From a32be88f6f29a2c2aaebeccacd471c23dc4f3aa6 Mon Sep 17 00:00:00 2001
From: juanf <juanf@bsse-bs-dock-dhcp-358.ethz.ch>
Date: Tue, 25 Sep 2018 13:07:06 +0200
Subject: [PATCH] SSDM-7235 : Continuous sample codes, project samples support
---
.../parser/SampleUploadSectionsParser.java | 62 +++++++++++++------
1 file changed, 43 insertions(+), 19 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
index 6d1aa623d4e..004ac406111 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
@@ -85,9 +85,29 @@ public class SampleUploadSectionsParser
List<String> generateCodes(int size);
}
+ /*
+ * This overloaded method has been kept to provide backwards compatibility for a couple of older uses
+ */
public static BatchSamplesOperation prepareSamples(
- final boolean projectSamplesEnabled,
- final SampleType sampleType,
+ final SampleType sampleType,
+ final String spaceIdentifierSilentOverrideOrNull,
+ final String experimentIdentifierSilentOverrideOrNull,
+ final Collection<NamedInputStream> files, String defaultGroupIdentifier,
+ final SampleCodeGenerator sampleCodeGeneratorOrNull, final boolean allowExperiments,
+ String excelSheetName, BatchOperationKind operationKind)
+ {
+ return prepareSamples(false,
+ sampleType,
+ spaceIdentifierSilentOverrideOrNull,
+ experimentIdentifierSilentOverrideOrNull,
+ files, defaultGroupIdentifier,
+ sampleCodeGeneratorOrNull, allowExperiments,
+ excelSheetName, operationKind);
+ }
+
+ public static BatchSamplesOperation prepareSamples(
+ final boolean projectSamplesEnabled,
+ final SampleType sampleType,
final String spaceIdentifierSilentOverrideOrNull,
final String experimentIdentifierSilentOverrideOrNull,
final Collection<NamedInputStream> files, String defaultGroupIdentifier,
@@ -269,8 +289,9 @@ public class SampleUploadSectionsParser
createSampleLoaderFromExcel(typeFromSection, isAutoGenerateCodes,
allowExperiments, operationKind);
String sectionInFile =
- sampleSections.size() == 1 ? "" : " (section:"
- + fs.getSectionName() + ")";
+ sampleSections.size() == 1 ? ""
+ : " (section:"
+ + fs.getSectionName() + ")";
final List<NewSample> loadedSamples =
excelFileLoader.load(fs.getSheet(), fs.getBegin(), fs.getEnd(),
fileName + sectionInFile, defaults);
@@ -313,8 +334,9 @@ public class SampleUploadSectionsParser
createSampleLoader(typeFromSection, isAutoGenerateCodes,
allowExperiments, operationKind);
String sectionInFile =
- sampleSections.size() == 1 ? "" : " (section:"
- + fs.getSectionName() + ")";
+ sampleSections.size() == 1 ? ""
+ : " (section:"
+ + fs.getSectionName() + ")";
final List<NewSample> loadedSamples =
tabFileLoader.load(new DelegatedReader(reader, fileName
+ sectionInFile), defaults);
@@ -335,7 +357,7 @@ public class SampleUploadSectionsParser
}
private static void generateIdentifiers(boolean projectSamplesEnabled,
- String defaultGroupIdentifier,
+ String defaultGroupIdentifier,
SampleCodeGenerator sampleCodeGenerator, boolean isAutoGenerateCodes,
List<NewSamplesWithTypes> newSamplesWithTypes)
{
@@ -347,25 +369,27 @@ public class SampleUploadSectionsParser
List<String> codes = sampleCodeGenerator.generateCodes(newSamples.size());
for (int i = 0; i < newSamples.size(); i++)
{
- String spaceCodeOrNull = null;
- if (newSamples.get(i).getDefaultSpaceIdentifier() == null || newSamples.get(i).getDefaultSpaceIdentifier().isEmpty())
+ String spaceCodeOrNull = null;
+ if (newSamples.get(i).getDefaultSpaceIdentifier() == null || newSamples.get(i).getDefaultSpaceIdentifier().isEmpty())
{
- spaceCodeOrNull = defaultGroupIdentifier;
+ spaceCodeOrNull = defaultGroupIdentifier;
} else
{
- spaceCodeOrNull = newSamples.get(i).getDefaultSpaceIdentifier();
+ spaceCodeOrNull = newSamples.get(i).getDefaultSpaceIdentifier();
}
- spaceCodeOrNull = spaceCodeOrNull.substring(1);
- String projectCodeOrNull = null;
- if(projectSamplesEnabled && newSamples.get(i).getExperimentIdentifier() != null && !newSamples.get(i).getExperimentIdentifier().isEmpty()) {
- String[] experimentIdentifierParts = newSamples.get(i).getExperimentIdentifier().split("/");
- projectCodeOrNull = experimentIdentifierParts[experimentIdentifierParts.length - 2];
- }
- newSamples.get(i).setIdentifier(createIdentifier(spaceCodeOrNull, projectCodeOrNull, codes.get(i)));
+ spaceCodeOrNull = spaceCodeOrNull.substring(1);
+ String projectCodeOrNull = null;
+ if (projectSamplesEnabled && newSamples.get(i).getExperimentIdentifier() != null
+ && !newSamples.get(i).getExperimentIdentifier().isEmpty())
+ {
+ String[] experimentIdentifierParts = newSamples.get(i).getExperimentIdentifier().split("/");
+ projectCodeOrNull = experimentIdentifierParts[experimentIdentifierParts.length - 2];
+ }
+ newSamples.get(i).setIdentifier(createIdentifier(spaceCodeOrNull, projectCodeOrNull, codes.get(i)));
}
}
}
-
+
private static String createIdentifier(String spaceCodeOrNull, String projectCodeOrNull, String sampleCode)
{
StringBuilder builder = new StringBuilder("/");
--
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