From 8f3a24508af3adb7c81ed893f1ec4ab1577d2094 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Fri, 19 May 2023 11:29:45 -0500 Subject: [PATCH 1/7] Switch to dev.jzarr:jzarr 0.3.7 This is the latest release based on https://github.com/zarr-developers/jzarr. --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 31934b7..b70d77a 100644 --- a/build.gradle +++ b/build.gradle @@ -49,7 +49,7 @@ dependencies { implementation 'ome:formats-gpl:6.13.0' implementation 'info.picocli:picocli:4.6.1' implementation 'com.univocity:univocity-parsers:2.8.4' - implementation 'com.bc.zarr:jzarr:0.3.5' + implementation 'dev.zarr:jzarr:0.3.7' // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT' // implementation 'io.nextflow:nxf-s3fs:1.1.0' implementation 'org.lasersonlab:s3fs:2.2.3' From 1737ceafec9a28e06095565c63dc0a0a13363a05 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Fri, 19 May 2023 11:31:09 -0500 Subject: [PATCH 2/7] Remove GS jzarr repos dev.jzarr:jzarr is in Maven central. --- build.gradle | 6 ------ 1 file changed, 6 deletions(-) diff --git a/build.gradle b/build.gradle index b70d77a..2067c5c 100644 --- a/build.gradle +++ b/build.gradle @@ -21,18 +21,12 @@ repositories { maven { url 'https://repo.glencoesoftware.com/repository/n5-zarr-snapshots/' } - maven { - url 'https://repo.glencoesoftware.com/repository/jzarr-snapshots' - } maven { url 'https://artifacts.glencoesoftware.com/artifactory/ome.external' } maven { url 'https://artifacts.glencoesoftware.com/artifactory/scijava-thirdparty' } - maven { - url 'https://artifacts.glencoesoftware.com/artifactory/jzarr-releases' - } maven { name 'Unidata' url 'https://artifacts.glencoesoftware.com/artifactory/unidata-releases' From 08d28f9f11e9357fb63f6aed9aa46ad2b934f1c6 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Fri, 19 May 2023 11:44:41 -0500 Subject: [PATCH 3/7] Remove one more unneeded repository --- build.gradle | 3 --- 1 file changed, 3 deletions(-) diff --git a/build.gradle b/build.gradle index 2067c5c..c291407 100644 --- a/build.gradle +++ b/build.gradle @@ -18,9 +18,6 @@ repositories { maven { url 'https://artifacts.glencoesoftware.com/artifactory/ome.releases' } - maven { - url 'https://repo.glencoesoftware.com/repository/n5-zarr-snapshots/' - } maven { url 'https://artifacts.glencoesoftware.com/artifactory/ome.external' } From 94c8ead04eef217a98d7956e65cabb59c657f7a3 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Wed, 28 Jun 2023 11:02:15 -0500 Subject: [PATCH 4/7] Update to dev.jzarr:jzarr 0.4.0 --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index c291407..52d809f 100644 --- a/build.gradle +++ b/build.gradle @@ -40,7 +40,7 @@ dependencies { implementation 'ome:formats-gpl:6.13.0' implementation 'info.picocli:picocli:4.6.1' implementation 'com.univocity:univocity-parsers:2.8.4' - implementation 'dev.zarr:jzarr:0.3.7' + implementation 'dev.zarr:jzarr:0.4.0' // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT' // implementation 'io.nextflow:nxf-s3fs:1.1.0' implementation 'org.lasersonlab:s3fs:2.2.3' From 321f268e88f887618c75e0929cb9302cc91b6a83 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Fri, 22 Sep 2023 10:34:39 -0500 Subject: [PATCH 5/7] Update test to use ZarrArray.getDimensionSeparator() --- .../java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java index 3acdb19..19f7aad 100644 --- a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java +++ b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java @@ -24,6 +24,7 @@ import java.util.stream.Stream; import com.bc.zarr.DataType; +import com.bc.zarr.DimensionSeparator; import com.bc.zarr.ZarrArray; import com.bc.zarr.ZarrGroup; import com.fasterxml.jackson.databind.JsonNode; @@ -270,7 +271,7 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception { // no getter for DimensionSeparator in ZarrArray // check that the correct separator was used by checking // that the expected first chunk file exists - assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists()); + assertEquals(series0.getDimensionSeparator(), DimensionSeparator.SLASH); // Also ensure we're using the latest .zarray metadata ObjectMapper objectMapper = new ObjectMapper(); From 609f092c171d3275521903283452a8c63091f455 Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Mon, 25 Sep 2023 09:47:30 -0500 Subject: [PATCH 6/7] Update test comment to reflect changes in jzarr 0.4.0 --- .../com/glencoesoftware/bioformats2raw/test/ZarrTest.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java index 19f7aad..b5b076a 100644 --- a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java +++ b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java @@ -268,9 +268,7 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception { ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0"); - // no getter for DimensionSeparator in ZarrArray - // check that the correct separator was used by checking - // that the expected first chunk file exists + // check that the correct separator was used assertEquals(series0.getDimensionSeparator(), DimensionSeparator.SLASH); // Also ensure we're using the latest .zarray metadata From a4bb062637271e13fdaed70ddc2b7ee61c6e6b9a Mon Sep 17 00:00:00 2001 From: Melissa Linkert Date: Tue, 31 Oct 2023 09:42:34 -0500 Subject: [PATCH 7/7] Update to jzarr 0.4.2 --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 52d809f..2bcad87 100644 --- a/build.gradle +++ b/build.gradle @@ -40,7 +40,7 @@ dependencies { implementation 'ome:formats-gpl:6.13.0' implementation 'info.picocli:picocli:4.6.1' implementation 'com.univocity:univocity-parsers:2.8.4' - implementation 'dev.zarr:jzarr:0.4.0' + implementation 'dev.zarr:jzarr:0.4.2' // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT' // implementation 'io.nextflow:nxf-s3fs:1.1.0' implementation 'org.lasersonlab:s3fs:2.2.3'