add support for updating cache from local archive

globalbioticinteractions · Mar 20, 2020 · 6548204 · 6548204
1 parent 9b256f0
commit 6548204
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Showing 6 changed files with 112 additions and 44 deletions.
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java
@@ -38,7 +38,9 @@ public void run() {
 
         List<DatasetRegistry> registries = new ArrayList<>();
         for (String registryName : registryNames) {
-            DatasetRegistryFactoryImpl datasetRegistryFactory = new DatasetRegistryFactoryImpl(inputStreamFactory);
+            DatasetRegistryFactoryImpl datasetRegistryFactory
+                    = new DatasetRegistryFactoryImpl(
+                            getWorkDir(), getCacheDir(), inputStreamFactory);
             try {
                 DatasetRegistry registry = datasetRegistryFactory.createRegistryByName(registryName);
                 registries.add(registry);

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImpl.java b/src/main/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImpl.java
@@ -6,22 +6,30 @@
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.dataset.DatasetRegistryGitHubArchive;
 import org.globalbioticinteractions.dataset.DatasetRegistryZenodo;
+import org.globalbioticinteractions.elton.util.DatasetRegistrySingleDir;
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
+import java.net.URI;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Set;
 import java.util.TreeMap;
 
 public class DatasetRegistryFactoryImpl implements DatasetRegistryFactory {
     private static final Map<String, Class<? extends DatasetRegistry>> REGISTRY_LOOKUP = MapUtils.unmodifiableMap(new TreeMap<String, Class<? extends DatasetRegistry>>() {{
+        put("local", DatasetRegistrySingleDir.class);
         put("zenodo", DatasetRegistryZenodo.class);
         put("github", DatasetRegistryGitHubArchive.class);
     }});
 
     private final InputStreamFactory inputStreamFactory;
+    private final URI workDir;
+    private final String cacheDir;
 
-    public DatasetRegistryFactoryImpl(InputStreamFactory inputStreamFactory) {
+    public DatasetRegistryFactoryImpl(URI workDir, String cacheDir, InputStreamFactory inputStreamFactory) {
+        this.workDir = workDir;
+        this.cacheDir = cacheDir;
         this.inputStreamFactory = inputStreamFactory;
     }
 
@@ -32,14 +40,40 @@ public DatasetRegistry createRegistryByName(String name) throws DatasetFinderExc
             throw new DatasetFinderException("failed to create registry for [" + name + "]: not supported");
         }
         try {
-            Constructor<? extends DatasetRegistry> constructor = registryClass.getConstructor(InputStreamFactory.class);
-            return constructor.newInstance(inputStreamFactory);
-        } catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException e) {
+            Class<?>[] paramTypes = {URI.class, String.class, InputStreamFactory.class};
+            Optional<Constructor<? extends DatasetRegistry>> constructor = constructorFor(registryClass, paramTypes);
+            if (!constructor.isPresent()) {
+                Class<?>[] paramTypesShort = {InputStreamFactory.class};
+                Optional<Constructor<? extends DatasetRegistry>> constructor2 = constructorFor(registryClass, paramTypesShort);
+                return constructor2
+                        .orElseThrow(() -> new DatasetFinderException("failed to create registry for [" + name + "]")
+                        ).newInstance(inputStreamFactory);
+            } else {
+                return constructor.get().newInstance(getWorkDir(), getCacheDir(), inputStreamFactory);
+            }
+        } catch (InstantiationException | IllegalAccessException | InvocationTargetException e) {
             throw new DatasetFinderException("failed to create registry for [" + name + "]", e);
         }
     }
 
+    private Optional<Constructor<? extends DatasetRegistry>> constructorFor(Class<? extends DatasetRegistry> registryClass, Class<?>[] paramTypes) {
+        try {
+            Constructor<? extends DatasetRegistry> constructor = registryClass.getConstructor(paramTypes);
+            return Optional.of(constructor);
+        } catch(NoSuchMethodException ex) {
+            return Optional.empty();
+        }
+    }
+
     public static Set<String> getSupportedRegistries() {
         return REGISTRY_LOOKUP.keySet();
     }
+
+    public URI getWorkDir() {
+        return workDir;
+    }
+
+    public String getCacheDir() {
+        return cacheDir;
+    }
 }
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/RegistryNameValidator.java b/src/main/java/org/globalbioticinteractions/elton/cmd/RegistryNameValidator.java
diff --git a/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistrySingleDir.java b/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistrySingleDir.java
@@ -0,0 +1,38 @@
+package org.globalbioticinteractions.elton.util;
+
+import org.eol.globi.util.InputStreamFactory;
+import org.globalbioticinteractions.cache.CachePullThrough;
+import org.globalbioticinteractions.dataset.Dataset;
+import org.globalbioticinteractions.dataset.DatasetFinderException;
+import org.globalbioticinteractions.dataset.DatasetImpl;
+import org.globalbioticinteractions.dataset.DatasetRegistry;
+import org.globalbioticinteractions.dataset.DatasetWithCache;
+
+import java.net.URI;
+import java.util.Collection;
+import java.util.Collections;
+
+public class DatasetRegistrySingleDir implements DatasetRegistry {
+    private final URI localArchiveDir;
+    private final InputStreamFactory streamFactory;
+    private final String cacheDir;
+
+    public DatasetRegistrySingleDir(URI localArchiveDir, String cacheDir, InputStreamFactory streamFactory) {
+        this.localArchiveDir = localArchiveDir;
+        this.cacheDir = cacheDir;
+        this.streamFactory = streamFactory;
+    }
+
+    @Override
+    public Collection<String> findNamespaces() throws DatasetFinderException {
+        return Collections.singletonList(DatasetRegistryUtil.NAMESPACE_LOCAL);
+    }
+
+    @Override
+    public Dataset datasetFor(String namespace) throws DatasetFinderException {
+        DatasetImpl local = new DatasetImpl(DatasetRegistryUtil.NAMESPACE_LOCAL, localArchiveDir, streamFactory);
+
+        return new DatasetWithCache(local,
+                new CachePullThrough(DatasetRegistryUtil.NAMESPACE_LOCAL, cacheDir, streamFactory));
+    }
+}
diff --git a/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistryUtil.java b/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistryUtil.java
@@ -1,41 +1,21 @@
 package org.globalbioticinteractions.elton.util;
 
-import org.globalbioticinteractions.dataset.Dataset;
 import org.globalbioticinteractions.dataset.DatasetFinderException;
-import org.globalbioticinteractions.dataset.DatasetImpl;
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.eol.globi.util.InputStreamFactory;
 import org.globalbioticinteractions.cache.CacheFactory;
 import org.globalbioticinteractions.cache.CacheLocalReadonly;
-import org.globalbioticinteractions.cache.CachePullThrough;
 import org.globalbioticinteractions.dataset.DatasetRegistryLocal;
-import org.globalbioticinteractions.dataset.DatasetWithCache;
 
 import java.net.URI;
 import java.util.Collection;
-import java.util.Collections;
 
 public class DatasetRegistryUtil {
 
     public static final String NAMESPACE_LOCAL = "local";
 
-    public static DatasetRegistry forLocalDir(final URI localDir, final String localCacheDir, InputStreamFactory streamFactory) {
-        return new DatasetRegistry() {
-            private final String localStaticNamespace = NAMESPACE_LOCAL;
-
-            @Override
-            public Collection<String> findNamespaces() throws DatasetFinderException {
-                return Collections.singletonList(localStaticNamespace);
-            }
-
-            @Override
-            public Dataset datasetFor(String namespace) throws DatasetFinderException {
-                DatasetImpl local = new DatasetImpl(NAMESPACE_LOCAL, localDir, streamFactory);
-
-                return new DatasetWithCache(local,
-                        new CachePullThrough(NAMESPACE_LOCAL, localCacheDir, streamFactory));
-            }
-        };
+    public static DatasetRegistry forLocalDir(final URI localArchiveDir, final String cacheDir, InputStreamFactory streamFactory) {
+        return new DatasetRegistrySingleDir(localArchiveDir, cacheDir, streamFactory);
     }
 
     private static CacheFactory getCacheFactoryLocal(String cacheDir, InputStreamFactory streamFactory) {
@@ -65,4 +45,5 @@ public static DatasetRegistry forCacheDirOrLocalDir(String cacheDir, URI workDir
         }
         return registry;
     }
+
 }
diff --git a/src/test/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImplTest.java b/src/test/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImplTest.java
@@ -0,0 +1,30 @@
+package org.globalbioticinteractions.elton.cmd;
+
+import org.globalbioticinteractions.dataset.DatasetFinderException;
+import org.globalbioticinteractions.dataset.DatasetRegistry;
+import org.hamcrest.core.Is;
+import org.junit.Test;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+
+public class DatasetRegistryFactoryImplTest {
+
+    @Test
+    public void list() throws DatasetFinderException {
+        List<DatasetRegistry> registries = new ArrayList<>();
+        Set<String> supportedRegistries = DatasetRegistryFactoryImpl.getSupportedRegistries();
+        for (String supportedRegistry : supportedRegistries) {
+            DatasetRegistry registry = new DatasetRegistryFactoryImpl(
+                    URI.create("some:uri"), "someCacheDir", in -> in)
+                    .createRegistryByName(supportedRegistry);
+            registries.add(registry);
+        }
+        assertThat(registries.size(), Is.is(supportedRegistries.size()));
+    }
+
+}