From 2aa8d54390a67c21a9cad1dd32da271d678aaa13 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 14 Dec 2010 14:57:27 +0000
Subject: [PATCH] LMS-1909 Fixed minor inconsistencies in the Sample/Data Set
registration processes. Fixed tests.
SVN: 19140
---
.../SampleAndDataSetControlFileProcessor.java | 41 +------------------
.../SampleAndDataSetRegistrator.java | 30 ++++++++++++++
.../entityregistration/SampleDataSetPair.java | 15 +++----
...mpleAndDatasetRegistrationHandlerTest.java | 10 ++---
.../test-data/basic-example/control.tsv | 9 ++--
.../test-data/basic-example/ds1/dataset.txt | 0
.../test-data/basic-example/ds2/dataset.txt | 0
.../test-data/basic-example/ds3/dataset.txt | 0
8 files changed, 48 insertions(+), 57 deletions(-)
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds1/dataset.txt
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds2/dataset.txt
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds3/dataset.txt
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
index 4284e2124b0..24403c55957 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
@@ -37,8 +37,6 @@ import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
import ch.systemsx.cisd.openbis.generic.shared.parser.GlobalProperties;
import ch.systemsx.cisd.openbis.generic.shared.parser.GlobalPropertiesLoader;
@@ -74,21 +72,6 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
properties = GlobalPropertiesLoader.load(controlFile);
}
- public String trySpaceCode()
- {
- return properties.get(SampleAndDataSetRegistrationHandler.DATA_SPACE_CONTROL_FILE_KEY);
- }
-
- public SpaceIdentifier trySpaceIdentifier()
- {
- String spaceCode = trySpaceCode();
- if (null == spaceCode)
- {
- return null;
- }
- return new SpaceIdentifier(DatabaseInstanceIdentifier.createHome(), spaceCode);
- }
-
public SampleType trySampleType()
{
String sampleTypeCode =
@@ -168,19 +151,6 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
return globalProperties;
}
- /**
- * Returns a space identifier. Call checkValidity first.
- */
- public SpaceIdentifier getSpaceIdentifier()
- {
- SpaceIdentifier spaceIdentifier = overrideProperties.trySpaceIdentifier();
- if (null == spaceIdentifier)
- {
- spaceIdentifier = globalProperties.trySpaceIdentifier();
- }
- return spaceIdentifier;
- }
-
public SampleType getSampleType()
{
SampleType sampleType = overrideProperties.trySampleType();
@@ -208,18 +178,12 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
public void checkValidity()
{
- SpaceIdentifier spaceIdentifier = getSpaceIdentifier();
SampleType sampleType = getSampleType();
DataSetType dataSetType = getDataSetType();
Person theUser = getUser();
StringBuilder sb = new StringBuilder();
boolean hasError = false;
- if (null == spaceIdentifier)
- {
- hasError = true;
- sb.append("\tNo default space identifier has been specified, and no space identifier was specified in the control file.");
- }
if (null == sampleType)
{
hasError = true;
@@ -340,10 +304,9 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
{
String message =
String.format(
- "Global properties extracted from file '%s': SAMPLE_TYPE(%s) DATA_SET_TYPE(%s) DEFAULT_SPACE(%s) USER(%s)",
+ "Global properties extracted from file '%s': SAMPLE_TYPE(%s) DATA_SET_TYPE(%s) USER(%s)",
controlFile.getName(), properties.trySampleType(),
- properties.tryDataSetType(), properties.trySpaceCode(),
- properties.tryUserString());
+ properties.tryDataSetType(), properties.tryUserString());
logInfo(message);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
index dbd23f6024d..b6ce51d9b92 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
@@ -18,10 +18,12 @@ package ch.systemsx.cisd.etlserver.entityregistration;
import java.io.File;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler;
import ch.systemsx.cisd.etlserver.TransferredDataSetHandler;
import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetControlFileProcessor.ControlFileRegistrationProperties;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
@@ -58,6 +60,12 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
public Exception register()
{
File dataSetFile = new File(folder, sampleDataSetPair.getFolderName());
+ Exception isEmptyException = checkDataSetFileNotEmpty(dataSetFile);
+ if (null != isEmptyException)
+ {
+ return isEmptyException;
+ }
+
if (globalState.getDelegator() instanceof IExtensibleDataSetHandler)
{
IExtensibleDataSetHandler handler =
@@ -71,6 +79,15 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
return failureException;
}
+ private Exception checkDataSetFileNotEmpty(File dataSetFile)
+ {
+ if (0 == dataSetFile.list().length)
+ {
+ return new UserFailureException("The data set folder cannot be empty");
+ }
+ return null;
+ }
+
private void logDataRegistered()
{
String message = String.format("Registered sample/data set pair %s", sampleDataSetPair);
@@ -79,6 +96,14 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
public void registerDataSetInApplicationServer(NewExternalData data)
{
+ data.setDataSetType(properties.getDataSetType());
+ if (null != sampleDataSetPair.getFileFormatTypeCode())
+ {
+ FileFormatType fileFormatType =
+ new FileFormatType(sampleDataSetPair.getFileFormatTypeCode());
+
+ data.setFileFormatType(fileFormatType);
+ }
try
{
Sample sample =
@@ -93,6 +118,11 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
didSucceed = false;
failureException = e;
throw e;
+ } catch (Exception e)
+ {
+ didSucceed = false;
+ failureException = e;
+ throw new CheckedExceptionTunnel(e);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
index 32a30518f52..b94344a616a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
@@ -44,8 +44,6 @@ public class SampleDataSetPair
private final static String DATA_SET_CODE = "D_code";
- private final static String DATA_SET_TYPE = "D_data_set_type";
-
private final static String DATA_SET_FILE_TYPE = "D_file_type";
private final static String FOLDER = "FOLDER";
@@ -58,6 +56,8 @@ public class SampleDataSetPair
private String folderName;
+ private String fileFormatTypeCode;
+
public SampleDataSetPair()
{
newSample = new NewSample();
@@ -84,7 +84,7 @@ public class SampleDataSetPair
return dataSetInformation;
}
- @BeanProperty(label = SAMPLE_IDENTIFIER, optional = true)
+ @BeanProperty(label = SAMPLE_IDENTIFIER, optional = false)
public void setSampleIdentifier(String sampleIdentifier)
{
this.newSample.setIdentifier(sampleIdentifier);
@@ -114,14 +114,15 @@ public class SampleDataSetPair
dataSetInformation.setDataSetCode(code);
}
- @BeanProperty(label = DATA_SET_TYPE, optional = true)
- public void setDataSetType(String parent)
+ public String getFileFormatTypeCode()
{
+ return fileFormatTypeCode;
}
@BeanProperty(label = DATA_SET_FILE_TYPE, optional = true)
- public void setDataSetFileType(String experimentIdentifier)
+ public void setFileFormatTypeCode(String fileFormatType)
{
+ this.fileFormatTypeCode = fileFormatType;
}
public String getFolderName()
@@ -129,7 +130,7 @@ public class SampleDataSetPair
return folderName;
}
- @BeanProperty(label = FOLDER, optional = true)
+ @BeanProperty(label = FOLDER, optional = false)
public void setFolderName(String folderName)
{
this.folderName = folderName;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index ff71b372cc3..40c4414e760 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -95,8 +95,6 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
setupOpenBisExpectations();
setupDataSetHandlerExpectations(dataSetInfoMatcher, newSampleMatcher);
- // setupSessionContextExpectations();
- // setupCallerDataSetInfoExpectations();
File workingCopy = createWorkingCopyOfTestFolder("basic-example");
@@ -104,10 +102,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(workingCopy);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DEFAULT_SPACE(MYSPACE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=<null>,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=<null>,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=<null>,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=<null>,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
checkAppenderContent(logText, "basic-example");
context.assertIsSatisfied();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
index 22f20fc3b70..a8d70ccf592 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
@@ -1,12 +1,11 @@
# Control Parameters
#! GLOBAL_PROPERTIES_START
-#! DEFAULT_SPACE = MYSPACE
#! SAMPLE_TYPE = MY_SAMPLE_TYPE
#! DATA_SET_TYPE = MY_DATA_SET_TYPE
#! USERID = test@test.test
#! GLOBAL_PROPERTIES_END
# Data
-S_experiment S_PROP1 S_PROP2 S_PROP3 D_file_type D_PROP1 D_PROP2 FOLDER
-/MYSPACE/MYPROJ/EXP1 VAL10 VAL20 VAL30 FILE_TYPE VAL40 VAL50 ds1/
-/MYSPACE/MYPROJ/EXP2 VAL11 VAL21 VAL31 FILE_TYPE VAL41 VAL51 ds2/
-/MYSPACE/MYPROJ/EXP3 VAL12 VAL22 VAL32 FILE_TYPE VAL42 VAL52 ds3/
+S_identifier S_experiment S_PROP1 S_PROP2 S_PROP3 D_file_type D_PROP1 D_PROP2 FOLDER
+/MYSPACE/S1 /MYSPACE/MYPROJ/EXP1 VAL10 VAL20 VAL30 FILE_TYPE VAL40 VAL50 ds1/
+/MYSPACE/S2 /MYSPACE/MYPROJ/EXP2 VAL11 VAL21 VAL31 FILE_TYPE VAL41 VAL51 ds2/
+/MYSPACE/S3 /MYSPACE/MYPROJ/EXP3 VAL12 VAL22 VAL32 FILE_TYPE VAL42 VAL52 ds3/
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds1/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds1/dataset.txt
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds2/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds2/dataset.txt
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds3/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/ds3/dataset.txt
new file mode 100644
index 00000000000..e69de29bb2d
--
GitLab