diff --git a/sanofi/.classpath b/sanofi/.classpath
new file mode 100644
index 0000000000000000000000000000000000000000..dc1aac1a05c9f18d34503f26441c2ecaa11697f0
--- /dev/null
+++ b/sanofi/.classpath
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="source/java"/>
+ <classpathentry kind="src" path="sourceTest/java"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/screening"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/common"/>
+ <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+ <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
+ <classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
+ <classpathentry kind="lib" path="/libraries/jaxb/jaxb-api.jar" sourcepath="/libraries/jaxb/jaxb-api-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jaxb/jsr173_1.0_api.jar"/>
+ <classpathentry kind="lib" path="/libraries/gwt2.0/gwt-isserializable.jar"/>
+ <classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
+ <classpathentry kind="lib" path="/libraries/cisd-args4j/cisd-args4j.jar" sourcepath="/libraries/cisd-args4j/cisd-args4j-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/poi/poi-3.7-20101029.jar"/>
+ <classpathentry kind="lib" path="/libraries/jython/standalone/jython.jar" sourcepath="/Users/gpawel/Downloads/jython_installer-2.2.1.jar"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
+ <classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
+ <classpathentry kind="output" path="targets/classes"/>
+</classpath>
diff --git a/sanofi/.project b/sanofi/.project
new file mode 100644
index 0000000000000000000000000000000000000000..36b7fe7a11e5e37c6e446a8a96ae69f0bf8d5d6d
--- /dev/null
+++ b/sanofi/.project
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>sanofi</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.python.pydev.PyDevBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.python.pydev.pythonNature</nature>
+ </natures>
+</projectDescription>
diff --git a/sanofi/.pydevproject b/sanofi/.pydevproject
new file mode 100644
index 0000000000000000000000000000000000000000..a9cca037b33037ebc3232e6b63f3f00283463a4e
--- /dev/null
+++ b/sanofi/.pydevproject
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?>
+
+<pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+</pydev_project>
diff --git a/sanofi/build/antrun.sh b/sanofi/build/antrun.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5ff1a62b259d6011d228440f2fb89ec0dbecf747
--- /dev/null
+++ b/sanofi/build/antrun.sh
@@ -0,0 +1,6 @@
+#! /bin/bash
+
+ME="$0"
+MYDIR=${ME%/*}
+cd $MYDIR
+ant -lib ../../build_resources/lib/ecj.jar "$@"
diff --git a/sanofi/build/build.xml b/sanofi/build/build.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5dd99be6cd1a5a153129d1bb5209d867f2e17df5
--- /dev/null
+++ b/sanofi/build/build.xml
@@ -0,0 +1,49 @@
+<project name="sanofi" default="ci" basedir="..">
+ <import file="../../datastore_server/build/build.xml" />
+ <project-classpath name="ecp" classes="${classes}" />
+
+ <property name="original.dist" value="dist" />
+ <property name="mainfolder" value="sanofi" />
+
+ <target name="compile" depends="build-common.compile, clean" />
+
+ <target name="run-tests">
+ <antcall target="build-common.run-tests">
+ <param name="test.suite" value="tests.xml" />
+ </antcall>
+ </target>
+
+ <!--
+ No jar files produced by the module yet.
+ <target name="jar" depends="compile">
+ <mkdir dir="${dist}" />
+ <build-info revision="revision.number" version="version.number" clean="clean.flag" />
+ <echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
+ <jar destfile="${plugin-jar.file}">
+ <fileset dir="${classes}">
+ <include name="ch/**/*.class" />
+ <include name="${build.info.filename}" />
+ </fileset>
+ <fileset dir="source">
+ <include name="**/*.sql" />
+ </fileset>
+ <manifest>
+ <attribute name="Version" value="${version.number}" />
+ <attribute name="Build-Number"
+ value="${version.number} (r${revision.number},${clean.flag})" />
+ </manifest>
+ </jar>
+ </target>
+ -->
+
+ <!--
+ // Task for creating distributions
+ <target name="dist" depends="jar" />
+ -->
+
+ <!--
+ // Task for continuous integration server.
+ -->
+ <target name="ci" depends="build-common.ci, check-dependencies" />
+
+</project>
\ No newline at end of file
diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
new file mode 100644
index 0000000000000000000000000000000000000000..6399023c81462c4bc39f087ba4d084f19f19d87d
--- /dev/null
+++ b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
@@ -0,0 +1,215 @@
+import ch.systemsx.cisd.etlserver.registrator.api.v1.MaterialIdentifierCollection as MaterialIdentifierCollection
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria as SearchCriteria
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause as MatchClause
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute as MatchClauseAttribute
+
+PLATE_TYPE = "PLATE"
+
+DATA_SET_TYPE = "HCS_IMAGE_RAW"
+DATA_SET_BATCH_PROPNAME = "ACQUISITION_BATCH"
+
+def findPlateByCode(code):
+ """
+ Finds a plate (openBIS sample) matching a specified bar code.
+ """
+ criteria = SearchCriteria()
+ criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, PLATE_TYPE))
+ criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, code))
+
+ searchService = transaction.getSearchService()
+ platesFound = list(searchService.searchForSamples(criteria))
+
+ if len(platesFound) > 0:
+ return platesFound[0]
+ else:
+ return None
+
+def parseIncomingDirname(dirName):
+ """
+ Parses the name of an incoming dataset folder from the format
+ 'AcquisitionBatch_BarCode_Timestamp' to a tuple (acquisitionBatch, barCode)
+ """
+ tokens = dirName.split("_")
+ assert len(tokens) >= 2, "Data set directory name does not match the pattern 'AcquisitionBatch_BarCode_Timestamp': " + dirName
+ acquisitionBatch = tokens[0]
+ barCode = tokens[1].split('.')[0]
+ return (acquisitionBatch, barCode)
+
+def removeDuplicates(list):
+ dict = {}
+ for item in list:
+ dict[item] = item
+ return dict.keys()
+
+class SanofiMaterial:
+ """
+ A data structure class holding compound materials as they exist in the Abase (Sanofi) database.
+ """
+ def __init__(self, wellCode, materialCode, sanofiId, sanofiBatchId):
+ self.wellCode = wellCode
+ self.materialCode = materialCode
+ self.sanofiId = sanofiId
+ self.sanofiBatchId = sanofiBatchId
+
+class PlateInitializer:
+ ABASE_DATA_SOURCE = "abase-datasource"
+ ABASE_QUERY = "TODO: this a query provided by Matt"
+
+ LIBRARY_TEMPLATE_PROPNAME = "LIBRARY_TEMPLATE"
+
+ WELL_TYPE = "COMPOUND_WELL"
+ WELL_CONCENTRATION_PROPNAME = "CONCENTRATION"
+ WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH"
+
+ MATERIAL_TYPE = "COMPOUND_BATCH"
+ MATERIAL_ID_PROPNAME = "COMPOUND_ID"
+ MATERIAL_BATCH_ID_PROPNAME = "COMPOUND_BATCH_ID"
+
+ def __init__(self, transaction):
+ self.transaction = transaction
+ self.plate = plate
+
+ def getWellCode(self, x, y):
+ return chr(ord('A') + x) + str(y)
+
+ def getPlateDimensions(self):
+ # TODO KE: implement me
+ return (2, 2)
+
+ def validateLibraryDimensions(self, csvLists):
+ (plateWidth, plateHeight) = self.getPlateDimensions()
+
+ assert plateHeight == len(csvLists), \
+ "Plate geometry (height=%i) does not agree with LIBRARY_TEMPLATE (height=%i)." % (plateHeight, len(csvLists))
+
+ for i in range(0, len(csvLists)):
+ assert plateWidth == len(csvLists[i]), \
+ "Plate geometry (width=%i) does not agree with LIBRARY_TEMPLATE (line=%i,width=%i)." % (plateWidth, i, len(csvLists[i]))
+
+ def parseLibraryTemplate(self):
+ experimentId = plate.getExperiment().getExperimentIdentifier()
+ experiment = transaction.getExperiment(experimentId)
+ template = experiment.getPropertyValue(self.LIBRARY_TEMPLATE_PROPNAME)
+
+ csvLists = [ line.split(",") for line in template.splitlines() ]
+ self.validateLibraryDimensions(csvLists)
+
+ library = {}
+ for x in range(0, len(csvLists)):
+ for y in range(0, len(csvLists[0])):
+ wellCode = self.getWellCode(x,y)
+ library[wellCode] = csvLists[x][y].strip()
+
+ return library
+
+
+ def fetchPlateCompounds(self):
+ """
+ Fetch well metadata from the Abase database.
+
+ @return: a list of tuples (one per well) in the form
+ (wellCode, openBisCompoundCode, abaseCompoundBatchId, abaseCompoundId).
+ In case the plate is not found in Abase return None.
+ """
+ queryService = service.getDataSourceQueryService()
+ queryResult = queryService.select(self.ABASE_DATA_SOURCE, self.ABASE_QUERY, [plate.code])
+
+ sanofiMaterials = []
+ for materialMap in list(queryResult):
+ wellCode = str(materialMap['WELLCODE'])
+ materialCode = str(materialMap['MATERIALCODE'])
+ sanofiId = str(materialMap['ABASE_COMPOUND_ID'])
+ sanofiBatchId = str(materialMap['ABASE_COMPOUND_BATCH_ID'])
+ material = SanofiMaterial(wellCode, materialCode, sanofiId, sanofiBatchId)
+ sanofiMaterials.append(material)
+
+ queryResult.close()
+
+ return sanofiMaterials
+
+ def createMaterial(self, sanofiMaterial):
+ material = transaction.createNewMaterial(sanofiMaterial.materialCode, self.MATERIAL_TYPE)
+ material.setPropertyValue(self.MATERIAL_ID_PROPNAME, sanofiMaterial.sanofiId)
+ material.setPropertyValue(self.MATERIAL_BATCH_ID_PROPNAME, sanofiMaterial.sanofiBatchId)
+ return material
+
+ def getOrCreateMaterials(self, library, sanofiMaterials):
+ materialCodes = [sanofiMaterial.materialCode for sanofiMaterial in sanofiMaterials]
+ materialCodes = removeDuplicates(materialCodes)
+
+ materialIdentifiers = MaterialIdentifierCollection()
+ for materialCode in materialCodes:
+ materialIdentifiers.addIdentifier(self.MATERIAL_TYPE, materialCode)
+ searchService = transaction.getSearchService()
+ preExistingMaterials = list(searchService.listMaterials(materialIdentifiers))
+
+ materialsByCode = {}
+ for material in preExistingMaterials:
+ materialsByCode[ material.getCode() ] = material
+
+ for materialCode in materialCodes:
+ if not materialCode in materialsByCode:
+ sanofiMaterial = self.getByMaterialCode(materialCode, sanofiMaterials)
+ openbisMaterial = self.createMaterial(sanofiMaterial)
+ materialsByCode[materialCode] = openbisMaterial
+
+ return materialsByCode
+
+ def getByMaterialCode(self, materialCode, sanofiMaterials):
+ for sanofiMaterial in sanofiMaterials:
+ if materialCode == sanofiMaterial.materialCode:
+ return sanofiMaterial
+
+ raise RuntimeError("No material found for materialCode " + wellCode)
+
+ def getByWellCode(self, wellCode, sanofiMaterials):
+ for sanofiMaterial in sanofiMaterials:
+ if wellCode == sanofiMaterial.wellCode:
+ return sanofiMaterial
+
+ raise RuntimeError("No material found for wellCode " + wellCode)
+
+ def createWells(self, library, sanofiMaterials, openbisMaterials):
+ controlWellTypes = { "H" : "posti", "L" : "negative"};
+ for wellCode in library:
+ libraryValue = library[wellCode].uppercase()
+ if libraryValue in controlWellTypes:
+ pass
+ else:
+ try
+ except ValueError:
+ raise RuntimeError("TODO...")
+ well = transaction.createNewSample(plate.code +":" + wellCode, self.WELL_TYPE)
+ well.setContainer(plate)
+ concentration = library[wellCode]
+ well.setPropertyValue(self.WELL_CONCENTRATION_PROPNAME, concentration)
+ materialCode = self.getByWellCode(wellCode, sanofiMaterials).materialCode
+ material = openbisMaterials[materialCode]
+ well.setMaterialPropertyValue(self.WELL_MATERIAL_PROPNAME, material)
+
+
+ def createWellsAndMaterials(self):
+ library = self.parseLibraryTemplate()
+ sanofiMaterials = self.fetchPlateCompounds()
+
+ # TODO KE: validate that library and sanofiMaterials data agrees
+ openbisMaterials = self.getOrCreateMaterials(library, sanofiMaterials)
+ self.createWells(library, sanofiMaterials, openbisMaterials)
+
+
+transaction = service.transaction()
+dataSet = transaction.createNewDataSet(DATA_SET_TYPE)
+
+(batchName, barCode) = parseIncomingDirname(incoming.getName())
+dataSet.setPropertyValue(DATA_SET_BATCH_PROPNAME, batchName)
+plate = findPlateByCode(barCode)
+
+if len(plate.getContainedSamples()) == 0:
+ plateInitializer = PlateInitializer(plate)
+ plateInitializer.createWellsAndMaterials()
+
+
+dataSet.setSample(plate)
+transaction.moveFile(incoming.getAbsolutePath(), dataSet)
+
+# TODO KE: send emails on ERROR/SUCCESS
diff --git a/sanofi/etc/log.xml b/sanofi/etc/log.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5cee0a68436a19a6c4ec4b14b580e6d9f75bf84f
--- /dev/null
+++ b/sanofi/etc/log.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+ <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
+ <layout class="org.apache.log4j.PatternLayout">
+ <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
+ </layout>
+ </appender>
+
+ <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
+
+ <root>
+ <priority value ="info" />
+ <appender-ref ref="STDOUT" />
+ </root>
+
+</log4j:configuration>
diff --git a/sanofi/.gitignore b/sanofi/source/java/.gitignore
similarity index 100%
rename from sanofi/.gitignore
rename to sanofi/source/java/.gitignore
diff --git a/sanofi/sourceTest/examples/batchNr_plateCode.variant_2011.06.28/sample.data b/sanofi/sourceTest/examples/batchNr_plateCode.variant_2011.06.28/sample.data
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f69e8b5b9de791cb0eecf2611fa5c57a8acdfd06
--- /dev/null
+++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
@@ -0,0 +1,234 @@
+/*
+ * Copyright 2011 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.sanofi.dss.test;
+
+import static ch.systemsx.cisd.common.Constants.IS_FINISHED_PREFIX;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+import org.apache.commons.io.FileUtils;
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.eodsql.MockDataSet;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.etlserver.registrator.AbstractJythonDataSetHandlerTest;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSourceQueryService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * <pre>
+ * Things not tested
+ * - skip well creation when plate library already exists
+ * - skip material creation for preexisting materials
+ * - error cases
+ * </pre>
+ *
+ * @author Kaloyan Enimanev
+ */
+public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
+{
+ private static final String PLATE_CODE = "plateCode";
+
+ private static final String LIBRARY_TEMPLATE_PROPNAME = "LIBRARY_TEMPLATE";
+
+ private static final String MATERIAL_TYPE = "COMPOUND_BATCH";
+
+ private static final String DATASET_DIR_NAME = "batchNr_plateCode.variant_2011.06.28";
+
+ private static final String DATA_SET_CODE = "data-set-code";
+
+ private static final DataSetType DATA_SET_TYPE = new DataSetType("DATA_SET_TYPE");
+
+ private static final String EXPERIMENT_IDENTIFIER = "/SANOFI/PROJECT/EXP";
+ private static final String PLATE_IDENTIFIER = "/SANOFI/TEST-PLATE";
+
+ private IDataSourceQueryService queryService;
+
+ @BeforeMethod
+ @Override
+ public void setUp() throws IOException
+ {
+ super.setUp();
+ queryService = context.mock(IDataSourceQueryService.class);
+ }
+
+ @Test(enabled = false)
+ public void testSimpleTransaction() throws IOException
+ {
+ setUpHomeDataBaseExpectations();
+ Properties properties = createThreadPropertiesRelativeToScriptsFolder("sanofi-dropbox.py");
+ createHandler(properties, false, true, queryService);
+ createData();
+
+ final String libraryTemplate = "1.45, H\n0.12, L";
+ final Sample plate = createPlate(libraryTemplate);
+ setUpPlateSearchExpectations(plate);
+ setUpLibraryTemplateExpectations(plate);
+
+ final MockDataSet<Map<String, Object>> queryResult = new MockDataSet<Map<String, Object>>();
+ queryResult.add(createQueryResult("A0"));
+ queryResult.add(createQueryResult("B0"));
+
+ final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
+ new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
+ final RecordingMatcher<ListMaterialCriteria> materialCriteria =
+ new RecordingMatcher<ListMaterialCriteria>();
+ context.checking(new Expectations()
+ {
+ {
+ one(queryService).select(with(any(String.class)), with(any(String.class)),
+ with(anything()));
+ will(returnValue(queryResult));
+
+ one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ will(returnValue(Collections.emptyList()));
+
+ one(openBisService).createPermId();
+ will(returnValue("A0-permId"));
+
+ one(openBisService).createPermId();
+ will(returnValue("B0-permId"));
+
+ one(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE));
+
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
+ new File(new File(stagingDirectory, DATA_SET_CODE), DATASET_DIR_NAME));
+
+ SampleIdentifier sampleIdentifier =
+ SampleIdentifierFactory.parse(plate.getIdentifier());
+ one(openBisService).tryGetSampleWithExperiment(sampleIdentifier);
+ will(returnValue(plate));
+
+ one(openBisService).getPropertiesOfTopSampleRegisteredFor(sampleIdentifier);
+ will(returnValue(new IEntityProperty[0]));
+
+ one(openBisService).performEntityOperations(with(atomicatOperationDetails));
+ will(returnValue(new AtomicEntityOperationResult()));
+ }
+ });
+
+ handler.handle(markerFile);
+
+ assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType());
+ assertEquals(true, queryResult.hasCloseBeenInvoked());
+
+ assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+
+ NewExternalData dataSet =
+ atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+
+ assertEquals(DATA_SET_CODE, dataSet.getCode());
+ assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());
+
+ context.assertIsSatisfied();
+ }
+
+ private void setUpPlateSearchExpectations(final Sample plate)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "PLATE"));
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ PLATE_CODE));
+ oneOf(openBisService).searchForSamples(sc);
+
+ will(returnValue(Arrays.asList(plate)));
+ }
+ });
+ }
+
+ private void setUpLibraryTemplateExpectations(final Sample plate)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ final String identifierString = plate.getExperiment().getIdentifier();
+ ExperimentIdentifier identifier =
+ ExperimentIdentifierFactory.parse(identifierString);
+ oneOf(openBisService).tryToGetExperiment(identifier);
+ will(returnValue(plate.getExperiment()));
+ }
+ });
+ }
+
+ private void createData() throws IOException
+ {
+ File dataDirectory = new File("./sourceTest/examples/" + DATASET_DIR_NAME);
+ FileUtils.copyDirectoryToDirectory(dataDirectory, workingDirectory);
+ incomingDataSetFile = new File(workingDirectory, dataDirectory.getName());
+
+ markerFile = new File(workingDirectory, IS_FINISHED_PREFIX + dataDirectory.getName());
+ FileUtilities.writeToFile(markerFile, "");
+ }
+
+ private Sample createPlate(String libraryTemplate)
+ {
+ ExperimentBuilder experimentBuilder =
+ new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER).property(
+ LIBRARY_TEMPLATE_PROPNAME,
+ libraryTemplate);
+
+ SampleBuilder sampleBuilder =
+ new SampleBuilder().identifier(PLATE_IDENTIFIER).experiment(
+ experimentBuilder.getExperiment());
+ final Sample plate = sampleBuilder.getSample();
+ return plate;
+ }
+
+ private Map<String, Object> createQueryResult(String wellCode)
+ {
+ Map<String, Object> result = new HashMap<String, Object>();
+ result.put("WELL_CODE", wellCode);
+ result.put("MATERIAL_CODE", wellCode + "_material_code");
+ result.put("ABASE_COMPOUND_ID", wellCode + "_compound_id");
+ result.put("ABASE_COMPOUND_BATCH_ID", wellCode + "_compound_batch_id");
+ return result;
+ }
+
+ @Override
+ protected String getRegistrationScriptsFolderPath()
+ {
+ return "dist/etc/sanofi-dropbox/";
+ }
+}
\ No newline at end of file
diff --git a/sanofi/sourceTest/java/tests.xml b/sanofi/sourceTest/java/tests.xml
new file mode 100644
index 0000000000000000000000000000000000000000..082bf00ea75a27c289e1b0fe079726fd9dc54245
--- /dev/null
+++ b/sanofi/sourceTest/java/tests.xml
@@ -0,0 +1,14 @@
+<!DOCTYPE suite SYSTEM "http://beust.com/testng/testng-1.0.dtd" >
+
+<suite name="All" verbose="1">
+ <test name="All">
+ <groups>
+ <run>
+ <exclude name="broken" />
+ </run>
+ </groups>
+ <packages>
+ <package name="eu.basynthec.cisd.dss.*" />
+ </packages>
+ </test>
+</suite>
diff --git a/sanofi/sourceTest/python/unit-tests.py b/sanofi/sourceTest/python/unit-tests.py
new file mode 100644
index 0000000000000000000000000000000000000000..ac84070940f3808e2195c57e543ae28e0ae09c9b
--- /dev/null
+++ b/sanofi/sourceTest/python/unit-tests.py
@@ -0,0 +1,11 @@
+import unittest
+
+class DropboxUnitTests(unittest.TestCase):
+
+ def test_parse_incoming_dir_name(self):
+ self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
+ self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
+
+ def test_parse_incoming_dir_name(self):
+ self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
+ self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
\ No newline at end of file