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Update to new jzarr 0.4.2 #203

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merged 7 commits into from
Nov 15, 2023
Merged

Update to new jzarr 0.4.2 #203

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8f3a245
Switch to dev.jzarr:jzarr 0.3.7
melissalinkert May 19, 2023
1737cea
Remove GS jzarr repos
melissalinkert May 19, 2023
08d28f9
Remove one more unneeded repository
melissalinkert May 19, 2023
94c8ead
Update to dev.jzarr:jzarr 0.4.0
melissalinkert Jun 28, 2023
321f268
Update test to use ZarrArray.getDimensionSeparator()
melissalinkert Sep 22, 2023
609f092
Update test comment to reflect changes in jzarr 0.4.0
melissalinkert Sep 25, 2023
a4bb062
Update to jzarr 0.4.2
melissalinkert Oct 31, 2023
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11 changes: 1 addition & 10 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -18,21 +18,12 @@ repositories {
maven {
url 'https://artifacts.glencoesoftware.com/artifactory/ome.releases'
}
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'
Expand All @@ -49,7 +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 'com.bc.zarr:jzarr:0.3.5'
implementation 'dev.zarr:jzarr:0.4.0'
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// 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'
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7 changes: 3 additions & 4 deletions src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -267,10 +268,8 @@ 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
assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());
// check that the correct separator was used
assertEquals(series0.getDimensionSeparator(), DimensionSeparator.SLASH);

// Also ensure we're using the latest .zarray metadata
ObjectMapper objectMapper = new ObjectMapper();
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