use cachedDir for local registry cache

globalbioticinteractions · Mar 20, 2020 · 9b256f0 · 9b256f0
1 parent bf6e303
commit 9b256f0
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Showing 10 changed files with 18 additions and 31 deletions.
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDatasets.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDatasets.java
@@ -45,7 +45,7 @@ void run(PrintStream out) {
             serializer.writeHeader();
         }
 
-        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), getTmpDir(), createInputStreamFactory());
+        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), createInputStreamFactory());
 
         try {
             CmdUtil.handleNamespaces(registry,

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDefaultParams.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDefaultParams.java
@@ -15,9 +15,6 @@ abstract class CmdDefaultParams implements Runnable {
     @Parameter(names = {"--cache-dir", "-c"}, description = "cache directory")
     private String cacheDir = "./datasets";
 
-    @Parameter(names = {"--tmp-dir"}, description = "tmp directory")
-    private String tmpDir = "./.elton/tmp";
-
     @Parameter(description = "[namespace1] [namespace2] ...")
     private List<String> namespaces = new ArrayList<>();
 
@@ -69,14 +66,6 @@ public void setCacheDir(String cacheDir) {
         this.cacheDir = cacheDir;
     }
 
-    public String getTmpDir() {
-        return tmpDir;
-    }
-
-    public String setTmpDir(String tmpDir) {
-        return this.tmpDir = tmpDir;
-    }
-
     public void setWorkDir(URI workingDir) {
         this.workDir = workingDir;
     }

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdInteractions.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdInteractions.java
@@ -189,7 +189,6 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                getTmpDir(),
                 createInputStreamFactory());
 
         NodeFactoryNull nodeFactory = new NodeFactoryForDataset(writer, new DatasetProcessorForTSV());

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdList.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdList.java
@@ -24,7 +24,7 @@ public void run() {
 
     public void run(PrintStream out) {
         InputStreamFactoryLogging inputStreamFactory = createInputStreamFactory();
-        DatasetRegistry registryLocal = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), getTmpDir(), inputStreamFactory);
+        DatasetRegistry registryLocal = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), inputStreamFactory);
         DatasetRegistry registry = isOnline()
                 ? new DatasetRegistryProxy(Arrays.asList(new DatasetRegistryZenodo(inputStreamFactory), new DatasetRegistryGitHubArchive(inputStreamFactory), registryLocal))
                 : registryLocal;

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNames.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNames.java
@@ -35,7 +35,7 @@ void run(PrintStream out) {
             writer.writeHeader();
         }
 
-        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), getTmpDir(), createInputStreamFactory());
+        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), createInputStreamFactory());
         NodeFactory nodeFactory = createFactory(writer);
         CmdUtil.handleNamespaces(registry, nodeFactory, getNamespaces(), "listing taxa", getStderr(), new NullImportLogger());
     }

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNanoPubs.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNanoPubs.java
@@ -39,7 +39,6 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                getTmpDir(),
                 createInputStreamFactory());
 
         InteractionWriter serializer = createSerializer(out);

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdReview.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdReview.java
@@ -113,7 +113,7 @@ private void checkCacheOrRemote(List<String> namespaces, InputStreamFactory inpu
     }
 
     private void reviewLocal(URI workDir, InputStreamFactory inputStreamFactory) throws StudyImporterException {
-        DatasetRegistry registryLocal = DatasetRegistryUtil.forLocalDir(workDir, getTmpDir(), inputStreamFactory);
+        DatasetRegistry registryLocal = DatasetRegistryUtil.forLocalDir(workDir, getCacheDir(), inputStreamFactory);
         review("local", registryLocal, inputStreamFactory);
     }
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImpl.java b/src/main/java/org/globalbioticinteractions/elton/cmd/DatasetRegistryFactoryImpl.java
@@ -9,7 +9,6 @@
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
-import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;

diff --git a/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistryUtil.java b/src/main/java/org/globalbioticinteractions/elton/util/DatasetRegistryUtil.java
@@ -43,10 +43,13 @@ private static CacheFactory getCacheFactoryLocal(String cacheDir, InputStreamFac
     }
 
     public static DatasetRegistry forCacheDir(String cacheDir, InputStreamFactory streamFactory) {
-        return new DatasetRegistryLocal(cacheDir, getCacheFactoryLocal(cacheDir, streamFactory), streamFactory);
+        return new DatasetRegistryLocal(
+                cacheDir,
+                getCacheFactoryLocal(cacheDir, streamFactory),
+                streamFactory);
     }
 
-    public static boolean emptyFinder(DatasetRegistry registry) {
+    private static boolean isEmpty(DatasetRegistry registry) {
         try {
             Collection<String> namespaces = registry.findNamespaces();
             return namespaces.isEmpty();
@@ -55,10 +58,10 @@ public static boolean emptyFinder(DatasetRegistry registry) {
         }
     }
 
-    public static DatasetRegistry forCacheDirOrLocalDir(String cacheDir, URI workDir, String tmpDir, InputStreamFactory streamFactory) {
+    public static DatasetRegistry forCacheDirOrLocalDir(String cacheDir, URI workDir, InputStreamFactory streamFactory) {
         DatasetRegistry registry = forCacheDir(cacheDir, streamFactory);
-        if (emptyFinder(registry)) {
-            registry = forLocalDir(workDir, tmpDir, streamFactory);
+        if (isEmpty(registry)) {
+            registry = forLocalDir(workDir, cacheDir, streamFactory);
         }
         return registry;
     }

diff --git a/src/test/java/org/globalbioticinteractions/elton/cmd/CmdReviewTest.java b/src/test/java/org/globalbioticinteractions/elton/cmd/CmdReviewTest.java
@@ -3,7 +3,6 @@
 import com.beust.jcommander.JCommander;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.Range;
 import org.apache.commons.lang3.StringUtils;
 import org.codehaus.jackson.map.ObjectMapper;
 import org.eol.globi.data.LogUtil;
@@ -26,7 +25,6 @@
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
-import java.util.MissingFormatArgumentException;
 import java.util.UUID;
 
 import static junit.framework.TestCase.fail;
@@ -38,12 +36,12 @@
 
 public class CmdReviewTest {
 
-    private String testTmpDir = "target/test-cache";
+    private String testCacheDir = "target/test-cache";
     private CmdReview cmdReview;
 
     @Before
     public void init() {
-        this.testTmpDir = "target/test-cache/" + UUID.randomUUID();
+        this.testCacheDir = "target/test-cache/" + UUID.randomUUID();
         this.cmdReview = new CmdReview();
         cmdReview.setDateFactory(() -> new Date(0));
         cmdReview.setReviewerName("elton-dev");
@@ -52,11 +50,11 @@ public void init() {
 
     @After
     public void cleanCache() {
-        FileUtils.deleteQuietly(new File(getTestTmpDir()));
+        FileUtils.deleteQuietly(new File(getTestCacheDir()));
     }
 
-    private String getTestTmpDir() {
-        return testTmpDir;
+    private String getTestCacheDir() {
+        return testCacheDir;
     }
 
     @Test
@@ -136,7 +134,7 @@ private void runCheck(String localTestPath, ByteArrayOutputStream errOs, ByteArr
         PrintStream out = new PrintStream(outOs);
         cmdReview.setStdout(out);
         cmdReview.setWorkDir(Paths.get(localTestPath).toUri());
-        cmdReview.setTmpDir(getTestTmpDir());
+        cmdReview.setCacheDir(getTestCacheDir());
         cmdReview.setMaxLines(maxLines);
         cmdReview.setDesiredReviewCommentTypes(commentTypes);
         cmdReview.run();