[GEOS-6992] Add gdalwarp/gdal_translate/gdaladdo transformation suppo…

…rt in importer

doc/en/user/source/extensions/importer/rest_examples.rst

@@ -401,4 +401,69 @@ If all goes well the new layer is created in PostGIS and registered in GeoServer
 
 In case the features in the CSV need to be appended to an existing layer a PUT request against the task might be performed, changing its
 updateMode from "CREATE" to "APPEND". Changing it to "REPLACE" instead will preserve the layer, but remove the old conents and replace
-them with the newly uploaded ones.
+them with the newly uploaded ones.
+
+Uploading and optimizing a GeoTiff with ground control points 
+-------------------------------------------------------------
+
+A data supplier is periodically providing GeoTiffs that we need to configure in GeoServer.
+The GeoTIFF is referenced via Ground Control Points, is organized by stripes, and has no overviews.
+The objective is to rectify, optimize and publish it via the importer.
+
+First, we are going to create a empty import with no store as the target::
+
+    curl -u admin:geoserver -XPOST -H "Content-type: application/json" -d @import.json "http://localhost:8080/geoserver/rest/imports"
+
+Where import.json is::
+
+    {
+       "import": {
+          "targetWorkspace": {
+             "workspace": {
+                "name": "sf"
+             }
+          }
+       }
+    }
+
+Then, we are going to POST the GeoTiff file to the tasks list, in order to create an import task for it::
+
+    curl -u admin:geoserver -F name=test -F filedata=@box_gcp_fixed.tif "http://localhost:8080/geoserver/rest/imports/0/tasks"
+    
+We are then going to append the transformations to rectify (gdalwarp), retile (gdal_translate) and add overviews (gdaladdo) to it:
+
+   curl -u admin:geoserver -XPOST -H "Content-type: application/json" -d @warp.json "http://localhost:8080/geoserver/rest/imports/0/tasks/0/transforms"
+   curl -u admin:geoserver -XPOST -H "Content-type: application/json" -d @gtx.json "http://localhost:8080/geoserver/rest/imports/0/tasks/0/transforms"
+   curl -u admin:geoserver -XPOST -H "Content-type: application/json" -d @gad.json "http://localhost:8080/geoserver/rest/imports/0/tasks/0/transforms"
+
+
+``warp.json`` is::
+
+    {
+      "type": "GdalWarpTransform",
+      "options": [ "-t_srs", "EPSG:4326"]
+    }
+
+
+``gtx.json`` is:
+
+    {
+      "type": "GdalTranslateTransform",
+      "options": [ "-co", "TILED=YES", "-co", "BLOCKXSIZE=512", "-co", "BLOCKYSIZE=512"]
+    }
+
+``gad.json`` is::
+
+    {
+      "type": "GdalAddoTransform",
+      "options": [ "-r", "average"],
+      "levels" : [2, 4, 8, 16]
+    }
+
+    
+Now the import is ready to run, and we'll execute it using::
+
+    curl -u admin:geoserver -XPOST "http://localhost:8080/geoserver/rest/imports/0"
+
+A new layer ``box_gcp_fixed`` layer will appear in GeoServer, with an underlying GeoTiff file ready
+for web serving.

doc/en/user/source/extensions/importer/rest_reference.rst

@@ -910,3 +910,54 @@ Reprojects a vector layer from a source CRS to a target CRS
      - N
      - Identifier of the target coordinate reference system
 
+GdalTranslateTransform
+""""""""""""""""""""""
+
+Applies ``gdal_translate`` to a single file raster input. Requires ``gdal_translate`` to be inside the PATH used by the web container running GeoServer.
+
+
+.. list-table::
+   :header-rows: 1
+
+   * - Parameter
+     - Optional
+     - Description
+   * - options
+     - N
+     - Array of options that will be passed to ``gdal_translate`` (beside the input and output names, which are internally managed)
+
+GdalWarpTransform
+"""""""""""""""""
+
+Applies ``gdalwarp`` to a single file raster input. Requires ``gdalwarp`` to be inside the PATH used by the web container running GeoServer.
+
+
+.. list-table::
+   :header-rows: 1
+
+   * - Parameter
+     - Optional
+     - Description
+   * - options
+     - N
+     - Array of options that will be passed to ``gdalwarp`` (beside the input and output names, which are internally managed)
+
+GdalAddoTransform
+"""""""""""""""""
+
+Applies ``gdaladdo`` to a single file raster input. Requires ``gdaladdo`` to be inside the PATH used by the web container running GeoServer.
+
+
+.. list-table::
+   :header-rows: 1
+
+   * - Parameter
+     - Optional
+     - Description
+   * - options
+     - N
+     - Array of options that will be passed to ``gdaladdo`` (beside the input file name, which is internally managed)
+   * - levels
+     - N
+     - Array of integers with the overview levels that will be passed to ``gdaladdo``
+

src/extension/importer/core/pom.xml

@@ -51,6 +51,10 @@
       <artifactId>javacsv</artifactId>
       <version>2.0</version>
     </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-exec</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.geotools</groupId>
       <artifactId>gt-epsg-wkt</artifactId>

src/extension/importer/core/src/main/java/org/geoserver/importer/Directory.java

@@ -26,8 +26,8 @@
 import org.apache.commons.fileupload.FileItem;
 import org.apache.commons.io.FilenameUtils;
 import org.geoserver.data.util.IOUtils;
-import org.geotools.util.logging.Logging;
 import org.geoserver.importer.job.ProgressMonitor;
+import org.geotools.util.logging.Logging;
 
 import com.google.common.base.Predicate;
 import com.google.common.collect.Iterables;
@@ -135,17 +135,23 @@ public void prepare(ProgressMonitor m) throws IOException {
         while(!q.isEmpty()) {
             File dir = q.poll();
 
-            if (m.isCanceled()){
+            if (m.isCanceled()) {
                 return;
             }
             m.setTask("Scanning " + dir.getPath());
 
             //get all the regular (non directory) files
-            Set<File> all = new LinkedHashSet<File>(Arrays.asList(dir.listFiles(new FilenameFilter() {
+            File[] fileList = dir.listFiles(new FilenameFilter() {
                 public boolean accept(File dir, String name) {
                     return !new File(dir, name).isDirectory();
                 }
-            })));
+            });
+            if (fileList == null) {
+                // it can be null in case of I/O error, even if the
+                // dir is indeed a directory
+                continue;
+            }
+            Set<File> all = new LinkedHashSet<File>(Arrays.asList(fileList));
 
             //scan all the files looking for spatial ones
             for (File f : dir.listFiles()) {

src/extension/importer/core/src/main/java/org/geoserver/importer/Importer.java

@@ -816,17 +816,17 @@ void doDirectImport(ImportTask task) throws IOException {
         task.setState(ImportTask.State.RUNNING);
 
         try {
-            //set up transform chain
+            // set up transform chain
             TransformChain tx = task.getTransform();
 
-            //apply pre transform
+            // apply pre transform
             if (!doPreTransform(task, task.getData(), tx)) {
                 return;
             }
 
             addToCatalog(task);
 
-            //apply pre transform
+            // apply post transform
             if (!doPostTransform(task, task.getData(), tx)) {
                 return;
             }