OMERO-zarr-pixel-buffer-push #21 Changes

build.gradle src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java src/main/java/com/bc/zarr/storage/OmeroFileSystemStore.java src/main/java/org/carlspring/cloud/storage/s3fs/OmeroS3FilesystemProvider.java src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java

d.lindner at 11:11 AM 5/13/26

Drop jzarr, only use zarr-java (v2/v3)

17caebc

build.gradle src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java src/main/java/com/bc/zarr/storage/OmeroFileSystemStore.java src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPath.java src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java src/main/java/org/carlspring/cloud/storage/s3fs/OmeroS3FilesystemProvider.java

d.lindner at 11:12 AM 5/13/26

Fix formatting

92279a4

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

d.lindner at 11:12 AM 5/13/26

Add tests again

57347d7

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelsServiceTest.java src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java

d.lindner at 11:14 AM 5/13/26

Check for ome key in attributes

cd2cb5f

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

d.lindner at 11:14 AM 5/13/26

Fix unsafe cast warnings

146db8a

src/main/java/com/glencoesoftware/omero/zarr/Utils.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

d.lindner at 11:15 AM 5/13/26

Add more info logging

76411f8

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

d.lindner at 11:25 AM 5/13/26

add tests

813c6fa

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java

d.lindner at 11:27 AM 5/13/26

Use UrlConnectionHttpClient instead of apache

f32b393

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

d.lindner at 11:46 AM 5/13/26

fix/add more tests

619866b

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java

d.lindner at 11:48 AM 5/13/26

Add anon s3 test

2589080

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java

d.lindner at 11:49 AM 5/13/26

update zarrjava to 0.1.0

2c10fc9

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

d.lindner at 11:57 AM 5/13/26

relax checkstyle.xml a bit

05882a7

config/checkstyle/checkstyle.xml

d.lindner at 12:11 PM 5/13/26

add deps to build.gradle

dd86948

build.gradle

d.lindner at 12:32 PM 5/13/26

Remove codeql

74f1356

.github/workflows/codeql.yml

d.lindner at 12:55 PM 5/13/26

fix entityID check

ee383a3

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java

d.lindner at 2:12 PM 5/14/26

Do not create a URI from the zarr path

03ac9b2

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 5:41 PM 5/15/26

Manually get query parameters

05bbbd5

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 7:30 PM 5/15/26

add settings.gradle

a44065d

settings.gradle

d.lindner at 2:51 PM 5/21/26

bump version to 0.7.1-SNAPSHOT to distingush from glencoesofware build

7a69fd6

build.gradle

d.lindner at 1:58 PM 5/22/26

Update PixelsService to handle old and new entity IDs

ed145cd

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelsServiceTest.java

kevin at 1:20 PM 5/28/26

Cleanup build.gradle changes

2246d83

build.gradle

kevin at 6:02 PM 6/4/26

Add codeql back

22837b9

.github/workflows/codeql.yml

kevin at 6:04 PM 6/4/26

Rever checkstyle and fix resulting issues

e01c23c

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java config/checkstyle/checkstyle.xml

kevin at 6:14 PM 6/4/26

Add copyrights

a34a85f

src/main/java/com/glencoesoftware/omero/zarr/ZarrPath.java src/main/java/com/glencoesoftware/omero/zarr/Utils.java src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 6:29 PM 6/4/26

Revert compileJava section of build.gradle

48a2596

build.gradle

kevin at 6:56 PM 6/4/26

Add newline at end of build.gradle

0d874f9

build.gradle

kevin at 12:49 PM 6/5/26

Make small changes as per review

ec9971e

src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java build.gradle

kevin at 2:03 PM 6/5/26

Use explicit version numbers

8e06bc4

build.gradle

kevin at 6:01 PM 6/5/26

Create ZarrStore in try block, add Instance Creds support, remove static cred support

c61f154

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java

kevin at 6:56 PM 6/5/26

checkstyle

fbfa684

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 7:10 PM 6/5/26

Use provider chain to allow for default profile

69a0254

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 7:20 PM 6/9/26

Bump version to 0.7.0-rc1

bab417b

build.gradle

sbesson at 7:55 PM 6/10/26

Bump version to 0.7.0-SNAPSHOT

e195bc0

build.gradle

sbesson at 7:56 PM 6/10/26

Handle ? properly

8dd8031

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 7:41 PM 6/29/26

Remove query string pattern from final section of path

7ff7d89

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 8:03 PM 7/2/26

Refactor regex work and add unit tests

a0b29c0

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java src/test/java/com/glencoesoftware/omero/zarr/ZarrStoreTest.java

kevin at 3:45 PM 7/14/26

Remove broken S3 tests until cause is determined

ad03ae1

src/test/java/com/glencoesoftware/omero/zarr/ZarrPixelBufferTest.java

kevin at 4:31 PM 7/14/26

Fix query handling for anonymous and profile

b40d06b

src/test/java/com/glencoesoftware/omero/zarr/ZarrStoreTest.java src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java

kevin at 5:38 PM 7/15/26

Consolidate and improve the utility of the query utility functions

78ea3e5

src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java src/test/java/com/glencoesoftware/omero/zarr/ZarrStoreTest.java

kevin at 7:19 PM 7/17/26

Bump version to 0.7.0-rc2

3108f9c

build.gradle

callan at 2:30 PM 7/20/26

Restore version to 0.7.0-SNAPSHOT

45627b5

build.gradle

callan at 2:36 PM 7/20/26