Update Plate/Image naming to match new design proposal

This removes the automatic setting of user-specified names in the importer, so that later calls to retrieve the user-specified name are guaranteed to return only what the user actually specified (or null by default). Plate and Image names supplied by the reader are trusted when the user has not specified a name. The name(s) will be set to the relative path of the imported file only if both the user- and reader-specified names are null. The issue of 255 character limits on name fields has not been addressed here, but a comment has been added so that it's easier to go back to later.
ome · Dec 9, 2016 · 94575d5 · 94575d5
1 parent 3746fbe
commit 94575d5
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Showing 4 changed files with 20 additions and 23 deletions.
diff --git a/components/blitz/src/ome/formats/importer/ImportCandidates.java b/components/blitz/src/ome/formats/importer/ImportCandidates.java
@@ -437,14 +437,7 @@ protected ImportContainer singleFile(File file, ImportConfig config)
                 ic.setDoThumbnails(config.doThumbnails.get());
                 ic.setNoStatsInfo(config.noStatsInfo.get());
                 String configImageName = config.userSpecifiedName.get();
-                if (configImageName == null)
-                {
-                    ic.setUserSpecifiedName(file.getName());
-                }
-                else
-                {
-                    ic.setUserSpecifiedName(configImageName);
-                }
+                ic.setUserSpecifiedName(configImageName);
                 ic.setUserSpecifiedDescription(config.userSpecifiedDescription.get());
                 ic.setCustomAnnotationList(config.annotations.get());
                 return ic;

diff --git a/components/blitz/src/ome/formats/importer/ImportFixture.java b/components/blitz/src/ome/formats/importer/ImportFixture.java
@@ -112,7 +112,6 @@ public void doImport() throws Throwable
         {
 		ic = new ImportContainer(file, fads.get(file),
 					null, null, null, null);
-		ic.setUserSpecifiedName(file.getAbsolutePath());
 		library.importImage(ic, 0, 0, 1);
         /*
 		library.importImage(file, 0, 0, 1, file.getAbsolutePath(),

diff --git a/components/blitz/src/ome/formats/model/PixelsProcessor.java b/components/blitz/src/ome/formats/model/PixelsProcessor.java
@@ -27,6 +27,7 @@
 
 import static ome.formats.model.UnitsFactory.makeLength;
 
+import java.io.File;
 import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
@@ -124,14 +125,18 @@ public void process(IObjectContainerStore store) throws ModelException {
       }
 
       // Ensure that the Image name is set
+
+      // name supplied by user
       String userSpecifiedName = store.getUserSpecifiedName();
       if (userSpecifiedName != null) {
         userSpecifiedName = userSpecifiedName.trim();
         if (userSpecifiedName.isEmpty()) {
           userSpecifiedName = null;
         }
       }
+      // name that will actually be set on the Image
       String saveName = "";
+      // name supplied by the reader
       String imageName;
       if (image.getName() != null && image.getName().getValue() != null) {
         imageName = image.getName().getValue().trim();
@@ -150,9 +155,17 @@ public void process(IObjectContainerStore store) throws ModelException {
           }
           saveName += " [" + imageName + "]";
         }
-      } else {
+      } else if (imageName != null) {
         saveName = imageName;
       }
+      else {
+        saveName = reader.getCurrentFile();
+        saveName = saveName.substring(saveName.lastIndexOf(File.separator) + 1);
+        if (reader.getSeriesCount() > 1) {
+          saveName += " [" + imageIndex + "]";
+        }
+      }
+      // TODO: remove this if/when name is switched to TEXT in the DB
       if (saveName != null && saveName.length() > 255) {
         saveName = '…' + saveName.substring(saveName.length() - 254);
       }

diff --git a/components/blitz/src/ome/formats/model/WellProcessor.java b/components/blitz/src/ome/formats/model/WellProcessor.java
@@ -26,6 +26,7 @@
 import static omero.rtypes.rint;
 import static omero.rtypes.rstring;
 
+import java.io.File;
 import java.util.LinkedHashMap;
 import java.util.List;
 
@@ -96,23 +97,14 @@ private Plate validatePlate(int plateIndex) {
     String userSpecifiedPlateName = store.getUserSpecifiedName();
     String userSpecifiedPlateDescription = store.getUserSpecifiedDescription();
 
-    // precedence order for plate naming:
-    //
-    // 1. user specified, if not default name of imported file
-    // 2. reader supplied, if not null
-    // 3. user specified (name of imported file)
-    // 4. "Plate"
     if (userSpecifiedPlateName != null) {
-      String currentFile = store.getReader().getCurrentFile();
-      if (!currentFile.endsWith(userSpecifiedPlateName) ||
-        plate.getName() == null)
-      {
-        plate.setName(rstring(userSpecifiedPlateName));
-      }
+      plate.setName(rstring(userSpecifiedPlateName));
     }
     if (plate.getName() == null) {
       log.warn("Missing plate name for: " + container.LSID);
-      plate.setName(rstring("Plate"));
+      String filename = store.getReader().getCurrentFile();
+      filename = filename.substring(filename.lastIndexOf(File.separator) + 1);
+      plate.setName(rstring(filename));
     }
 
     if (userSpecifiedPlateDescription != null) {