Fix getWellSamples/getPlateAcquisitions

GReD-Clermont · Oct 25, 2023 · 567c052 · 567c052
1 parent ea00830
commit 567c052
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Showing 8 changed files with 102 additions and 36 deletions.
diff --git a/.omeroci/test-data b/.omeroci/test-data
@@ -54,10 +54,10 @@ touch "$WORKDIR/screen1.fake"
 {
     echo "screens=1"
     echo "plates=1"
-    echo "plateAcqs=1"
+    echo "plateAcqs=2"
     echo "plateRows=3"
     echo "plateCols=3"
-    echo "fields=4"
+    echo "fields=2"
 } > "$WORKDIR/screen1.fake.ini"
 
 touch "$WORKDIR/screen2.fake"

diff --git a/src/main/java/fr/igred/omero/repository/ImageWrapper.java b/src/main/java/fr/igred/omero/repository/ImageWrapper.java
@@ -324,6 +324,7 @@ public List<WellSampleWrapper> getWellSamples() {
      */
     public List<WellSampleWrapper> getWellSamples(Client client)
     throws AccessException, ServiceException, ExecutionException {
+        reload(client);
         List<WellSampleWrapper> samples = getWellSamples();
         for (WellSampleWrapper sample : samples) {
             sample.reload(client);
@@ -345,17 +346,12 @@ public List<WellSampleWrapper> getWellSamples(Client client)
      */
     public List<WellWrapper> getWells(Client client)
     throws AccessException, ServiceException, ExecutionException {
-        List<WellSampleWrapper> wellSamples = getWellSamples();
+        List<WellSampleWrapper> wellSamples = getWellSamples(client);
         Collection<WellWrapper> wells       = new ArrayList<>(wellSamples.size());
         for (WellSampleWrapper ws : wellSamples) {
             wells.add(ws.getWell(client));
         }
-        Long[] ids = wells.stream()
-                          .map(WellWrapper::getId)
-                          .sorted()
-                          .distinct()
-                          .toArray(Long[]::new);
-        return client.getWells(ids);
+        return distinct(wells);
     }
 
 
@@ -372,13 +368,13 @@ public List<WellWrapper> getWells(Client client)
      */
     public List<PlateAcquisitionWrapper> getPlateAcquisitions(Client client)
     throws AccessException, ServiceException, ExecutionException {
-        List<WellWrapper> wells = getWells(client);
+        List<WellSampleWrapper> wellSamples = getWellSamples(client);
 
-        Collection<List<PlateAcquisitionWrapper>> acqs = new ArrayList<>(wells.size());
-        for (WellWrapper w : wells) {
-            acqs.add(w.getPlateAcquisitions(client));
+        Collection<PlateAcquisitionWrapper> acqs = new ArrayList<>(wellSamples.size());
+        for (WellSampleWrapper ws : wellSamples) {
+            acqs.add(ws.getPlateAcquisition());
         }
-        return flatten(acqs);
+        return distinct(acqs);
     }
 
 

diff --git a/src/main/java/fr/igred/omero/repository/PlateAcquisitionWrapper.java b/src/main/java/fr/igred/omero/repository/PlateAcquisitionWrapper.java
@@ -20,21 +20,19 @@
 
 import fr.igred.omero.Browser;
 import fr.igred.omero.Client;
-import fr.igred.omero.GenericObjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
 import omero.gateway.model.AnnotationData;
 import omero.gateway.model.PlateAcquisitionData;
+import omero.gateway.model.WellSampleData;
 import omero.model.IObject;
 import omero.model.PlateAcquisitionAnnotationLink;
 import omero.model.PlateAcquisitionAnnotationLinkI;
 import omero.model._PlateAcquisitionOperationsNC;
 
 import java.sql.Timestamp;
-import java.util.Collection;
-import java.util.Comparator;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
@@ -215,6 +213,51 @@ public List<WellWrapper> getWells(Client client)
     }
 
 
+    /**
+     * Retrieves the well samples for this plate acquisition.
+     *
+     * @return See above.
+     */
+    public List<WellSampleWrapper> getWellSamples() {
+        _PlateAcquisitionOperationsNC pa = (_PlateAcquisitionOperationsNC) data.asIObject();
+        return pa.copyWellSample()
+                 .stream()
+                 .map(WellSampleData::new)
+                 .map(WellSampleWrapper::new)
+                 .collect(Collectors.toList());
+    }
+
+
+    /**
+     * Retrieves the well samples for this plate acquisition from OMERO and updates the object.
+     *
+     * @param browser The data browser.
+     *
+     * @return See above.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<WellSampleWrapper> getWellSamples(Browser browser)
+    throws AccessException, ServiceException, ExecutionException {
+        reload(browser);
+        return getWellSamples();
+    }
+
+
+    /**
+     * Retrieves the images contained in the well samples.
+     *
+     * @return See above
+     */
+    public List<ImageWrapper> getImages() {
+        return getWellSamples().stream()
+                               .map(WellSampleWrapper::getImage)
+                               .collect(Collectors.toList());
+    }
+
+
     /**
      * Retrieves the images contained in the wells in the parent plate.
      *
@@ -228,14 +271,9 @@ public List<WellWrapper> getWells(Client client)
      */
     public List<ImageWrapper> getImages(Client client)
     throws ServiceException, AccessException, ExecutionException {
-        return getWells(client).stream()
-                               .map(WellWrapper::getImages)
-                               .flatMap(Collection::stream)
-                               .collect(Collectors.toMap(GenericObjectWrapper::getId, i -> i, (i1, i2) -> i1))
-                               .values()
-                               .stream()
-                               .sorted(Comparator.comparing(GenericObjectWrapper::getId))
-                               .collect(Collectors.toList());
+        return getWellSamples(client).stream()
+                                     .map(WellSampleWrapper::getImage)
+                                     .collect(Collectors.toList());
     }
 
 

diff --git a/src/main/java/fr/igred/omero/repository/WellSampleWrapper.java b/src/main/java/fr/igred/omero/repository/WellSampleWrapper.java
@@ -26,6 +26,7 @@
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
 import ome.model.units.BigResult;
+import omero.gateway.model.PlateAcquisitionData;
 import omero.gateway.model.WellSampleData;
 import omero.model.IObject;
 import omero.model.Length;
@@ -99,6 +100,16 @@ public List<PlateWrapper> getPlates(Client client)
     }
 
 
+    /**
+     * Returns the plate acquisition containing this well sample.
+     *
+     * @return See above.
+     */
+    public PlateAcquisitionWrapper getPlateAcquisition() {
+        return new PlateAcquisitionWrapper(new PlateAcquisitionData(data.asWellSample().getPlateAcquisition()));
+    }
+
+
     /**
      * Returns the plate acquisitions linked to the parent Well.
      *

diff --git a/src/test/java/fr/igred/omero/repository/ImageTest.java b/src/test/java/fr/igred/omero/repository/ImageTest.java
@@ -91,9 +91,13 @@ void testGetPlates() throws Exception {
 
     @Test
     void testGetPlateAcquisitions() throws Exception {
-        final long   id   = 5L;
-        final String name = "PlateAcquisition Name 0";
-        assertEquals(name, client.getImage(id).getPlateAcquisitions(client).get(0).getName());
+        PlateAcquisitionWrapper pa = client.getPlate(PLATE1.id).getPlateAcquisitions().get(0);
+
+        String                        name  = pa.getName();
+        ImageWrapper                  image = pa.getImages(client).get(0);
+        List<PlateAcquisitionWrapper> acqs  = image.getPlateAcquisitions(client);
+        assertEquals(1, acqs.size());
+        assertEquals(name, acqs.get(0).getName());
     }
 
 
@@ -109,7 +113,7 @@ void testGetWells() throws Exception {
 
     @Test
     void testGetWellSamples() throws Exception {
-        final long wellId = 1L;
+        final long        wellId = 1L;
         WellSampleWrapper sample = client.getWell(wellId).getWellSamples().get(0);
 
         ImageWrapper image = sample.getImage();

diff --git a/src/test/java/fr/igred/omero/repository/PlateAcquisitionTest.java b/src/test/java/fr/igred/omero/repository/PlateAcquisitionTest.java
@@ -57,11 +57,21 @@ void testGetWells() throws Exception {
 
 
     @Test
-    void testGetImages() throws Exception {
+    void testGetImages1() throws Exception {
         PlateWrapper            plate  = client.getPlate(PLATE1.id);
         PlateAcquisitionWrapper acq    = plate.getPlateAcquisitions().get(0);
         List<ImageWrapper>      images = acq.getImages(client);
-        assertEquals(36, images.size());
+        assertEquals(18, images.size());
+    }
+
+
+    @Test
+    void testGetImages2() throws Exception {
+        PlateWrapper            plate = client.getPlate(PLATE1.id);
+        PlateAcquisitionWrapper acq   = plate.getPlateAcquisitions().get(0);
+        acq.reload(client);
+        List<ImageWrapper> images = acq.getImages();
+        assertEquals(18, images.size());
     }
 
 

diff --git a/src/test/java/fr/igred/omero/repository/PlateTest.java b/src/test/java/fr/igred/omero/repository/PlateTest.java
@@ -72,13 +72,11 @@ void testGetWellsFromPlate2() throws Exception {
 
     @Test
     void testGetPlateAcquisitionsFromPlate() throws Exception {
-        final String name = "PlateAcquisition Name 0";
-
         PlateWrapper plate = client.getPlate(PLATE1.id);
 
         List<PlateAcquisitionWrapper> acquisitions = plate.getPlateAcquisitions();
-        assertEquals(1, acquisitions.size());
-        assertEquals(name, acquisitions.get(0).getName());
+        assertEquals(2, acquisitions.size());
+        assertEquals(1L, acquisitions.get(0).getId());
     }
 
 

diff --git a/src/test/java/fr/igred/omero/repository/WellSampleTest.java b/src/test/java/fr/igred/omero/repository/WellSampleTest.java
@@ -50,12 +50,21 @@ void testGetPlates() throws Exception {
     }
 
 
+    @Test
+    void testGetPlateAcquisition() throws Exception {
+        PlateWrapper            plate  = client.getPlate(1L);
+        PlateAcquisitionWrapper acq    = plate.getPlateAcquisitions().get(0);
+        WellSampleWrapper       sample = acq.getWellSamples(client).get(0);
+        assertEquals(acq.getId(), sample.getPlateAcquisition().getId());
+    }
+
+
     @Test
     void testGetPlateAcquisitions() throws Exception {
         WellWrapper                   well   = client.getWell(1L);
         WellSampleWrapper             sample = well.getWellSamples().get(0);
         List<PlateAcquisitionWrapper> acqs   = sample.getPlateAcquisitions(client);
-        assertEquals(1, acqs.size());
+        assertEquals(2, acqs.size());
     }