Resolve even more fields when exporing to Nahima

src/main/java/edu/harvard/mcz/imagecapture/CandidateImageFile.java

@@ -1050,7 +1050,7 @@ private TextStatus checkSourceForBarcode(LuminanceSource source,
             returnValue.setText(result.getText());
             returnValue.setStatus(RESULT_BARCODE_SCANNED);
         } catch (ReaderException e) {
-            log.error(e.getClass().toString() + " " + e.getMessage());
+            log.error(e.getClass() + " " + e.getMessage());
             if (!Singleton.getSingletonInstance()
                     .getProperties()
                     .getProperties()
@@ -1076,13 +1076,13 @@ private TextStatus checkSourceForBarcode(LuminanceSource source,
                     returnValue.setStatus(RESULT_ERROR);
                 } catch (ArrayIndexOutOfBoundsException e1) {
                     log.error(e.getMessage());
-                    returnValue.setText(e1.toString() + " " + e1.getMessage());
+                    returnValue.setText(e1 + " " + e1.getMessage());
                     returnValue.setStatus(RESULT_ERROR);
                 }
             }
         } catch (ArrayIndexOutOfBoundsException e) {
             log.error(e.getMessage());
-            returnValue.setText(e.toString() + " " + e.getMessage());
+            returnValue.setText(e + " " + e.getMessage());
             returnValue.setStatus(RESULT_ERROR);
         }
         return returnValue;

src/main/java/edu/harvard/mcz/imagecapture/ConvertTesseractOCR.java

@@ -146,17 +146,17 @@ public String getOCRText() throws OCRReadException {
                 // String runCommand = "convert temptiff.jpg -depth 8 temptiff.tif";
                 List<String> runCommand = new ArrayList<>();
                 runCommand.addAll(Arrays.asList(Singleton.getSingletonInstance()
-                        .getProperties()
-                        .getProperties()
-                        .getProperty(ImageCaptureProperties.KEY_CONVERT_EXECUTABLE),
+                                .getProperties()
+                                .getProperties()
+                                .getProperty(ImageCaptureProperties.KEY_CONVERT_EXECUTABLE),
                         "temptiff.jpg",
                         Singleton.getSingletonInstance()
                                 .getProperties()
                                 .getProperties()
                                 .getProperty(ImageCaptureProperties.KEY_CONVERT_PARAMETERS),
                         "temptiff.tif"));
                 log.debug("in ConvertTesseractOCR.getOCRText() 11 runCommand is " +
-                        runCommand.toString());
+                        runCommand);
                 Runtime r = Runtime.getRuntime();
                 log.debug("in ConvertTesseractOCR.getOCRText() 12");
                 Process proc = r.exec((String[]) runCommand.toArray());

src/main/java/edu/harvard/mcz/imagecapture/ImageCaptureProperties.java

@@ -231,12 +231,11 @@ public class ImageCaptureProperties extends AbstractTableModel {
     public static String KEY_NAHIMA_URL = "nahima.url";
     public static String KEY_NAHIMA_PASSWORD = "nahima.password";
     public static String KEY_NAHIMA_USER = "nahima.user";
-
+    private final String propertiesFilename = "imagecapture.properties";
     /**
      * Private properties
      */
     private Properties properties = null;
-    private final String propertiesFilename = "imagecapture.properties";
     private String propertiesFilePath = null;
 
     public ImageCaptureProperties() {

src/main/java/edu/harvard/mcz/imagecapture/TesseractOCR.java

@@ -127,9 +127,9 @@ public String getOCRText() throws OCRReadException {
             // Run tesseract to OCR the target file.
             List<String> runCommand = new ArrayList<>();
             runCommand.addAll(Arrays.asList(Singleton.getSingletonInstance()
-                    .getProperties()
-                    .getProperties()
-                    .getProperty(ImageCaptureProperties.KEY_TESSERACT_EXECUTABLE),
+                            .getProperties()
+                            .getProperties()
+                            .getProperty(ImageCaptureProperties.KEY_TESSERACT_EXECUTABLE),
                     target, tempFileBase, language));
 
             Process proc = r.exec((String[]) runCommand.toArray());

src/main/java/edu/harvard/mcz/imagecapture/data/NahimaManager.java

@@ -25,7 +25,7 @@ public class NahimaManager extends AbstractRestClient {
     private final String username;
     private final String password;
     private String token;
-    private Map<String, Map<String, JSONObject>> resolveCache = new HashMap<String, Map<String, JSONObject>>();
+    private final Map<String, Map<String, JSONObject>> resolveCache = new HashMap<String, Map<String, JSONObject>>();
 
     public NahimaManager(String url, String username, String password) throws IOException, InterruptedException, RuntimeException {
         // normalize URL
@@ -191,6 +191,28 @@ public JSONObject searchForString(String searchString, String objectType, boolea
         return searchForString(searchString, objectType, "fulltext", ignoreCache);
     }
 
+    /**
+     * Search in Nahima for one string, get result only if just one result though
+     *
+     * @param search     the string to search for
+     * @param objectType the object type that is searched
+     * @return the object if there is only one, null if not
+     * @throws IOException
+     * @throws InterruptedException
+     */
+    public JSONObject resolveStringSearchToOne(String search, String objectType) throws IOException, InterruptedException {
+        JSONObject results = this.searchForString(search, objectType);
+
+        JSONArray foundObjects = (JSONArray) results.get("objects");
+        if (foundObjects.length() == 1) {
+            return (JSONObject) foundObjects.get(0);
+        } else {
+            // TODO: create / select correct
+            log.info("Got != 1 " + objectType + " status. {}", results);
+            return null;
+        }
+    }
+
     /**
      * Find a person in Nahima
      *
@@ -200,18 +222,10 @@ public JSONObject searchForString(String searchString, String objectType, boolea
      * @throws InterruptedException
      */
     public JSONObject resolvePerson(String personName) throws IOException, InterruptedException {
-        JSONObject results = this.searchForString(personName, "person");
+        JSONObject results = this.resolveStringSearchToOne(personName, "person");
         // TODO: check compliance, does it really match well? We use "must", so let's hope so, but the resolution could still go wrong.
-        // also, multiple could be returned.
-        // or, none, in which case we might need to create one
-        JSONArray foundPersons = (JSONArray) results.get("objects");
-        if (foundPersons.length() == 1) {
-            return (JSONObject) foundPersons.get(0);
-        } else {
-            // TODO: create / select correct
-            log.info("Got != 1 person. {}", results);
-            return null;
-        }
+        // TODO: create / select correct
+        return results;
     }
 
     /**
@@ -223,29 +237,38 @@ public JSONObject resolvePerson(String personName) throws IOException, Interrupt
      * @throws InterruptedException
      */
     public JSONObject resolveLocation(String location) throws IOException, InterruptedException {
-        JSONObject results = this.searchForString(location, "gazetteer");
+        JSONObject results = this.resolveStringSearchToOne(location, "gazetteer");
+        // TODO: create / select correct
+        return results;
+    }
 
-        JSONArray foundLocations = (JSONArray) results.get("objects");
-        if (foundLocations.length() == 1) {
-            return (JSONObject) foundLocations.get(0);
-        } else {
-            // TODO: create / select correct
-            log.info("Got != 1 location. {}", results);
-            return null;
-        }
+    /**
+     * Find a typusstatus in Nahima
+     *
+     * @param status the search string
+     * @return the nahima returned object if only one
+     * @throws IOException
+     * @throws InterruptedException
+     */
+    public JSONObject resolveTypeStatus(String status) throws IOException, InterruptedException {
+        JSONObject results = this.resolveStringSearchToOne(status, "typusstatus");
+        // TODO: create / select correct
+        return results;
     }
 
+    /**
+     * Generic function to resolve unit for a certain field
+     *
+     * @param unit        the unit to find in Nahima
+     * @param unitSubject the unit type
+     * @return
+     * @throws IOException
+     * @throws InterruptedException
+     */
     public JSONObject resolveUnitFor(String unit, String unitSubject) throws IOException, InterruptedException {
-        JSONObject results = this.searchForString(unit, unitSubject, "token");
-
-        JSONArray foundUnits = (JSONArray) results.get("objects");
-        if (foundUnits.length() == 1) {
-            return (JSONObject) foundUnits.get(0);
-        } else {
-            // TODO: create / select correct
-            log.info("Got != 1 unit. {}", results);
-            return null;
-        }
+        JSONObject results = this.resolveStringSearchToOne(unit, unitSubject);
+        // TODO: create / select correct
+        return results;
     }
 
     /**
@@ -274,6 +297,7 @@ public JSONObject resolveUnitForErrorRadius(String unit) throws IOException, Int
 
     /**
      * Find the location "Datum" in Nahima
+     *
      * @param format the datum to search for
      * @return the nahima returned object if only one
      * @throws IOException
@@ -294,22 +318,16 @@ public JSONObject resolveDatumFormat(String format) throws IOException, Interrup
 
     /**
      * Find the collection method in Nahima
+     *
      * @param method the collection method to search for
      * @return the nahima returned object if only one
      * @throws IOException
      * @throws InterruptedException
      */
     public JSONObject resolveCollectionMethod(String method) throws IOException, InterruptedException {
-        JSONObject results = this.searchForString(method, "sammlungsmethoden");
-
-        JSONArray foundMethods = (JSONArray) results.get("objects");
-        if (foundMethods.length() == 1) {
-            return (JSONObject) foundMethods.get(0);
-        } else {
-            // TODO: create / select correct
-            log.info("Got != 1 collecting method. {}", results);
-            return null;
-        }
+        JSONObject results = this.resolveStringSearchToOne(method, "sammlungsmethoden");
+        // TODO: create / select correct
+        return results;
     }
 
     /**

src/main/java/edu/harvard/mcz/imagecapture/jobs/NahimaExportJob.java

@@ -86,6 +86,7 @@ public void start() {
                         put("preferred", true);
                         put("_id", imageJsonObj.get("_id"));
                     }})));
+                    put("barcode", specimen.getBarcode());
                     put("urspruelicherdateiname", imageJsonObj.get("original_filename"));
                 }};
                 JSONObject reducedImageMediaAsset = new JSONObject(reducedMediaAssetMap);

src/main/java/edu/harvard/mcz/imagecapture/serializer/ToJSONSerializerInterface.java

@@ -3,6 +3,7 @@
 import org.json.JSONObject;
 
 public interface ToJSONSerializerInterface {
-    public JSONObject serialize2JSON(Object target);
-    public boolean supportsSerializationOf(Object target);
+    JSONObject serialize2JSON(Object target);
+
+    boolean supportsSerializationOf(Object target);
 }

src/main/java/edu/harvard/mcz/imagecapture/serializer/nahima/Specimen2JSONSerializer.java

@@ -1,10 +1,7 @@
 package edu.harvard.mcz.imagecapture.serializer.nahima;
 
 import edu.harvard.mcz.imagecapture.data.NahimaManager;
-import edu.harvard.mcz.imagecapture.entity.Collector;
-import edu.harvard.mcz.imagecapture.entity.Determination;
-import edu.harvard.mcz.imagecapture.entity.LatLong;
-import edu.harvard.mcz.imagecapture.entity.Specimen;
+import edu.harvard.mcz.imagecapture.entity.*;
 import edu.harvard.mcz.imagecapture.serializer.ToJSONSerializerInterface;
 import org.apache.commons.lang3.time.DateUtils;
 import org.json.JSONArray;
@@ -50,6 +47,16 @@ public JSONObject serialize2JSON(Object target) {
                 put("_pool", NahimaManager.defaultPool);
                 put("_id", JSONObject.NULL);
                 put("typusid", det.getTypeStatus());
+                put("typusstatustrans", det.getTypeStatus());
+                put("autortrans", det.getAuthorship()); // TODO: resolve
+                put("taxonnametrans", toSerialize.getAssociatedTaxon()); // TODO: resolve
+                put("familietrans", toSerialize.getFamily()); // TODO: resolve
+                put("genustrans", det.getGenus()); // TODO: resolve
+                put("subspezifischesarttrans", det.getSubspecificEpithet()); // TODO: resolve
+                put("bestimmertrans", det.getIdentifiedBy());
+                put("infraspezifischestaxontrans", det.getInfraspecificEpithet()); // TODO: resolve
+                put("infrapezifischerrangtrans", det.getInfraspecificRank()); // TODO: resolve
+                put("arttrans", det.getSpecificEpithet()); // TODO: resolve
             }};
 
             JSONObject reverseNestedDetermination = new JSONObject(reverseNestedCollectionMap);
@@ -63,12 +70,6 @@ public JSONObject serialize2JSON(Object target) {
                 log.error("Failed to parse bestimmungsdatum", e);
             }
 
-            reverseNestedDetermination.put("autortrans", det.getAuthorship()); // TODO: resolve
-            reverseNestedDetermination.put("taxonnametrans", toSerialize.getAssociatedTaxon()); // TODO: resolve
-            reverseNestedDetermination.put("familietrans", toSerialize.getFamily()); // TODO: resolve
-            reverseNestedDetermination.put("genustrans", det.getGenus()); // TODO: resolve
-            reverseNestedDetermination.put("subspezifischesarttrans", det.getSubspecificEpithet()); // TODO: resolve
-            reverseNestedDetermination.put("bestimmertrans", det.getIdentifiedBy());
             JSONArray identifierPersons = new JSONArray();
             try {
                 JSONObject identifierPerson = nahimaManager.resolvePerson(det.getIdentifiedBy());
@@ -79,6 +80,13 @@ public JSONObject serialize2JSON(Object target) {
                 log.info("Failed to resolve person", e);
             }
             reverseNestedDetermination.put("_nested:bestimmung__bestimmer_person", identifierPersons);
+
+            try {
+                JSONObject resolvedTypeStatus = nahimaManager.resolveTypeStatus(det.getTypeStatus());
+                reverseNestedDetermination.put("typusstatus", resolvedTypeStatus);
+            } catch (IOException | InterruptedException e) {
+                log.info("Failed to resolve type status", e);
+            }
             // TODO: other fields
 
             // finally,
@@ -96,6 +104,7 @@ public JSONObject serialize2JSON(Object target) {
             put("kommentare", toSerialize.getSpecimenNotes());
             put("habitattrans", toSerialize.getHabitat());
             put("sammelorttrans", toSerialize.getVerbatimLocality());
+            put("lokalitaet", toSerialize.getSpecificLocality());
             put("neuhabitat", wrapInLan(toSerialize.getHabitat()));
             put("mikrohabitat", wrapInLan(toSerialize.getMicrohabitat()));
             put("traegerorganismustrans", toSerialize.getAssociatedTaxon());
@@ -105,6 +114,7 @@ public JSONObject serialize2JSON(Object target) {
             put("fehlerradius", georef == null ? null : georef.getMaxErrorDistance());
             put("hoehemin", toSerialize.getMinimum_elevation());
             put("hoehemax", toSerialize.getMaximum_elevation());
+            put("lokalitaettrans", toSerialize.getVerbatimLocality());
             put("__idx", 0);
             put("_version", 1);
             put("_id", JSONObject.NULL);
@@ -169,7 +179,7 @@ public JSONObject serialize2JSON(Object target) {
                 reverseNestedCollection.put("datum", this.dateToNahima(toSerialize.getDateEmerged()));
             }
         } catch (ParseException e) {
-            log.error("Failed to parse datum " + toSerialize.getDateEmerged(), e);
+            log.error("Failed to parse datum " + toSerialize.getDateEmerged() + " " + toSerialize.getDateNos(), e);
         }
         reverseNestedCollection.put("indikator_fuer_kultur_zucht", toSerialize.getDateEmergedIndicator());
         reverseNestedCollection.put("sammeldatumtrans", toSerialize.getDateCollected());
@@ -183,6 +193,16 @@ public JSONObject serialize2JSON(Object target) {
         reverseNestedCollections.put(reverseNestedCollection);
         result.put("_reverse_nested:aufsammlung:entomologie", reverseNestedCollections);
 
+        JSONArray parts = new JSONArray();
+        for (SpecimenPart part : toSerialize.getSpecimenParts()) {
+            JSONObject partJson = new JSONObject(new HashMap<>() {{
+                put("anzahlpraeparatteile", part.getLotCount());
+            }});
+            // TODO: (resolve) other fields
+            parts.put(partJson);
+        }
+        result.put("_nested:entomologie__praeparatteile", parts);
+
 
         // TODO: other fields
 

src/main/java/edu/harvard/mcz/imagecapture/ui/component/JAccordionPanel.java

@@ -16,9 +16,9 @@ public class JAccordionPanel extends JPanel {
 
     private static final Logger log =
             LoggerFactory.getLogger(JAccordionPanel.class);
+    private final JScrollPane mainContent;
     private String titleOpen = "";
     private String titleClosed = "";
-    private final JScrollPane mainContent;
     private JButton toggleButton = null;
     private boolean contentVisible = false;
 

src/main/java/edu/harvard/mcz/imagecapture/ui/dialog/BatchUpdateDialog.java

@@ -157,7 +157,7 @@ private void doApplyChange() {
 
             int numAffected = updateQuery.executeUpdate();
             session.getTransaction().commit();
-            JOptionPane.showMessageDialog(this, "Changed " + String.valueOf(numAffected) + " values", "Success",
+            JOptionPane.showMessageDialog(this, "Changed " + numAffected + " values", "Success",
                     JOptionPane.INFORMATION_MESSAGE);
         } catch (Exception e) {
             log.error("Failed to do query update: " + e.getMessage(), e);

src/main/java/edu/harvard/mcz/imagecapture/ui/dialog/MeliaStatisticsDialog.java

@@ -4,7 +4,6 @@
 import edu.harvard.mcz.imagecapture.utility.CastUtility;
 import net.miginfocom.swing.MigLayout;
 import org.hibernate.Session;
-import org.hibernate.Transaction;
 import org.hibernate.query.Query;
 import org.jdatepicker.JDatePicker;
 import org.jdatepicker.UtilDateModel;

src/main/java/edu/harvard/mcz/imagecapture/ui/dialog/NahimaExportDialog.java

@@ -8,7 +8,6 @@
 
 import javax.swing.*;
 import java.awt.*;
-import java.awt.event.ActionListener;
 
 public class NahimaExportDialog extends JDialog implements ProgressListener {
     private static final Logger log =
@@ -44,7 +43,7 @@ private void initialize() {
                 didRunSuccessfully = false;
                 getResultsTextField().setText("Error: " + job.getLastException().getMessage());
             } else if (didRunSuccessfully) {
-                getResultsTextField().setText("Finished processing " + String.valueOf(job.getTotalCount()) + " Specimen");
+                getResultsTextField().setText("Finished processing " + job.getTotalCount() + " Specimen");
             }
             getCloseButton().setEnabled(true);
         });

src/main/java/edu/harvard/mcz/imagecapture/ui/frame/MainFrame.java

@@ -40,7 +40,6 @@
 import javax.swing.*;
 import javax.swing.text.DefaultEditorKit;
 import java.awt.*;
-import java.awt.event.ActionEvent;
 import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 import java.io.File;