From 7508cd7e3f75f292cc8886d16eeca5a11933051b Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Thu, 1 Nov 2018 11:35:13 +0100
Subject: [PATCH] SSDM-7166: monitoring-support module with core plugin
dss-monitoring-initialization added
---
.../SetEnableTechnologiesVariableAction.java | 2 +-
...tEnableTechnologiesVariableActionTest.java | 16 +--
.../dss-monitoring-initialization.py | 103 ++++++++++++++++++
.../plugin.properties | 3 +
4 files changed, 115 insertions(+), 9 deletions(-)
create mode 100644 openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/dss-monitoring-initialization.py
create mode 100644 openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/plugin.properties
diff --git a/installation/source/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableAction.java b/installation/source/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableAction.java
index 1a247d1f54d..822b8ef6e9f 100644
--- a/installation/source/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableAction.java
+++ b/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";
diff --git a/installation/sourceTest/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableActionTest.java b/installation/sourceTest/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableActionTest.java
index a59e0dc2ded..32a8c1b4ec8 100644
--- a/installation/sourceTest/java/ch/systemsx/cisd/openbis/installer/izpack/SetEnableTechnologiesVariableActionTest.java
+++ b/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());
}
diff --git a/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/dss-monitoring-initialization.py b/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/dss-monitoring-initialization.py
new file mode 100644
index 00000000000..fc10827bd41
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/dss-monitoring-initialization.py
@@ -0,0 +1,103 @@
+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
diff --git a/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/plugin.properties b/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/plugin.properties
new file mode 100644
index 00000000000..da4af6eba30
--- /dev/null
+++ b/openbis_standard_technologies/dist/core-plugins/monitoring-support/1/dss/reporting-plugins/dss-monitoring-initialization/plugin.properties
@@ -0,0 +1,3 @@
+label = DSS Monitoring Initialization
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
+script-path = dss-monitoring-initialization.py
--
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