tools for migrating codex data into wildbook

devops/development/.dockerfiles/smtp/dkim-keys/README.md

@@ -0,0 +1,2 @@
+your DKIM keys should go in here
+see: https://hub.docker.com/r/boky/postfix/

devops/development/.dockerfiles/tomcat/commonConfiguration.properties

@@ -56,9 +56,9 @@ allowAdoptions = false
 
 #email addresses and parameters
 sendEmailNotifications=true
-autoEmailAddress=info@wildbook.org
-newSubmissionEmail=donotreply@wildbook.org
-mailHost=localhost
+autoEmailAddress=noreply@wildme.org
+newSubmissionEmail=noreply@wildme.org
+mailHost=smtp
 removeEmailString=Do you want to REMOVE your email address from this database? Click the link below to remove it. You will no longer receive updates on your encounters.
 
 #HTML metadata for each page

devops/development/_env.template

@@ -6,6 +6,14 @@
 WILDBOOK_BASE_DIR=~/wildbook-dev
 
 
+# for smtp (postfix) usage:
+MAIL_HOSTNAME=example.com
+MAIL_ALLOWED_SENDER_DOMAINS=example.com
+MAIL_PORT=1587
+MAIL_RELAYHOST=example.com:587
+MAIL_RELAYHOST_USERNAME=changeme
+MAIL_RELAYHOST_PASSWORD=changeme
+
 
 
 # these rest of these settings are fine for a development environment, but can be changed if you desire

devops/development/docker-compose.yml

@@ -95,6 +95,23 @@ services:
       - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
       - "OPENSEARCH_INITIAL_ADMIN_PASSWORD=${OPENSEARCH_INITIAL_ADMIN_PASSWORD}"
 
+  # https://hub.docker.com/r/boky/postfix/
+  #  TODO dkim and spf needs to be added/supported
+  smtp:
+    image: boky/postfix
+    networks:
+      - intranet
+    ports:
+      - $MAIL_PORT:587
+    volumes:
+      - .dockerfiles/smtp/dkim-keys:/etc/opendkim/keys
+    environment:
+      - "HOSTNAME=${MAIL_HOSTNAME}"
+      - "ALLOWED_SENDER_DOMAINS=${MAIL_ALLOWED_SENDER_DOMAINS}"
+      - "RELAYHOST=${MAIL_RELAYHOST}"
+      - "RELAYHOST_USERNAME=${MAIL_RELAYHOST_USERNAME}"
+      - "RELAYHOST_PASSWORD=${MAIL_RELAYHOST_PASSWORD}"
+
   autoheal:
     image: willfarrell/autoheal
     volumes:

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

@@ -1427,6 +1427,12 @@ public boolean hasMarkedIndividual() {
         return (individual != null);
     }
 
+    public boolean hasMarkedIndividual(MarkedIndividual match) {
+        if (match == null) return false;
+        if (individual == null) return false;
+        return (match.getId().equals(individual.getId()));
+    }
+
     public void assignToMarkedIndividual(MarkedIndividual indiv) {
         setIndividual(indiv);
     }
@@ -2989,13 +2995,13 @@ public void setAnnotations(ArrayList<Annotation> anns) {
     public void addAnnotations(List<Annotation> anns) {
         if (annotations == null) annotations = new ArrayList<Annotation>();
         for (Annotation ann : anns) {
-            annotations.add(ann);
+            if (!annotations.contains(ann)) annotations.add(ann);
         }
     }
 
     public void addAnnotation(Annotation ann) {
         if (annotations == null) annotations = new ArrayList<Annotation>();
-        annotations.add(ann);
+        if (!annotations.contains(ann)) annotations.add(ann);
     }
 
     public void useAnnotationsForMatching(boolean use) {

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

@@ -1129,7 +1129,11 @@ public void setTaxonomyString(String tax) {
             setSpecificEpithet(tax);
         } else {
             setGenus(parts[0]);
-            setSpecificEpithet(parts[1]);
+            String ep = parts[1];
+            for (int i = 2 ; i < parts.length ; i++) {
+                ep += " " + parts[i];
+            }
+            setSpecificEpithet(ep);
         }
     }
 

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

@@ -155,22 +155,15 @@ public Occurrence(String occurrenceID) {
         System.out.println("Created new occurrence with only ID" + this.occurrenceID);
     }
 
+    public boolean hasEncounter(Encounter enc) {
+        return ((encounters != null) && encounters.contains(enc));
+    }
+
     public boolean addEncounter(Encounter enc) {
-        if (encounters == null) { encounters = new ArrayList<Encounter>(); }
-        // prevent duplicate addition
-        boolean isNew = true;
-        for (int i = 0; i < encounters.size(); i++) {
-            Encounter tempEnc = (Encounter)encounters.get(i);
-            if (tempEnc.getEncounterNumber().equals(enc.getEncounterNumber())) {
-                return false;
-            }
-        }
-        if (isNew) {
-            encounters.add(enc);
-            // updateNumberOfEncounters();
-        }
-        // if((locationID!=null) && (enc.getLocationID()!=null)&&(!enc.getLocationID().equals("None"))){this.locationID=enc.getLocationID();}
-        return isNew;
+        if (encounters == null) encounters = new ArrayList<Encounter>();
+        if (encounters.contains(enc)) return false;
+        encounters.add(enc);
+        return true;
     }
 
     // private void updateNumberOfEncounters() {

src/main/java/org/ecocean/OpenSearch.java

@@ -121,6 +121,10 @@ public static boolean isValidIndexName(String indexName) {
         return Arrays.asList(VALID_INDICES).contains(indexName);
     }
 
+    public static boolean skipAutoIndexing() {
+        return new java.io.File("/tmp/skipAutoIndexing").exists();
+    }
+
 // http://localhost:9200/encounter/_search?pretty=true&q=*:*
 // http://localhost:9200/_cat/indices?v
 

src/main/java/org/ecocean/WildbookLifecycleListener.java

@@ -4,6 +4,7 @@
 import javax.jdo.listener.*;
 import org.datanucleus.enhancement.Persistable;
 import org.ecocean.Base;
+import org.ecocean.OpenSearch;
 
 // https://www.datanucleus.org/products/accessplatform_4_1/jdo/lifecycle_callbacks.html#listeners
 
@@ -40,6 +41,11 @@ public void preStore(InstanceLifecycleEvent event) {}
     public void postStore(InstanceLifecycleEvent event) {
         Persistable obj = (Persistable)event.getSource();
 
+        if (OpenSearch.skipAutoIndexing()) {
+            System.out.println("WildbookLifecycleListener skipAutoIndexing set");
+            return;
+        }
+
         System.out.println("WildbookLifecycleListener postStore() event type=" +
             event.getEventType() + "; source=" + obj + "; target=" + event.getTarget() +
             "; detachedInstance=" + event.getDetachedInstance() + "; persistentInstance=" +

src/main/java/org/ecocean/social/Relationship.java

@@ -162,6 +162,11 @@ public void setBidirectional(Boolean direction) {
         if (direction != null) { bidirectional = direction; } else { bidirectional = null; }
     }
 
+    public String toString() {
+        return this.type + ": " + this.individual1.getId() + "[" + this.getMarkedIndividualRole1() + "] + " +
+            this.individual2.getId() + "[" + this.getMarkedIndividualRole2() + "]";
+    }
+
     public JSONObject decorateJson(HttpServletRequest request, JSONObject jobj)
     throws JSONException {
         if (individual1 != null) jobj.put("individual1", this.individual1.uiJson(request, false));

src/main/resources/bundles/codexMigration.properties

@@ -0,0 +1,3 @@
+codexDbUrl=jdbc:postgresql://localhost:5432/codex
+codexDbUsername=example
+codexDbPassword=example