diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ServiceProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ServiceProvider.java
index 10c3304f8c6632ef60fba8d73cae168e06d42c68..ce8fd97fbac6ae13180a5026ea4403ee32cf33a6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ServiceProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ServiceProvider.java
@@ -138,6 +138,11 @@ public class ServiceProvider
return ((IApplicationServerApi) getApplicationContext().getBean(V3_APPLICATION_SERVICE_BEAN));
}
+ public static IDataStoreServerApi getV3DataStoreService()
+ {
+ return ((IDataStoreServerApi) getApplicationContext().getBean(DataStoreServerApi.INTERNAL_SERVICE_NAME));
+ }
+
public static IGeneralInformationService getGeneralInformationService()
{
return ((IGeneralInformationService) getApplicationContext().getBean(
diff --git a/integration-tests/TEST_PYTHON_LIBRARIES_LOCALLY b/integration-tests/TEST_PYTHON_LIBRARIES_LOCALLY
new file mode 100644
index 0000000000000000000000000000000000000000..025024e43c90b61c001bfd13aa4bcc7a55f0fd69
--- /dev/null
+++ b/integration-tests/TEST_PYTHON_LIBRARIES_LOCALLY
@@ -0,0 +1,17 @@
+# add the source folder to the PYTHONPATH:
+
+export PYTHONPATH=/Users/vermeul/openbis/integration-tests/source:/Users/vermeul/openbis/integration-tests/sourceTest:$PYTHONPATH
+
+# make sure you test the develop-version of pybis or obis
+
+cd ~/openbis/pybis/src/python
+pip install -e .
+
+# ... and prevent this test-suite to install pybis from some source
+vim openbis/integration-tests/source/test_pybis.py
+
+# on line 34, make sure that
+
+ #self.installPybis()
+
+# is commented out, otherwise your installation is being overwritten
diff --git a/integration-tests/source/systemtest/testcase.py b/integration-tests/source/systemtest/testcase.py
index 1bb35a7792e50c1cec256efb97a6aa25e22ae235..63d1fa64f3c76dd8ce76c490bd36325bdcd7d04f 100644
--- a/integration-tests/source/systemtest/testcase.py
+++ b/integration-tests/source/systemtest/testcase.py
@@ -280,17 +280,20 @@ class TestCase(object):
return ScreeningTestClient(self, installPath)
def installPybis(self):
- zipFile = self.artifactRepository.getPathToArtifact(OPENBIS_STANDARD_TECHNOLOGIES_PROJECT, 'pybis-')
- installPath = "%s/pybis" % self.playgroundFolder
- util.unzip(zipFile, installPath)
- util.executeCommand(['pip', 'install', installPath + '/src/python'], "Installation of pybis failed.")
+ #zipFile = self.artifactRepository.getPathToArtifact(OPENBIS_STANDARD_TECHNOLOGIES_PROJECT, 'pybis-')
+ #installPath = "%s/pybis" % self.playgroundFolder
+ #util.unzip(zipFile, installPath)
+ #util.executeCommand(['pip', 'install', installPath + '/src/python'], "Installation of pybis failed.")
+ # install the local pybis in editable-mode (-e)
+ util.executeCommand(['pip', 'install', '-e', '../pybis/src/python'], "Installation of pybis failed.")
def installObis(self):
- zipFile = self.artifactRepository.getPathToArtifact(OPENBIS_STANDARD_TECHNOLOGIES_PROJECT, 'obis-')
- installPath = "%s/obis" % self.playgroundFolder
- util.unzip(zipFile, installPath)
- print('pip install ' + installPath + '/src/python')
- util.executeCommand(['pip', 'install', installPath + '/src/python'], "Installation of obis failed.")
+ #zipFile = self.artifactRepository.getPathToArtifact(OPENBIS_STANDARD_TECHNOLOGIES_PROJECT, 'obis-')
+ #installPath = "%s/obis" % self.playgroundFolder
+ #util.unzip(zipFile, installPath)
+ #print('pip install ' + installPath + '/src/python')
+ #util.executeCommand(['pip', 'install', installPath + '/src/python'], "Installation of obis failed.")
+ util.executeCommand(['pip', 'install', '-e', '../obis/src/python'], "Installation of pybis failed.")
def getTemplatesFolder(self):
@@ -815,4 +818,4 @@ class OpenbisController(_Controller):
for line in lines:
f.write("%s\n" % line)
-
\ No newline at end of file
+
diff --git a/integration-tests/test_pybis.py b/integration-tests/test_pybis.py
index 34a6e06daff835b51b97e13083965219f756fcf5..12e38db131349e0ae71299617c2e096ee3b114d2 100755
--- a/integration-tests/test_pybis.py
+++ b/integration-tests/test_pybis.py
@@ -31,7 +31,7 @@ class TestCase(systemtest.testcase.TestCase):
self.FILE = 'TEST_FILE_' + str(randrange(100000))
self.installOpenbis()
- #self.installPybis()
+ self.installPybis()
self.openbisController = self.createOpenbisController()
self.openbisController.createTestDatabase("openbis")
self.openbisController.allUp()
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/SingleSignOnServlet.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/SingleSignOnServlet.java
index f370f8c7d41928d8d4bfcb43303f671e0bec0faf..dd45e86850433efcc9ddaddbbc062192444d829e 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/SingleSignOnServlet.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/SingleSignOnServlet.java
@@ -17,6 +17,8 @@
package ch.ethz.sis.openbis.generic.server;
import java.io.IOException;
+import java.util.Arrays;
+import java.util.Enumeration;
import java.util.HashMap;
import java.util.Map;
@@ -108,6 +110,18 @@ public class SingleSignOnServlet extends AbstractServlet
{
String sessionId = getHeader(request, SESSION_ID_KEY, DEFAULT_SESSION_ID_KEY);
String sessionToken = sessionTokenBySessionId.get(sessionId);
+ String returnURL = request.getParameter("return");
+ if (returnURL != null)
+ {
+ handleLogOut(request, response, sessionId, sessionToken, returnURL);
+ } else
+ {
+ handleLogIn(request, response, sessionId, sessionToken);
+ }
+ }
+
+ private void handleLogIn(HttpServletRequest request, HttpServletResponse response, String sessionId, String sessionToken) throws IOException
+ {
if (sessionToken != null)
{
Session session = sessionManager.tryGetSession(sessionToken);
@@ -138,13 +152,40 @@ public class SingleSignOnServlet extends AbstractServlet
redirectToApp(request, response, sessionToken);
}
- protected void redirectToApp(HttpServletRequest request, HttpServletResponse response, String sessionToken) throws IOException
+ private void handleLogOut(HttpServletRequest request, HttpServletResponse response, String sessionId, String sessionToken, String returnURL)
+ throws IOException
+ {
+ operationLog.info("log out session id: " + sessionId);
+ if (sessionToken != null)
+ {
+ Session session = sessionManager.tryGetSession(sessionToken);
+ if (session != null)
+ {
+ sessionManager.closeSession(sessionToken);
+ operationLog.info("Session " + sessionToken + " closed.");
+ }
+ }
+ operationLog.info("Redirect to " + returnURL);
+ removeOpenbisCookies(request, response);
+ response.sendRedirect(returnURL);
+ }
+
+ private void redirectToApp(HttpServletRequest request, HttpServletResponse response, String sessionToken) throws IOException
{
String host = request.getHeader("X-Forwarded-Host");
Template template = this.template.createFreshCopy();
template.bind("host", host);
String redirectUrl = configurer.getResolvedProps().getProperty(REDIRECT_URL_KEY, template.createText());
operationLog.info("redirect to " + redirectUrl);
+ removeOpenbisCookies(request, response);
+ Cookie cookie = new Cookie("openbis", sessionToken);
+ cookie.setPath("/");
+ response.addCookie(cookie);
+ response.sendRedirect(redirectUrl);
+ }
+
+ private void removeOpenbisCookies(HttpServletRequest request, HttpServletResponse response)
+ {
Cookie[] cookies = request.getCookies();
for (Cookie cookie : cookies)
{
@@ -156,10 +197,6 @@ public class SingleSignOnServlet extends AbstractServlet
response.addCookie(cookie);
}
}
- Cookie cookie = new Cookie("openbis", sessionToken);
- cookie.setPath("/");
- response.addCookie(cookie);
- response.sendRedirect(redirectUrl);
}
private String getHeader(HttpServletRequest request, String keyProperty, String defaultKey)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/DefaultFullTextIndexer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/DefaultFullTextIndexer.java
index 0d1b6ac00d43e9d33828be7ec3f63b20680905df..3060eb00acdbc0899db194ff5b5d9627951c500f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/DefaultFullTextIndexer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/DefaultFullTextIndexer.java
@@ -148,6 +148,9 @@ final class DefaultFullTextIndexer implements IFullTextIndexer
List<Long> subList = ids.subList(index, nextIndex);
final List<T> results =
listEntitiesWithRestrictedId(fullTextSession, clazz, subList);
+ if (subList.size() != results.size()) {
+ operationLog.error(String.format("The system tried to index %d but only found %d on the database.", subList.size(), results.size()));
+ }
indexEntities(fullTextSession, results);
index = nextIndex;
operationLog.info(String.format("%d/%d %ss have been reindexed...", index,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
index 3416d16c13051a66faa0542a7bdfd38f2f0a08c1..978e14e2ef7b11b458fb26acc9a3fc595ff29e59 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
@@ -93,7 +93,7 @@ public class BasicConstant
/**
* Canonical date format pattern used to render dates in GUI in a more readable way.
*/
- public static final String RENDERED_CANONICAL_DATE_FORMAT_PATTERN = "yyyy-MM-dd HH:mm:ss ZZZ";
+ public static final String RENDERED_CANONICAL_DATE_FORMAT_PATTERN = "yyyy-MM-dd HH:mm:ss Z";
/**
* Date format which does not include time zone.
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
index f682ae31ed44532ac9bccc4a6c47c2d71b803c2c..d76ed8acd11035a28bd2b1b8c72d737f68e93147 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/initialize-master-data.py
@@ -16,7 +16,6 @@
# MasterDataRegistrationTransaction Class
from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
-from ch.systemsx.cisd.openbis.generic.server import ComponentNames
from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
from ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl import MasterDataRegistrationHelper
@@ -25,19 +24,10 @@ import sys
helper = MasterDataRegistrationHelper(sys.path)
api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
sessionToken = api.loginAsSystem()
-props = CustomASServiceExecutionOptions().withParameter('xls', helper.listXlsByteArrays())\
- .withParameter('xls_name', 'ELN-LIMS-LIFE-SCIENCES').withParameter('update_mode', 'IGNORE_EXISTING')\
+props = CustomASServiceExecutionOptions().withParameter('xls', helper.listXlsByteArrays()) \
+ .withParameter('xls_name', 'ELN-LIMS-LIFE-SCIENCES').withParameter('update_mode', 'IGNORE_EXISTING') \
.withParameter('scripts', helper.getAllScripts())
-result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import-api"), props);
-# Updating MULTILINE_VARCHAR to use "Word Processor" for all Properties
-daoFactory = CommonServiceProvider.getApplicationContext().getBean(ComponentNames.DAO_FACTORY);
-currentSession = daoFactory.getSessionFactory().getCurrentSession();
-SQL = "UPDATE property_types SET meta_data = cast(:meta_data AS jsonb) WHERE id IN (SELECT id FROM property_types WHERE daty_id = (SELECT id FROM data_types WHERE code = 'MULTILINE_VARCHAR'))";
-meta_data = "{ \"custom_widget\" : \"Word Processor\" }";
-sqlQuery = currentSession.createSQLQuery(SQL);
-sqlQuery.setParameter("meta_data", meta_data);
-sqlQuery.executeUpdate();
-#
+result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import-api"), props)
print("======================== master-data xls ingestion result ========================")
print(result)
print("======================== master-data xls ingestion result ========================")
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls
index b6725cb9c04a7e5c2b7e09d1e0be48893d3fa778..e2755043112873eaa41408f7a01ab4e152444d93 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims-life-sciences/1/as/master-data/data-model.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls
index 4d69110b10b17aa7e664af2f3bc8fc636427f53f..c061f53d70d87bbbb9cf15446655855d2d1bf0ce 100644
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls and b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/master-data/data-model.xls differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
index b898b2b7b3fb242a979ca33933c46a083d92c1cf..f4e5c0d716dbd1b4bf84461a4a7a6646b2db7184 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/services/publication-api/publication-api.py
@@ -89,7 +89,7 @@ def getDefaultDataStoreCode(v3, sessionToken):
def createPublicationSample(parameters, sessionToken, v3):
publicationOrganization = parameters.get('publicationOrganization')
if publicationOrganization is None:
- raise ValueError('publicationOrganization parameter is None.')
+ publicationOrganization = ''
name = parameters.get('name')
if name is None:
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
index 2ed7d10ad30493b50d6f2ef725993e9b5a61454e..aa154b6a24013efa7ce3540fbf74cd1cec3f32bc 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/index.html
@@ -258,6 +258,10 @@
<script type="text/javascript" src="./js/views/ResearchCollectionExport/ResearchCollectionExportModel.js"></script>
<script type="text/javascript" src="./js/views/ResearchCollectionExport/ResearchCollectionExportView.js"></script>
+ <script type="text/javascript" src="./js/views/ZenodoExport/ZenodoExportController.js"></script>
+ <script type="text/javascript" src="./js/views/ZenodoExport/ZenodoExportModel.js"></script>
+ <script type="text/javascript" src="./js/views/ZenodoExport/ZenodoExportView.js"></script>
+
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsController.js"></script>
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsModel.js"></script>
<script type="text/javascript" src="./js/views/DrawingBoards/DrawingBoardsView.js"></script>
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
index b713b303923d04fa508d679c6db1851f4d2ce138..8b1a0d7ebb7f7f357ea1016d155394606e58f0fd 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/Profile.js
@@ -135,6 +135,7 @@ $.extend(DefaultProfile.prototype, {
// "ADMIN-BS-MBPR28.D.ETHZ.CH-E96954A7" : "http://localhost:8080/download"
}
this.singleSignOnUrlTemplate = null;
+ this.singleSignOnUrlLogoutTemplate = null;
this.singleSignOnLinkLabel = 'Single Sign On Login';
this.customWidgetSettings = {};
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
index 142198f6bab65d4da0dce1cf78171022e97001b4..1294aec2ba78fe8eec0fbf4992a436edea3db223 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/controllers/MainController.js
@@ -389,6 +389,13 @@ function MainController(profile) {
newResearchCollectionExportView.init(researchCollectionExportViews);
this.currentView = newResearchCollectionExportView;
break;
+ case "showZenodoExportPage":
+ document.title = "Zenodo Export Builder";
+ var newZenodoExportView = new ZenodoExportController(this);
+ var zenodoExportViews = this._getNewViewModel(true, true, false);
+ newZenodoExportView.init(zenodoExportViews);
+ this.currentView = newZenodoExportView;
+ break;
case "showLabNotebookPage":
document.title = "Lab Notebook";
var newView = new LabNotebookController(this);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
index 10486e4a5bbe79d136de70edc36f315712adf67a..96e277604e4a4ba2387881404142543ed6e52463 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/server/ServerFacade.js
@@ -396,6 +396,51 @@ function ServerFacade(openbisServer) {
});
};
+ this.exportZenodo = function(entities, includeRoot, metadataOnly, userInformation, callbackFunction) {
+ this.asyncExportZenodo({
+ "method": "exportAll",
+ "includeRoot": includeRoot,
+ "entities": entities,
+ "metadataOnly": metadataOnly,
+ "userInformation": userInformation,
+ "originUrl": window.location.origin,
+ "sessionToken": this.openbisServer.getSession(),
+ }, callbackFunction, "zenodo-exports-api");
+ };
+
+ this.asyncExportZenodo = function(parameters, callbackFunction, serviceId) {
+ require(["as/dto/service/execute/ExecuteAggregationServiceOperation",
+ "as/dto/operation/AsynchronousOperationExecutionOptions", "as/dto/service/id/DssServicePermId",
+ "as/dto/datastore/id/DataStorePermId", "as/dto/service/execute/AggregationServiceExecutionOptions"],
+ function(ExecuteAggregationServiceOperation, AsynchronousOperationExecutionOptions, DssServicePermId, DataStorePermId,
+ AggregationServiceExecutionOptions) {
+ var dataStoreCode = profile.getDefaultDataStoreCode();
+ var dataStoreId = new DataStorePermId(dataStoreCode);
+ var dssServicePermId = new DssServicePermId(serviceId, dataStoreId);
+ var options = new AggregationServiceExecutionOptions();
+
+ options.withParameter("sessionToken", parameters["sessionToken"]);
+
+ options.withParameter("entities", parameters["entities"]);
+ options.withParameter("includeRoot", parameters["includeRoot"]);
+ options.withParameter("metadataOnly", parameters["metadataOnly"]);
+ options.withParameter("method", parameters["method"]);
+ options.withParameter("originUrl", parameters["originUrl"]);
+ options.withParameter("submissionType", parameters["submissionType"]);
+ options.withParameter("submissionUrl", parameters["submissionUrl"]);
+ options.withParameter("entities", parameters["entities"]);
+ options.withParameter("userId", parameters["userInformation"]["id"]);
+ options.withParameter("userEmail", parameters["userInformation"]["email"]);
+ options.withParameter("userFirstName", parameters["userInformation"]["firstName"]);
+ options.withParameter("userLastName", parameters["userInformation"]["lastName"]);
+
+ var operation = new ExecuteAggregationServiceOperation(dssServicePermId, options);
+ mainController.openbisV3.executeOperations([operation], new AsynchronousOperationExecutionOptions()).done(function(results) {
+ callbackFunction(results.executionId.permId);
+ });
+ });
+ };
+
//
// Gets submission types
//
@@ -1476,33 +1521,70 @@ function ServerFacade(openbisServer) {
});
}
+ this.getResultsWithBrokenEqualsFix = function(hackFixForBrokenEquals, results, operator) {
+ if (!operator) {
+ operator = "AND";
+ }
+
+ if(hackFixForBrokenEquals.length > 0 && results) {
+ var filteredResults = [];
+ var resultsValid = new Array(results.length);
+ for (var vIdx = 0; vIdx < resultsValid.length; vIdx++) {
+ switch(operator) {
+ case "AND":
+ resultsValid[vIdx] = true;
+ break;
+ case "OR":
+ resultsValid[vIdx] = false;
+ break;
+ }
+ }
+
+ for(var rIdx = 0; rIdx < results.length; rIdx++) {
+ var result = results[rIdx];
+ for(var fIdx = 0; fIdx < hackFixForBrokenEquals.length; fIdx++) {
+ if( result &&
+ result.properties &&
+ result.properties[hackFixForBrokenEquals[fIdx].propertyCode] === hackFixForBrokenEquals[fIdx].value) {
+ switch(operator) {
+ case "AND":
+ resultsValid[rIdx] = resultsValid[rIdx] && true;
+ break;
+ case "OR":
+ resultsValid[rIdx] = resultsValid[rIdx] || true;
+ break;
+ }
+ } else {
+ switch(operator) {
+ case "AND":
+ resultsValid[rIdx] = resultsValid[rIdx] && false;
+ break;
+ case "OR":
+ resultsValid[rIdx] = resultsValid[rIdx] || false;
+ break;
+ }
+ }
+ }
+ }
+
+ for(var rIdx = 0; rIdx < results.length; rIdx++) {
+ if(resultsValid[rIdx]) {
+ filteredResults.push(results[rIdx]);
+ }
+ }
+
+ results = filteredResults;
+ }
+
+ return results;
+ }
+
this.searchForEntityAdvanced = function(advancedSearchCriteria, advancedFetchOptions, callback, criteriaClass, fetchOptionsClass, searchMethodName) {
+ var _this = this;
var searchFunction = function(searchCriteria, fetchOptions, hackFixForBrokenEquals) {
mainController.openbisV3[searchMethodName](searchCriteria, fetchOptions)
.done(function(apiResults) {
- //
- // Fix For broken equals PART 2
- //
- var results = apiResults.objects;
- var filteredResults = [];
- if(hackFixForBrokenEquals.length > 0 && results) {
- for(var rIdx = 0; rIdx < results.length; rIdx++) {
- var result = results[rIdx];
- for(var fIdx = 0; fIdx < hackFixForBrokenEquals.length; fIdx++) {
- if( result &&
- result.properties &&
- result.properties[hackFixForBrokenEquals[fIdx].propertyCode] === hackFixForBrokenEquals[fIdx].value) {
- filteredResults.push(result);
- }
- }
- }
- } else {
- filteredResults = results;
- }
- apiResults.objects = filteredResults;
- //
- // Fix For broken equals PART 2 - END
- //
+ apiResults.objects = _this.getResultsWithBrokenEqualsFix(hackFixForBrokenEquals, apiResults.objects, advancedSearchCriteria.logicalOperator);
callback(apiResults);
})
.fail(function(result) {
@@ -1825,14 +1907,14 @@ function ServerFacade(openbisServer) {
var localReference = this;
//
- // Fix For broken equals PART 1
+ // Collection Rules for broken equals Fix
// Currently the back-end matches whole words instead doing a standard EQUALS
// This fixes some most used cases for the storage system, but other use cases that use subcriterias can fail
//
var hackFixForBrokenEquals = [];
if(sampleCriteria.matchClauses) {
for(var cIdx = 0; cIdx < sampleCriteria.matchClauses.length; cIdx++) {
- if(sampleCriteria.matchClauses[cIdx]["@type"] === "PropertyMatchClause" &&
+ if(sampleCriteria.matchClauses[cIdx]["@type"] === "PropertyMatchClause" &&
sampleCriteria.matchClauses[cIdx]["compareMode"] === "EQUALS") {
hackFixForBrokenEquals.push({
propertyCode : sampleCriteria.matchClauses[cIdx].propertyCode,
@@ -1844,32 +1926,11 @@ function ServerFacade(openbisServer) {
//
// Fix For broken equals PART 1 - END
//
-
+ var _this = this;
this.openbisServer.searchForSamplesWithFetchOptions(sampleCriteria, options, function(data) {
var results = localReference.getInitializedSamples(data.result);
- //
- // Fix For broken equals PART 2
- //
- var filteredResults = [];
- if(hackFixForBrokenEquals.length > 0 && results) {
- for(var rIdx = 0; rIdx < results.length; rIdx++) {
- var result = results[rIdx];
- for(var fIdx = 0; fIdx < hackFixForBrokenEquals.length; fIdx++) {
- if( result &&
- result.properties &&
- result.properties[hackFixForBrokenEquals[fIdx].propertyCode] === hackFixForBrokenEquals[fIdx].value) {
- filteredResults.push(result);
- }
- }
- }
- } else {
- filteredResults = results;
- }
- //
- // Fix For broken equals PART 2 - END
- //
-
- callbackFunction(filteredResults);
+ results = _this.getResultsWithBrokenEqualsFix(hackFixForBrokenEquals, results, "AND");
+ callbackFunction(results);
});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
index 9658d70d42f076133974dd2075ce5654b55951de..19a34eb8422cac3228815ef88103b4e019eafa83 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/util/FormUtil.js
@@ -1176,7 +1176,17 @@ var FormUtil = new function() {
}
this._getDropboxFolderName = function(nameElements, dataSetTypeCode, name) {
- var folderName = nameElements.join("+");
+ var folderName = "";
+
+ for(var nIdx = 0; nIdx < nameElements.length; nIdx++) {
+ if(nameElements[nIdx]) {
+ if(nIdx !== 0) {
+ folderName += "+";
+ }
+ folderName += nameElements[nIdx];
+ }
+ }
+
for (var optionalPart of [dataSetTypeCode, name]) {
if (optionalPart) {
folderName += "+" + optionalPart;
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
index 514b6a15d2dcc03336b6c499ac7ad13528fbe454..df2a9b1fce2acd81bf794a0f7702ad527bde11a2 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportController.js
@@ -22,7 +22,7 @@ function ResearchCollectionExportController(parentController) {
researchCollectionExportView.repaint(views);
};
- this.initialiseSubmissionTypesDropdown = function(callback) {
+ this.initialiseSubmissionTypesDropdown = function() {
Util.blockUI();
mainController.serverFacade.listSubmissionTypes(function(error, result) {
Util.unblockUI();
@@ -56,6 +56,8 @@ function ResearchCollectionExportController(parentController) {
if (toExport.length === 0) {
Util.showInfo('First select something to export.');
+ } else if (!this.isValid(toExport)) {
+ Util.showInfo('Not only spaces and the root should be selected. It will result in an empty export file.');
} else if (!submissionUrl) {
Util.showInfo('First select submission type.');
} else {
@@ -82,6 +84,16 @@ function ResearchCollectionExportController(parentController) {
}
};
+ this.isValid = function(toExport) {
+ for (var i = 0; i < toExport.length; i++) {
+ var value = toExport[i];
+ if (value.type !== 'ROOT' && value.type !== 'SPACE' || value.expand) {
+ return true;
+ }
+ }
+ return false;
+ };
+
this.waitForOpExecutionResponse = function(operationExecutionPermIdString, callbackFunction) {
var _this = this;
require(["as/dto/operation/id/OperationExecutionPermId",
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
index 7945f200cb3b4bdf5591f784dbeff1a6335ce1f0..fa97054bbcc0ef9b17d3cc9d3cdb4c2e1ff6beae 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ResearchCollectionExport/ResearchCollectionExportView.js
@@ -15,8 +15,6 @@
*/
function ResearchCollectionExportView(researchCollectionExportController, researchCollectionExportModel) {
- var exportTreeView = new ExportTreeView(researchCollectionExportController, researchCollectionExportModel);
-
this.repaint = function(views) {
researchCollectionExportController.initialiseSubmissionTypesDropdown();
@@ -52,7 +50,7 @@ function ResearchCollectionExportView(researchCollectionExportController, resear
var $formTitle = $('<h2>').append('Research Collection Export Builder');
$header.append($formTitle);
- var $exportButton = $('<input>', { 'type': 'submit', 'class': 'btn btn-primary', 'value': 'Export Selected',
+ var $exportButton = $('<input>', {'type': 'submit', 'class': 'btn btn-primary', 'value': 'Export Selected',
'onClick': '$("form[name=\'rcExportForm\']").submit()'});
$header.append($exportButton);
};
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
index 5f1a59eb228352e90f692b6a428337bb6204f7a8..a4b303cd98b51654a4aa5817221b0ef10342324e 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SampleForm/SampleFormView.js
@@ -361,8 +361,6 @@ function SampleFormView(sampleFormController, sampleFormModel) {
sample = results.objects[rIdx];
}
}
- _this._sampleFormModel.sample.properties = sample.properties;
- delete _this._sampleFormModel.sample.properties[profile.propertyReplacingCode];
if(_this._sampleFormModel.views.header) {
_this._sampleFormModel.views.header.empty();
@@ -1245,7 +1243,7 @@ function SampleFormView(sampleFormController, sampleFormModel) {
this._allowedToCreateChild = function() {
var sample = this._sampleFormModel.v3_sample;
- return sample.frozenForChildren == false && sample.experiment.frozenForSamples == false;
+ return sample.frozenForChildren == false && (!sample.experiment || sample.experiment.frozenForSamples == false);
}
this._allowedToEdit = function() {
@@ -1255,21 +1253,21 @@ function SampleFormView(sampleFormController, sampleFormModel) {
this._allowedToMove = function() {
var sample = this._sampleFormModel.v3_sample;
- return sample.experiment.frozenForSamples == false;
+ return !sample.experiment || sample.experiment.frozenForSamples == false;
}
this._allowedToDelete = function() {
var sample = this._sampleFormModel.v3_sample;
- return sample.frozen == false && sample.experiment.frozenForSamples == false;
+ return sample.frozen == false && (!sample.experiment || sample.experiment.frozenForSamples == false);
}
this._allowedToCopy = function() {
var sample = this._sampleFormModel.v3_sample;
- return sample.experiment.frozenForSamples == false;
+ return !sample.experiment || sample.experiment.frozenForSamples == false;
}
this._allowedToRegisterDataSet = function() {
var sample = this._sampleFormModel.v3_sample;
- return sample.frozenForDataSets == false && sample.experiment.frozenForDataSets == false;
+ return sample.frozenForDataSets == false && (!sample.experiment || sample.experiment.frozenForDataSets == false);
}
}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
index 78ddfd0bd3f5f1b5219a904641976de2414d1ba3..787b3cf4ee32ec7eb542cd5b7f0afa72acde69e0 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
@@ -39,6 +39,27 @@ function SettingsFormController(mainController, settingsSample, mode) {
}
this.save = function(settings, widgetSettings) {
+ if(widgetSettings) { // Validate Widget Settings
+ for(var idx = 0; idx < widgetSettings.length; idx++) {
+ var widget = widgetSettings[idx];
+ var property = profile.getPropertyType(widget["Property Type"]);
+ switch(widget.Widget) {
+ case "Word Processor":
+ if(property.dataType !== "MULTILINE_VARCHAR") {
+ Util.showUserError("Word Processor only works with MULTILINE_VARCHAR data type.", function() {}, true);
+ return;
+ }
+ break;
+ case "Spreadsheet":
+ if(property.dataType !== "XML") {
+ Util.showUserError("Spreadsheet only works with XML data type.", function() {}, true);
+ return;
+ }
+ break;
+ }
+ }
+ }
+
var _this = this;
var onSave = function() {
_this._settingsManager.validateAndsave(_this._settingsFormModel.settingsSample, settings, (function() {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
index 03d1f8e2c9581b2f078153158d33a037359c596b..c7f77e5c4cd57151ba75599ade67fbfcd3b60f52 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SideMenu/SideMenuWidgetView.js
@@ -106,9 +106,14 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
searchElement.css({"margin-right" : "2px"});
var logoutButton = FormUtil.getButtonWithIcon("glyphicon-off", function() {
- Â Â Â Â $('body').addClass('bodyLogin');
- mainController.serverFacade.logout();
- });
+ $('body').addClass('bodyLogin');
+ var logoutTemplate = mainController.profile.singleSignOnUrlLogoutTemplate;
+ if (logoutTemplate) {
+ window.location = logoutTemplate.replace("${host}", window.location.hostname);
+ } else {
+ mainController.serverFacade.logout();
+ }
+ });
var $searchForm = $("<form>", { "onsubmit": "return false;" })
                    .append(logoutButton)
@@ -203,7 +208,7 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
                sortField = "displayName";
            }
            // descending order for registrationDate
-Â Â Â Â Â Â Â Â Â Â Â Â if (sortField == "registrationDate") {
+Â Â Â Â Â Â Â Â Â Â Â Â if (sortField === "registrationDate") {
                return naturalSort(resultB[sortField], resultA[sortField]);
            }
            return naturalSort(resultA[sortField], resultB[sortField]);
@@ -226,8 +231,8 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
}
if(profile.mainMenu.showStock) {
- Â Â Â Â var inventoryLink = _this.getLinkForNode("Stock", "STOCK", "showStockPage", null);
- Â Â Â Â treeModel.push({ displayName: "Stock", title : inventoryLink, entityType: "STOCK", key : "STOCK", folder : true, lazy : true, view : "showStockPage", icon: "fa fa-shopping-cart" });
+ Â Â Â Â var stockLink = _this.getLinkForNode("Stock", "STOCK", "showStockPage", null);
+ Â Â Â Â treeModel.push({ displayName: "Stock", title : stockLink, entityType: "STOCK", key : "STOCK", folder : true, lazy : true, view : "showStockPage", icon: "fa fa-shopping-cart" });
}
var treeModelUtils = [];
@@ -241,8 +246,8 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
}
if(profile.mainMenu.showUserProfile && profile.isFileAuthenticationService && profile.isFileAuthenticationUser) {
- Â Â Â Â var settingsLink = _this.getLinkForNode("User Profile", "USER_PROFILE", "showUserProfilePage", null);
- Â Â Â Â treeModelUtils.push({ title : settingsLink, entityType: "USER_PROFILE", key : "USER_PROFILE", folder : false, lazy : false, view : "showUserProfilePage", icon : "glyphicon glyphicon-user" });
+ Â Â Â Â var userProfileLink = _this.getLinkForNode("User Profile", "USER_PROFILE", "showUserProfilePage", null);
+ Â Â Â Â treeModelUtils.push({ title : userProfileLink, entityType: "USER_PROFILE", key : "USER_PROFILE", folder : false, lazy : false, view : "showUserProfilePage", icon : "glyphicon glyphicon-user" });
}
if(profile.mainMenu.showDrawingBoard) {
@@ -264,19 +269,38 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
    var advancedSearchLink = _this.getLinkForNode("Advanced Search", "ADVANCED_SEARCH", "showAdvancedSearchPage", null);
    treeModelUtils.push({ displayName: "Advanced Search", title : advancedSearchLink, entityType: "ADVANCED_SEARCH", key : "ADVANCED_SEARCH", folder : false, lazy : false, view : "showAdvancedSearchPage", icon : "glyphicon glyphicon-search" });
}
-
- if(profile.mainMenu.showExports) {
- Â Â Â Â var exportBuilderLink = _this.getLinkForNode("Export Builder", "EXPORT_BUILDER", "showExportTreePage", null);
- Â Â Â Â treeModelUtils.push({ displayName: "Export Builder", title : exportBuilderLink, entityType: "EXPORT_BUILDER", key : "EXPORT_BUILDER",
- folder : false, lazy : false, view : "showExportTreePage", icon : "glyphicon glyphicon-export" });
- }
- if (profile.mainMenu.showResearchCollectionExportBuilder) {
- var researchCollectionExportBuilderLink = _this.getLinkForNode("Research Collection Export Builder", "RESEARCH_COLLECTION_EXPORT_BUILDER",
- "showResearchCollectionExportPage", null);
- treeModelUtils.push({ displayName: "Research Collection Export Builder", title: researchCollectionExportBuilderLink,
- entityType: "RESEARCH_COLLECTION_EXPORT_BUILDER", key: "RESEARCH_COLLECTION_EXPORT_BUILDER", folder: false, lazy: false,
- view: "showResearchCollectionExportPage" });
+ if (profile.mainMenu.showExports || profile.mainMenu.showResearchCollectionExportBuilder || profile.mainMenu.showZenodoExportBuilder) {
+ var treeModelExports = [];
+
+ if (profile.mainMenu.showExports) {
+ var exportBuilderLink = _this.getLinkForNode("Export to ZIP", "EXPORT_TO_ZIP", "showExportTreePage", null);
+ treeModelExports.push({
+ displayName: "Export to ZIP", title: exportBuilderLink, entityType: "EXPORT_TO_ZIP", key: "EXPORT_TO_ZIP",
+ folder: false, lazy: false, view: "showExportTreePage", icon: "glyphicon glyphicon-export"
+ });
+ }
+
+ if (profile.mainMenu.showResearchCollectionExportBuilder) {
+ var researchCollectionExportBuilderLink = _this.getLinkForNode("Export to Research Collection",
+ "EXPORT_TO_RESEARCH_COLLECTION", "showResearchCollectionExportPage", null);
+ treeModelExports.push({
+ displayName: "Export to Research Collection", title: researchCollectionExportBuilderLink,
+ entityType: "EXPORT_TO_RESEARCH_COLLECTION", key: "EXPORT_TO_RESEARCH_COLLECTION", folder: false, lazy: false,
+ view: "showResearchCollectionExportPage", icon: "./img/research-collection-icon.png"
+ });
+ }
+
+ if (profile.mainMenu.showZenodoExportBuilder) {
+ var zenodoExportBuilderLink = _this.getLinkForNode("Export to Zenodo", "EXPORT_TO_ZENODO", "showZenodoExportPage", null);
+ treeModelExports.push({
+ displayName: "Export to Zenodo", title: zenodoExportBuilderLink, entityType: "EXPORT_TO_ZENODO",
+ key: "EXPORT_TO_ZENODO", folder: false, lazy: false, view: "showZenodoExportPage", icon: "glyphicon glyphicon-export"
+ });
+ }
+
+ treeModelUtils.push({ displayName: "Exports", title: "Exports", entityType: "EXPORTS", key: "EXPORTS", folder: true, lazy: false,
+ expanded: false, children: treeModelExports, view: "showBlancPage", icon: "glyphicon glyphicon-export" });
}
if(profile.mainMenu.showStorageManager) {
@@ -299,26 +323,26 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
    treeModelUtils.push({ displayName: "Settings", title : settingsLink, entityType: "SETTINGS", key : "SETTINGS", folder : false, lazy : false, view : "showSettingsPage", icon : "glyphicon glyphicon-cog" });
}
- treeModel.push({ displayName: "Utilities", title : "Utilities", entityType: "UTILITIES", key : "UTILITIES", folder : true, lazy : false, expanded : true, children : treeModelUtils, icon : "glyphicon glyphicon-wrench" });
+ treeModel.push({ displayName: "Utilities", title : "Utilities", entityType: "UTILITIES", key : "UTILITIES", folder : true, lazy : false, expanded : true, children : treeModelUtils, view: "showBlancPage", icon : "glyphicon glyphicon-wrench" });
treeModel.push({ displayName: "About", title : "About", entityType: "ABOUT", key : "ABOUT", folder : false, lazy : false, view : "showAbout", icon : "glyphicon glyphicon-info-sign" });
        var glyph_opts = {
- Â Â Â Â map: {
- Â Â Â Â doc: "glyphicon glyphicon-file",
- Â Â Â Â docOpen: "glyphicon glyphicon-file",
- Â Â Â Â checkbox: "glyphicon glyphicon-unchecked",
- Â Â Â Â checkboxSelected: "glyphicon glyphicon-check",
- Â Â Â Â checkboxUnknown: "glyphicon glyphicon-share",
- Â Â Â Â dragHelper: "glyphicon glyphicon-play",
- Â Â Â Â dropMarker: "glyphicon glyphicon-arrow-right",
- Â Â Â Â error: "glyphicon glyphicon-warning-sign",
- Â Â Â Â expanderClosed: "glyphicon glyphicon-plus-sign",
- Â Â Â Â expanderLazy: "glyphicon glyphicon-plus-sign", // glyphicon-expand
- Â Â Â Â expanderOpen: "glyphicon glyphicon-minus-sign", // glyphicon-collapse-down
- Â Â Â Â folder: "glyphicon glyphicon-folder-close",
- Â Â Â Â folderOpen: "glyphicon glyphicon-folder-open",
- Â Â Â Â loading: "glyphicon glyphicon-refresh"
- Â Â Â Â }
+ Â Â Â Â map: {
+ Â Â Â Â doc: "glyphicon glyphicon-file",
+ Â Â Â Â docOpen: "glyphicon glyphicon-file",
+ Â Â Â Â checkbox: "glyphicon glyphicon-unchecked",
+ Â Â Â Â checkboxSelected: "glyphicon glyphicon-check",
+ Â Â Â Â checkboxUnknown: "glyphicon glyphicon-share",
+ Â Â Â Â dragHelper: "glyphicon glyphicon-play",
+ Â Â Â Â dropMarker: "glyphicon glyphicon-arrow-right",
+ Â Â Â Â error: "glyphicon glyphicon-warning-sign",
+ Â Â Â Â expanderClosed: "glyphicon glyphicon-plus-sign",
+ Â Â Â Â expanderLazy: "glyphicon glyphicon-plus-sign", // glyphicon-expand
+ Â Â Â Â expanderOpen: "glyphicon glyphicon-minus-sign", // glyphicon-collapse-down
+ Â Â Â Â folder: "glyphicon glyphicon-folder-close",
+ Â Â Â Â folderOpen: "glyphicon glyphicon-folder-open",
+ Â Â Â Â loading: "glyphicon glyphicon-refresh"
+ Â Â Â Â }
};
   Â
    var onLazyLoad = function(event, data) {
@@ -381,7 +405,7 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
    });
                });
            });
- Â Â Â Â }
+ Â Â Â Â };
   Â
    switch(type) {
        case "LAB_NOTEBOOK":
@@ -450,7 +474,7 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
                                    registrationDate: space.registrationDate,
                                };
    if(!space.getCode().endsWith("STOCK_CATALOG") && !space.getCode().endsWith("STOCK_ORDERS")) {
- Â Â Â Â Â Â Â Â Â Â Â Â results.push(spaceNode);
+ Â Â Â Â Â Â Â Â Â Â Â Â results.push(spaceNode);
    }
    }
    }
@@ -661,24 +685,24 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
            });
       Â
        }
- Â Â Â Â }
+ Â Â Â Â };
   Â
    var getCancelResultsFunction = function(dfd) {
- Â Â Â Â Â Â Â Â Â Â Â Â return function() {
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â dfd.resolve([]);
- Â Â Â Â Â Â Â Â Â Â Â Â }
- Â Â Â Â }
+Â Â Â Â Â Â Â Â Â Â Â Â return function() {
+Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â dfd.resolve([]);
+Â Â Â Â Â Â Â Â Â Â Â Â }
+ Â Â Â Â };
   Â
    if(samplesToShow.length > 50) {
- Â Â Â Â Â Â Â Â Â Â Â Â var toExecute = function() {
-Â Â Â Â Â Â Â Â Â Â Â Â Util.blockUIConfirm("Do you want to show " + samplesWithoutELNParents.length + " " + ELNDictionary.Samples + " on the tree?",
-Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â getOkResultsFunction(dfd, samplesToShow),
-Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â getCancelResultsFunction(dfd));
- Â Â Â Â }
+Â Â Â Â Â Â Â Â Â Â Â Â var toExecute = function() {
+Â Â Â Â Â Â Â Â Â Â Â Â Util.blockUIConfirm("Do you want to show " + samplesWithoutELNParents.length + " " + ELNDictionary.Samples + " on the tree?",
+ Â Â Â Â Â Â Â Â Â Â Â Â getOkResultsFunction(dfd, samplesToShow),
+ Â Â Â Â Â Â Â Â Â Â Â Â getCancelResultsFunction(dfd));
+ Â Â Â Â };
       Â
- Â Â Â Â Â Â Â Â Â Â Â Â setTimeout(toExecute, 1000);
+ Â Â Â Â Â Â Â Â setTimeout(toExecute, 1000);
    } else {
- Â Â Â Â Â Â Â Â Â Â Â Â getOkResultsFunction(dfd, samplesToShow)();
+ Â Â Â Â Â Â Â Â getOkResultsFunction(dfd, samplesToShow)();
    }
            });
            break;
@@ -820,10 +844,9 @@ function SideMenuWidgetView(sideMenuWidgetController, sideMenuWidgetModel) {
            stock.setExpanded(true);
        }
       Â
- setCustomIcon($tree, "RESEARCH_COLLECTION_EXPORT_BUILDER", "./img/research-collection-icon.png");
        setCustomIcon($tree, "JUPYTER_WORKSPACE", "./img/jupyter-icon.png");
        setCustomIcon($tree, "NEW_JUPYTER_NOTEBOOK", "./img/jupyter-icon.png");
- }
+ };
function setCustomIcon($tree, nodeKey, iconImage) {
        var node = $tree.fancytree("getTree").getNodeByKey(nodeKey);
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js
new file mode 100644
index 0000000000000000000000000000000000000000..34f489234de0f0119b948bb8139ea5a7e76855ff
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportController.js
@@ -0,0 +1,112 @@
+/*
+ * 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.
+ */
+
+function ZenodoExportController(parentController) {
+ var exportModel = new ZenodoExportModel();
+ var exportView = new ZenodoExportView(this, exportModel);
+
+ this.init = function(views) {
+ exportView.repaint(views);
+ };
+
+ this.exportSelected = function() {
+ var _this = this;
+ var selectedNodes = $(exportModel.tree).fancytree('getTree').getSelectedNodes();
+
+ var toExport = [];
+ for (var eIdx = 0; eIdx < selectedNodes.length; eIdx++) {
+ var node = selectedNodes[eIdx];
+ toExport.push({type: node.data.entityType, permId: node.key, expand: !node.expanded});
+ }
+
+ if (toExport.length === 0) {
+ Util.showInfo('First select something to export.');
+ } else if (!this.isValid(toExport)) {
+ Util.showInfo('Not only spaces and the root should be selected. It will result in an empty export file.');
+ } else {
+ Util.blockUI();
+ this.getUserInformation(function(userInformation) {
+ mainController.serverFacade.exportZenodo(toExport, true, false, userInformation,
+ function(operationExecutionPermId) {
+ _this.waitForOpExecutionResponse(operationExecutionPermId, function(error, result) {
+ Util.unblockUI();
+ if (result && result.data && result.data.url) {
+ var win = window.open(result.data.url, '_blank');
+ win.focus();
+ mainController.refreshView();
+ } else {
+ if (error) {
+ Util.showError(error);
+ } else {
+ Util.showError('Returned result format is not correct.');
+ }
+ }
+ });
+ });
+ });
+ }
+ };
+
+ this.isValid = function(toExport) {
+ for (var i = 0; i < toExport.length; i++) {
+ var value = toExport[i];
+ if (value.type !== 'ROOT' && value.type !== 'SPACE' || value.expand) {
+ return true;
+ }
+ }
+ return false;
+ };
+
+ this.waitForOpExecutionResponse = function(operationExecutionPermIdString, callbackFunction) {
+ var _this = this;
+ require(['as/dto/operation/id/OperationExecutionPermId',
+ 'as/dto/operation/fetchoptions/OperationExecutionFetchOptions'],
+ function(OperationExecutionPermId, OperationExecutionFetchOptions) {
+ var operationExecutionPermId = new OperationExecutionPermId(operationExecutionPermIdString);
+ var fetchOptions = new OperationExecutionFetchOptions();
+ var fetchOptionsDetails = fetchOptions.withDetails();
+ fetchOptionsDetails.withResults();
+ fetchOptionsDetails.withError();
+ mainController.openbisV3.getOperationExecutions([operationExecutionPermId], fetchOptions).done(function(results) {
+ var result = results[operationExecutionPermIdString];
+ var v2Result = null;
+ if (result && result.details && result.details.results) {
+ v2Result = result.details.results[0];
+ }
+
+ if (result && result.state === 'FINISHED') {
+ mainController.serverFacade.customELNApiCallbackHandler(v2Result, callbackFunction);
+ } else if (!result || result.state === 'FAILED') {
+ mainController.serverFacade.customELNApiCallbackHandler(v2Result, callbackFunction);
+ } else {
+ setTimeout(function() {
+ _this.waitForOpExecutionResponse(operationExecutionPermIdString, callbackFunction);
+ }, 3000);
+ }
+ });
+ });
+ };
+
+ this.getUserInformation = function(callback) {
+ var userId = mainController.serverFacade.getUserId();
+ mainController.serverFacade.getSessionInformation(function(sessionInfo) {
+ var userInformation = {
+ id: userId,
+ };
+ callback(userInformation);
+ });
+ };
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js
new file mode 100644
index 0000000000000000000000000000000000000000..f555844b57e82e8c640965767f2077b1b66f213e
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportModel.js
@@ -0,0 +1,18 @@
+/*
+ * 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.
+ */
+
+function ZenodoExportModel() {
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js
new file mode 100644
index 0000000000000000000000000000000000000000..775a8893be6bbaed639dd4409ab6e73e14e56b43
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/ZenodoExport/ZenodoExportView.js
@@ -0,0 +1,60 @@
+/*
+ * 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.
+ */
+
+function ZenodoExportView(exportController, exportModel) {
+ this.repaint = function(views) {
+ var $header = views.header;
+ var $container = views.content;
+
+ var $form = $("<div>");
+ var $formColumn = $("<form>", {
+ 'name': 'rcExportForm',
+ 'role': 'form',
+ 'action': 'javascript:void(0);',
+ 'onsubmit': 'mainController.currentView.exportSelected();'
+ });
+ $form.append($formColumn);
+
+ var $infoBox1 = FormUtil.getInfoBox('You can select any parts of the accessible openBIS structure to export:', [
+ 'If you select a tree node and do not expand it, everything below this node will be exported by default.',
+ 'To export selectively only parts of a tree, open the nodes and select what to export.'
+ ]);
+ $infoBox1.css('border', 'none');
+ $container.append($infoBox1);
+
+ var $infoBox2 = FormUtil.getInfoBox('Publication time constraint', [
+ 'After the resource has been exported it should be published in Zenodo UI within 2 hours.',
+ 'Otherwise, the publication metadata will not be registered in openBIS.'
+ ]);
+ $infoBox2.css('border', 'none');
+ $container.append($infoBox2);
+
+ var $tree = $('<div>', { 'id' : 'exportsTree' });
+ $formColumn.append($('<br>'));
+ $formColumn.append(FormUtil.getBox().append($tree));
+
+ $container.append($form);
+
+ exportModel.tree = TreeUtil.getCompleteTree($tree);
+
+ var $formTitle = $('<h2>').append('Zenodo Export Builder');
+ $header.append($formTitle);
+
+ var $exportButton = $('<input>', { 'type': 'submit', 'class': 'btn btn-primary', 'value': 'Export Selected',
+ 'onClick': '$("form[name=\'rcExportForm\']").submit()'});
+ $header.append($exportButton);
+ };
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
index 50c8297589fcd2df04625c1510e88306723ac95c..71b0971ba7ed85a576b6b53fc307f89dbb4474f5 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/drop-boxes/eln-lims-dropbox/eln-lims-dropbox.py
@@ -32,22 +32,15 @@ def process(transaction):
# Parse entity Kind Format
if entityKind == "O":
-
- if len(datasetInfo) >= 4:
+ OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis"
+ v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
+ projectSamplesEnabled = v3.getServerInformation(transaction.getOpenBisServiceSessionToken())['project-samples-enabled'] == 'true'
+
+ if len(datasetInfo) >= 4 and projectSamplesEnabled:
sampleSpace = datasetInfo[1];
projectCode = datasetInfo[2];
sampleCode = datasetInfo[3];
-
- OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis"
- v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
- projectSamplesEnabled = v3.getServerInformation(transaction.getOpenBisServiceSessionToken())['project-samples-enabled'] == 'true'
-
- sample = None
- if projectSamplesEnabled:
- sample = transaction.getSample("/" +sampleSpace + "/" + projectCode + "/" + sampleCode);
- else:
- sample = transaction.getSample("/" +sampleSpace + "/" + sampleCode);
-
+ sample = transaction.getSample("/" +sampleSpace + "/" + projectCode + "/" + sampleCode);
if sample is None:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE);
if len(datasetInfo) >= 5:
@@ -56,9 +49,20 @@ def process(transaction):
name = datasetInfo[5];
if len(datasetInfo) > 6:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
+ elif len(datasetInfo) >= 3 and not projectSamplesEnabled:
+ sampleSpace = datasetInfo[1];
+ sampleCode = datasetInfo[2];
+ sample = transaction.getSample("/" +sampleSpace + "/" + sampleCode);
+ if sample is None:
+ raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + SAMPLE_MISSING_ERROR_MESSAGE);
+ if len(datasetInfo) >= 4:
+ datasetType = datasetInfo[3];
+ if len(datasetInfo) >= 5:
+ name = datasetInfo[4];
+ if len(datasetInfo) > 5:
+ raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
else:
raise UserFailureException(INVALID_FORMAT_ERROR_MESSAGE + ":" + FAILED_TO_PARSE_SAMPLE_ERROR_MESSAGE);
-
if entityKind == "E":
if len(datasetInfo) >= 4:
experimentSpace = datasetInfo[1];
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
index 932c0fa302302c30bd0dc8174b5fd680c62a0707..7af095aa70a2bb27e997ae05a1d669464da3fd5c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/exportsApi.py
@@ -645,4 +645,33 @@ def getConfigurationProperty(transaction, propertyName):
try:
return threadProperties.getProperty(propertyName);
except:
- return None
\ No newline at end of file
+ return None
+
+
+def generateZipFile(entities, params, tempDirPath, tempZipFilePath):
+ # Generates ZIP file with selected item for export
+
+ sessionToken = params.get('sessionToken')
+ includeRoot = params.get('includeRoot')
+
+ fos = None
+ zos = None
+ try:
+ fos = FileOutputStream(tempZipFilePath)
+ zos = ZipOutputStream(fos)
+
+ fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
+ finally:
+ if zos is not None:
+ zos.close()
+ if fos is not None:
+ fos.close()
+
+ return fileMetadata
+
+
+def checkResponseStatus(response):
+ status = response.getStatus()
+ if status >= 300:
+ reason = response.getReason()
+ raise ValueError('Unsuccessful response from the server: %s %s' % (status, reason))
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
index 99f41ac9578a20a317c6af933a733e5e6b407d00..66e91990f86074101ad93186f4f6c7aac001b285 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/rc-exports-api/rcExports.py
@@ -35,7 +35,8 @@ from org.eclipse.jetty.client.util import BasicAuthentication
from org.eclipse.jetty.http import HttpMethod
from org.eclipse.jetty.util.ssl import SslContextFactory
-from exportsApi import displayResult, findEntitiesToExport, validateDataSize, getConfigurationProperty, generateFilesInZip, addToZipFile, cleanUp
+from exportsApi import displayResult, findEntitiesToExport, validateDataSize, getConfigurationProperty, generateFilesInZip, addToZipFile, cleanUp, \
+ generateZipFile, checkResponseStatus
operationLog = Logger.getLogger(str(LogCategory.OPERATION) + '.rcExports.py')
@@ -106,7 +107,7 @@ def export(entities, tr, params, userInformation):
exportZipFilePath = exportDirPath + '.zip'
exportZipFileName = exportDirName + '.zip'
- generateInternalZipFile(entities, params, contentDirPath, contentZipFilePath)
+ generateZipFile(entities, params, contentDirPath, contentZipFilePath)
FileUtils.forceDelete(File(contentDirPath))
generateExternalZipFile(params=params, exportDirPath=exportDirPath, contentZipFilePath=contentZipFilePath, contentZipFileName=contentZipFileName,
@@ -189,35 +190,6 @@ def fetchServiceDocument(url, httpClient):
return json.dumps(map(collectionToDictionaryMapper, collections))
-def checkResponseStatus(response):
- status = response.getStatus()
- if status >= 300:
- reason = response.getReason()
- raise ValueError('Unsuccessful response from the server: %s %s' % (status, reason))
-
-
-def generateInternalZipFile(entities, params, tempDirPath, tempZipFilePath):
- # Generates ZIP file with selected item for export
-
- sessionToken = params.get('sessionToken')
- includeRoot = params.get('includeRoot')
-
- fos = None
- zos = None
- try:
- fos = FileOutputStream(tempZipFilePath)
- zos = ZipOutputStream(fos)
-
- fileMetadata = generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
- finally:
- if zos is not None:
- zos.close()
- if fos is not None:
- fos.close()
-
- return fileMetadata
-
-
def generateExternalZipFile(params, exportDirPath, contentZipFilePath, contentZipFileName, exportZipFileName, userInformation, entities):
# Generates ZIP file which will go to the research collection server
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/exportsApi.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/exportsApi.py
new file mode 120000
index 0000000000000000000000000000000000000000..ccb8a49feb33c9712b493e377365bd0b7dad5f8d
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/exportsApi.py
@@ -0,0 +1 @@
+../exports-api/exportsApi.py
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/job-scheduler-source/JobScheduler.java b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/job-scheduler-source/JobScheduler.java
new file mode 100644
index 0000000000000000000000000000000000000000..23558319831415c5d4b1a912d720553ce45efc7d
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/job-scheduler-source/JobScheduler.java
@@ -0,0 +1,51 @@
+/*
+ * 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.ethz.sis;
+
+import java.util.Timer;
+import java.util.TimerTask;
+import java.util.concurrent.atomic.AtomicInteger;
+
+public class JobScheduler
+{
+
+ public static void scheduleRepeatedRequest(final long period, final int repCount, final BooleanCallable callable)
+ {
+ final Timer timer = new Timer(false);
+
+ final AtomicInteger remainingRepCount = new AtomicInteger(repCount);
+ timer.scheduleAtFixedRate(new TimerTask()
+ {
+ @Override
+ public void run()
+ {
+ final boolean returnedValue = callable.call();
+ if (returnedValue || remainingRepCount.decrementAndGet() <= 0)
+ {
+ timer.cancel();
+ }
+ }
+
+ }, period, period);
+ }
+
+ public interface BooleanCallable
+ {
+ boolean call();
+ }
+
+}
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/lib/job-scheduler.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/lib/job-scheduler.jar
new file mode 100644
index 0000000000000000000000000000000000000000..3ab019d90a01dc5cb77d1c80b8f37dab09761137
Binary files /dev/null and b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/lib/job-scheduler.jar differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..46637e2ba22178234ec544460bef0591959e8a9a
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties
@@ -0,0 +1,7 @@
+label = Zenodo Exports API
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
+script-path = zenodoExports.py
+service-document-url=https://test.research-collection.ethz.ch/swordv2/servicedocument
+limit-data-size-megabytes = 50000
+zenodoUrl=https://localhost
+accessToken=
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py
new file mode 100644
index 0000000000000000000000000000000000000000..4934cac3586e661ffe31a3142a24b52af2876ba7
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/zenodoExports.py
@@ -0,0 +1,260 @@
+#
+# Copyright 2016 ETH Zuerich, Scientific IT Services
+#
+# 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.
+#
+
+from __future__ import print_function
+
+import json
+import traceback
+
+import time
+from ch.systemsx.cisd.common.logging import LogCategory
+from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.service.id import CustomASServiceCode
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExecutionOptions
+from java.io import File
+from java.nio.file import Paths
+from org.apache.commons.io import FileUtils
+from org.apache.log4j import Logger
+from org.eclipse.jetty.client import HttpClient
+from org.eclipse.jetty.client.util import MultiPartContentProvider
+from org.eclipse.jetty.client.util import PathContentProvider
+from org.eclipse.jetty.client.util import StringContentProvider
+from org.eclipse.jetty.http import HttpMethod
+from org.eclipse.jetty.util.ssl import SslContextFactory
+from org.json import JSONObject
+
+from ch.ethz.sis import JobScheduler
+from exportsApi import findEntitiesToExport, validateDataSize, getConfigurationProperty, generateZipFile, checkResponseStatus, displayResult, cleanUp
+
+operationLog = Logger.getLogger(str(LogCategory.OPERATION) + '.zenodoExports.py')
+
+
+def process(tr, params, tableBuilder):
+ method = params.get('method')
+
+ # Set user using the service
+ tr.setUserId(userId)
+
+ if method == 'exportAll':
+ resultUrl = expandAndExport(tr, params)
+ displayResult(resultUrl is not None, tableBuilder, '{"url": "' + resultUrl + '"}' if resultUrl is not None else None)
+
+
+def expandAndExport(tr, params):
+ entitiesToExport = findEntitiesToExport(params)
+ validateDataSize(entitiesToExport, tr)
+
+ operationLog.info('Found ' + str(len(entitiesToExport)) + ' entities to export')
+ exportUrl = export(entities=entitiesToExport, tr=tr, params=params)
+
+ return exportUrl
+
+
+def export(entities, tr, params):
+ #Create temporal folder
+ timeNow = time.time()
+
+ exportDirName = 'export_' + str(timeNow)
+ exportDir = File.createTempFile(exportDirName, None)
+ exportDirPath = exportDir.getCanonicalPath()
+ exportDir.delete()
+ exportDir.mkdir()
+
+ contentZipFileName = 'content.zip'
+ contentDirName = 'content_' + str(timeNow)
+ contentDir = File.createTempFile(contentDirName, None, exportDir)
+ contentDirPath = contentDir.getCanonicalPath()
+ contentDir.delete()
+ contentDir.mkdir()
+
+ contentZipFilePath = exportDirPath + '/' + contentZipFileName
+
+ generateZipFile(entities, params, contentDirPath, contentZipFilePath)
+ FileUtils.forceDelete(File(contentDirPath))
+
+ resultUrl = sendToZenodo(tr=tr, params=params, tempZipFilePath=contentZipFilePath, entities=entities)
+ FileUtils.forceDelete(File(exportDirPath))
+ return resultUrl
+
+
+def sendToZenodo(tr, params, tempZipFilePath, entities):
+ depositRootUrl = str(getConfigurationProperty(tr, 'zenodoUrl')) + '/api/deposit/depositions'
+
+ accessToken = str(getConfigurationProperty(tr, 'accessToken'))
+ operationLog.info('accessToken: %s' % accessToken)
+
+ httpClient = None
+ try:
+ httpClient = createHttpClient()
+
+ httpClient.setFollowRedirects(False)
+ httpClient.start()
+
+ depositionData = createDepositionResource(httpClient.newRequest(depositRootUrl), accessToken)
+
+ depositionLinks = depositionData.get('links')
+ depositUrl = depositionLinks.get('files')
+ selfUrl = depositionLinks.get('self')
+
+ submitFile(httpClient.newRequest(depositUrl), accessToken, tempZipFilePath)
+ addMetadata(httpClient.newRequest(selfUrl), accessToken)
+
+ entityPermIds = map(lambda entity: entity['permId'], entities)
+ zenodoCallable = ZenodoCallable(params, accessToken, selfUrl,
+ reduce(lambda str, permId: str + ',' + permId, entityPermIds))
+ zenodoCallable.scheduleMetadataCheck()
+
+ result = depositionLinks.get('html')
+ return result
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ raise e
+ finally:
+ if httpClient is not None:
+ httpClient.stop()
+
+
+def submitFile(request, accessToken, tempZipFilePath):
+ multiPart = MultiPartContentProvider()
+ multiPart.addFilePart('file', 'content.zip', PathContentProvider(Paths.get(tempZipFilePath)), None)
+ multiPart.close()
+ addAuthenticationHeader(accessToken, request)
+ response = request.method(HttpMethod.POST).content(multiPart).send()
+ checkResponseStatus(response)
+ contentStr = response.getContentAsString()
+
+ return JSONObject(contentStr)
+
+
+def addMetadata(request, accessToken):
+ data = {
+ 'metadata': {
+ 'title': str(time.time()),
+ 'license': 'cc-zero',
+ 'upload_type': 'dataset',
+ 'description': 'Add some description.',
+ 'creators': [{'name': userId}]
+ }
+ }
+
+ addAuthenticationHeader(accessToken, request)
+ jsonString = json.dumps(data)
+ response = request.method(HttpMethod.PUT).content(StringContentProvider(jsonString), 'application/json').send()
+
+ checkResponseStatus(response)
+
+
+def retrieve(request, accessToken):
+ addAuthenticationHeader(accessToken, request)
+ response = request.method(HttpMethod.GET).send()
+ contentStr = response.getContentAsString()
+
+ # If the resource has been deleted instead of published return None.
+ if response.getStatus() == 410:
+ return None
+
+ checkResponseStatus(response)
+
+ return JSONObject(contentStr)
+
+
+def createDepositionResource(request, accessToken):
+ addAuthenticationHeader(accessToken, request)
+ response = request.method(HttpMethod.POST).content(StringContentProvider('{}'), 'application/json').send()
+ checkResponseStatus(response)
+
+ contentStr = response.getContentAsString()
+ return JSONObject(contentStr)
+
+
+def addAuthenticationHeader(accessToken, request):
+ request.header('Authorization', 'Bearer ' + accessToken)
+
+
+def createHttpClient():
+ sslContextFactory = SslContextFactory()
+ sslContextFactory.setTrustAll(True)
+ return HttpClient(sslContextFactory)
+
+
+class ZenodoCallable(object):
+ params = None
+ accessToken = None
+ selfUrl = None
+ permIdsStr = None
+
+ def __init__(self, params, accessToken, selfUrl, permIdsStr):
+ self.params = params
+ self.accessToken = accessToken
+ self.selfUrl = selfUrl
+ self.permIdsStr = permIdsStr
+
+ def scheduleMetadataCheck(self):
+ JobScheduler.scheduleRepeatedRequest(120000, 60, self.call)
+
+ def call(self):
+ httpClient = None
+
+ # Whether this method returned a completion result and it should not be called repeatedly.
+ actionCompleted = False
+
+ try:
+ httpClient = createHttpClient()
+
+ httpClient.setFollowRedirects(False)
+ httpClient.start()
+
+ try:
+ publicationJson = retrieve(httpClient.newRequest(self.selfUrl), self.accessToken)
+ if publicationJson is None:
+ operationLog.info('Publication at the URL has been deleted.' % self.selfUrl)
+ actionCompleted = True
+ elif publicationJson.get('submitted'):
+ operationLog.info('Publication #%d submitted. Registering metadata.' % publicationJson.get('id'))
+ self.registerPublicationInOpenbis(publicationJson.get('metadata'))
+ actionCompleted = True
+ else:
+ operationLog.info('Publication #%d not submitted yet.' % publicationJson.get('id'))
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ actionCompleted = False
+ except Exception as e:
+ operationLog.error('Exception at: ' + traceback.format_exc())
+ operationLog.error('Exception: ' + str(e))
+ raise e
+ finally:
+ if httpClient is not None:
+ httpClient.stop()
+
+ return actionCompleted
+
+
+ def registerPublicationInOpenbis(self, publicationMetadataJson):
+ sessionToken = self.params.get('sessionToken')
+ v3 = ServiceProvider.getV3ApplicationService()
+ id = CustomASServiceCode('publication-api')
+ options = CustomASServiceExecutionOptions() \
+ .withParameter('method', 'insertPublication') \
+ .withParameter('publicationURL', self.selfUrl) \
+ .withParameter('openBISRelatedIdentifiers', self.permIdsStr) \
+ .withParameter('name', publicationMetadataJson.get('title')) \
+ .withParameter('publicationDescription', publicationMetadataJson.get('description')) \
+ .withParameter('publicationType', publicationMetadataJson.get('upload_type')) \
+ .withParameter('publicationIdentifier', publicationMetadataJson.get('doi'))
+ result = v3.executeCustomASService(sessionToken, id, options)
+ return result
diff --git a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/entrypoint.py b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/entrypoint.py
index adf93431d3e19e72826f8cff495710a536a4e5d5..9806b27718bb3855c9f0eff450b44c2edb637b3b 100644
--- a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/entrypoint.py
+++ b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/entrypoint.py
@@ -26,9 +26,9 @@ def validate_data(xls_byte_arrays, update_mode, xls_name):
def get_property(key, defaultValue):
- propertyConfigurer = CommonServiceProvider.getApplicationContext().getBean("propertyConfigurer");
- properties = propertyConfigurer.getResolvedProps();
- return properties.getProperty(key, defaultValue);
+ propertyConfigurer = CommonServiceProvider.getApplicationContext().getBean("propertyConfigurer")
+ properties = propertyConfigurer.getResolvedProps()
+ return properties.getProperty(key, defaultValue)
def read_versioning_information(xls_version_filepath):
@@ -93,7 +93,8 @@ def process(context, parameters):
if code in versioning_information:
version = versioning_information[code]
else:
- version = creations_metadata.get_metadata_for(creation_type, creation).version if update_mode != "UPDATE_IF_EXISTS" else 0
+ version = creations_metadata.get_metadata_for(creation_type,
+ creation).version if update_mode != "UPDATE_IF_EXISTS" else 0
versioning_information[code] = int(version)
else:
versioning_information = {}
@@ -101,12 +102,14 @@ def process(context, parameters):
if creation_type in versionable_types:
for creation in creation_collection:
code = get_metadata_name_for(creation_type, creation)
- versioning_information[code] = creations_metadata.get_metadata_for(creation_type, creation).version if update_mode != "UPDATE_IF_EXISTS" else 0
+ versioning_information[code] = creations_metadata.get_metadata_for(creation_type,
+ creation).version if update_mode != "UPDATE_IF_EXISTS" else 0
existing_elements = search_engine.find_all_existing_elements(creations)
entity_kinds = search_engine.find_existing_entity_kind_definitions_for(creations)
existing_vocabularies = search_engine.find_all_existing_vocabularies()
- existing_unified_kinds = unify_properties_representation_of(creations, entity_kinds, existing_vocabularies, existing_elements)
+ existing_unified_kinds = unify_properties_representation_of(creations, entity_kinds, existing_vocabularies,
+ existing_elements)
creations = PropertiesLabelHandler.rewrite_property_labels_to_codes(creations, existing_unified_kinds)
server_duplicates_handler = OpenbisDuplicatesHandler(creations, creations_metadata, existing_elements,
versioning_information, update_mode)
@@ -117,4 +120,3 @@ def process(context, parameters):
all_versioning_information[xls_version_name] = versioning_information
save_versioning_information(all_versioning_information, xls_version_filepath)
return res
-
diff --git a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/creation_to_update/update_parsers.py b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/creation_to_update/update_parsers.py
index a9be5e9003d550f3a6ebf87aaeaa15f251cd60b6..93daca6f0a0b5e766fb24526a148da944271c4e9 100644
--- a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/creation_to_update/update_parsers.py
+++ b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/creation_to_update/update_parsers.py
@@ -8,14 +8,14 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.update import SpaceUpdate
from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.update import ProjectUpdate
from ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.update import PluginUpdate
from java.lang import UnsupportedOperationException
-from ..definition_to_creation import PropertyTypeDefinitionToCreationType, VocabularyDefinitionToCreationType, VocabularyTermDefinitionToCreationType, \
- PropertyAssignmentDefinitionToCreationType, SampleTypeDefinitionToCreationType, ExperimentTypeDefinitionToCreationType, \
- DatasetTypeDefinitionToCreationType, SpaceDefinitionToCreationType, ProjectDefinitionToCreationType, ExperimentDefinitionToCreationType, \
- SampleDefinitionToCreationType, ScriptDefinitionToCreationType
-from .update_types import PropertyTypeCreationToUpdateType, VocabularyCreationToUpdateType, PropertyAssignmentCreationToUpdateType, \
- SampleTypeCreationToUpdateType, ExperimentTypeCreationToUpdateType, DatasetTypeCreationToUpdateType, \
- SpaceCreationToUpdateType, ProjectCreationToUpdateType, ExperimentCreationToUpdateType, \
- SampleCreationToUpdateType, ScriptCreationToUpdateType, VocabularyTermCreationToUpdateType
+from ..definition_to_creation import PropertyTypeDefinitionToCreationType, VocabularyDefinitionToCreationType, \
+ VocabularyTermDefinitionToCreationType, SampleTypeDefinitionToCreationType, ExperimentTypeDefinitionToCreationType, \
+ DatasetTypeDefinitionToCreationType, SpaceDefinitionToCreationType, ProjectDefinitionToCreationType, \
+ ExperimentDefinitionToCreationType, SampleDefinitionToCreationType, ScriptDefinitionToCreationType
+from .update_types import PropertyTypeCreationToUpdateType, VocabularyCreationToUpdateType, \
+ SampleTypeCreationToUpdateType, ExperimentTypeCreationToUpdateType, DatasetTypeCreationToUpdateType, \
+ SpaceCreationToUpdateType, ProjectCreationToUpdateType, ExperimentCreationToUpdateType, SampleCreationToUpdateType, \
+ ScriptCreationToUpdateType, VocabularyTermCreationToUpdateType
class CreationToUpdateParserFactory(object):
@@ -81,6 +81,13 @@ class PropertyTypeCreationToUpdateParser(object):
property_type_update.typeId = existing_property_type.permId
property_type_update.setLabel(creation.label)
property_type_update.setDescription(creation.description)
+ metadata_update = property_type_update.getMetaData()
+ if existing_property_type.metaData:
+ for metaDataEntry in existing_property_type.metaData:
+ if creation.metaData and metaDataEntry not in creation.metaData:
+ metadata_update.remove(metaDataEntry)
+ if creation.metaData:
+ metadata_update.add(creation.metaData)
return property_type_update
def get_type(self):
@@ -91,8 +98,10 @@ class EntityTypeCreationToUpdateParser(object):
def parseAssignments(self, creation, existing_entity_type):
assignments_update = ListUpdateValue()
- creationPropertyAssignmentCodes = [str(property_assignment.propertyTypeId) for property_assignment in creation.propertyAssignments]
- existingPropertyAssignmentCodes = [str(property_assignment.propertyType.code) for property_assignment in existing_entity_type.propertyAssignments]
+ creationPropertyAssignmentCodes = [str(property_assignment.propertyTypeId) for property_assignment in
+ creation.propertyAssignments]
+ existingPropertyAssignmentCodes = [str(property_assignment.propertyType.code) for property_assignment in
+ existing_entity_type.propertyAssignments]
for property_assignment in existing_entity_type.propertyAssignments:
if str(property_assignment.propertyType.code) in creationPropertyAssignmentCodes:
continue
@@ -205,9 +214,11 @@ class SampleCreationToUpdateParser(object):
for child in existing_sample.children:
existing_children_identifiers.extend([str(child.permId), str(child.identifier)])
- parentsToRemove = [parent.permId for parent in existing_sample.parents if parent.permId not in creation.parentIds and parent.identifier not in creation.parentIds]
+ parentsToRemove = [parent.permId for parent in existing_sample.parents if
+ parent.permId not in creation.parentIds and parent.identifier not in creation.parentIds]
parentsToAdd = [parent for parent in creation.parentIds if str(parent) not in existing_parent_identifiers]
- childrenToRemove = [child.permId for child in existing_sample.children if child.permId not in creation.childIds and child.identifier not in creation.parentIds]
+ childrenToRemove = [child.permId for child in existing_sample.children if
+ child.permId not in creation.childIds and child.identifier not in creation.parentIds]
childrenToAdd = [child for child in creation.childIds if str(child) not in existing_children_identifiers]
sample_update.childIds.remove([parent.permId for parent in existing_sample.children])
sample_update.parentIds.remove([child.permId for child in existing_sample.parents])
@@ -230,4 +241,3 @@ class ScriptCreationToUpdateParser(object):
def get_type(self):
return ScriptCreationToUpdateType
-
diff --git a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/definition_to_creation/creation_parsers.py b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/definition_to_creation/creation_parsers.py
index 9a9f1918639be04793de2877c4264970cfae4852..d1681a5a469899b943903533b91f04474c3a82de 100644
--- a/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/definition_to_creation/creation_parsers.py
+++ b/openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/definition_to_creation/creation_parsers.py
@@ -17,15 +17,20 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id import VocabularyPer
from java.lang import UnsupportedOperationException
from ch.systemsx.cisd.common.exceptions import UserFailureException
from utils.openbis_utils import is_internal_namespace, get_script_name_for
-from .creation_types import PropertyTypeDefinitionToCreationType, VocabularyDefinitionToCreationType, VocabularyTermDefinitionToCreationType, \
- PropertyAssignmentDefinitionToCreationType, SampleTypeDefinitionToCreationType, ExperimentTypeDefinitionToCreationType, \
- DatasetTypeDefinitionToCreationType, SpaceDefinitionToCreationType, ProjectDefinitionToCreationType, ExperimentDefinitionToCreationType, \
- SampleDefinitionToCreationType, ScriptDefinitionToCreationType
+from .creation_types import PropertyTypeDefinitionToCreationType, VocabularyDefinitionToCreationType, \
+ VocabularyTermDefinitionToCreationType, \
+ PropertyAssignmentDefinitionToCreationType, SampleTypeDefinitionToCreationType, \
+ ExperimentTypeDefinitionToCreationType, \
+ DatasetTypeDefinitionToCreationType, SpaceDefinitionToCreationType, ProjectDefinitionToCreationType, \
+ ExperimentDefinitionToCreationType, \
+ SampleDefinitionToCreationType, ScriptDefinitionToCreationType
+import json
def get_boolean_from_string(text):
if text.lower() not in [u'true', u'false']:
- raise UserFailureException("Boolean field should either be 'true' or 'false' (case insensitive) but was " + text)
+ raise UserFailureException(
+ "Boolean field should either be 'true' or 'false' (case insensitive) but was " + text)
return True if text and text.lower() == u'true' else False
@@ -73,7 +78,10 @@ class PropertyTypeDefinitionToCreationParser(object):
property_type_creation.description = prop.get(u'description')
property_type_creation.dataType = DataType.valueOf(prop.get(u'data type'))
property_type_creation.internalNameSpace = is_internal_namespace(prop.get(u'code'))
- property_type_creation.vocabularyId = VocabularyPermId(prop.get(u'vocabulary code')) if prop.get(u'vocabulary code') is not None else None
+ property_type_creation.vocabularyId = VocabularyPermId(prop.get(u'vocabulary code')) if prop.get(
+ u'vocabulary code') is not None else None
+ metadata = json.loads(prop.get(u'metadata')) if prop.get(u'metadata') is not None else None
+ property_type_creation.metaData = metadata
property_creations.append(property_type_creation)
return property_creations
@@ -150,7 +158,8 @@ class SampleTypeDefinitionToCreationParser(object):
generatedCodePrefix = definition.attributes.get(u'generated code prefix')
if generatedCodePrefix is not None:
sample_creation.generatedCodePrefix = generatedCodePrefix
- if u'validation script' in definition.attributes and definition.attributes.get(u'validation script') is not None:
+ if u'validation script' in definition.attributes and definition.attributes.get(
+ u'validation script') is not None:
validation_script_path = definition.attributes.get(u'validation script')
sample_creation.validationPluginId = PluginPermId(get_script_name_for(code, validation_script_path))
@@ -174,9 +183,11 @@ class ExperimentTypeDefinitionToCreationParser(object):
experiment_type_creation = ExperimentTypeCreation()
experiment_type_creation.code = code
experiment_type_creation.description = definition.attributes.get(u'description')
- if u'validation script' in definition.attributes and definition.attributes.get(u'validation script') is not None:
+ if u'validation script' in definition.attributes and definition.attributes.get(
+ u'validation script') is not None:
validation_script_path = definition.attributes.get(u'validation script')
- experiment_type_creation.validationPluginId = PluginPermId(get_script_name_for(code, validation_script_path))
+ experiment_type_creation.validationPluginId = PluginPermId(
+ get_script_name_for(code, validation_script_path))
property_assignment_creations = []
property_assignment_parser = PropertyAssignmentDefinitionToCreationParser()
@@ -198,7 +209,8 @@ class DatasetTypeDefinitionToCreationParser(object):
code = definition.attributes.get(u'code')
dataset_type_creation.code = code
dataset_type_creation.description = definition.attributes.get(u'description')
- if u'validation script' in definition.attributes and definition.attributes.get(u'validation script') is not None:
+ if u'validation script' in definition.attributes and definition.attributes.get(
+ u'validation script') is not None:
validation_script_path = definition.attributes.get(u'validation script')
dataset_type_creation.validationPluginId = PluginPermId(get_script_name_for(code, validation_script_path))
@@ -277,7 +289,7 @@ class SampleDefinitionToCreationParser(object):
def parse(self, definition):
samples = []
sample_attributes = [u'$', u'code', u'space', u'project', u'experiment', u'auto generate code', u'parents',
- u'children']
+ u'children']
for sample_properties in definition.properties:
sample_creation = SampleCreation()
sample_creation.typeId = EntityTypePermId(definition.attributes.get(u'sample type'))
@@ -288,9 +300,11 @@ class SampleDefinitionToCreationParser(object):
if u'$' in sample_properties and sample_properties.get(u'$') is not None:
# may overwrite creationId from code, which is intended
sample_creation.creationId = CreationId(sample_properties.get(u'$'))
- if u'auto generate code' in sample_properties and sample_properties.get(u'auto generate code') is not None and \
+ if u'auto generate code' in sample_properties and sample_properties.get(
+ u'auto generate code') is not None and \
sample_properties.get(u'auto generate code') != '':
- sample_creation.autoGeneratedCode = get_boolean_from_string(sample_properties.get(u'auto generate code'))
+ sample_creation.autoGeneratedCode = get_boolean_from_string(
+ sample_properties.get(u'auto generate code'))
if u'space' in sample_properties and sample_properties.get(u'space') is not None:
sample_creation.spaceId = CreationId(sample_properties.get(u'space'))
if u'project' in sample_properties and sample_properties.get(u'project') is not None:
diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index 4ba563b5f32628fd97bd1378de9904040d4d3d28..1c68708da418d638fa3158a6d438d9e08b63e341 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -1,3 +1,8 @@
+## Changes with pybis-1.9.1
+
+* bugfix: controlled vocabulary
+
+
## Changes with pybis-1.9.0
* new: search, create, update and delete Property Types
@@ -6,6 +11,7 @@
* freeze entities to prevent changes
* added more tests
+
## Changes with pybis-1.8.5
* changed to v3 API when fetching datastores
diff --git a/pybis/src/python/pybis/__init__.py b/pybis/src/python/pybis/__init__.py
index 2ca20089ea36d860b51223bba7c30326c7957f96..4aa2b995675dc04f0874952732c359ada99bdd0f 100644
--- a/pybis/src/python/pybis/__init__.py
+++ b/pybis/src/python/pybis/__init__.py
@@ -1,7 +1,7 @@
name = 'pybis'
__author__ = 'Swen Vermeul'
__email__ = 'swen@ethz.ch'
-__version__ = '1.9.0'
+__version__ = '1.9.1'
from . import pybis
from .pybis import Openbis
diff --git a/pybis/src/python/pybis/property.py b/pybis/src/python/pybis/property.py
index 9dd9bf6c31f89a0868f743a03e04f97868aa485e..9d2a6431abf9304559c0fb9ddae52bf6b2e89f2f 100644
--- a/pybis/src/python/pybis/property.py
+++ b/pybis/src/python/pybis/property.py
@@ -60,7 +60,7 @@ class PropertyHolder():
if name in self._property_names:
property_type = self._property_names[name]
if property_type['dataType'] == 'CONTROLLEDVOCABULARY':
- return self._get_terms(property_type['vocabulary']['code'])
+ return self._get_terms(property_type['code'])
else:
syntax = { property_type["label"] : property_type["dataType"]}
if property_type["dataType"] == "TIMESTAMP":
@@ -82,7 +82,7 @@ class PropertyHolder():
property_type = self._property_names[name]
data_type = property_type['dataType']
if data_type == 'CONTROLLEDVOCABULARY':
- voc = self._get_terms(property_type['vocabulary']['code'])
+ voc = self._get_terms(property_type['code'])
value = str(value).upper()
if value not in voc.df['code'].values:
raise ValueError("Value for attribute {} must be one of these terms: {}".format(
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index ba3e2a12cd1d6c1af822210f2223dee6324fe419..723fcda825c708e6a385739579d327aa8d44c80e 100644
--- a/pybis/src/python/setup.py
+++ b/pybis/src/python/setup.py
@@ -11,7 +11,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name='PyBIS',
- version= '1.9.0',
+ version= '1.9.1',
author='Swen Vermeul • ID SIS • ETH Zürich',
author_email='swen@ethz.ch',
description='openBIS connection and interaction, optimized for using with Jupyter',