Merge branch 'master' of https://sissource.ethz.ch/sispub/openbis

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/hotfix/ELNCollectionTypeMigration.java

@@ -135,6 +135,7 @@ public class ELNCollectionTypeMigration {
     }
 
     private static List executeQuery(String SQL, String key, Object value) {
+        //System.out.println("SQL: " + SQL + " Key: " + key + " Value: " + value);
         DAOFactory daoFactory = (DAOFactory) CommonServiceProvider.getApplicationContext().getBean(ComponentNames.DAO_FACTORY);
         Session currentSession = daoFactory.getSessionFactory().getCurrentSession();
         NativeQuery nativeQuery = currentSession.createNativeQuery(SQL);
@@ -165,7 +166,8 @@ public class ELNCollectionTypeMigration {
         for (String experimentCode:experimentsOfTypeCollection) {
             Set<ExperimentType> experimentTypes = getExperimentTypes(new String[]{experimentCode});
             if (!experimentTypes.isEmpty()) {
-                ExperimentType experimentType = getExperimentTypes(new String[]{experimentCode}).iterator().next();
+                //System.out.println("EXPERIMENT_CODE: " + experimentCode + " IS OF TYPE: " + experimentTypes.iterator().next().getCode());
+                ExperimentType experimentType = experimentTypes.iterator().next();
                 if (!experimentType.getCode().equals(COLLECTION)) {
                     // Property Type used
                     Set<PropertyType> propertyTypes = getPropertyTypes(experimentType);

openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/initialize-master-data.py

@@ -21,13 +21,17 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.service import CustomASServiceExec
 from ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl import MasterDataRegistrationHelper
 import sys
 
+from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNCollectionTypeMigration
+
+ELNCollectionTypeMigration.migrate()
+
 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').withParameter('update_mode', 'UPDATE_IF_EXISTS')\
     .withParameter('scripts', helper.getAllScripts())
-result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import-api"), props);
+result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import-api"), props)
 print("======================== master-data xls ingestion result ========================")
 print(result)
 print("======================== master-data xls ingestion result ========================")

openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/zenodo-exports-api/plugin.properties

@@ -2,4 +2,4 @@ label = Zenodo Exports API
 class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
 script-path = zenodoExports.py
 limit-data-size-megabytes=${zenodo-exports-api-limit-data-size-megabytes:4000}
-zenodoUrl=${zenodo-exports-api-zenodoUrl:https://localhost}
\ No newline at end of file
+zenodoUrl=${zenodo-exports-api-zenodoUrl:https://zenodo.org}
\ No newline at end of file

openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/entrypoint.py

@@ -121,11 +121,6 @@ def process(context, parameters):
     entity_type_creation_operations, entity_creation_operations, entity_type_update_operations, entity_update_operations = CreationOrUpdateToOperationParser.parse(
         creations)
 
-    print(entity_type_creation_operations)
-    print(entity_creation_operations)
-    print(entity_type_update_operations)
-    print(entity_update_operations)
-
     entity_type_update_results = str(api.executeOperations(session_token, entity_type_update_operations,
                                                            SynchronousOperationExecutionOptions()).getResults())
     entity_type_creation_results = str(api.executeOperations(session_token, entity_type_creation_operations,

openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/parsers/definition_to_creation/creation_parsers.py

@@ -14,6 +14,8 @@ from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create import SpaceCreation
 from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyCreation
 from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.create import VocabularyTermCreation
 from ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id import VocabularyPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id import ProjectIdentifier
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentIdentifier
 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
@@ -271,7 +273,7 @@ class ExperimentDefinitionToCreationParser(object):
             experiment_creation = ExperimentCreation()
             experiment_creation.typeId = EntityTypePermId(definition.attributes.get(u'experiment type'))
             experiment_creation.code = experiment_properties.get(u'code')
-            experiment_creation.projectId = CreationId(experiment_properties.get(u'project'))
+            experiment_creation.projectId = ProjectIdentifier(experiment_properties.get(u'project'))
             creation_id = experiment_properties.get(u'code')
             experiment_creation.creationId = CreationId(creation_id)
             for prop, value in experiment_properties.items():
@@ -308,9 +310,9 @@ class SampleDefinitionToCreationParser(object):
             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:
-                sample_creation.projectId = CreationId(sample_properties.get(u'project'))
+                sample_creation.projectId = ProjectIdentifier(sample_properties.get(u'project'))
             if u'experiment' in sample_properties and sample_properties.get(u'experiment') is not None:
-                sample_creation.experimentId = CreationId(sample_properties.get(u'experiment'))
+                sample_creation.experimentId = ExperimentIdentifier(sample_properties.get(u'experiment'))
             if u'parents' in sample_properties and sample_properties.get(u'parents') is not None:
                 parent_creation_ids = []
                 parents = sample_properties.get(u'parents').split('\n')

openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/processors/openbis_duplicates_handler.py

@@ -28,12 +28,12 @@ class OpenbisDuplicatesHandler(object):
                     if existing_element.code == str(creation.spaceId):
                         creation.spaceId = existing_element.permId
                         break
-        if ExperimentDefinitionToCreationType in self.creations:
-            for creation in self.creations[ExperimentDefinitionToCreationType]:
-                for existing_element in self.existing_elements[ProjectDefinitionToCreationType]:
-                    if existing_element.code == str(creation.projectId):
-                        creation.projectId = existing_element.permId
-                        break
+        # if ExperimentDefinitionToCreationType in self.creations:
+        #     for creation in self.creations[ExperimentDefinitionToCreationType]:
+        #         for existing_element in self.existing_elements[ProjectDefinitionToCreationType]:
+        #             if existing_element.code == str(creation.projectId):
+        #                 creation.projectId = existing_element.permId
+        #                 break
         if SampleDefinitionToCreationType in self.creations:
             for creation in self.creations[SampleDefinitionToCreationType]:
                 if creation.spaceId is not None:
@@ -41,16 +41,16 @@ class OpenbisDuplicatesHandler(object):
                         if existing_element.code == str(creation.spaceId):
                             creation.spaceId = existing_element.permId
                             break
-                if creation.projectId is not None:
-                    for existing_element in self.existing_elements[ProjectDefinitionToCreationType]:
-                        if existing_element.code == str(creation.projectId):
-                            creation.projectId = existing_element.identifier
-                            break
-                if creation.experimentId is not None:
-                    for existing_element in self.existing_elements[ExperimentDefinitionToCreationType]:
-                        if existing_element.code == str(creation.experimentId):
-                            creation.experimentId = existing_element.permId
-                            break
+                # if creation.projectId is not None:
+                #     for existing_element in self.existing_elements[ProjectDefinitionToCreationType]:
+                #         if existing_element.code == str(creation.projectId):
+                #             creation.projectId = existing_element.identifier
+                #             break
+                # if creation.experimentId is not None:
+                #     for existing_element in self.existing_elements[ExperimentDefinitionToCreationType]:
+                #         if existing_element.code == str(creation.experimentId):
+                #             creation.experimentId = existing_element.permId
+                #             break
 
                 rewritten_children = []
                 if creation.childIds is not None:

openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/search_engines/search_criteria_factory.py

@@ -38,7 +38,7 @@ class SampleCreationSampleChildrenParentSearchCriteria(object):
             sample_code = identifier.sampleCode
             search_criteria.withCode().thatEquals(sample_code)
             if project_code is not None:
-                search_criteria.withProject().withCode().thatEquals(project_code)
+                search_criteria.withProject().withIdentifier().thatEquals(project_code)
             else:
                 search_criteria.withoutProject()
 
@@ -66,12 +66,15 @@ class SampleCreationSampleSearchCriteria(object):
             if creation.code is not None:
                 search_criteria.withCode().thatEquals(creation.code)
                 if creation.experimentId is not None:
-                    search_criteria.withExperiment().withCode().thatEquals(str(creation.experimentId))
+                    search_criteria.withExperiment().withIdentifier().thatEquals(str(creation.experimentId))
                 else:
                     search_criteria.withoutExperiment()
 
                 if creation.projectId is not None:
-                    search_criteria.withProject().withCode().thatEquals(str(creation.projectId))
+                    space_code, project_code = str(creation.projectId)[1:].split('/')
+                    project_search_criteria = search_criteria.withProject()
+                    project_search_criteria.withCode().thatEquals(project_code)
+                    project_search_criteria.withSpace().withCode().thatEquals(space_code)
                 else:
                     search_criteria.withoutProject()
 
@@ -104,11 +107,12 @@ class ProjectFromPropertiesSearchCriteria(object):
         self.search_criteria = search_criteria_class
 
     def get_search_criteria(self, specific_creations):
-        project_codes = [dotdict({'code': str(creation.projectId)}) for creation in
-                         specific_creations if
+        space_project = [tuple(str(creation.projectId)[1:].split('/')) for creation in specific_creations if
                          creation.projectId is not None]
+        project_codes = [dotdict({'code': project, 'spaceId': space}) for (space, project) in space_project]
         if project_codes == []:
             return None
+
         default_search_criteria_builder = ProjectFromProjectCreationSearchCriteria(self.search_criteria)
         return default_search_criteria_builder.get_search_criteria(project_codes)
 
@@ -119,11 +123,11 @@ class ExperimentFromPropertiesSearchCriteria(object):
         self.search_criteria = search_criteria_class
 
     def get_search_criteria(self, specific_creations):
-        experiment_codes = [dotdict({'code': str(creation.experimentId)}) for creation in specific_creations if
+        experiment_codes = [dotdict({'identifier': str(creation.experimentId)}) for creation in specific_creations if
                             creation.experimentId is not None]
         if not experiment_codes:
             return None
-        default_search_criteria_builder = DefaultCreationElementSearchCriteria(self.search_criteria)
+        default_search_criteria_builder = ExperimentFromExperimentCreationSearchCriteria(self.search_criteria)
         return default_search_criteria_builder.get_search_criteria(experiment_codes)
 
 
@@ -155,6 +159,19 @@ class ProjectFromProjectCreationSearchCriteria(object):
         return self.search_criteria
 
 
+class ExperimentFromExperimentCreationSearchCriteria(object):
+
+    def __init__(self, search_criteria_class):
+        self.search_criteria = search_criteria_class()
+
+    def get_search_criteria(self, specific_creations):
+        for creation in specific_creations:
+            if creation.identifier:
+                self.search_criteria.withIdentifier().thatEquals(creation.identifier)
+        self.search_criteria.withOrOperator()
+        return self.search_criteria
+
+
 class VocabularyTermCreationVocabularyTermSearchCriteria(object):
 
     def __init__(self, search_criteria_class):

openbis_standard_technologies/dist/core-plugins/xls-import/1/as/services/xls-import-api/search_engines/search_engine.py

@@ -278,39 +278,25 @@ class SearchEngine():
                         # explicitly mentioned in xls sheet, it is ok.
                         existing_elements[results_key].extend(existing_specific_elements)
 
+        print("DEBUGDEBUG")
+        print(existing_elements)
+
         return existing_elements
 
     def _get_existing_elements(self, search_criterias, **kwargs):
         search_operation = kwargs['search_operation']
-        print("SSSOOOO")
         fetch_options = kwargs['fetch_options']
-        print("FFFFFSSSOOOO")
         if not search_criterias:
             return None
         search_criterias = search_criterias if type(search_criterias) == list else [search_criterias]
-        print("SCCSCSCSCS")
-        print(search_criterias)
         operations = [search_operation(search_criteria, fetch_options) for search_criteria in search_criterias]
-        print("OOOOOOOOOO301")
-        print(operations)
         return self._execute_search_operation(operations)
 
     def _execute_search_operation(self, operations):
-        print(operations)
-        print("BRBRBRBRBRBRBRB")
-        print(self.api)
         execution_results = self.api.executeOperations(self.session_token, operations,
                                                        SynchronousOperationExecutionOptions())
-        print("WWWWWWWWWW")
+
         result_objects = []
-        print(operations)
-        print(execution_results)
-        print(execution_results.getResults())
-        print(execution_results.getResults()[0])
-        print(execution_results.getResults()[0].getSearchResult())
-        print(execution_results.getResults()[0].getSearchResult().getObjects())
         for search_result in execution_results.getResults():
             result_objects.extend(search_result.getSearchResult().getObjects())
-        print("PRINTED THINGS")
-        print(result_objects)
         return result_objects