Set wildcard classpath on Windows

[melissalinkert]

Fixes #14.

This worked for me on Windows. Without this PR, built and unzipped bioformats2raw-0.7.0-SNAPSHOT.zip, then:

> mv bioformats2raw-0.7.0-SNAPSHOT C:\Users\melissa\data\long-path-name-test\
> cd C:\Users\melissa\data\long-path-name-test\bioformats2raw-0.7.0-SNAPSHOT
> .\bin\bioformats2raw.bat test.fake test.zarr --compression null
The input line is too long.
The syntax of the command is incorrect.

With this PR, the same test should successfully create test.zarr.

If we're happy with this approach, raw2ometiff can get the same fix.

/cc @jburel

[sbesson]

Comparing this to the artifact built with this PR from the ones build from HEAD

(base) sbesson@Sebastiens-MacBook-Pro-2 Downloads % diff -ur bioformats2raw-0.7.0-SNAPSHOT bioformats2raw-0.7.0-SNAPSHOT\ 2
diff -ur bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw.bat bioformats2raw-0.7.0-SNAPSHOT 2/bin/bioformats2raw.bat
--- bioformats2raw-0.7.0-SNAPSHOT/bin/bioformats2raw.bat	2023-04-24 14:26:32
+++ bioformats2raw-0.7.0-SNAPSHOT 2/bin/bioformats2raw.bat	2023-05-15 16:09:58
@@ -67,7 +67,7 @@
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\lib\bioformats2raw-0.7.0-SNAPSHOT.jar;%APP_HOME%\lib\jzarr-0.3.5.jar;%APP_HOME%\lib\jblosc-1.0.1.jar;%APP_HOME%\lib\jna-5.10.0.jar;%APP_HOME%\lib\formats-gpl-6.12.0.jar;%APP_HOME%\lib\picocli-4.6.1.jar;%APP_HOME%\lib\univocity-parsers-2.8.4.jar;%APP_HOME%\lib\s3fs-2.2.3.jar;%APP_HOME%\lib\jaxb-api-2.3.0.jar;%APP_HOME%\lib\logback-classic-1.3.4.jar;%APP_HOME%\lib\logback-core-1.3.4.jar;%APP_HOME%\lib\opencv-3.4.2-1.jar;%APP_HOME%\lib\progressbar-0.9.0.jar;%APP_HOME%\lib\formats-bsd-6.12.0.jar;%APP_HOME%\lib\formats-api-6.12.0.jar;%APP_HOME%\lib\ome-xml-6.3.2.jar;%APP_HOME%\lib\metakit-5.3.5.jar;%APP_HOME%\lib\ome-poi-5.3.7.jar;%APP_HOME%\lib\ome-codecs-0.4.4.jar;%APP_HOME%\lib\ome-common-6.0.14.jar;%APP_HOME%\lib\ome-mdbtools-5.3.2.jar;%APP_HOME%\lib\cdm-core-5.3.3.jar;%APP_HOME%\lib\jcl-over-slf4j-1.7.5.jar;%APP_HOME%\lib\jxrlib-all-0.2.4.jar;%APP_HOME%\lib\native-lib-loader-2.1.4.jar;%APP_HOME%\lib\udunits-5.3.3.jar;%APP_HOME%\lib\httpservices-5.3.3.jar;%APP_HOME%\lib\slf4j-api-2.0.1.jar;%APP_HOME%\lib\JWlz-1.4.0.jar;%APP_HOME%\lib\minio-5.0.2.jar;%APP_HOME%\lib\aws-java-sdk-s3-1.11.232.jar;%APP_HOME%\lib\aws-java-sdk-kms-1.11.232.jar;%APP_HOME%\lib\aws-java-sdk-core-1.11.232.jar;%APP_HOME%\lib\joda-time-2.10.3.jar;%APP_HOME%\lib\kryo-4.0.2.jar;%APP_HOME%\lib\json-20090211.jar;%APP_HOME%\lib\sqlite-jdbc-3.28.0.jar;%APP_HOME%\lib\jmespath-java-1.11.232.jar;%APP_HOME%\lib\jackson-annotations-2.14.1.jar;%APP_HOME%\lib\jackson-dataformat-cbor-2.14.1.jar;%APP_HOME%\lib\jackson-core-2.14.1.jar;%APP_HOME%\lib\jackson-databind-2.14.1.jar;%APP_HOME%\lib\guava-29.0-jre.jar;%APP_HOME%\lib\tika-core-1.5.jar;%APP_HOME%\lib\jsr305-3.0.2.jar;%APP_HOME%\lib\javax.mail-1.6.2.jar;%APP_HOME%\lib\jline-3.16.0.jar;%APP_HOME%\lib\xalan-2.7.2.jar;%APP_HOME%\lib\serializer-2.7.2.jar;%APP_HOME%\lib\specification-6.3.2.jar;%APP_HOME%\lib\turbojpeg-6.12.0.jar;%APP_HOME%\lib\jgoodies-forms-1.7.2.jar;%APP_HOME%\lib\commons-lang-2.6.jar;%APP_HOME%\lib\perf4j-0.9.16.jar;%APP_HOME%\lib\jhdf5-19.04.0.jar;%APP_HOME%\lib\metadata-extractor-2.18.0.jar;%APP_HOME%\lib\xercesImpl-2.12.2.jar;%APP_HOME%\lib\xml-apis-1.4.01.jar;%APP_HOME%\lib\snakeyaml-1.32.jar;%APP_HOME%\lib\httpmime-4.5.9.jar;%APP_HOME%\lib\google-http-client-xml-1.20.0.jar;%APP_HOME%\lib\google-http-client-1.20.0.jar;%APP_HOME%\lib\httpclient-4.5.9.jar;%APP_HOME%\lib\commons-logging-1.2.jar;%APP_HOME%\lib\jdom2-2.0.6.jar;%APP_HOME%\lib\protobuf-java-3.9.1.jar;%APP_HOME%\lib\jcommander-1.78.jar;%APP_HOME%\lib\httpcore-4.4.11.jar;%APP_HOME%\lib\re2j-1.3.jar;%APP_HOME%\lib\reflectasm-1.11.3.jar;%APP_HOME%\lib\minlog-1.3.0.jar;%APP_HOME%\lib\objenesis-2.5.1.jar;%APP_HOME%\lib\junit-4.12.jar;%APP_HOME%\lib\activation-1.1.jar;%APP_HOME%\lib\failureaccess-1.0.1.jar;%APP_HOME%\lib\listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar;%APP_HOME%\lib\checker-qual-2.11.1.jar;%APP_HOME%\lib\error_prone_annotations-2.3.4.jar;%APP_HOME%\lib\j2objc-annotations-1.3.jar;%APP_HOME%\lib\okhttp-3.7.0.jar;%APP_HOME%\lib\okio-1.12.0.jar;%APP_HOME%\lib\ome-jai-0.1.3.jar;%APP_HOME%\lib\aircompressor-0.21.jar;%APP_HOME%\lib\jgoodies-common-1.7.0.jar;%APP_HOME%\lib\base-18.09.0.jar;%APP_HOME%\lib\commons-io-2.7.jar;%APP_HOME%\lib\commons-lang3-3.10.jar;%APP_HOME%\lib\xmpcore-6.1.11.jar;%APP_HOME%\lib\asm-5.0.4.jar;%APP_HOME%\lib\hamcrest-core-1.3.jar;%APP_HOME%\lib\ion-java-1.0.2.jar;%APP_HOME%\lib\xpp3-1.1.4c.jar;%APP_HOME%\lib\commons-codec-1.11.jar;%APP_HOME%\lib\config
+set CLASSPATH=.;%APP_HOME%/lib/*
 
 
 @rem Execute bioformats2raw
Binary files bioformats2raw-0.7.0-SNAPSHOT/lib/bioformats2raw-0.7.0-SNAPSHOT.jar and bioformats2raw-0.7.0-SNAPSHOT 2/lib/bioformats2raw-0.7.0-SNAPSHOT.jar differ

This looks inline with the patch applied in https://github.com/ome/conda-bioformats2raw/blob/master/bioformats2raw/windows-bat-classpath-wildcard.patch. Only immediate question is whether using a forward slash rather than a backwards slash might cause problems under some Windows environments?

[melissalinkert]

I'm fairly certain a forward-slash in this case wouldn't be a problem in any modern Windows environment, but 916a0e0 switches to backslashes for completeness.

[muhanadz]

Without PR:

PS C:\Users\Muhan\Documents\bioformats2raw> & "C:\Users\Muhan\Downloads\bioformats2raw-0.7.0-SNAPSHOT (1)\bioformats2raw-0.7.0-SNAPSHOT\bin\bioformats2raw.bat" "C:\Users\Muhan\Documents\bioformats2raw\realy_long_file_name_for_testing_purposes_only_and_for_fun\test.fake" test2.zarr --compression null
The input line is too long.
The syntax of the command is incorrect.

With PR:

PS C:\Users\Muhan\Documents\bioformats2raw> & "C:\Users\Muhan\Documents\bioformats2raw\realy_long_file_name_for_testing_purposes_only_and_for_fun\bioformats2raw-0.7.0-SNAPSHOT\bin\bioformats2raw.bat" "C:\Users\Muhan\Documents\bioformats2raw\realy_long_file_name_for_testing_purposes_only_and_for_fun\test.fake" test.zarr --compression null

LGTM