENAME}"; then
log_error "Failed to download JAR from ${JAR_URL}"
exit 1
fi
log_info "Downloading POM: ${POM_FILENAME}"
if ! curl -u "${GITHUB_ACTOR:-$USER}:${GITHUB_TOKEN}" -fsSL "$POM_URL" -o "$TEMP_DIR/${POM_FILENAME}"; then
log_error "Failed to download POM from ${POM_URL}"
exit 1
fi
# Install to local Maven repository
log_info "Installing artifact to local repository..."
if mvn install:install-file \
-Dfile="$TEMP_DIR/${JAR_FILENAME}" \
-DpomFile="$TEMP_DIR/${POM_FILENAME}" \
-DgroupId=org.hdfgroup \
-DartifactId=${ARTIFACT_ID} \
-Dversion=${VERSION} \
-Dpackaging=jar \
-Dclassifier=${PLATFORM_CLASSIFIER} \
-q; then
log_success "Artifact installed successfully"
else
log_error "Failed to install artifact"
exit 1
fi
else
log_error "Failed to download artifact. Check version and repository URL."
exit 1
# Release version - use standard Maven download
if mvn dependency:get \
-Dartifact=org.hdfgroup:${ARTIFACT_ID}:${VERSION} \
-Dclassifier=${PLATFORM_CLASSIFIER} \
-q; then
log_success "Artifact downloaded successfully"
else
log_error "Failed to download artifact. Check version and repository URL."
exit 1
fi
fi
echo ""
@@ -307,36 +450,118 @@ CLASS_COUNT=$(jar tf "$JAR_PATH" | grep "hdf/hdf5lib.*\.class" | wc -l)
log_info "Found $CLASS_COUNT HDF5 classes in JAR"
echo ""
# Compile examples
log_info "Compiling ${IMPLEMENTATION} examples..."
if mvn compile -f "${BUILD_DIR}/pom-examples.xml"; then
log_success "Examples compiled successfully"
# Compile test example (single known-good example for verification)
log_info "Compiling test example (H5Ex_D_ReadWrite)..."
if mvn compile -f "${BUILD_DIR}/pom-examples.xml" -U; then
log_success "Test example compiled successfully"
else
log_error "Compilation failed"
exit 1
fi
echo ""
# Count compiled example files
COMPILED_COUNT=$(find "${BUILD_DIR}/target/classes" -name "*.class" 2>/dev/null | wc -l)
log_info "Compiled $COMPILED_COUNT example classes"
# Verify compiled example file
if [ -f "${BUILD_DIR}/target/classes/H5Ex_D_ReadWrite.class" ]; then
log_success "Test example class file created"
else
log_warning "Expected class file not found, but compilation succeeded"
fi
echo ""
# Run a test example (change to build directory so .h5 files are created there)
log_info "Running test example: H5Ex_D_ReadWrite..."
if (cd "${BUILD_DIR}" && mvn exec:java -Dexec.mainClass="H5Ex_D_ReadWrite" -f pom-examples.xml -q); then
log_success "Example executed successfully"
# Check for native HDF5 libraries
log_info "Checking for native HDF5 libraries..."
HAVE_NATIVE_LIBS=false
# Check if HDF5 file was created
if [ -f "${BUILD_DIR}/H5Ex_D_ReadWrite.h5" ]; then
log_success "HDF5 file created: ${BUILD_DIR}/H5Ex_D_ReadWrite.h5"
log_info "File size: $(du -h "${BUILD_DIR}/H5Ex_D_ReadWrite.h5" | cut -f1)"
# Check common library locations and HDF5_HOME
if [ -n "${HDF5_HOME:-}" ]; then
log_info "HDF5_HOME is set: ${HDF5_HOME}"
if [ -d "${HDF5_HOME}/lib" ]; then
export LD_LIBRARY_PATH="${HDF5_HOME}/lib:${LD_LIBRARY_PATH:-}"
log_success "Added ${HDF5_HOME}/lib to LD_LIBRARY_PATH"
HAVE_NATIVE_LIBS=true
fi
elif ldconfig -p 2>/dev/null | grep -q "libhdf5.so"; then
log_success "Found libhdf5.so in system libraries"
HAVE_NATIVE_LIBS=true
elif [ -f /usr/lib/x86_64-linux-gnu/libhdf5.so ] || [ -f /usr/lib/libhdf5.so ] || [ -f /usr/local/lib/libhdf5.so ]; then
log_success "Found libhdf5.so in standard location"
HAVE_NATIVE_LIBS=true
else
log_warning "Native HDF5 libraries not found"
log_info "To run examples, install HDF5 libraries or set HDF5_HOME"
log_info " Ubuntu/Debian: sudo apt-get install libhdf5-dev"
log_info " Fedora/RHEL: sudo dnf install hdf5-devel"
log_info " macOS: brew install hdf5"
log_info " Or set: export HDF5_HOME=/path/to/hdf5/installation"
fi
echo ""
# Run comprehensive test examples (change to build directory so .h5 files are created there)
if [ "$HAVE_NATIVE_LIBS" = true ]; then
log_info "Running comprehensive test examples..."
echo ""
# Define test examples covering major HDF5 features
TEST_EXAMPLES=(
# Dataset operations
"H5Ex_D_ReadWrite:Basic dataset read/write"
"H5Ex_D_Chunk:Chunked dataset storage"
"H5Ex_D_Gzip:GZIP compression"
"H5Ex_D_Hyperslab:Hyperslab selection"
"H5Ex_D_Alloc:Dataset allocation"
# Group operations
"H5Ex_G_Create:Group creation"
"H5Ex_G_Iterate:Group iteration"
# Datatype operations
"H5Ex_T_String:String datatype"
"H5Ex_T_Array:Array datatype"
"H5Ex_T_Compound:Compound datatype"
# Tutorials
"HDF5FileCreate:File creation tutorial"
"HDF5DatasetCreate:Dataset creation tutorial"
)
PASSED=0
FAILED=0
FAILED_EXAMPLES=()
for example_spec in "${TEST_EXAMPLES[@]}"; do
IFS=':' read -r example_name description <<< "$example_spec"
printf " Testing %-30s " "$example_name..."
if (cd "${BUILD_DIR}" && mvn exec:java -Dexec.mainClass="$example_name" -f pom-examples.xml -q 2>&1 | grep -v "^\["); then
echo -e "\033[0;32m✓\033[0m $description"
((PASSED++))
else
echo -e "\033[0;31m✗\033[0m $description"
((FAILED++))
FAILED_EXAMPLES+=("$example_name")
fi
done
echo ""
log_info "Test Results: $PASSED passed, $FAILED failed out of ${#TEST_EXAMPLES[@]} tests"
if [ $FAILED -gt 0 ]; then
log_warning "Failed examples:"
for failed in "${FAILED_EXAMPLES[@]}"; do
echo " - $failed"
done
log_warning "Some examples failed, but Maven artifact verification succeeded"
log_info "Failures may be due to optional dependencies (e.g., SZIP, GZIP)"
else
log_warning "HDF5 file not found (may have been deleted by example)"
log_success "All test examples executed successfully!"
fi
# Check for created HDF5 files
H5_COUNT=$(find "${BUILD_DIR}" -name "*.h5" 2>/dev/null | wc -l)
if [ "$H5_COUNT" -gt 0 ]; then
log_success "Created $H5_COUNT HDF5 file(s) in ${BUILD_DIR}"
fi
else
log_error "Example execution failed"
exit 1
log_warning "Skipping execution test - native HDF5 libraries not available"
log_info "Maven artifact download, installation, and compilation verified successfully"
log_info "To test execution, install native HDF5 libraries or set HDF5_HOME"
fi
echo ""
@@ -348,10 +573,14 @@ log_success "All tests passed!"
echo ""
echo "Summary:"
echo " - Artifact: org.hdfgroup:${ARTIFACT_ID}:${VERSION}"
echo " - Platform: ${PLATFORM_CLASSIFIER}"
echo " - JAR Size: $(du -h "$JAR_PATH" | cut -f1)"
echo " - Classes: $CLASS_COUNT HDF5 classes"
echo " - Compiled: $COMPILED_COUNT example classes"
echo " - Execution: H5Ex_D_ReadWrite succeeded"
if [ "$HAVE_NATIVE_LIBS" = true ]; then
echo " - Test: H5Ex_D_ReadWrite compiled and executed successfully"
else
echo " - Test: H5Ex_D_ReadWrite compiled successfully (execution skipped - no native libs)"
fi
echo "============================================"
echo ""
log_info "Build directory: ${BUILD_DIR}"