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Remove S3 handling #108

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7cc04b9
Remove S3 handling
dominikl Nov 6, 2025
018efa4
add jackson dep again
dominikl May 12, 2026
7605d6d
remove location-server
dominikl Jun 16, 2026
4a1461b
clean up pom.xml
dominikl Jun 16, 2026
96b8c16
remove URLType
dominikl Jun 16, 2026
25c43aa
remove unused code
dominikl Jun 16, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
.vscode
.DS_Store
target
.idea
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5 changes: 0 additions & 5 deletions location-server/.gitignore
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This file was deleted.

34 changes: 0 additions & 34 deletions location-server/start-location.sh
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44 changes: 0 additions & 44 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -87,51 +87,11 @@
</ciManagement>

<dependencies>
<dependency>
<groupId>io.minio</groupId>
<artifactId>minio</artifactId>
<version>5.0.2</version>
<exclusions>
<exclusion>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</exclusion>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>

@sbesson sbesson Jun 18, 2026

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Is there a reason to keep jackson-databind?

<version>2.14.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>2.14.2</version>
</dependency>
<dependency>
<groupId>com.esotericsoftware</groupId>
<artifactId>kryo</artifactId>
Expand Down Expand Up @@ -260,10 +220,6 @@
<suiteXmlFiles>
<suiteXmlFile>src/test/java/loci/common/utests/testng-template.xml</suiteXmlFile>
</suiteXmlFiles>
<systemPropertyVariables>
<testng.runHttpRemoteTests>0</testng.runHttpRemoteTests>
<testng.runS3RemoteTests>0</testng.runS3RemoteTests>
</systemPropertyVariables>
</configuration>
</plugin>

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1 change: 0 additions & 1 deletion src/main/java/loci/common/CaseInsensitiveLocation.java
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Expand Up @@ -35,7 +35,6 @@
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;

/**
* Case insensitive variant of Location.
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2 changes: 0 additions & 2 deletions src/main/java/loci/common/DateTools.java
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Expand Up @@ -32,8 +32,6 @@

package loci.common;

import java.text.FieldPosition;
import java.text.ParsePosition;
import java.util.Locale;

import org.joda.time.DateTime;
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78 changes: 6 additions & 72 deletions src/main/java/loci/common/Location.java
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Expand Up @@ -37,7 +37,6 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UncheckedIOException;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
Expand Down Expand Up @@ -68,12 +67,6 @@ public class Location {
private static final boolean IS_WINDOWS =
System.getProperty("os.name").startsWith("Windows");

// -- Enumerations --
protected enum UrlType {
GENERIC,
S3
};

// -- Static fields --

/** Map from given filenames to actual filenames. */
Expand Down Expand Up @@ -113,7 +106,6 @@ protected class ListingsResult {
// -- Fields --

private boolean isURL = false;
private UrlType urlType;
private URL url;
private URI uri;
private File file;
Expand Down Expand Up @@ -203,21 +195,13 @@ public Location(String parent, String child) {
pathname = child;
uri = new URI(mapped);
isURL = true;
if (S3Handle.canHandleScheme(uri.toString())) {
urlType = UrlType.S3;
url = null;
}
else {
urlType = UrlType.GENERIC;
url = uri.toURL();
}
url = uri.toURL();
}
catch (URISyntaxException | MalformedURLException e) {
// Readers such as FilePatternReader may pass invalid URI paths
// containing <> so don't throw, instead treat as a non-URL
LOGGER.debug("Invalid URL: {} {}", child, e);
isURL = false;
urlType = null;
url = null;
uri = null;
}
Expand Down Expand Up @@ -486,23 +470,8 @@ public static IRandomAccess getHandle(String id, boolean writable,
LOGGER.trace("no handle was mapped for this ID");
String mapId = getMappedId(id);

if (S3Handle.canHandleScheme(id)) {
StreamHandle.Settings ss = new StreamHandle.Settings();
if (ss.getRemoteCacheRootDir() != null) {
String cachedFile = S3Handle.cacheObject(mapId, ss);
if (bufferSize > 0) {
handle = new NIOFileHandle(
new File(cachedFile), "r", bufferSize);
}
else {
handle = new NIOFileHandle(cachedFile, "r");
}
}
else {
handle = new S3Handle(mapId);
}
}
else if (id.startsWith("http://") || id.startsWith("https://")) {
if (id.startsWith("http://") || id.startsWith("https://")
|| id.startsWith("s3://")) {
handle = new URLHandle(mapId);
}
else if (allowArchiveHandles && ZipHandle.isZipFile(mapId)) {
Expand Down Expand Up @@ -575,18 +544,6 @@ public String[] list(boolean noHiddenFiles) {
final List<String> files = new ArrayList<String>();
if (isURL) {
try {
if (urlType == UrlType.S3) {
if (isDirectory()) {
// TODO: This is complicated, not sure what to do here
// See comment in isDirectory()
LOGGER.trace("list s3 {}: Returning []", uri);
return new String[0];
}
else {
LOGGER.trace("list s3 {}: Returning null", uri);
return null;
}
}
URLConnection c = url.openConnection();
InputStream is = c.getInputStream();
boolean foundEnd = false;
Expand Down Expand Up @@ -918,32 +875,9 @@ public boolean isAbsolute() {
public boolean isDirectory() {
LOGGER.trace("isDirectory()");
if (isURL) {
if (urlType == UrlType.S3) {
// TODO: This is complicated
//
// S3 doesn't have directories, but keys can contain / which we
// can pretend is a file path. However this "directory" doesn't
// actually exist, only the "contents" of the directory exist.
//
// Minio.listObjects() lists all objects in a bucket that
// match an optional prefix so this could be an option for checking
// whether to trest this as a directory.
//
// S3 buckets are the closest thing to a proper directory
// so for now
try {
S3Handle h = new S3Handle(uri.toString());
boolean isBucket = h.isBucket();
h.close();
return isBucket;
} catch (IOException e) {
throw new UncheckedIOException(e);
}
} else {
// TODO: this should be removed as well.
String[] list = list();
return list != null;
}
// TODO: this should be removed as well.
String[] list = list();
return list != null;
}
return file.isDirectory();
}
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