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Dependency updates #38

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merged 8 commits into from
Jun 27, 2022
Merged

Dependency updates #38

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45ec49f
Bump formats-api to 6.10.0
dgault Jun 9, 2022
feb1492
Remove dependency on commons-io and netty-nio-client
dgault Jun 9, 2022
a195d7c
Remove AWS dependencies
dgault Jun 10, 2022
81f05cb
Merge branch 'main' into dependency-updates
dgault Jun 20, 2022
0b73f24
Reorder formats-api dependency
dgault Jun 23, 2022
0a49867
Add objenesis dependency
dgault Jun 23, 2022
a7942b4
Bump testing in ZarrReader to 6.10
dgault Jun 23, 2022
af893b9
Update location of test files and scope of test dependencies
dgault Jun 23, 2022
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45 changes: 12 additions & 33 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,12 +56,21 @@
</pluginRepositories>

<dependencies>

<dependency>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
<version>6.10.0</version>
</dependency>
<dependency>
<groupId>com.bc.zarr</groupId>
<artifactId>jzarr</artifactId>
<version>0.3.4</version>
</dependency>
<dependency>
<groupId>org.objenesis</groupId>
<artifactId>objenesis</artifactId>
<version>2.5.1</version>
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This is the version shipped in ome-common (via kryo 4.0.2). From mvn dependency:tree -Dverbose it looks like it is conflicting with the version from org.mockito:mockito-inline:3.7.7.

Declaring it in the POM should suffice although I assume an alternative would be to add and exclude in the mockito dependency?

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From a quick discussion with @dgault and @jburel, a possible simpler and more effective option would simply be to declare mockito and testng as test dependencies (via scope). This might suffice to exclude these from the openmicroscopy Ivy resolution and prevent the copying of unnecessary JARs into the lib folder

</dependency>

<dependency>
<groupId>org.mockito</groupId>
Expand All @@ -72,31 +81,10 @@
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<version>6.10</version>
</dependency>

<dependency>
<groupId>software.amazon.awssdk</groupId>
<artifactId>s3</artifactId>
<version>2.13.8</version>
</dependency>
<dependency>
<groupId>software.amazon.awssdk</groupId>
<artifactId>netty-nio-client</artifactId>
<version>2.13.8</version>
</dependency>
<dependency>
<groupId>software.amazon.awssdk</groupId>
<artifactId>sts</artifactId>
<version>2.13.8</version>
</dependency>

<dependency>
<groupId>software.amazon.awssdk</groupId>
<artifactId>bom</artifactId>
<version>2.11.10</version>
<type>pom</type>
</dependency>
<dependency>
<!-- NB: We want this, despite warning from dependency:analyze. -->
<groupId>xalan</groupId>
Expand All @@ -111,16 +99,7 @@
<version>2.7.2</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.8.0</version>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-api</artifactId>
<version>6.7.0</version>
</dependency>



</dependencies>
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263 changes: 0 additions & 263 deletions src/loci/formats/S3FileSystemStore.java
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27 changes: 9 additions & 18 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,18 +32,19 @@

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;

import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;

import org.apache.commons.io.FileUtils;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;

Expand All @@ -62,7 +63,6 @@
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.S3FileSystemStore;
import loci.formats.meta.MetadataStore;
import loci.formats.ome.OMEXMLMetadata;
import loci.formats.services.JZarrServiceImpl;
Expand Down Expand Up @@ -832,22 +832,13 @@ public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
ArrayList<String> usedFiles = new ArrayList<String>();
if (!zarrRootPath.toLowerCase().contains("s3:")) {
File folder = new File(zarrRootPath);
Collection<File> libs = FileUtils.listFiles(folder, null, true);
for (File file : libs) {
if (!file.isDirectory()) {
usedFiles.add(file.getAbsolutePath());
}
}
}
else {
try {
usedFiles.addAll(new S3FileSystemStore(Paths.get(zarrRootPath)).getFiles());
} catch (IOException e) {
e.printStackTrace();
}
try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath))) {
paths.filter(Files::isRegularFile)
.forEach(path -> usedFiles.add(path.toFile().getAbsolutePath()));
} catch (IOException e) {
e.printStackTrace();
}

String[] fileArr = new String[usedFiles.size()];
fileArr = usedFiles.toArray(fileArr);
return fileArr;
Expand Down
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