From b40191067d907bda84cb15a23467fcf0fc216e79 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 15 Jun 2010 08:18:20 +0000
Subject: [PATCH] LMS-1569 Refactored code to get/create {experiment,
container, dataset}.
SVN: 16492
---
.../openbis/dss/etl/HCSDatasetUploader.java | 38 ++-----
.../ScreeningContainerDatasetInfoHelper.java | 103 ++++++++++++++++++
2 files changed, 110 insertions(+), 31 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index 00f409f35a1..74bc81e66d7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -31,8 +31,6 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgAcquiredImageDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelStackDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgContainerDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgSpotDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -239,7 +237,8 @@ public class HCSDatasetUploader
private static AcquiredImageInStack makeAcquiredImageInStack(AcquiredPlateImage image)
{
- return new AcquiredImageInStack(image.getChannelName(), image.getImageReference(), image.getThumbnailFilePathOrNull());
+ return new AcquiredImageInStack(image.getChannelName(), image.getImageReference(), image
+ .getThumbnailFilePathOrNull());
}
private static ImgChannelStackDTO makeStackDTO(AcquiredPlateImage image, Long[][] spotIds,
@@ -283,15 +282,14 @@ public class HCSDatasetUploader
{
long imageId = addImage(image.getImageFilePath());
Long thumbnailId = addImage(image.getThumbnailPathOrNull());
- ImgAcquiredImageDTO acquiredImage =
- new ImgAcquiredImageDTO();
+ ImgAcquiredImageDTO acquiredImage = new ImgAcquiredImageDTO();
acquiredImage.setImageId(imageId);
acquiredImage.setThumbnailId(thumbnailId);
acquiredImage.setChannelStackId(stackId);
acquiredImage.setChannelId(channelTechId);
dao.addAcquiredImage(acquiredImage);
}
-
+
private Long addImage(RelativeImageReference imageReferenceOrNull)
{
if (imageReferenceOrNull == null)
@@ -423,38 +421,16 @@ public class HCSDatasetUploader
private long createDataset(long contId, ScreeningContainerDatasetInfo info)
{
- ImgDatasetDTO dataset =
- new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(), info
- .getTileColumns(), contId);
- return dao.addDataset(dataset);
+ return ScreeningContainerDatasetInfoHelper.createDataset(dao, info, contId);
}
private long getOrCreateContainer(long expId, ScreeningContainerDatasetInfo info)
{
- String containerPermId = info.getContainerPermId();
- Long containerId = dao.tryGetContainerIdPermId(containerPermId);
- if (containerId != null)
- {
- return containerId;
- } else
- {
- ImgContainerDTO container =
- new ImgContainerDTO(containerPermId, info.getContainerRows(), info
- .getContainerColumns(), expId);
- return dao.addContainer(container);
- }
+ return ScreeningContainerDatasetInfoHelper.getOrCreateContainer(dao, info, expId);
}
private long getOrCreateExperiment(ScreeningContainerDatasetInfo info)
{
- String experimentPermId = info.getExperimentPermId();
- Long expId = dao.tryGetExperimentIdByPermId(experimentPermId);
- if (expId != null)
- {
- return expId;
- } else
- {
- return dao.addExperiment(experimentPermId);
- }
+ return ScreeningContainerDatasetInfoHelper.getOrCreateExperiment(dao, info);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
new file mode 100644
index 00000000000..8ce0d018c68
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
@@ -0,0 +1,103 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl;
+
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
+
+/**
+ * Helper class for retrieving and/or creating entities associated with the screening container data
+ * set info in the DB.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ScreeningContainerDatasetInfoHelper
+{
+ private final ScreeningContainerDatasetInfo info;
+
+ private final IImagingUploadDAO dao;
+
+ public ScreeningContainerDatasetInfoHelper(IImagingUploadDAO dao,
+ ScreeningContainerDatasetInfo info)
+ {
+ this.dao = dao;
+ this.info = info;
+ }
+
+ public long getOrCreateExperiment()
+ {
+ return getOrCreateExperiment(dao, info);
+ }
+
+ public long getOrCreateContainer(long expId)
+ {
+ return getOrCreateContainer(dao, info, expId);
+ }
+
+ public long getOrCreateDataset(long contId)
+ {
+ ImgDatasetDTO dataset = dao.tryGetDatasetByPermId(info.getDatasetPermId());
+ if (null != dataset)
+ {
+ return dataset.getId();
+ } else
+ {
+ return createDataset(dao, info, contId);
+ }
+
+ }
+
+ // Package-visible static methods
+ static long createDataset(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info, long contId)
+ {
+ ImgDatasetDTO dataset =
+ new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(), info
+ .getTileColumns(), contId);
+ return dao.addDataset(dataset);
+ }
+
+ static long getOrCreateContainer(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
+ long expId)
+ {
+ String containerPermId = info.getContainerPermId();
+ Long containerId = dao.tryGetContainerIdPermId(containerPermId);
+ if (containerId != null)
+ {
+ return containerId;
+ } else
+ {
+ ImgContainerDTO container =
+ new ImgContainerDTO(containerPermId, info.getContainerRows(), info
+ .getContainerColumns(), expId);
+ return dao.addContainer(container);
+ }
+ }
+
+ static long getOrCreateExperiment(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info)
+ {
+ String experimentPermId = info.getExperimentPermId();
+ Long expId = dao.tryGetExperimentIdByPermId(experimentPermId);
+ if (expId != null)
+ {
+ return expId;
+ } else
+ {
+ return dao.addExperiment(experimentPermId);
+ }
+ }
+}
--
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