build(deps): bump bio-formats and maven plugins for 1.2.7
Add Maven Wrapper scripts and wrapper properties for reproducible builds. Update project and documentation version references from 1.2.6 to 1.2.7. Refresh plugin and dependency versions, including Bio-Formats 8.5.0.
This commit is contained in:
+3
@@ -0,0 +1,3 @@
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wrapperVersion=3.3.4
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distributionType=only-script
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distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.11/apache-maven-3.9.11-bin.zip
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Vendored
+19
-2
@@ -7,8 +7,25 @@
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"editor.defaultFormatter": "esbenp.prettier-vscode"
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},
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// Extensions - Code Spell Checker
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"cSpell.ignoreWords": ["endianness", "noflat", "nopix", "omexml"],
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"cSpell.words": ["appassembler", "bioformats", "codehaus", "imageinfo", "neurodata", "riken", "unidata"],
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"cSpell.ignoreWords": [
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"appassembler", //
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"codehaus",
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"Dloci",
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"endianness",
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"noflat",
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"nopix",
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"println"
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],
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"cSpell.words": [
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"bioformats", //
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"DICOM",
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"imageinfo",
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"neurodata",
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"neuroinformatics",
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"omexml",
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"riken",
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"unidata"
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],
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// Extentions - Prettier
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"prettier.printWidth": 120,
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"prettier.singleQuote": true,
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@@ -1,22 +1,22 @@
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# BioFormatsImageInfo
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[](https://www.oracle.com/java/)
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[](https://www.openmicroscopy.org/bio-formats/)
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[](https://www.openmicroscopy.org/bio-formats/)
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BioFormatsImageInfo is a metadata extraction and thumbnail generation tool for biomedical images, based on the [Bio-Formats](https://www.openmicroscopy.org/bio-formats/) library. It supports over 150 image formats and can be used both as a command-line tool and as a Java library.
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## Features
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- **Wide Format Support**: Leverages Bio-Formats' extensive format support
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- **Metadata Extraction**: Outputs detailed image information in JSON format
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- **Thumbnail Generation**: Creates high-quality thumbnail images
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- **Command-Line Ready**: Suitable for batch processing and scripting
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- **Library Integration**: Can be embedded into Java applications
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- **Wide Format Support**: Leverages Bio-Formats' extensive format support
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- **Metadata Extraction**: Outputs detailed image information in JSON format
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- **Thumbnail Generation**: Creates high-quality thumbnail images
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- **Command-Line Ready**: Suitable for batch processing and scripting
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- **Library Integration**: Can be embedded into Java applications
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## Requirements
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- Java 1.8 or higher
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- Maven 3.0 or higher (for building)
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- Java 1.8 or higher
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- Maven 3.6.3 or higher (for building)
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## Installation & Build
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@@ -30,9 +30,9 @@ mvn package
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After the build completes, the following files will be generated:
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- `target/dist/` - Executable distribution
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- `target/bioformats-imageinfo-1.2.6.jar` - Standard JAR file
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- `target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar` - Fat JAR with dependencies
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- `target/dist/` - Executable distribution
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- `target/bioformats-imageinfo-1.2.7.jar` - Standard JAR file
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- `target/bioformats-imageinfo-1.2.7-jar-with-dependencies.jar` - Fat JAR with dependencies
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## Usage
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@@ -47,13 +47,13 @@ After the build completes, the following files will be generated:
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#### Running from JAR File
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```shell
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java -jar ./target/dist/lib/bioformats-imageinfo-1.2.6.jar [OPTION] [path to image file]
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java -jar ./target/dist/lib/bioformats-imageinfo-1.2.7.jar [OPTION] [path to image file]
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```
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#### Running from Fat JAR
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```shell
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java -jar ./target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar [OPTION] [path to image file]
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java -jar ./target/bioformats-imageinfo-1.2.7-jar-with-dependencies.jar [OPTION] [path to image file]
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```
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### Options
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@@ -86,7 +86,7 @@ Example of using as a library in Java applications:
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<dependency>
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<groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
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<artifactId>bioformats-imageinfo</artifactId>
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<version>1.2.6</version>
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<version>1.2.7</version>
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</dependency>
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```
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@@ -128,10 +128,10 @@ try {
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As this tool uses the Bio-Formats library, it supports a wide variety of biomedical image formats including:
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- **Microscopy Images**: LSM, CZI, ND2, OIB, OIF, LIF, etc.
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- **Common Images**: TIFF, JPEG, PNG, BMP, etc.
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- **Medical Images**: DICOM
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- **Others**: Over 150 formats
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- **Microscopy Images**: LSM, CZI, ND2, OIB, OIF, LIF, etc.
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- **Common Images**: TIFF, JPEG, PNG, BMP, etc.
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- **Medical Images**: DICOM
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- **Others**: Over 150 formats
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For detailed format support information, please refer to the [Bio-Formats official website](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html).
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@@ -139,15 +139,15 @@ For detailed format support information, please refer to the [Bio-Formats offici
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### Metadata Output
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- Structured metadata in JSON format
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- Image size, pixel information, acquisition conditions, etc.
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- Detailed information for each series
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- Structured metadata in JSON format
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- Image size, pixel information, acquisition conditions, etc.
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- Detailed information for each series
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### Thumbnail Output
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- Thumbnail images in JPEG format
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- Base64 encoding support for embedding
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- Adjustable quality (default: 85%)
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- Thumbnail images in JPEG format
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- Base64 encoding support for embedding
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- Adjustable quality (default: 85%)
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## License
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@@ -157,8 +157,8 @@ Please refer to the `LICENSE.txt` file for the license of this project.
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Developed by the Neuroinformatics Unit, RIKEN Center for Brain Science. Contributions are welcome via pull requests or issues on the repository.
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- **Developer**: Neuroinformatics Unit, RIKEN Center for Brain Science
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- **Project URL**: https://neurodata.riken.jp
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- **Developer**: Neuroinformatics Unit, RIKEN Center for Brain Science
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- **Project URL**: <https://neurodata.riken.jp>
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## Troubleshooting
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@@ -167,7 +167,7 @@ Developed by the Neuroinformatics Unit, RIKEN Center for Brain Science. Contribu
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1. **Out of Memory Error**
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```shell
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java -Xmx4g -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
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java -Xmx4g -jar bioformats-imageinfo-1.2.7-jar-with-dependencies.jar -M image.tif
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```
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2. **Processing Large Files**
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@@ -183,5 +183,5 @@ Developed by the Neuroinformatics Unit, RIKEN Center for Brain Science. Contribu
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When detailed logs are needed:
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```shell
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java -Dloci.common.DebugTools.enableLogging=true -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
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java -Dloci.common.DebugTools.enableLogging=true -jar bioformats-imageinfo-1.2.7-jar-with-dependencies.jar -M image.tif
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```
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@@ -0,0 +1,295 @@
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#!/bin/sh
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# ----------------------------------------------------------------------------
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# Licensed to the Apache Software Foundation (ASF) under one
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# or more contributor license agreements. See the NOTICE file
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# distributed with this work for additional information
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# regarding copyright ownership. The ASF licenses this file
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# to you under the Apache License, Version 2.0 (the
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# "License"); you may not use this file except in compliance
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# with the License. You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing,
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# software distributed under the License is distributed on an
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# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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# KIND, either express or implied. See the License for the
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# specific language governing permissions and limitations
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# under the License.
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# ----------------------------------------------------------------------------
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# ----------------------------------------------------------------------------
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# Apache Maven Wrapper startup batch script, version 3.3.4
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#
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# Optional ENV vars
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# -----------------
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# JAVA_HOME - location of a JDK home dir, required when download maven via java source
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# MVNW_REPOURL - repo url base for downloading maven distribution
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# MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven
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# MVNW_VERBOSE - true: enable verbose log; debug: trace the mvnw script; others: silence the output
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# ----------------------------------------------------------------------------
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set -euf
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[ "${MVNW_VERBOSE-}" != debug ] || set -x
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# OS specific support.
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native_path() { printf %s\\n "$1"; }
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case "$(uname)" in
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CYGWIN* | MINGW*)
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[ -z "${JAVA_HOME-}" ] || JAVA_HOME="$(cygpath --unix "$JAVA_HOME")"
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native_path() { cygpath --path --windows "$1"; }
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;;
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esac
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# set JAVACMD and JAVACCMD
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set_java_home() {
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# For Cygwin and MinGW, ensure paths are in Unix format before anything is touched
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if [ -n "${JAVA_HOME-}" ]; then
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if [ -x "$JAVA_HOME/jre/sh/java" ]; then
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# IBM's JDK on AIX uses strange locations for the executables
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JAVACMD="$JAVA_HOME/jre/sh/java"
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JAVACCMD="$JAVA_HOME/jre/sh/javac"
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else
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JAVACMD="$JAVA_HOME/bin/java"
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JAVACCMD="$JAVA_HOME/bin/javac"
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if [ ! -x "$JAVACMD" ] || [ ! -x "$JAVACCMD" ]; then
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echo "The JAVA_HOME environment variable is not defined correctly, so mvnw cannot run." >&2
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echo "JAVA_HOME is set to \"$JAVA_HOME\", but \"\$JAVA_HOME/bin/java\" or \"\$JAVA_HOME/bin/javac\" does not exist." >&2
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return 1
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fi
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fi
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else
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JAVACMD="$(
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'set' +e
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'unset' -f command 2>/dev/null
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'command' -v java
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)" || :
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JAVACCMD="$(
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'set' +e
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'unset' -f command 2>/dev/null
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'command' -v javac
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)" || :
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if [ ! -x "${JAVACMD-}" ] || [ ! -x "${JAVACCMD-}" ]; then
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echo "The java/javac command does not exist in PATH nor is JAVA_HOME set, so mvnw cannot run." >&2
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return 1
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fi
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fi
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}
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# hash string like Java String::hashCode
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hash_string() {
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str="${1:-}" h=0
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while [ -n "$str" ]; do
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char="${str%"${str#?}"}"
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h=$(((h * 31 + $(LC_CTYPE=C printf %d "'$char")) % 4294967296))
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str="${str#?}"
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done
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printf %x\\n $h
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}
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verbose() { :; }
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[ "${MVNW_VERBOSE-}" != true ] || verbose() { printf %s\\n "${1-}"; }
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die() {
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printf %s\\n "$1" >&2
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exit 1
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}
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trim() {
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# MWRAPPER-139:
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# Trims trailing and leading whitespace, carriage returns, tabs, and linefeeds.
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# Needed for removing poorly interpreted newline sequences when running in more
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# exotic environments such as mingw bash on Windows.
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printf "%s" "${1}" | tr -d '[:space:]'
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}
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scriptDir="$(dirname "$0")"
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scriptName="$(basename "$0")"
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# parse distributionUrl and optional distributionSha256Sum, requires .mvn/wrapper/maven-wrapper.properties
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while IFS="=" read -r key value; do
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case "${key-}" in
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distributionUrl) distributionUrl=$(trim "${value-}") ;;
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distributionSha256Sum) distributionSha256Sum=$(trim "${value-}") ;;
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esac
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done <"$scriptDir/.mvn/wrapper/maven-wrapper.properties"
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[ -n "${distributionUrl-}" ] || die "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties"
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case "${distributionUrl##*/}" in
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maven-mvnd-*bin.*)
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MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/
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case "${PROCESSOR_ARCHITECTURE-}${PROCESSOR_ARCHITEW6432-}:$(uname -a)" in
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*AMD64:CYGWIN* | *AMD64:MINGW*) distributionPlatform=windows-amd64 ;;
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:Darwin*x86_64) distributionPlatform=darwin-amd64 ;;
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:Darwin*arm64) distributionPlatform=darwin-aarch64 ;;
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:Linux*x86_64*) distributionPlatform=linux-amd64 ;;
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*)
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echo "Cannot detect native platform for mvnd on $(uname)-$(uname -m), use pure java version" >&2
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distributionPlatform=linux-amd64
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;;
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esac
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distributionUrl="${distributionUrl%-bin.*}-$distributionPlatform.zip"
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;;
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maven-mvnd-*) MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ ;;
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*) MVN_CMD="mvn${scriptName#mvnw}" _MVNW_REPO_PATTERN=/org/apache/maven/ ;;
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esac
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# apply MVNW_REPOURL and calculate MAVEN_HOME
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# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-<version>,maven-mvnd-<version>-<platform>}/<hash>
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[ -z "${MVNW_REPOURL-}" ] || distributionUrl="$MVNW_REPOURL$_MVNW_REPO_PATTERN${distributionUrl#*"$_MVNW_REPO_PATTERN"}"
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distributionUrlName="${distributionUrl##*/}"
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distributionUrlNameMain="${distributionUrlName%.*}"
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distributionUrlNameMain="${distributionUrlNameMain%-bin}"
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MAVEN_USER_HOME="${MAVEN_USER_HOME:-${HOME}/.m2}"
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MAVEN_HOME="${MAVEN_USER_HOME}/wrapper/dists/${distributionUrlNameMain-}/$(hash_string "$distributionUrl")"
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exec_maven() {
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unset MVNW_VERBOSE MVNW_USERNAME MVNW_PASSWORD MVNW_REPOURL || :
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exec "$MAVEN_HOME/bin/$MVN_CMD" "$@" || die "cannot exec $MAVEN_HOME/bin/$MVN_CMD"
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}
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if [ -d "$MAVEN_HOME" ]; then
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verbose "found existing MAVEN_HOME at $MAVEN_HOME"
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exec_maven "$@"
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fi
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case "${distributionUrl-}" in
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*?-bin.zip | *?maven-mvnd-?*-?*.zip) ;;
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*) die "distributionUrl is not valid, must match *-bin.zip or maven-mvnd-*.zip, but found '${distributionUrl-}'" ;;
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esac
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# prepare tmp dir
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if TMP_DOWNLOAD_DIR="$(mktemp -d)" && [ -d "$TMP_DOWNLOAD_DIR" ]; then
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clean() { rm -rf -- "$TMP_DOWNLOAD_DIR"; }
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trap clean HUP INT TERM EXIT
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else
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die "cannot create temp dir"
|
||||
fi
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mkdir -p -- "${MAVEN_HOME%/*}"
|
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|
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# Download and Install Apache Maven
|
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verbose "Couldn't find MAVEN_HOME, downloading and installing it ..."
|
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verbose "Downloading from: $distributionUrl"
|
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verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName"
|
||||
|
||||
# select .zip or .tar.gz
|
||||
if ! command -v unzip >/dev/null; then
|
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distributionUrl="${distributionUrl%.zip}.tar.gz"
|
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distributionUrlName="${distributionUrl##*/}"
|
||||
fi
|
||||
|
||||
# verbose opt
|
||||
__MVNW_QUIET_WGET=--quiet __MVNW_QUIET_CURL=--silent __MVNW_QUIET_UNZIP=-q __MVNW_QUIET_TAR=''
|
||||
[ "${MVNW_VERBOSE-}" != true ] || __MVNW_QUIET_WGET='' __MVNW_QUIET_CURL='' __MVNW_QUIET_UNZIP='' __MVNW_QUIET_TAR=v
|
||||
|
||||
# normalize http auth
|
||||
case "${MVNW_PASSWORD:+has-password}" in
|
||||
'') MVNW_USERNAME='' MVNW_PASSWORD='' ;;
|
||||
has-password) [ -n "${MVNW_USERNAME-}" ] || MVNW_USERNAME='' MVNW_PASSWORD='' ;;
|
||||
esac
|
||||
|
||||
if [ -z "${MVNW_USERNAME-}" ] && command -v wget >/dev/null; then
|
||||
verbose "Found wget ... using wget"
|
||||
wget ${__MVNW_QUIET_WGET:+"$__MVNW_QUIET_WGET"} "$distributionUrl" -O "$TMP_DOWNLOAD_DIR/$distributionUrlName" || die "wget: Failed to fetch $distributionUrl"
|
||||
elif [ -z "${MVNW_USERNAME-}" ] && command -v curl >/dev/null; then
|
||||
verbose "Found curl ... using curl"
|
||||
curl ${__MVNW_QUIET_CURL:+"$__MVNW_QUIET_CURL"} -f -L -o "$TMP_DOWNLOAD_DIR/$distributionUrlName" "$distributionUrl" || die "curl: Failed to fetch $distributionUrl"
|
||||
elif set_java_home; then
|
||||
verbose "Falling back to use Java to download"
|
||||
javaSource="$TMP_DOWNLOAD_DIR/Downloader.java"
|
||||
targetZip="$TMP_DOWNLOAD_DIR/$distributionUrlName"
|
||||
cat >"$javaSource" <<-END
|
||||
public class Downloader extends java.net.Authenticator
|
||||
{
|
||||
protected java.net.PasswordAuthentication getPasswordAuthentication()
|
||||
{
|
||||
return new java.net.PasswordAuthentication( System.getenv( "MVNW_USERNAME" ), System.getenv( "MVNW_PASSWORD" ).toCharArray() );
|
||||
}
|
||||
public static void main( String[] args ) throws Exception
|
||||
{
|
||||
setDefault( new Downloader() );
|
||||
java.nio.file.Files.copy( java.net.URI.create( args[0] ).toURL().openStream(), java.nio.file.Paths.get( args[1] ).toAbsolutePath().normalize() );
|
||||
}
|
||||
}
|
||||
END
|
||||
# For Cygwin/MinGW, switch paths to Windows format before running javac and java
|
||||
verbose " - Compiling Downloader.java ..."
|
||||
"$(native_path "$JAVACCMD")" "$(native_path "$javaSource")" || die "Failed to compile Downloader.java"
|
||||
verbose " - Running Downloader.java ..."
|
||||
"$(native_path "$JAVACMD")" -cp "$(native_path "$TMP_DOWNLOAD_DIR")" Downloader "$distributionUrl" "$(native_path "$targetZip")"
|
||||
fi
|
||||
|
||||
# If specified, validate the SHA-256 sum of the Maven distribution zip file
|
||||
if [ -n "${distributionSha256Sum-}" ]; then
|
||||
distributionSha256Result=false
|
||||
if [ "$MVN_CMD" = mvnd.sh ]; then
|
||||
echo "Checksum validation is not supported for maven-mvnd." >&2
|
||||
echo "Please disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2
|
||||
exit 1
|
||||
elif command -v sha256sum >/dev/null; then
|
||||
if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | sha256sum -c - >/dev/null 2>&1; then
|
||||
distributionSha256Result=true
|
||||
fi
|
||||
elif command -v shasum >/dev/null; then
|
||||
if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | shasum -a 256 -c >/dev/null 2>&1; then
|
||||
distributionSha256Result=true
|
||||
fi
|
||||
else
|
||||
echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available." >&2
|
||||
echo "Please install either command, or disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2
|
||||
exit 1
|
||||
fi
|
||||
if [ $distributionSha256Result = false ]; then
|
||||
echo "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised." >&2
|
||||
echo "If you updated your Maven version, you need to update the specified distributionSha256Sum property." >&2
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
|
||||
# unzip and move
|
||||
if command -v unzip >/dev/null; then
|
||||
unzip ${__MVNW_QUIET_UNZIP:+"$__MVNW_QUIET_UNZIP"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -d "$TMP_DOWNLOAD_DIR" || die "failed to unzip"
|
||||
else
|
||||
tar xzf${__MVNW_QUIET_TAR:+"$__MVNW_QUIET_TAR"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -C "$TMP_DOWNLOAD_DIR" || die "failed to untar"
|
||||
fi
|
||||
|
||||
# Find the actual extracted directory name (handles snapshots where filename != directory name)
|
||||
actualDistributionDir=""
|
||||
|
||||
# First try the expected directory name (for regular distributions)
|
||||
if [ -d "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" ]; then
|
||||
if [ -f "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain/bin/$MVN_CMD" ]; then
|
||||
actualDistributionDir="$distributionUrlNameMain"
|
||||
fi
|
||||
fi
|
||||
|
||||
# If not found, search for any directory with the Maven executable (for snapshots)
|
||||
if [ -z "$actualDistributionDir" ]; then
|
||||
# enable globbing to iterate over items
|
||||
set +f
|
||||
for dir in "$TMP_DOWNLOAD_DIR"/*; do
|
||||
if [ -d "$dir" ]; then
|
||||
if [ -f "$dir/bin/$MVN_CMD" ]; then
|
||||
actualDistributionDir="$(basename "$dir")"
|
||||
break
|
||||
fi
|
||||
fi
|
||||
done
|
||||
set -f
|
||||
fi
|
||||
|
||||
if [ -z "$actualDistributionDir" ]; then
|
||||
verbose "Contents of $TMP_DOWNLOAD_DIR:"
|
||||
verbose "$(ls -la "$TMP_DOWNLOAD_DIR")"
|
||||
die "Could not find Maven distribution directory in extracted archive"
|
||||
fi
|
||||
|
||||
verbose "Found extracted Maven distribution directory: $actualDistributionDir"
|
||||
printf %s\\n "$distributionUrl" >"$TMP_DOWNLOAD_DIR/$actualDistributionDir/mvnw.url"
|
||||
mv -- "$TMP_DOWNLOAD_DIR/$actualDistributionDir" "$MAVEN_HOME" || [ -d "$MAVEN_HOME" ] || die "fail to move MAVEN_HOME"
|
||||
|
||||
clean || :
|
||||
exec_maven "$@"
|
||||
@@ -0,0 +1,189 @@
|
||||
<# : batch portion
|
||||
@REM ----------------------------------------------------------------------------
|
||||
@REM Licensed to the Apache Software Foundation (ASF) under one
|
||||
@REM or more contributor license agreements. See the NOTICE file
|
||||
@REM distributed with this work for additional information
|
||||
@REM regarding copyright ownership. The ASF licenses this file
|
||||
@REM to you under the Apache License, Version 2.0 (the
|
||||
@REM "License"); you may not use this file except in compliance
|
||||
@REM with the License. You may obtain a copy of the License at
|
||||
@REM
|
||||
@REM http://www.apache.org/licenses/LICENSE-2.0
|
||||
@REM
|
||||
@REM Unless required by applicable law or agreed to in writing,
|
||||
@REM software distributed under the License is distributed on an
|
||||
@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
|
||||
@REM KIND, either express or implied. See the License for the
|
||||
@REM specific language governing permissions and limitations
|
||||
@REM under the License.
|
||||
@REM ----------------------------------------------------------------------------
|
||||
|
||||
@REM ----------------------------------------------------------------------------
|
||||
@REM Apache Maven Wrapper startup batch script, version 3.3.4
|
||||
@REM
|
||||
@REM Optional ENV vars
|
||||
@REM MVNW_REPOURL - repo url base for downloading maven distribution
|
||||
@REM MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven
|
||||
@REM MVNW_VERBOSE - true: enable verbose log; others: silence the output
|
||||
@REM ----------------------------------------------------------------------------
|
||||
|
||||
@IF "%__MVNW_ARG0_NAME__%"=="" (SET __MVNW_ARG0_NAME__=%~nx0)
|
||||
@SET __MVNW_CMD__=
|
||||
@SET __MVNW_ERROR__=
|
||||
@SET __MVNW_PSMODULEP_SAVE=%PSModulePath%
|
||||
@SET PSModulePath=
|
||||
@FOR /F "usebackq tokens=1* delims==" %%A IN (`powershell -noprofile "& {$scriptDir='%~dp0'; $script='%__MVNW_ARG0_NAME__%'; icm -ScriptBlock ([Scriptblock]::Create((Get-Content -Raw '%~f0'))) -NoNewScope}"`) DO @(
|
||||
IF "%%A"=="MVN_CMD" (set __MVNW_CMD__=%%B) ELSE IF "%%B"=="" (echo %%A) ELSE (echo %%A=%%B)
|
||||
)
|
||||
@SET PSModulePath=%__MVNW_PSMODULEP_SAVE%
|
||||
@SET __MVNW_PSMODULEP_SAVE=
|
||||
@SET __MVNW_ARG0_NAME__=
|
||||
@SET MVNW_USERNAME=
|
||||
@SET MVNW_PASSWORD=
|
||||
@IF NOT "%__MVNW_CMD__%"=="" ("%__MVNW_CMD__%" %*)
|
||||
@echo Cannot start maven from wrapper >&2 && exit /b 1
|
||||
@GOTO :EOF
|
||||
: end batch / begin powershell #>
|
||||
|
||||
$ErrorActionPreference = "Stop"
|
||||
if ($env:MVNW_VERBOSE -eq "true") {
|
||||
$VerbosePreference = "Continue"
|
||||
}
|
||||
|
||||
# calculate distributionUrl, requires .mvn/wrapper/maven-wrapper.properties
|
||||
$distributionUrl = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionUrl
|
||||
if (!$distributionUrl) {
|
||||
Write-Error "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties"
|
||||
}
|
||||
|
||||
switch -wildcard -casesensitive ( $($distributionUrl -replace '^.*/','') ) {
|
||||
"maven-mvnd-*" {
|
||||
$USE_MVND = $true
|
||||
$distributionUrl = $distributionUrl -replace '-bin\.[^.]*$',"-windows-amd64.zip"
|
||||
$MVN_CMD = "mvnd.cmd"
|
||||
break
|
||||
}
|
||||
default {
|
||||
$USE_MVND = $false
|
||||
$MVN_CMD = $script -replace '^mvnw','mvn'
|
||||
break
|
||||
}
|
||||
}
|
||||
|
||||
# apply MVNW_REPOURL and calculate MAVEN_HOME
|
||||
# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-<version>,maven-mvnd-<version>-<platform>}/<hash>
|
||||
if ($env:MVNW_REPOURL) {
|
||||
$MVNW_REPO_PATTERN = if ($USE_MVND -eq $False) { "/org/apache/maven/" } else { "/maven/mvnd/" }
|
||||
$distributionUrl = "$env:MVNW_REPOURL$MVNW_REPO_PATTERN$($distributionUrl -replace "^.*$MVNW_REPO_PATTERN",'')"
|
||||
}
|
||||
$distributionUrlName = $distributionUrl -replace '^.*/',''
|
||||
$distributionUrlNameMain = $distributionUrlName -replace '\.[^.]*$','' -replace '-bin$',''
|
||||
|
||||
$MAVEN_M2_PATH = "$HOME/.m2"
|
||||
if ($env:MAVEN_USER_HOME) {
|
||||
$MAVEN_M2_PATH = "$env:MAVEN_USER_HOME"
|
||||
}
|
||||
|
||||
if (-not (Test-Path -Path $MAVEN_M2_PATH)) {
|
||||
New-Item -Path $MAVEN_M2_PATH -ItemType Directory | Out-Null
|
||||
}
|
||||
|
||||
$MAVEN_WRAPPER_DISTS = $null
|
||||
if ((Get-Item $MAVEN_M2_PATH).Target[0] -eq $null) {
|
||||
$MAVEN_WRAPPER_DISTS = "$MAVEN_M2_PATH/wrapper/dists"
|
||||
} else {
|
||||
$MAVEN_WRAPPER_DISTS = (Get-Item $MAVEN_M2_PATH).Target[0] + "/wrapper/dists"
|
||||
}
|
||||
|
||||
$MAVEN_HOME_PARENT = "$MAVEN_WRAPPER_DISTS/$distributionUrlNameMain"
|
||||
$MAVEN_HOME_NAME = ([System.Security.Cryptography.SHA256]::Create().ComputeHash([byte[]][char[]]$distributionUrl) | ForEach-Object {$_.ToString("x2")}) -join ''
|
||||
$MAVEN_HOME = "$MAVEN_HOME_PARENT/$MAVEN_HOME_NAME"
|
||||
|
||||
if (Test-Path -Path "$MAVEN_HOME" -PathType Container) {
|
||||
Write-Verbose "found existing MAVEN_HOME at $MAVEN_HOME"
|
||||
Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD"
|
||||
exit $?
|
||||
}
|
||||
|
||||
if (! $distributionUrlNameMain -or ($distributionUrlName -eq $distributionUrlNameMain)) {
|
||||
Write-Error "distributionUrl is not valid, must end with *-bin.zip, but found $distributionUrl"
|
||||
}
|
||||
|
||||
# prepare tmp dir
|
||||
$TMP_DOWNLOAD_DIR_HOLDER = New-TemporaryFile
|
||||
$TMP_DOWNLOAD_DIR = New-Item -Itemtype Directory -Path "$TMP_DOWNLOAD_DIR_HOLDER.dir"
|
||||
$TMP_DOWNLOAD_DIR_HOLDER.Delete() | Out-Null
|
||||
trap {
|
||||
if ($TMP_DOWNLOAD_DIR.Exists) {
|
||||
try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null }
|
||||
catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" }
|
||||
}
|
||||
}
|
||||
|
||||
New-Item -Itemtype Directory -Path "$MAVEN_HOME_PARENT" -Force | Out-Null
|
||||
|
||||
# Download and Install Apache Maven
|
||||
Write-Verbose "Couldn't find MAVEN_HOME, downloading and installing it ..."
|
||||
Write-Verbose "Downloading from: $distributionUrl"
|
||||
Write-Verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName"
|
||||
|
||||
$webclient = New-Object System.Net.WebClient
|
||||
if ($env:MVNW_USERNAME -and $env:MVNW_PASSWORD) {
|
||||
$webclient.Credentials = New-Object System.Net.NetworkCredential($env:MVNW_USERNAME, $env:MVNW_PASSWORD)
|
||||
}
|
||||
[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
|
||||
$webclient.DownloadFile($distributionUrl, "$TMP_DOWNLOAD_DIR/$distributionUrlName") | Out-Null
|
||||
|
||||
# If specified, validate the SHA-256 sum of the Maven distribution zip file
|
||||
$distributionSha256Sum = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionSha256Sum
|
||||
if ($distributionSha256Sum) {
|
||||
if ($USE_MVND) {
|
||||
Write-Error "Checksum validation is not supported for maven-mvnd. `nPlease disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties."
|
||||
}
|
||||
Import-Module $PSHOME\Modules\Microsoft.PowerShell.Utility -Function Get-FileHash
|
||||
if ((Get-FileHash "$TMP_DOWNLOAD_DIR/$distributionUrlName" -Algorithm SHA256).Hash.ToLower() -ne $distributionSha256Sum) {
|
||||
Write-Error "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised. If you updated your Maven version, you need to update the specified distributionSha256Sum property."
|
||||
}
|
||||
}
|
||||
|
||||
# unzip and move
|
||||
Expand-Archive "$TMP_DOWNLOAD_DIR/$distributionUrlName" -DestinationPath "$TMP_DOWNLOAD_DIR" | Out-Null
|
||||
|
||||
# Find the actual extracted directory name (handles snapshots where filename != directory name)
|
||||
$actualDistributionDir = ""
|
||||
|
||||
# First try the expected directory name (for regular distributions)
|
||||
$expectedPath = Join-Path "$TMP_DOWNLOAD_DIR" "$distributionUrlNameMain"
|
||||
$expectedMvnPath = Join-Path "$expectedPath" "bin/$MVN_CMD"
|
||||
if ((Test-Path -Path $expectedPath -PathType Container) -and (Test-Path -Path $expectedMvnPath -PathType Leaf)) {
|
||||
$actualDistributionDir = $distributionUrlNameMain
|
||||
}
|
||||
|
||||
# If not found, search for any directory with the Maven executable (for snapshots)
|
||||
if (!$actualDistributionDir) {
|
||||
Get-ChildItem -Path "$TMP_DOWNLOAD_DIR" -Directory | ForEach-Object {
|
||||
$testPath = Join-Path $_.FullName "bin/$MVN_CMD"
|
||||
if (Test-Path -Path $testPath -PathType Leaf) {
|
||||
$actualDistributionDir = $_.Name
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (!$actualDistributionDir) {
|
||||
Write-Error "Could not find Maven distribution directory in extracted archive"
|
||||
}
|
||||
|
||||
Write-Verbose "Found extracted Maven distribution directory: $actualDistributionDir"
|
||||
Rename-Item -Path "$TMP_DOWNLOAD_DIR/$actualDistributionDir" -NewName $MAVEN_HOME_NAME | Out-Null
|
||||
try {
|
||||
Move-Item -Path "$TMP_DOWNLOAD_DIR/$MAVEN_HOME_NAME" -Destination $MAVEN_HOME_PARENT | Out-Null
|
||||
} catch {
|
||||
if (! (Test-Path -Path "$MAVEN_HOME" -PathType Container)) {
|
||||
Write-Error "fail to move MAVEN_HOME"
|
||||
}
|
||||
} finally {
|
||||
try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null }
|
||||
catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" }
|
||||
}
|
||||
|
||||
Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD"
|
||||
@@ -5,13 +5,13 @@
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
|
||||
<artifactId>bioformats-imageinfo</artifactId>
|
||||
<version>1.2.6</version>
|
||||
<version>1.2.7</version>
|
||||
|
||||
<name>bioformats-imageinfo</name>
|
||||
<url>https://neurodata.riken.jp</url>
|
||||
|
||||
<properties>
|
||||
<bio-formats.version>8.3.0</bio-formats.version>
|
||||
<bio-formats.version>8.5.0</bio-formats.version>
|
||||
<bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
|
||||
|
||||
<java.version>1.8</java.version>
|
||||
@@ -40,7 +40,7 @@
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-enforcer-plugin</artifactId>
|
||||
<version>3.6.2</version>
|
||||
<version>3.6.3</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>enforce-maven</id>
|
||||
@@ -60,7 +60,7 @@
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<version>3.9.0</version>
|
||||
<version>3.11.0</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-dependencies</id>
|
||||
@@ -77,7 +77,7 @@
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<version>3.4.2</version>
|
||||
<version>3.5.0</version>
|
||||
<configuration>
|
||||
<archive>
|
||||
<manifest>
|
||||
@@ -114,7 +114,7 @@
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<version>3.7.1</version>
|
||||
<version>3.8.0</version>
|
||||
<configuration>
|
||||
<descriptorRefs>
|
||||
<descriptorRef>jar-with-dependencies</descriptorRef>
|
||||
@@ -141,7 +141,7 @@
|
||||
<plugin>
|
||||
<groupId>org.owasp</groupId>
|
||||
<artifactId>dependency-check-maven</artifactId>
|
||||
<version>12.1.8</version>
|
||||
<version>12.2.2</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<goals>
|
||||
|
||||
Reference in New Issue
Block a user