diff --git a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
index d4d77f278cd9155a30443f1289f1ea8659626726..921be04420e9c41dc4e53aeec4657cc12cad6825 100644
--- a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
+++ b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
@@ -19,8 +19,6 @@ from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, I
from ch.systemsx.cisd.openbis.dss.etl.custom.geexplorer import GEExplorerImageAnalysisResultParser
from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
-from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
-
# Switch this off if there is more then one dropbox using this module,
# in this case it should be switched on manually only after the module's code has been changed on the fly
reload(plateinit)
@@ -79,21 +77,52 @@ def isUserError(ex):
return ex.value and (ex.value.getClass() == ValidationException("").getClass())
def getAdminEmails():
- admins = ServiceProvider.getOpenBISService().listAdministrators()
+ admins = state.getOpenBisService().listAdministrators()
adminEmails = [ admin.getEmail() for admin in admins if admin.getEmail() ]
return adminEmails
+def getUserEmails():
+ global experiment
+
+ recipients = []
+
+ if experiment:
+ recipientsProp = experiment.getPropertyValue(EXPERIMENT_RECIPIENTS_PROPCODE)
+ if recipientsProp:
+ recipients = [ email.strip() for email in recipientsProp.split(",") ]
+
+ return recipients
+
+def getAllEmailRecipients():
+ return getAdminEmails() + getUserEmails()
+
+def commit_transaction(service, transaction):
+ global plateCode
+
+ incomingFileName = incoming.getName()
+ plateLink = createPlateLink(OPENBIS_URL, plateCode)
+ sendEmail("openBIS: New data registered for %s" % (plateCode), """
+ Dear openBIS user,
+
+ New data from folder '%(incomingFileName)s' has been successfully registered in plate %(plateLink)s.
+
+ This email has been generated automatically.
+
+ Have a nice day!
+
+ Administrator
+ """ % vars(), getAllEmailRecipients())
def rollback_service(service, ex):
if isUserError(ex):
shortErrorMessage = ex.getMessage()
if not shortErrorMessage:
shortErrorMessage = ex.value.getMessage()
- sendUserError(service, shortErrorMessage, getDefaultEmailRecipients())
+ sendUserError(service, shortErrorMessage, getAllEmailRecipients())
else:
fullErrorMessage = ExceptionUtils.getFullStackTrace(ex)
sendAdminError(service, fullErrorMessage, getAdminEmails())
- sendSystemErrorNotificationToUser(service, getDefaultEmailRecipients())
+ sendSystemErrorNotificationToUser(service, getUserEmails())
def sendUserError(service, errorDetails, recipients):
global plateCode
@@ -158,35 +187,6 @@ def sendSystemErrorNotificationToUser(service, recipients):
openBIS Administrators
""" % vars(), recipients)
-def commit_transaction(service, transaction):
- global plateCode
-
- incomingFileName = incoming.getName()
- plateLink = createPlateLink(OPENBIS_URL, plateCode)
- sendEmail("openBIS: New data registered for %s" % (plateCode), """
- Dear openBIS user,
-
- New data from folder '%(incomingFileName)s' has been successfully registered in plate %(plateLink)s.
-
- This email has been generated automatically.
-
- Have a nice day!
-
- Administrator
- """ % vars(), getDefaultEmailRecipients())
-
-def getDefaultEmailRecipients():
- global experiment
-
- recipients = []
-
- if experiment:
- recipientsProp = experiment.getPropertyValue(EXPERIMENT_RECIPIENTS_PROPCODE)
- if recipientsProp:
- recipients = [ email.strip() for email in recipientsProp.split(",") ]
-
- return recipients
-
def sendEmail(title, content, recipients):
global experiment
@@ -321,7 +321,7 @@ class MyImageDataSetConfig(SimpleImageDataConfig):
global experiment
global plateCode
global plate
-
+
if incoming.isDirectory():
experiment = None
plateCode = None
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
index 5169bb35198f7de0de881f4cdd7e65d7626980ab..524114c30482b8e3691eb195fc599558b855a0a3 100644
--- a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
+++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
@@ -1,5 +1,6 @@
/*
* 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.
@@ -32,7 +33,6 @@ import java.util.Properties;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
import org.jmock.Expectations;
-import org.springframework.beans.factory.BeanFactory;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -51,7 +51,6 @@ import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.DataSetStorageAlgorithmRunner;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProviderTestWrapper;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
@@ -93,8 +92,14 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String EXPERIMENT_RECIPIENTS_PROPNAME = "OBSERVER_EMAILS";
- private static final String[] EXPERIMENT_RECIPIENTS = new String[]
- { "admin@sanofi.com", "mickey@mouse.org" };
+ private static final String[] USER_EMAILS = new String[]
+ { "donald@duck.com", "mickey@mouse.org" };
+
+ final String[] ADMIN_EMAILS = new String[]
+ { "admin@sanofi.com", "admin@openbis.org" };
+
+ final String[] ALL_EMAILS = new String[]
+ { "admin@sanofi.com", "admin@openbis.org", "donald@duck.com", "mickey@mouse.org" };
private static final String MATERIAL_TYPE = "COMPOUND";
@@ -139,15 +144,11 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private RecordingMatcher<String> email;
- private BeanFactory applicationContext;
-
@Override
@BeforeMethod
public void setUp() throws IOException
{
super.setUp();
-
- applicationContext = context.mock(BeanFactory.class);
extendJythonLibPath(getRegistrationScriptsFolderPath());
@@ -155,29 +156,14 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
materialCriteria = new RecordingMatcher<ListMaterialCriteria>();
email = new RecordingMatcher<String>();
-
- ServiceProviderTestWrapper.setApplicationContext(applicationContext);
- context.checking(new Expectations()
- {
- {
- allowing(applicationContext).getBean("openBIS-service");
- will(returnValue(openBisService));
- }
- });
- }
-
- @Override
- public void tearDown() throws IOException
- {
- super.tearDown();
-
- ServiceProviderTestWrapper.restoreApplicationContext();
}
@Test
public void testLibraryWider() throws IOException
{
createDataSetHandler(false, false);
+ setUpListAdministratorExpectations();
+
final Sample plate =
plateWithLibTemplateAndGeometry("1.45\t\tH\n0.12\t0.002\tL", "10_WELLS_1X10");
context.checking(new Expectations()
@@ -191,7 +177,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -217,6 +203,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
createDataSetHandler(false, false);
final Sample plate =
plateWithLibTemplateAndGeometry("1.45\t\tH\n0.12\t0.002\tL", "5_WELLS_5X1");
+ setUpListAdministratorExpectations();
+
context.checking(new Expectations()
{
{
@@ -228,7 +216,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -253,6 +241,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
public void testLibraryTemplateWithWellNotPresentInAbase() throws IOException
{
createDataSetHandler(false, false);
+ setUpListAdministratorExpectations();
final MockDataSet<Map<String, Object>> queryResult = new MockDataSet<Map<String, Object>>();
queryResult.add(createQueryResult("A1"));
@@ -272,7 +261,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -293,6 +282,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
public void testLibraryTemplateIncompleteAccordingToAbase() throws IOException
{
createDataSetHandler(false, false);
+ setUpListAdministratorExpectations();
final MockDataSet<Map<String, Object>> queryResult = new MockDataSet<Map<String, Object>>();
queryResult.add(createQueryResult("A1"));
@@ -313,7 +303,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -343,6 +333,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
queryResult.add(createQueryResult("B2"));
setDataSetExpectations();
+ setUpListAdministratorExpectations();
+
context.checking(new Expectations()
{
{
@@ -371,7 +363,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -424,12 +416,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
createDataSetHandler(false, false);
final Sample plate = plateWithLibTemplateAndGeometry("0.75\tH\n54.12\tL", "8_WELLS_2X4");
- final String[] adminEmails = new String[]
- { "admin@sanofi.com", null, "admin@openbis.org", "" };
-
- final String[] nonEmptyAdminEmails = new String[]
- { "admin@sanofi.com", "admin@openbis.org" };
-
+ setUpListAdministratorExpectations();
context.checking(new Expectations()
{
{
@@ -443,17 +430,13 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(openBisService).tryGetSampleWithExperiment(sampleIdentifier);
will(returnValue(plate));
- one(openBisService).listAdministrators();
- List<String> adminEmailsList = Arrays.asList(adminEmails);
- will(returnValue(createAdministrators(adminEmailsList)));
-
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(nonEmptyAdminEmails)));
+ with(equal(ADMIN_EMAILS)));
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(USER_EMAILS)));
}
@@ -480,18 +463,6 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
context.assertIsSatisfied();
}
- private List<Person> createAdministrators(List<String> adminEmails)
- {
- List<Person> result = new ArrayList<Person>();
- for (String adminEmail : adminEmails)
- {
- Person person = new Person();
- person.setEmail(adminEmail);
- result.add(person);
- }
- return result;
- }
-
@Test
public void testHappyCaseWithLibraryCreationAndNonUniqueMaterials() throws IOException
{
@@ -503,6 +474,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
queryResult.add(createQueryResult("B1", "material-1"));
setDataSetExpectations();
+ setUpListAdministratorExpectations();
+
context.checking(new Expectations()
{
{
@@ -530,7 +503,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(mailClient).sendMessage(with(any(String.class)), with(email),
with(aNull(String.class)), with(any(From.class)),
- with(equal(EXPERIMENT_RECIPIENTS)));
+ with(equal(ALL_EMAILS)));
}
});
@@ -742,6 +715,30 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
});
}
+ private void setUpListAdministratorExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openBisService).listAdministrators();
+ List<String> adminEmailsList = Arrays.asList(ADMIN_EMAILS);
+ will(returnValue(createAdministrators(adminEmailsList)));
+ }
+ });
+ }
+
+ private List<Person> createAdministrators(List<String> adminEmails)
+ {
+ List<Person> result = new ArrayList<Person>();
+ for (String adminEmail : adminEmails)
+ {
+ Person person = new Person();
+ person.setEmail(adminEmail);
+ result.add(person);
+ }
+ return result;
+ }
+
private void createData() throws IOException
{
File dataDirectory = new File("./sourceTest/examples/" + IMAGE_DATA_SET_DIR_NAME);
@@ -757,7 +754,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
ExperimentBuilder experimentBuilder = new ExperimentBuilder();
experimentBuilder.identifier(EXPERIMENT_IDENTIFIER);
experimentBuilder.property(LIBRARY_TEMPLATE_PROPNAME, libraryTemplate);
- String recipients = StringUtils.join(Arrays.asList(EXPERIMENT_RECIPIENTS), ",");
+ String recipients = StringUtils.join(Arrays.asList(USER_EMAILS), ",");
experimentBuilder.property(EXPERIMENT_RECIPIENTS_PROPNAME, recipients);
SampleBuilder sampleBuilder = new SampleBuilder();