replace hard-coded config values with properties settings

src/main/java/org/ecocean/Base.java

@@ -6,10 +6,13 @@
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import java.io.File;
 import java.io.IOException;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ExecutorService;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+
 import javax.jdo.Query;
 import org.ecocean.api.ApiException;
 import org.ecocean.OpenSearch;
@@ -113,9 +116,25 @@ public void opensearchIndexDeep()
 
     public void opensearchUnindex()
     throws IOException {
-        OpenSearch opensearch = new OpenSearch();
+        // unindexing should be non-blocking and backgrounded
+        String opensearchIndexName = this.opensearchIndexName();
+        String objectId = this.getId();
+        ExecutorService executor = Executors.newFixedThreadPool(4);
+        Runnable rn = new Runnable() {
+            OpenSearch opensearch = new OpenSearch();
+            public void run() {
+                try {
+                    opensearch.delete(opensearchIndexName, objectId);
+                } catch (Exception e) {
+                    System.out.println("opensearchUnindex() backgrounding Object " + objectId +
+                        " hit an exception.");
+                    e.printStackTrace();
+                }
+                executor.shutdown();
+            }
+        };
 
-        opensearch.delete(this.opensearchIndexName(), this);
+        executor.execute(rn);
     }
 
     public void opensearchUnindexQuiet() {
@@ -135,12 +154,8 @@ public void opensearchUnindexDeep()
     }
 
     // should be overridden
-    public void opensearchDocumentSerializer(JsonGenerator jgen)
+    public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd)
     throws IOException, JsonProcessingException {
-        Shepherd myShepherd = new Shepherd("context0");
-
-        myShepherd.setAction("BaseSerializer");
-        myShepherd.beginDBTransaction();
         jgen.writeStringField("id", this.getId());
         jgen.writeNumberField("version", this.getVersion());
 
@@ -157,8 +172,19 @@ public void opensearchDocumentSerializer(JsonGenerator jgen)
             jgen.writeString(id);
         }
         jgen.writeEndArray();
-        myShepherd.rollbackDBTransaction();
-        myShepherd.closeDBTransaction();
+    }
+
+    public void opensearchDocumentSerializer(JsonGenerator jgen)
+    throws IOException, JsonProcessingException {
+        Shepherd myShepherd = new Shepherd("context0");
+
+        myShepherd.setAction("BaseSerializer");
+        myShepherd.beginDBTransaction();
+        try {
+            opensearchDocumentSerializer(jgen, myShepherd);
+        } catch (Exception e) {} finally {
+            myShepherd.rollbackAndClose();
+        }
     }
 
     public static JSONObject opensearchQuery(final String indexname, final JSONObject query,

src/main/java/org/ecocean/Encounter.java

@@ -8,6 +8,8 @@
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ExecutorService;
 import java.util.concurrent.ThreadPoolExecutor;
 import java.util.Calendar;
 import java.util.Collection;
@@ -154,7 +156,6 @@ public void setSampleTakenForDiet(Boolean sampleTakenForDiet) {
     private static HashMap<String, ArrayList<Encounter> > _matchEncounterCache = new HashMap<String,
         ArrayList<Encounter> >();
 
-
     // An URL to a thumbnail image representing the encounter.
     private String dwcImageURL;
 
@@ -678,13 +679,12 @@ public boolean hasRightSpotImage() {
         return (this.getNumRightSpots() > 0);
     }
 
-
     // Sets the recorded length of the shark for this encounter.
     public void setSize(Double mysize) {
         if (mysize != null) { size = mysize; } else { size = null; }
     }
 
-    // @return the length of the shark 
+    // @return the length of the shark
     public double getSize() {
         return size.doubleValue();
     }
@@ -2450,9 +2450,10 @@ public void setTissueSamples(List<TissueSample> samps) {
     public Set<String> getTissueSampleIDs() {
         Set<String> ids = new HashSet<String>();
 
-        if (tissueSamples != null) for (TissueSample ts : tissueSamples) {
-            ids.add(ts.getSampleID());
-        }
+        if (tissueSamples != null)
+            for (TissueSample ts : tissueSamples) {
+                ids.add(ts.getSampleID());
+            }
         return ids;
     }
 
@@ -3860,10 +3861,20 @@ public static org.json.JSONObject opensearchQuery(final org.json.JSONObject quer
 
     public void opensearchDocumentSerializer(JsonGenerator jgen)
     throws IOException, JsonProcessingException {
-        super.opensearchDocumentSerializer(jgen);
         Shepherd myShepherd = new Shepherd("context0");
+
         myShepherd.setAction("Encounter.opensearchDocumentSerializer");
         myShepherd.beginDBTransaction();
+        try {
+            opensearchDocumentSerializer(jgen, myShepherd);
+        } catch (Exception e) {} finally {
+            myShepherd.rollbackAndClose();
+        }
+    }
+
+    public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd)
+    throws IOException, JsonProcessingException {
+        super.opensearchDocumentSerializer(jgen, myShepherd);
 
         jgen.writeStringField("locationId", this.getLocationID());
         jgen.writeStringField("locationName", this.getLocationName());
@@ -4052,7 +4063,6 @@ public void opensearchDocumentSerializer(JsonGenerator jgen)
                 encDate = Util.getISO8601Date(encs[encs.length - 1].getDate());
                 if (encDate != null) jgen.writeStringField("individualLastEncounterDate", encDate);
             }
-
             jgen.writeArrayFieldStart("individualSocialUnits");
             for (SocialUnit su : myShepherd.getAllSocialUnitsForMarkedIndividual(indiv)) {
                 Membership mem = su.getMembershipForMarkedIndividual(indiv);
@@ -4117,7 +4127,6 @@ public void opensearchDocumentSerializer(JsonGenerator jgen)
             jgen.writeNumberField(type, bmeas.get(type).getValue());
         }
         jgen.writeEndObject();
-        myShepherd.rollbackAndClose();
     }
 
     @Override public long getVersion() {
@@ -4335,9 +4344,13 @@ public static Object validateFieldValue(String fieldName, org.json.JSONObject da
                 // this is throwaway read-only shepherd
                 Shepherd myShepherd = new Shepherd("context0");
                 myShepherd.setAction("Encounter.validateFieldValue");
+                boolean validTaxonomy = false;
                 myShepherd.beginDBTransaction();
-                boolean validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue);
-                myShepherd.rollbackDBTransaction();
+                try {
+                    validTaxonomy = myShepherd.isValidTaxonomyName((String)returnValue);
+                } catch (Exception e) { e.printStackTrace(); } finally {
+                    myShepherd.rollbackAndClose();
+                }
                 if (!validTaxonomy) {
                     error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
                     error.put("value", returnValue);
@@ -4479,4 +4492,33 @@ public void sendCreationEmails(Shepherd myShepherd, String langCode) {
             myShepherd.rollbackDBTransaction();
         }
     }
+
+    public void opensearchIndexDeep()
+    throws IOException {
+        final String encId = this.getId();
+        ExecutorService executor = Executors.newFixedThreadPool(4);
+        Runnable rn = new Runnable() {
+            public void run() {
+                Shepherd bgShepherd = new Shepherd("context0");
+                bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId);
+                bgShepherd.beginDBTransaction();
+                try {
+                    Encounter enc = bgShepherd.getEncounter(encId);
+                    if (enc == null) {
+                        bgShepherd.rollbackAndClose();
+                        executor.shutdown();
+                        return;
+                    }
+                    enc.opensearchIndex();
+                } catch (Exception e) {
+                    e.printStackTrace();
+                } finally {
+                    bgShepherd.rollbackAndClose();
+                }
+                executor.shutdown();
+            }
+        };
+
+        executor.execute(rn);
+    }
 }

src/main/java/org/ecocean/MarkedIndividual.java

@@ -2602,7 +2602,7 @@ public void opensearchIndexDeep()
         Runnable rn = new Runnable() {
             public void run() {
                 Shepherd bgShepherd = new Shepherd("context0");
-                bgShepherd.setAction("MarkedIndividual.opensearchIndexDeep");
+                bgShepherd.setAction("MarkedIndividual.opensearchIndexDeep_" + indivId);
                 bgShepherd.beginDBTransaction();
                 try {
                     MarkedIndividual indiv = bgShepherd.getMarkedIndividual(indivId);
@@ -2625,6 +2625,10 @@ public void run() {
                             ex.printStackTrace();
                         }
                     }
+                } catch (Exception e) {
+                    System.out.println("opensearchIndexDeep() backgrounding MarkedIndividual " +
+                        indivId + " hit an exception.");
+                    e.printStackTrace();
                 } finally {
                     bgShepherd.rollbackAndClose();
                 }

src/main/java/org/ecocean/Occurrence.java

@@ -3,6 +3,8 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ExecutorService;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -95,7 +97,7 @@ public class Occurrence extends Base implements java.io.Serializable {
     private Integer numCalves;
     private String observer;
 
-    private String submitterID; 
+    private String submitterID;
     private List<User> submitters;
     private List<User> informOthers;
 
@@ -383,12 +385,12 @@ public ArrayList<String> getMarkedIndividualNamesForThisOccurrence() {
         return names;
     }
 
-    //TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
+    // TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
     public void setID(String id) {
         occurrenceID = id;
     }
 
-    //TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
+    // TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
     public String getID() {
         return occurrenceID;
     }
@@ -401,7 +403,7 @@ public String getWebUrl(HttpServletRequest req) {
         return getWebUrl(getOccurrenceID(), req);
     }
 
-    //TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
+    // TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
     public String getOccurrenceID() {
         return occurrenceID;
     }
@@ -416,7 +418,7 @@ public String getOccurrenceID() {
         occurrenceID = id;
     }
 
-    //TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
+    // TODO: validate and remove if ##DEPRECATED #509 - Base class setId() method
     public void setOccurrenceID(String id) {
         occurrenceID = id;
     }
@@ -1354,11 +1356,50 @@ public org.json.JSONObject getJSONSummary() {
     // has to be handled at the point of removal, e.g. OccurrenceRemoveEncounter servlet
     public void opensearchIndexDeep()
     throws IOException {
-        if (this.encounters != null)
-            for (Encounter enc : this.encounters) {
-                enc.opensearchIndex();
-            }
         this.opensearchIndex();
+
+        final String occurId = this.getId();
+        ExecutorService executor = Executors.newFixedThreadPool(4);
+        Runnable rn = new Runnable() {
+            public void run() {
+                Shepherd bgShepherd = new Shepherd("context0");
+                bgShepherd.setAction("Occurrence.opensearchIndexDeep_" + occurId);
+                bgShepherd.beginDBTransaction();
+                try {
+                    Occurrence occur = bgShepherd.getOccurrence(occurId);
+                    if ((occur == null) || (occur.getEncounters() == null)) {
+                        bgShepherd.rollbackAndClose();
+                        executor.shutdown();
+                        return;
+                    }
+                    int total = occur.getNumberEncounters();
+                    int ct = 0;
+                    for (Encounter enc : occur.getEncounters()) {
+                        ct++;
+                        System.out.println("opensearchIndexDeep() background indexing " +
+                            enc.getId() + " via " + occurId + " [" + ct + "/" + total + "]");
+                        try {
+                            enc.opensearchIndex();
+                        } catch (Exception ex) {
+                            System.out.println("opensearchIndexDeep() background indexing " +
+                                enc.getId() + " FAILED: " + ex.toString());
+                            ex.printStackTrace();
+                        }
+                    }
+                } catch (Exception e) {
+                    System.out.println("opensearchIndexDeep() backgrounding Occurrence " + occurId +
+                        " hit an exception.");
+                    e.printStackTrace();
+                } finally {
+                    bgShepherd.rollbackAndClose();
+                }
+                System.out.println("opensearchIndexDeep() backgrounding Occurrence " + occurId +
+                    " finished.");
+                executor.shutdown();
+            }
+        };
+
+        executor.execute(rn);
     }
 
     @Override public long getVersion() {