From 2248742c126547e5bfb29604eccb8ab1df1770c4 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Fri, 28 Oct 2011 11:26:15 +0000
Subject: [PATCH] LMS-2608 add sql queries to ask about wells with images
SVN: 23452
---
.../dataaccess/IImagingReadonlyQueryDAO.java | 21 +++++++++++++++++
.../shared/imaging/dataaccess/ImgSpotDTO.java | 3 +--
.../etl/dataaccess/ImagingQueryDAOTest.java | 23 +++++++++++++++++++
3 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index 20d96ba1ddf..437e496887a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -87,6 +87,12 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// " and CHANNEL_STACKS.T_in_SEC IS NULL "
// + " and CHANNEL_STACKS.Z_in_M IS NULL ";
+ public static final String SQL_HCS_WELLS_WITH_IMAGES =
+ "select distinct s.* "
+ + "from CHANNEL_STACKS ch, SPOTS s, ACQUIRED_IMAGES ai "
+ + "where ch.is_representative = 'T' and ch.DS_ID = ?{1} and "
+ + " ai.CHANNEL_STACK_ID = ch.ID and ch.SPOT_ID = s.ID";
+
// ---------------- HCS ---------------------------------
/**
@@ -138,6 +144,21 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ " where d.perm_id = ?{1} and ch.code = upper(?{2}) and s.id is NOT NULL")
public List<ImgImageEnrichedDTO> listHCSImages(String datasetPermId, String channelCode);
+ /**
+ * @return list of wells for which there are any thumbnail or original images (any tile, any
+ * channel).
+ */
+ @Select(SQL_HCS_WELLS_WITH_IMAGES)
+ public List<ImgSpotDTO> listWellsWithAnyImages(long datasetId);
+
+ /** @return list of wells for which there are any thumbnail images (any tile, any channel). */
+ @Select(SQL_HCS_WELLS_WITH_IMAGES + " and ai.thumbnail_id is not null")
+ public List<ImgSpotDTO> listWellsWithAnyThumbnails(long datasetId);
+
+ /** @return list of wells for which there are any original images (any tile, any channel). */
+ @Select(SQL_HCS_WELLS_WITH_IMAGES + " and ai.img_id is not null")
+ public List<ImgSpotDTO> listWellsWithAnyOriginalImages(long datasetId);
+
// ---------------- Microscopy ---------------------------------
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
index 689d17b6857..0bf32b80421 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
@@ -40,9 +40,8 @@ public class ImgSpotDTO extends AbstractImgIdentifiable
// All Data-Object classes must have a default constructor.
}
- public ImgSpotDTO(/* String permId, */Integer row, Integer column, long containerId)
+ public ImgSpotDTO(Integer row, Integer column, long containerId)
{
- /* this.permId = permId; */
this.column = column;
this.row = row;
this.containerId = containerId;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index cc200d14aee..6ed8e649a48 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -247,9 +247,32 @@ public class ImagingQueryDAOTest extends AbstractDBTest
addAcquiredImage(imageId2, channelStackId, experimentChannelId2);
testGetHCSImage(datasetId, channelStackId, datasetChannelId1, experimentChannelId2, spotId);
+ testGetAnyHCSImage(datasetId);
testListChannelStacksAndSpots(datasetId, channelStackId, spotId);
}
+ private void testGetAnyHCSImage(long datasetId)
+ {
+ List<ImgSpotDTO> anyImgSpots = dao.listWellsWithAnyImages(datasetId);
+ assertEquals(1, anyImgSpots.size());
+ ImgSpotDTO spot = anyImgSpots.get(0);
+ assertDefaultSpot(spot);
+
+ List<ImgSpotDTO> thumbnailImgSpots = dao.listWellsWithAnyThumbnails(datasetId);
+ assertEquals(1, thumbnailImgSpots.size());
+ assertEquals(spot, thumbnailImgSpots.get(0));
+
+ List<ImgSpotDTO> originalImgSpots = dao.listWellsWithAnyOriginalImages(datasetId);
+ assertEquals(1, originalImgSpots.size());
+ assertEquals(spot, originalImgSpots.get(0));
+ }
+
+ private void assertDefaultSpot(ImgSpotDTO spot)
+ {
+ assertEquals(X_WELL_COLUMN, 0L + spot.getColumn());
+ assertEquals(Y_WELL_ROW, 0L + spot.getRow());
+ }
+
private void testListChannelStacksAndSpots(long datasetId, long channelStackId, long spotId)
{
ImgChannelStackDTO stackDTO = testListChannelStacks(datasetId, channelStackId);
--
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