Refactor render client parameters to use ParameterDelegate references…

… so that common parameter sets can be easily shared by different clients. Add parameter parsing unit tests for each client.

render-app/src/main/java/org/janelia/alignment/match/RenderableCanvasIdPairs.java

@@ -1,10 +1,15 @@
 package org.janelia.alignment.match;
 
+import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
+import java.nio.file.FileSystems;
+import java.nio.file.Path;
 import java.util.List;
 
 import org.janelia.alignment.json.JsonUtils;
+import org.janelia.alignment.util.FileUtil;
+import org.slf4j.LoggerFactory;
 
 /**
  * List of {@link OrderedCanvasIdPair} objects with a common render parameters URL template.
@@ -61,11 +66,36 @@ public List<OrderedCanvasIdPair> getNeighborPairs() {
         return neighborPairs;
     }
 
+    /**
+     * @return pairs object loaded from the specified file.
+     */
+    public static RenderableCanvasIdPairs load(final String dataFile)
+            throws IOException, IllegalArgumentException {
+
+        final RenderableCanvasIdPairs renderableCanvasIdPairs;
+
+        final Path path = FileSystems.getDefault().getPath(dataFile).toAbsolutePath();
+
+        LOG.info("load: entry, path={}", path);
+
+        try (final Reader reader = FileUtil.DEFAULT_INSTANCE.getExtensionBasedReader(path.toString())) {
+            renderableCanvasIdPairs = RenderableCanvasIdPairs.fromJson(reader);
+        }
+
+        LOG.info("load: exit, loaded {} pairs", renderableCanvasIdPairs.size());
+
+
+        return renderableCanvasIdPairs;
+    }
+
+
     public static RenderableCanvasIdPairs fromJson(final Reader json) {
         return JSON_HELPER.fromJson(json);
     }
 
     private static final JsonUtils.Helper<RenderableCanvasIdPairs> JSON_HELPER =
             new JsonUtils.Helper<>(RenderableCanvasIdPairs.class);
 
+    private static final org.slf4j.Logger LOG = LoggerFactory.getLogger(RenderableCanvasIdPairs.class);
+
 }

render-ws-java-client/src/main/java/org/janelia/render/client/FileUtil.java → render-app/src/main/java/org/janelia/alignment/util/FileUtil.java

@@ -1,4 +1,4 @@
-package org.janelia.render.client;
+package org.janelia.alignment.util;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
@@ -24,7 +24,7 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Utility for reading and writing files.
+ * Shared file management utilities.
  *
  * @author Eric Trautman
  */
@@ -110,7 +110,33 @@ public static void ensureWritableDirectory(final File directory) {
         }
     }
 
+    public static boolean deleteRecursive(final File file) {
+
+        // could use Apache Commons FileUtils.delete but to have the logging, need to implement here
+
+        boolean deleteSuccessful = true;
+
+        if (file.isDirectory()){
+            final File[] files = file.listFiles();
+            if (files != null) {
+                for (final File f : files) {
+                    deleteSuccessful = deleteSuccessful && deleteRecursive(f);
+                }
+            }
+        }
+
+        if (file.delete()) {
+            LOG.info("deleted " + file.getAbsolutePath());
+        } else {
+            LOG.warn("failed to delete " + file.getAbsolutePath());
+            deleteSuccessful = false;
+        }
+
+        return deleteSuccessful;
+    }
+
     private static final Logger LOG = LoggerFactory.getLogger(FileUtil.class);
 
     private static final int DEFAULT_BUFFER_SIZE = 65536;
+
 }

render-app/src/test/java/org/janelia/alignment/MipmapGeneratorTest.java

@@ -4,6 +4,7 @@
 
 import org.janelia.alignment.spec.ChannelSpec;
 import org.janelia.alignment.spec.TileSpec;
+import org.janelia.alignment.util.FileUtil;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -38,7 +39,7 @@ public void setUp() throws Exception {
 
     @After
     public void tearDown() throws Exception {
-        deleteRecursive(baseMipmapDirectory);
+        FileUtil.deleteRecursive(baseMipmapDirectory);
     }
 
     @Test
@@ -125,29 +126,6 @@ private void validateMask(final ChannelSpec channelSpec,
         }
     }
 
-    private static boolean deleteRecursive(final File file) {
-
-        boolean deleteSuccessful = true;
-
-        if (file.isDirectory()){
-            final File[] files = file.listFiles();
-            if (files != null) {
-                for (final File f : files) {
-                    deleteSuccessful = deleteSuccessful && deleteRecursive(f);
-                }
-            }
-        }
-
-        if (file.delete()) {
-            LOG.info("deleted " + file.getAbsolutePath());
-        } else {
-            LOG.warn("failed to delete " + file.getAbsolutePath());
-            deleteSuccessful = false;
-        }
-
-        return deleteSuccessful;
-    }
-
     private static final Logger LOG = LoggerFactory.getLogger(MipmapGeneratorTest.class);
 
 }

render-app/src/test/java/org/janelia/alignment/mipmap/BoxMipmapGeneratorTest.java

@@ -28,6 +28,7 @@
 
 import org.janelia.alignment.ArgbRenderer;
 import org.janelia.alignment.RenderParameters;
+import org.janelia.alignment.util.FileUtil;
 import org.janelia.alignment.Utils;
 import org.janelia.alignment.spec.Bounds;
 import org.janelia.alignment.util.LabelImageProcessorCache;
@@ -85,7 +86,8 @@ public void setup() throws Exception {
 
     @After
     public void tearDown() throws Exception {
-        deleteRecursive(testDirectory);
+
+        FileUtil.deleteRecursive(testDirectory);
     }
 
     @Test
@@ -219,29 +221,5 @@ private BoxMipmapGenerator validateNextLevel(final BoxMipmapGenerator boxMipmapG
         return nextLevelGenerator;
     }
 
-    // TODO: replace with Apache Commons FileUtils.delete
-    public static boolean deleteRecursive(final File file) {
-
-        boolean deleteSuccessful = true;
-
-        if (file.isDirectory()){
-            final File[] files = file.listFiles();
-            if (files != null) {
-                for (final File f : files) {
-                    deleteSuccessful = deleteSuccessful && deleteRecursive(f);
-                }
-            }
-        }
-
-        if (file.delete()) {
-            LOG.info("deleted " + file.getAbsolutePath());
-        } else {
-            LOG.warn("failed to delete " + file.getAbsolutePath());
-            deleteSuccessful = false;
-        }
-
-        return deleteSuccessful;
-    }
-
     private static final Logger LOG = LoggerFactory.getLogger(BoxMipmapGeneratorTest.class);
 }

render-ws-java-client/src/main/java/org/janelia/acquire/client/AcquisitionDataImportClient.java

@@ -1,7 +1,23 @@
 package org.janelia.acquire.client;
 
 import com.beust.jcommander.Parameter;
-import org.janelia.acquire.client.model.*;
+import com.beust.jcommander.ParametersDelegate;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+
+import org.janelia.acquire.client.model.Acquisition;
+import org.janelia.acquire.client.model.AcquisitionTile;
+import org.janelia.acquire.client.model.AcquisitionTileIdList;
+import org.janelia.acquire.client.model.AcquisitionTileList;
+import org.janelia.acquire.client.model.AcquisitionTileState;
+import org.janelia.acquire.client.model.Calibration;
 import org.janelia.alignment.spec.ResolvedTileSpecCollection;
 import org.janelia.alignment.spec.TileSpec;
 import org.janelia.alignment.spec.TransformSpec;
@@ -12,25 +28,26 @@
 import org.janelia.render.client.ClientRunner;
 import org.janelia.render.client.ImportJsonClient;
 import org.janelia.render.client.RenderDataClient;
-import org.janelia.render.client.RenderDataClientParametersWithValidator;
+import org.janelia.render.client.parameter.CommandLineParameters;
+import org.janelia.render.client.parameter.RenderWebServiceParameters;
+import org.janelia.render.client.parameter.TileSpecValidatorParameters;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.util.*;
-
 /**
  * Java client that pulls tile data from an acquisition system and stores it in the render database.
  *
  * @author Cristian Goina (based on Eric Trautman's LowLatencyMontageClient)
  */
 public class AcquisitionDataImportClient {
 
-    @SuppressWarnings("ALL")
-    static class Parameters extends RenderDataClientParametersWithValidator {
+    public static class Parameters extends CommandLineParameters {
+
+        @ParametersDelegate
+        RenderWebServiceParameters renderWeb = new RenderWebServiceParameters();
 
-        // NOTE: --baseDataUrl, --owner, --project, --validatorClass, and --validatorData parameters defined in RenderDataClientParameters
-        // NOTE: --validatorClass and --validatorData parameters defined in RenderDataClientParametersWithValidator
+        @ParametersDelegate
+        TileSpecValidatorParameters tileSpecValidator = new TileSpecValidatorParameters();
 
         @Parameter(names = "--finalStackState", description = "State render stack should have after import (default is COMPLETE)", required = false)
         StackMetaData.StackState finalStackState;
@@ -85,7 +102,7 @@ public static void main(final String[] args) {
             @Override
             public void runClient(final String[] args) throws Exception {
                 final Parameters parameters = new Parameters();
-                parameters.parse(args, AcquisitionDataImportClient.class);
+                parameters.parse(args);
 
                 LOG.info("runClient: entry, parameters={}", parameters);
 
@@ -121,7 +138,7 @@ public void runClient(final String[] args) throws Exception {
     public AcquisitionDataImportClient(final Parameters parameters)
             throws IOException {
         this.parameters = parameters;
-        this.tileSpecValidator = parameters.getValidatorInstance();
+        this.tileSpecValidator = parameters.tileSpecValidator.getValidatorInstance();
 
         this.acquisitionDataClient = new AcquisitionDataClient(parameters.baseAcquisitionUrl);
 
@@ -199,7 +216,7 @@ public void processAcquisition(final Acquisition acquisition) {
         try {
             String ownerName = acquisition.getProjectOwner();
             if (parameters.overrideOwnerFromParameter) {
-                ownerName = parameters.owner;
+                ownerName = parameters.renderWeb.owner;
             }
             if (ownerName == null || ownerName.trim().length() == 0) {
                 throw new IllegalArgumentException("Owner for acquisition " + acqId + " is null");
@@ -218,7 +235,7 @@ public void processAcquisition(final Acquisition acquisition) {
 
             final String acquireStackName = baseStackName + "_acquire";
 
-            final RenderDataClient renderDataClient = new RenderDataClient(parameters.baseDataUrl,
+            final RenderDataClient renderDataClient = new RenderDataClient(parameters.renderWeb.baseDataUrl,
                                                                            ownerName,
                                                                            projectName);