Various minor improvements to Nahima export

BernhardWebstudio · Jan 31, 2024 · fe320bc · fe320bc
1 parent 41ba32c
commit fe320bc
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Showing 3 changed files with 15 additions and 7 deletions.
diff --git a/src/main/java/edu/harvard/mcz/imagecapture/jobs/NahimaExportJob.java b/src/main/java/edu/harvard/mcz/imagecapture/jobs/NahimaExportJob.java
@@ -23,6 +23,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.*;
+import java.util.stream.Collectors;
 
 public class NahimaExportJob implements RunnableJob, Runnable {
     private static final Logger log = LoggerFactory.getLogger(NahimaExportJob.class);
@@ -37,15 +38,15 @@ public class NahimaExportJob implements RunnableJob, Runnable {
     private int status = STATUS_RUNNING_FINE;
     private Exception lastError = null;
     private String oneSpecimenBarcode = null;
-    private List<Specimen> specimenToExport = null;
+    private List<Long> specimenToExport = null;
     private boolean anon = false;
 
     public void setOneSpecimenToExportBarcode(String oneSpecimenBarcode) {
         this.oneSpecimenBarcode = oneSpecimenBarcode;
     }
 
     public void setSpecimenToExport(List<Specimen> specimenToExport) {
-        this.specimenToExport = specimenToExport;
+        this.specimenToExport = specimenToExport.stream().map(spec -> spec.getSpecimenId()).collect(Collectors.toList());
     }
 
     public void goAnon() {
@@ -66,9 +67,9 @@ public void start() {
                 Map<String, Object> queryParams = new HashMap<>();
                 queryParams.put("nahimaExported", false);
                 queryParams.put("barcode", this.oneSpecimenBarcode);
-                specimenToExport = sls.findBy(queryParams);
+                specimenToExport = sls.findBy(queryParams).stream().map(spec -> spec.getSpecimenId()).collect(Collectors.toList());
             } else {
-                specimenToExport = sls.findToExport();
+                specimenToExport = sls.findIdsToExport();
             }
         }
         Collections.shuffle(specimenToExport);
@@ -94,8 +95,14 @@ public void start() {
 
         Specimen2JSONSerializer serializer = new Specimen2JSONSerializer(manager);
 
-        for (Specimen specimen : specimenToExport) {
+        for (Long specimenId : specimenToExport) {
+            Specimen specimen = sls.findById(specimenId);
             currentIndex = currentIndex + 1;
+            // check if it hasn't been exported by another instance already
+            if (specimen.getDateLastNahimaUpdated() != null && specimen.getDateLastNahimaUpdated().after(specimen.getDateLastUpdated())) {
+                continue;
+            }
+
             log.debug("Exporting specimen " + currentIndex + "/" + nrOfSpecimenToProcess + " with id " + specimen.getSpecimenId() + " and barcode " + specimen.getBarcode());
             notifyWorkStatusChanged("Exporting specimen " + currentIndex + "/" + nrOfSpecimenToProcess + " with id " + specimen.getSpecimenId() + " and barcode " + specimen.getBarcode());
 

diff --git a/src/main/java/edu/harvard/mcz/imagecapture/lifecycle/SpecimenLifeCycle.java b/src/main/java/edu/harvard/mcz/imagecapture/lifecycle/SpecimenLifeCycle.java
@@ -464,7 +464,7 @@ public List<Specimen> findAllPage(int startAt, int fetchSize) {
      *
      * @return
      */
-    public List<Specimen> findToExport() {
+    public List<Long> findIdsToExport() {
         try {
             Session session = this.getSession();
             try {
@@ -480,7 +480,7 @@ public List<Specimen> findToExport() {
                 Query q = session.createQuery(cr);
                 List<Long> ids = q.list();
                 session.getTransaction().commit();
-                return this.findByIds(ids);
+                return ids;
             } catch (HibernateException e) {
                 session.getTransaction().rollback();
                 log.error("find images failed", e);

diff --git a/src/main/java/edu/harvard/mcz/imagecapture/serializer/nahima/Specimen2JSONSerializer.java b/src/main/java/edu/harvard/mcz/imagecapture/serializer/nahima/Specimen2JSONSerializer.java
@@ -368,6 +368,7 @@ protected JSONObject dateToNahima(String date, boolean allowInvalid) throws Pars
         if (date == null || date.equals("")) {
             return null;
         }
+        date = date.trim();
         try {
             Date parsedDate = DateUtils.parseDate(date);
             return dateToNahima(parsedDate);