generator) {
+
+ backendTest = test;
+ backendGenerator = generator;
+ }
+
+ @Override public KeyValueAccess apply(final URI uri, final N5Factory factory) {
+
+ if (test(uri))
+ return backendGenerator.apply(uri, factory);
+ return null;
+ }
+
+ @Override public boolean test(URI uri) {
+
+ return backendTest.test(uri);
+ }
+
+ /**
+ * Test the provided {@link URI} to and return the appropriate {@link KeyValueAccess}.
+ * If no appropriate {@link KeyValueAccess} is found, may be null
+ *
+ * @param uri to create a {@link KeyValueAccess} from.
+ * @return the {@link KeyValueAccess} and container path, or null if none are valid
+ */
+ @Nullable
+ public static KeyValueAccess getKeyValueAccess(final URI uri) {
+
+ return getKeyValueAccess(uri, N5Factory.FACTORY);
+ }
+
+ @Nullable
+ static KeyValueAccess getKeyValueAccess(final URI uri, final N5Factory factory) {
+
+ /*NOTE: The order of these tests is very important, as the predicates for each
+ * backend take into account reasonable defaults when possible.
+ * Here we test from most to least restrictive.
+ * See the Javadoc for more details. */
+ for (final KeyValueAccessBackend backend : KeyValueAccessBackend.values()) {
+ final KeyValueAccess kva = backend.apply(uri, factory);
+ if (kva != null)
+ return kva;
+ }
+ return null;
+ }
+
+ private static GoogleCloudStorageKeyValueAccess newGoogleCloudKeyValueAccess(final URI uri, final N5Factory factory) {
+
+ final GoogleCloudStorageURI googleCloudUri = new GoogleCloudStorageURI(uri);
+ return new GoogleCloudStorageKeyValueAccess(factory.createGoogleCloudStorage(), googleCloudUri, true);
+ }
+
+ private static AmazonS3KeyValueAccess newAmazonS3KeyValueAccess(final URI uri, final N5Factory factory) {
+
+ final String uriString = uri.toString();
+ final AmazonS3 s3 = factory.createS3(uriString);
+
+ return new AmazonS3KeyValueAccess(s3, uri, true);
+ }
+
+ private static FileSystemKeyValueAccess newFileSystemKeyValueAccess(final URI uri, final N5Factory factory) {
+
+ return new FileSystemKeyValueAccess(FileSystems.getDefault());
+ }
+}
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/universe/N5Factory.java b/src/main/java/org/janelia/saalfeldlab/n5/universe/N5Factory.java
index a808a95..1250688 100644
--- a/src/main/java/org/janelia/saalfeldlab/n5/universe/N5Factory.java
+++ b/src/main/java/org/janelia/saalfeldlab/n5/universe/N5Factory.java
@@ -26,21 +26,16 @@
*/
package org.janelia.saalfeldlab.n5.universe;
-import java.io.File;
import java.io.Serializable;
import java.net.URI;
import java.net.URISyntaxException;
-import java.nio.file.FileSystems;
import java.nio.file.Paths;
import java.util.function.BiFunction;
-import java.util.function.Predicate;
-import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.annotation.Nullable;
import org.apache.commons.lang3.function.TriFunction;
-import org.janelia.saalfeldlab.googlecloud.GoogleCloudStorageURI;
import org.janelia.saalfeldlab.googlecloud.GoogleCloudUtils;
import org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess;
import org.janelia.saalfeldlab.n5.KeyValueAccess;
@@ -50,11 +45,8 @@
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5URI;
import org.janelia.saalfeldlab.n5.N5Writer;
-import org.janelia.saalfeldlab.n5.googlecloud.GoogleCloudStorageKeyValueAccess;
-import org.janelia.saalfeldlab.n5.hdf5.HDF5Utils;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer;
-import org.janelia.saalfeldlab.n5.s3.AmazonS3KeyValueAccess;
import org.janelia.saalfeldlab.n5.s3.AmazonS3Utils;
import org.janelia.saalfeldlab.n5.zarr.N5ZarrReader;
import org.janelia.saalfeldlab.n5.zarr.N5ZarrWriter;
@@ -69,7 +61,6 @@
import com.google.gson.GsonBuilder;
import net.imglib2.util.Pair;
-import net.imglib2.util.ValuePair;
/**
* Factory for various N5 readers and writers. Implementation specific
@@ -83,11 +74,11 @@
*/
public class N5Factory implements Serializable {
- private static final N5Factory FACTORY = new N5Factory();
+ static final N5Factory FACTORY = new N5Factory();
private static final long serialVersionUID = -6823715427289454617L;
- private final static Pattern HTTPS_SCHEME = Pattern.compile("http(s)?", Pattern.CASE_INSENSITIVE);
- private final static Pattern FILE_SCHEME = Pattern.compile("file", Pattern.CASE_INSENSITIVE);
+ final static Pattern HTTPS_SCHEME = Pattern.compile("http(s)?", Pattern.CASE_INSENSITIVE);
+ final static Pattern FILE_SCHEME = Pattern.compile("file", Pattern.CASE_INSENSITIVE);
private int[] hdf5DefaultBlockSize = {64, 64, 64, 1, 1};
private boolean hdf5OverrideBlockSize = false;
private GsonBuilder gsonBuilder = new GsonBuilder();
@@ -102,25 +93,6 @@ public class N5Factory implements Serializable {
private boolean s3Anonymous = true;
private String s3Endpoint;
- private static GoogleCloudStorageKeyValueAccess newGoogleCloudKeyValueAccess(final URI uri, final N5Factory factory) {
-
- final GoogleCloudStorageURI googleCloudUri = new GoogleCloudStorageURI(uri);
- return new GoogleCloudStorageKeyValueAccess(factory.createGoogleCloudStorage(), googleCloudUri, true);
- }
-
- private static AmazonS3KeyValueAccess newAmazonS3KeyValueAccess(final URI uri, final N5Factory factory) {
-
- final String uriString = uri.toString();
- final AmazonS3 s3 = factory.createS3(uriString);
-
- return new AmazonS3KeyValueAccess(s3, uri, true);
- }
-
- private static FileSystemKeyValueAccess newFileSystemKeyValueAccess(final URI uri, final N5Factory factory) {
-
- return new FileSystemKeyValueAccess(FileSystems.getDefault());
- }
-
public N5Factory hdf5DefaultBlockSize(final int... blockSize) {
hdf5DefaultBlockSize = blockSize;
@@ -225,26 +197,21 @@ Storage createGoogleCloudStorage() {
return GoogleCloudUtils.createGoogleCloudStorage(googleCloudProjectId);
}
+
+
/**
* Test the provided {@link URI} to and return the appropriate {@link KeyValueAccess}.
* If no appropriate {@link KeyValueAccess} is found, may be null
+ *
+ * This differs subtly from {@link KeyValueAccessBackend#getKeyValueAccess(URI)} in that
+ * the resulting {@link KeyValueAccess} may use configured fields from this {@link N5Factory}.
*
* @param uri to create a {@link KeyValueAccess} from.
* @return the {@link KeyValueAccess} and container path, or null if none are valid
*/
@Nullable
- KeyValueAccess getKeyValueAccess(final URI uri) {
-
- /*NOTE: The order of these tests is very important, as the predicates for each
- * backend take into account reasonable defaults when possible.
- * Here we test from most to least restrictive.
- * See the Javadoc for more details. */
- for (final KeyValueAccessBackend backend : KeyValueAccessBackend.values()) {
- final KeyValueAccess kva = backend.apply(uri, this);
- if (kva != null)
- return kva;
- }
- return null;
+ public KeyValueAccess getKeyValueAccess(final URI uri) {
+ return KeyValueAccessBackend.getKeyValueAccess(uri ,this);
}
/**
@@ -536,7 +503,9 @@ private T openN5ContainerWithBackend(
final Pair formatAndUri = StorageFormat.parseUri(containerUri);
final URI uri = formatAndUri.getB();
final KeyValueAccess kva = backend.apply(uri, this);
- return openWithBackend.apply(formatAndUri.getA(), kva, uri.toString());
+ StorageFormat format = formatAndUri.getA();
+ format = format != null? format : StorageFormat.guessStorageFromKeys(uri, kva);
+ return openWithBackend.apply(format, kva, uri.toString());
}
private T openN5Container(
@@ -547,7 +516,8 @@ private T openN5Container(
final KeyValueAccess kva = getKeyValueAccess(uri);
if (kva == null)
throw new N5Exception("Cannot get KeyValueAccess at " + uri);
- return openWithKva.apply(storageFormat, kva, uri.toString());
+ final StorageFormat format = storageFormat != null ? storageFormat : StorageFormat.guessStorageFromKeys(uri, kva);
+ return openWithKva.apply(format, kva, uri.toString());
}
private T openN5Container(
@@ -569,113 +539,6 @@ private T openN5Container(
return openN5Container(null, uri, openWithKva);
}
- /**
- * Enum to discover and provide {@link KeyValueAccess} for {@link N5Reader}s and {@link N5Writer}s.
- * IMPORTANT: If ever new {@link KeyValueAccess} backends are adding, they MUST be re-ordered
- * such that the earliest predicates are the most restrictive, and the later predicates
- * are the least restrictive. This ensures that when iterating through the values of
- * {@link KeyValueAccessBackend} you can test them in order, and stop at the first
- * {@link KeyValueAccess} that is generated.
- */
- enum KeyValueAccessBackend implements Predicate, BiFunction {
- GOOGLE_CLOUD(uri -> {
- final String scheme = uri.getScheme();
- final boolean hasScheme = scheme != null;
- return hasScheme && GoogleCloudUtils.GS_SCHEME.asPredicate().test(scheme)
- || hasScheme && HTTPS_SCHEME.asPredicate().test(scheme)
- && uri.getHost() != null && GoogleCloudUtils.GS_HOST.asPredicate().test(uri.getHost());
- }, N5Factory::newGoogleCloudKeyValueAccess),
- AWS(uri -> {
- final String scheme = uri.getScheme();
- final boolean hasScheme = scheme != null;
- return hasScheme && AmazonS3Utils.S3_SCHEME.asPredicate().test(scheme)
- || uri.getHost() != null && hasScheme && HTTPS_SCHEME.asPredicate().test(scheme);
- }, N5Factory::newAmazonS3KeyValueAccess),
- FILE(uri -> {
- final String scheme = uri.getScheme();
- final boolean hasScheme = scheme != null;
- return !hasScheme || FILE_SCHEME.asPredicate().test(scheme);
- }, N5Factory::newFileSystemKeyValueAccess);
-
- private final Predicate backendTest;
- private final BiFunction backendGenerator;
-
- KeyValueAccessBackend(Predicate test, BiFunction generator) {
-
- backendTest = test;
- backendGenerator = generator;
- }
-
- @Override public KeyValueAccess apply(final URI uri, final N5Factory factory) {
-
- if (test(uri))
- return backendGenerator.apply(uri, factory);
- return null;
- }
-
- @Override public boolean test(URI uri) {
-
- return backendTest.test(uri);
- }
- }
-
- public enum StorageFormat {
- ZARR(Pattern.compile("zarr", Pattern.CASE_INSENSITIVE), uri -> Pattern.compile("\\.zarr$", Pattern.CASE_INSENSITIVE).matcher(new File(uri.getPath()).toString()).find()),
- N5(Pattern.compile("n5", Pattern.CASE_INSENSITIVE), uri -> Pattern.compile("\\.n5$", Pattern.CASE_INSENSITIVE).matcher(new File(uri.getPath()).toString()).find()),
- HDF5(Pattern.compile("h(df)?5", Pattern.CASE_INSENSITIVE), uri -> {
- final boolean hasHdf5Extension = Pattern.compile("\\.h(df)?5$", Pattern.CASE_INSENSITIVE).matcher(uri.getPath()).find();
- return hasHdf5Extension || HDF5Utils.isHDF5(uri.getPath());
- });
-
- static final Pattern STORAGE_SCHEME_PATTERN = Pattern.compile("^(\\s*(?(n5|h(df)?5|zarr)):(//)?)?(?.*)$", Pattern.CASE_INSENSITIVE);
- private final static String STORAGE_SCHEME_GROUP = "storageScheme";
- private final static String URI_GROUP = "uri";
-
- final Pattern schemePattern;
- private final Predicate uriTest;
-
- StorageFormat(final Pattern schemePattern, final Predicate test) {
-
- this.schemePattern = schemePattern;
- this.uriTest = test;
- }
-
- public static StorageFormat guessStorageFromUri(URI uri) {
-
- for (final StorageFormat format : StorageFormat.values()) {
- if (format.uriTest.test(uri))
- return format;
- }
- return null;
- }
-
- public static Pair parseUri(String uri) throws URISyntaxException {
-
- final Pair storageFromScheme = getStorageFromNestedScheme(uri);
- final URI asUri = parseUriFromString(storageFromScheme.getB());
- if (storageFromScheme.getA() != null)
- return new ValuePair<>(storageFromScheme.getA(), asUri);
- else
- return new ValuePair<>(guessStorageFromUri(asUri), asUri);
-
- }
-
- public static Pair getStorageFromNestedScheme(String uri) {
-
- final Matcher storageSchemeMatcher = StorageFormat.STORAGE_SCHEME_PATTERN.matcher(uri);
- storageSchemeMatcher.matches();
- final String storageFormatScheme = storageSchemeMatcher.group(STORAGE_SCHEME_GROUP);
- final String uriGroup = storageSchemeMatcher.group(URI_GROUP);
- if (storageFormatScheme != null) {
- for (final StorageFormat format : StorageFormat.values()) {
- if (format.schemePattern.asPredicate().test(storageFormatScheme))
- return new ValuePair<>(format, uriGroup);
- }
- }
- return new ValuePair<>(null, uriGroup);
- }
- }
-
/**
* Creates an N5 writer for the specified container URI with default N5Factory configuration.
*
@@ -698,7 +561,7 @@ public static N5Reader createReader(String containerUri) {
return FACTORY.openReader(containerUri);
}
- private static URI parseUriFromString(String uri) {
+ static URI parseUriFromString(String uri) {
try {
return URI.create(uri);
} catch (final Throwable ignore) {}
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/universe/StorageFormat.java b/src/main/java/org/janelia/saalfeldlab/n5/universe/StorageFormat.java
new file mode 100644
index 0000000..03d5527
--- /dev/null
+++ b/src/main/java/org/janelia/saalfeldlab/n5/universe/StorageFormat.java
@@ -0,0 +1,94 @@
+package org.janelia.saalfeldlab.n5.universe;
+
+import net.imglib2.util.Pair;
+import net.imglib2.util.ValuePair;
+import org.janelia.saalfeldlab.n5.KeyValueAccess;
+import org.janelia.saalfeldlab.n5.hdf5.HDF5Utils;
+
+import javax.annotation.Nullable;
+import java.io.File;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.function.Predicate;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public enum StorageFormat {
+ ZARR(Pattern.compile("zarr", Pattern.CASE_INSENSITIVE), uri -> Pattern.compile("\\.zarr$", Pattern.CASE_INSENSITIVE).matcher(new File(uri.getPath()).toString()).find()),
+ N5(Pattern.compile("n5", Pattern.CASE_INSENSITIVE), uri -> Pattern.compile("\\.n5$", Pattern.CASE_INSENSITIVE).matcher(new File(uri.getPath()).toString()).find()),
+ HDF5(Pattern.compile("h(df)?5", Pattern.CASE_INSENSITIVE), uri -> {
+ final boolean hasHdf5Extension = Pattern.compile("\\.h(df)?5$", Pattern.CASE_INSENSITIVE).matcher(uri.getPath()).find();
+ return hasHdf5Extension || HDF5Utils.isHDF5(uri.getPath());
+ });
+
+ static final Pattern STORAGE_SCHEME_PATTERN = Pattern.compile("^(\\s*(?(n5|h(df)?5|zarr)):(//)?)?(?.*)$", Pattern.CASE_INSENSITIVE);
+ private final static String STORAGE_SCHEME_GROUP = "storageScheme";
+ private final static String URI_GROUP = "uri";
+
+ final Pattern schemePattern;
+ private final Predicate uriTest;
+
+ StorageFormat(final Pattern schemePattern, final Predicate test) {
+
+ this.schemePattern = schemePattern;
+ this.uriTest = test;
+ }
+
+ public static StorageFormat guessStorageFromUri(URI uri) {
+
+ for (final StorageFormat format : StorageFormat.values()) {
+ if (format.uriTest.test(uri))
+ return format;
+ }
+ return null;
+ }
+
+ public static Pair parseUri(String uri) throws URISyntaxException {
+
+ final Pair storageFromScheme = getStorageFromNestedScheme(uri);
+ final URI asUri = N5Factory.parseUriFromString(storageFromScheme.getB());
+ if (storageFromScheme.getA() != null)
+ return new ValuePair<>(storageFromScheme.getA(), asUri);
+ else
+ return new ValuePair<>(guessStorageFromUri(asUri), asUri);
+
+ }
+
+ public static Pair getStorageFromNestedScheme(String uri) {
+
+ final Matcher storageSchemeMatcher = StorageFormat.STORAGE_SCHEME_PATTERN.matcher(uri);
+ storageSchemeMatcher.matches();
+ final String storageFormatScheme = storageSchemeMatcher.group(STORAGE_SCHEME_GROUP);
+ final String uriGroup = storageSchemeMatcher.group(URI_GROUP);
+ if (storageFormatScheme != null) {
+ for (final StorageFormat format : StorageFormat.values()) {
+ if (format.schemePattern.asPredicate().test(storageFormatScheme))
+ return new ValuePair<>(format, uriGroup);
+ }
+ }
+ return new ValuePair<>(null, uriGroup);
+ }
+
+ private static final String ZARRAY = ".zarray";
+ private static final String ZGROUP = ".zgroup";
+ private static final String ZATTRS = ".zattrs";
+ private static final String[] ZARR2_KEYS = new String[]{ZARRAY, ZGROUP, ZATTRS};
+ private static final String Z3ATTRS = ".zattrs";
+ private static final String N5_ATTRIBUTES = "attributes.json";
+
+ public static @Nullable StorageFormat guessStorageFromKeys(final URI root, final KeyValueAccess kva) {
+ final URI uri;
+ if (root.isAbsolute())
+ uri = root;
+ else
+ uri = URI.create("file://" + root);
+ if (Arrays.stream(ZARR2_KEYS).anyMatch(it -> kva.exists(kva.compose(uri, it))))
+ return StorageFormat.ZARR;
+ else if (kva.exists(kva.compose(uri, N5_ATTRIBUTES)))
+ return StorageFormat.N5;
+ else return null;
+ }
+}
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/universe/N5FactoryTests.java b/src/test/java/org/janelia/saalfeldlab/n5/universe/N5FactoryTests.java
index f84884a..de8ba69 100644
--- a/src/test/java/org/janelia/saalfeldlab/n5/universe/N5FactoryTests.java
+++ b/src/test/java/org/janelia/saalfeldlab/n5/universe/N5FactoryTests.java
@@ -7,7 +7,6 @@
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer;
-import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
import org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader;
import org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter;
import org.junit.Test;
@@ -40,39 +39,39 @@ public void testStorageFormatGuesses() throws URISyntaxException {
final URI zarrExtSlash = new URI("file:///tmp/a.zarr/");
final URI unknownExt = new URI("file:///tmp/a.abc");
- assertNull("no extension null", N5Factory.StorageFormat.guessStorageFromUri(noExt));
+ assertNull("no extension null", StorageFormat.guessStorageFromUri(noExt));
/**
* h5 tests fail now because these test whether the file exists. It
* should not do that, if, for example, we're making a writer.
*/
- assertEquals("h5 extension == h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(h5Ext));
- assertNotEquals("h5 extension != n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(h5Ext));
- assertNotEquals("h5 extension != zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(h5Ext));
+ assertEquals("h5 extension == h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(h5Ext));
+ assertNotEquals("h5 extension != n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(h5Ext));
+ assertNotEquals("h5 extension != zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(h5Ext));
- assertEquals("hdf5 extension == h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(hdf5Ext));
- assertNotEquals("hdf5 extension != n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(hdf5Ext));
- assertNotEquals("hdf5 extension != zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(hdf5Ext));
+ assertEquals("hdf5 extension == h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(hdf5Ext));
+ assertNotEquals("hdf5 extension != n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(hdf5Ext));
+ assertNotEquals("hdf5 extension != zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(hdf5Ext));
- assertNotEquals("n5 extension != h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(n5Ext));
- assertEquals("n5 extension == n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(n5Ext));
- assertNotEquals("n5 extension != zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(n5Ext));
+ assertNotEquals("n5 extension != h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(n5Ext));
+ assertEquals("n5 extension == n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(n5Ext));
+ assertNotEquals("n5 extension != zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(n5Ext));
- assertNotEquals("n5 extension slash != h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(n5ExtSlash));
- assertEquals("n5 extension slash == n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(n5ExtSlash));
- assertNotEquals("n5 extension slash != zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(n5ExtSlash));
+ assertNotEquals("n5 extension slash != h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(n5ExtSlash));
+ assertEquals("n5 extension slash == n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(n5ExtSlash));
+ assertNotEquals("n5 extension slash != zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(n5ExtSlash));
- assertNotEquals("zarr extension != h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(zarrExt));
- assertNotEquals("zarr extension != n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(zarrExt));
- assertEquals("zarr extension == zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(zarrExt));
+ assertNotEquals("zarr extension != h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(zarrExt));
+ assertNotEquals("zarr extension != n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(zarrExt));
+ assertEquals("zarr extension == zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(zarrExt));
- assertNotEquals("zarr extension slash != h5", StorageFormat.HDF5, N5Factory.StorageFormat.guessStorageFromUri(zarrExtSlash));
- assertNotEquals("zarr extension slash != n5", StorageFormat.N5, N5Factory.StorageFormat.guessStorageFromUri(zarrExtSlash));
- assertEquals("zarr extension slash == zarr", StorageFormat.ZARR, N5Factory.StorageFormat.guessStorageFromUri(zarrExtSlash));
+ assertNotEquals("zarr extension slash != h5", StorageFormat.HDF5, StorageFormat.guessStorageFromUri(zarrExtSlash));
+ assertNotEquals("zarr extension slash != n5", StorageFormat.N5, StorageFormat.guessStorageFromUri(zarrExtSlash));
+ assertEquals("zarr extension slash == zarr", StorageFormat.ZARR, StorageFormat.guessStorageFromUri(zarrExtSlash));
- assertNull("unknown extension != h5", N5Factory.StorageFormat.guessStorageFromUri(unknownExt));
- assertNull("unknown extension != n5", N5Factory.StorageFormat.guessStorageFromUri(unknownExt));
- assertNull("unknown extension != zarr", N5Factory.StorageFormat.guessStorageFromUri(unknownExt));
+ assertNull("unknown extension != h5", StorageFormat.guessStorageFromUri(unknownExt));
+ assertNull("unknown extension != n5", StorageFormat.guessStorageFromUri(unknownExt));
+ assertNull("unknown extension != zarr", StorageFormat.guessStorageFromUri(unknownExt));
}
@Test
@@ -192,10 +191,10 @@ public void testDefaultForAmbiguousWriters() throws IOException {
final Class[] writerTypes = new Class[]{
null,
N5HDF5Writer.class,
- ZarrKeyValueWriter.class,
- ZarrKeyValueWriter.class,
- ZarrKeyValueWriter.class,
- ZarrKeyValueWriter.class
+ ZarrKeyValueWriter.class, //valid zarr, correct by key match
+ N5KeyValueWriter.class, //valid n5, correct by key match
+ ZarrKeyValueWriter.class, // empty directory, create new zarr
+ ZarrKeyValueWriter.class //directory doesn't exist, create new zarr
};
for (int i = 0; i < paths.length; i++) {
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/universe/N5StorageTests.java b/src/test/java/org/janelia/saalfeldlab/n5/universe/N5StorageTests.java
index 33cb6e7..a143b56 100644
--- a/src/test/java/org/janelia/saalfeldlab/n5/universe/N5StorageTests.java
+++ b/src/test/java/org/janelia/saalfeldlab/n5/universe/N5StorageTests.java
@@ -1,7 +1,6 @@
package org.janelia.saalfeldlab.n5.universe;
import com.amazonaws.services.s3.AmazonS3;
-import com.google.cloud.storage.Bucket;
import com.google.cloud.storage.Storage;
import com.google.gson.GsonBuilder;
import org.janelia.saalfeldlab.n5.AbstractN5Test;
@@ -58,9 +57,9 @@ public N5FactoryTest() {
return factory;
}
- @Override public N5Factory.StorageFormat getStorageFormat() {
+ @Override public StorageFormat getStorageFormat() {
- return N5Factory.StorageFormat.N5;
+ return StorageFormat.N5;
}
@Override protected N5Reader createN5Reader(String location, GsonBuilder gson) {
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/universe/StorageSchemeWrappedN5Test.java b/src/test/java/org/janelia/saalfeldlab/n5/universe/StorageSchemeWrappedN5Test.java
index 0336647..9e8a38a 100644
--- a/src/test/java/org/janelia/saalfeldlab/n5/universe/StorageSchemeWrappedN5Test.java
+++ b/src/test/java/org/janelia/saalfeldlab/n5/universe/StorageSchemeWrappedN5Test.java
@@ -17,7 +17,7 @@ public interface StorageSchemeWrappedN5Test {
N5Factory getFactory();
- N5Factory.StorageFormat getStorageFormat();
+ StorageFormat getStorageFormat();
Class getBackendTargetClass();
diff --git a/src/test/java/org/janelia/saalfeldlab/n5/universe/ZarrStorageTests.java b/src/test/java/org/janelia/saalfeldlab/n5/universe/ZarrStorageTests.java
index 3f7f9a1..e35d105 100644
--- a/src/test/java/org/janelia/saalfeldlab/n5/universe/ZarrStorageTests.java
+++ b/src/test/java/org/janelia/saalfeldlab/n5/universe/ZarrStorageTests.java
@@ -1,7 +1,6 @@
package org.janelia.saalfeldlab.n5.universe;
import com.amazonaws.services.s3.AmazonS3;
-import com.google.cloud.storage.Bucket;
import com.google.cloud.storage.Storage;
import com.google.gson.GsonBuilder;
import org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess;
@@ -55,9 +54,9 @@ public ZarrFactoryTest() {
return factory;
}
- @Override public N5Factory.StorageFormat getStorageFormat() {
+ @Override public StorageFormat getStorageFormat() {
- return N5Factory.StorageFormat.ZARR;
+ return StorageFormat.ZARR;
}
@Override protected N5Writer createN5Writer() {