SSDM-7166: monitoring-support module with core plugin dss-monitoring-initialization added

installation/source/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableAction.java

@@ -37,7 +37,7 @@ import ch.systemsx.cisd.common.shared.basic.string.CommaSeparatedListBuilder;
  */
 public class SetEnableTechnologiesVariableAction implements PanelAction
 {
-    private static final String[] MODULES = { "dropbox-monitor", "dataset-uploader", "dataset-file-search" };
+    private static final String[] MODULES = { "monitoring-support", "dropbox-monitor", "dataset-uploader", "dataset-file-search" };
 
     static final String ENABLED_TECHNOLOGIES_VARNAME = "ENABLED_TECHNOLOGIES";
 

installation/sourceTest/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableActionTest.java

@@ -93,7 +93,7 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
         variables.setProperty(TECHNOLOGY_SCREENING, "true");
 
         updateEnabledTechnologyProperties(variables, false);
-        assertEquals("[, enabled-modules = dropbox-monitor, dataset-uploader, dataset-file-search, screening]",
+        assertEquals("[, enabled-modules = monitoring-support, dropbox-monitor, dataset-uploader, dataset-file-search, screening]",
                 FileUtilities.loadToStringList(corePluginsProperties).toString());
     }
 
@@ -101,14 +101,14 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
     public void testUpdateInstallationWithOtherEnabledTechnologiesInAs()
     {
         FileUtilities.writeToFile(corePluginsProperties, "abc = 123\n" + ENABLED_TECHNOLOGIES_KEY
-                + "=dropbox-monitor, dataset-uploader, dataset-file-search, proteomics, my-tech");
+                + "=monitoring-support, dropbox-monitor, dataset-uploader, dataset-file-search, proteomics, my-tech");
         Properties variables = new Properties();
         variables.setProperty(TECHNOLOGY_PROTEOMICS, "true");
         variables.setProperty(TECHNOLOGY_SCREENING, "false");
 
         updateEnabledTechnologyProperties(variables, false);
 
-        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + "=dropbox-monitor, dataset-uploader, "
+        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + "=monitoring-support, dropbox-monitor, dataset-uploader, "
                 + "dataset-file-search, proteomics, my-tech]",
                 FileUtilities.loadToStringList(corePluginsProperties).toString());
     }
@@ -117,14 +117,14 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
     public void testUpdateUnchangedProperty()
     {
         FileUtilities.writeToFile(corePluginsProperties, "abc = 123\n" + ENABLED_TECHNOLOGIES_KEY
-                + "=dropbox-monitor, dataset-uploader, dataset-file-search, proteomics");
+                + "=monitoring-support, dropbox-monitor, dataset-uploader, dataset-file-search, proteomics");
         Properties variables = new Properties();
         variables.setProperty(TECHNOLOGY_PROTEOMICS, "true");
         variables.setProperty(TECHNOLOGY_SCREENING, "false");
 
         updateEnabledTechnologyProperties(variables, false);
 
-        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + "=dropbox-monitor, dataset-uploader, "
+        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + "=monitoring-support, dropbox-monitor, dataset-uploader, "
                 + "dataset-file-search, proteomics]", FileUtilities
                 .loadToStringList(corePluginsProperties).toString());
     }
@@ -140,7 +140,7 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
 
         updateEnabledTechnologyProperties(variables, false);
 
-        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + " = dropbox-monitor, dataset-uploader, "
+        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + " = monitoring-support, dropbox-monitor, dataset-uploader, "
                 + "dataset-file-search, proteomics, screening, answer = 42]",
                 FileUtilities
                         .loadToStringList(corePluginsProperties).toString());
@@ -156,7 +156,7 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
 
         updateEnabledTechnologyProperties(variables, false);
 
-        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + " = dropbox-monitor, dataset-uploader, "
+        assertEquals("[abc = 123, " + ENABLED_TECHNOLOGIES_KEY + " = monitoring-support, dropbox-monitor, dataset-uploader, "
                 + "dataset-file-search, screening]", FileUtilities
                 .loadToStringList(corePluginsProperties).toString());
     }
@@ -172,7 +172,7 @@ public class SetEnableTechnologiesVariableActionTest extends AbstractFileSystemT
 
         updateEnabledTechnologyProperties(variables, false);
 
-        assertEquals("[a = b, " + ENABLED_TECHNOLOGIES_KEY + " = dropbox-monitor, dataset-uploader, "
+        assertEquals("[a = b, " + ENABLED_TECHNOLOGIES_KEY + " = monitoring-support, dropbox-monitor, dataset-uploader, "
                 + "dataset-file-search, screening, gamma = alpha]", 
                 FileUtilities.loadToStringList(corePluginsProperties).toString());
     }

openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/dss-monitoring-initialization.py

+import subprocess
+from ch.systemsx.cisd.common.exceptions import UserFailureException
+from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id import SpacePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions import SpaceFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.space.create import SpaceCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id import SampleIdentifier
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import SampleCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id import EntityTypePermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleTypeFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.create import SampleTypeCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions import DataSetTypeFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create import DataSetTypeCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.person.id import PersonPermId
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.person.fetchoptions import PersonFetchOptions
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.person.create import PersonCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create import RoleAssignmentCreation
+from ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment import Role
+
+def process(tr, parameters, tableBuilder):
+    session_token = _get_mandatory_parameter(parameters, "sessionToken")
+    data_set_code = _get_mandatory_parameter(parameters, "data set code")
+    space_code = _get_mandatory_parameter(parameters, "space code")
+    sample_code = _get_mandatory_parameter(parameters, "sample code")
+    user_id = _get_mandatory_parameter(parameters, "user id")
+    password = _get_mandatory_parameter(parameters, "password")
+
+    data_set_type_code = _get_parameter(parameters, "data set type code", "MONITORED_DATA_SET")
+    sample_type_code = _get_parameter(parameters, "sample type code", "MONITOR_SAMPLE")
+    file_name = _get_parameter(parameters, "file name", "info.txt")
+    file_content = _get_parameter(parameters, "file content", "blab blah")
+    
+    if tr.getSearchService().getDataSet(data_set_code) is None:
+        _create_data_set_type(session_token, data_set_type_code)
+        data_set = tr.createNewDataSet(data_set_type_code, data_set_code)
+        sample_id = _create_sample(tr, session_token, space_code, sample_code, sample_type_code)
+        data_set.setSample(sample_id)
+        with open(tr.createNewFile(data_set, file_name), "w") as file:
+            file.write(file_content)
+    _create_user(session_token, user_id, password, space_code)
+    
+    tableBuilder.addHeader("STATUS")
+    tableBuilder.addHeader("MESSAGE")
+    tableBuilder.addHeader("RESULT")
+    row = tableBuilder.addRow()
+    row.setCell("STATUS","OK")
+    row.setCell("MESSAGE", "Operation Successful")
+    row.setCell("RESULT", "done")
+
+def _create_data_set_type(session_token, data_set_type_code):
+    v3 = ServiceProvider.getV3ApplicationService()
+    data_set_type_permid = EntityTypePermId(data_set_type_code)
+    if v3.getDataSetTypes(session_token, [data_set_type_permid], DataSetTypeFetchOptions()).get(data_set_type_permid) is None:
+        data_set_type_creation = DataSetTypeCreation()
+        data_set_type_creation.setCode(data_set_type_code)
+        v3.createDataSetTypes(session_token, [data_set_type_creation])
+
+def _create_sample(tr, session_token, space_code, sample_code, sample_type_code):
+    v3 = ServiceProvider.getV3ApplicationService()
+    space_permid = SpacePermId(space_code)
+    if v3.getSpaces(session_token, [space_permid], SpaceFetchOptions()).get(space_permid) is None:
+        space_creation = SpaceCreation()
+        space_creation.setCode(space_code)
+        v3.createSpaces(session_token, [space_creation])
+    sample_id = SampleIdentifier(space_code, None, sample_code)
+    if v3.getSamples(session_token, [sample_id], SampleFetchOptions()).get(sample_id) is None:
+        sample_type_permid = EntityTypePermId(sample_type_code)
+        if v3.getSampleTypes(session_token, [sample_type_permid], SampleTypeFetchOptions()).get(sample_type_permid) is None:
+            sample_type_creation = SampleTypeCreation()
+            sample_type_creation.setCode(sample_type_code)
+            v3.createSampleTypes(session_token, [sample_type_creation])
+        sample_creation = SampleCreation()
+        sample_creation.setTypeId(sample_type_permid)
+        sample_creation.setSpaceId(space_permid)
+        sample_creation.setCode(sample_code)
+        v3.createSamples(session_token, [sample_creation])
+    return tr.getSearchService().getSample(sample_id.getIdentifier())
+
+def _create_user(session_token, user_id, password, space_code):
+    v3 = ServiceProvider.getV3ApplicationService()
+    person_permid = PersonPermId(user_id)
+    if v3.getPersons(session_token, [person_permid], PersonFetchOptions()).get(person_permid) is None:
+        passwdShPath = '../openBIS-server/jetty/bin/passwd.sh'
+        subprocess.call([passwdShPath, 'add', user_id, '-p', password])
+        creation = PersonCreation()
+        creation.setUserId(user_id)
+        v3.createPersons(session_token, [creation])
+        role_assignment_creation = RoleAssignmentCreation()
+        role_assignment_creation.setUserId(person_permid)
+        role_assignment_creation.setRole(Role.OBSERVER)
+        role_assignment_creation.setSpaceId(SpacePermId(space_code))
+        v3.createRoleAssignments(session_token, [role_assignment_creation])
+
+def _get_parameter(parameters, key, default_value):
+    p = parameters.get(key)
+    return p if p is not None else default_value
+
+def _get_mandatory_parameter(parameters, key):
+    p = parameters.get(key)
+    if p is None:
+        raise UserFailureException("Parameter '%s' not specified." % key)
+    return p

openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/plugin.properties

+label = DSS Monitoring Initialization
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
+script-path = dss-monitoring-initialization.py