From 2ded4be4582aac3372e56e9008957e25eec9c087 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Thu, 9 Nov 2023 17:09:11 +0100
Subject: [PATCH] BIS-716: Added simple data model and validator for
imaging_data_set
---
.../imaging/1/as/initialize-master-data.py | 73 ++++++++
.../1/as/master-data/imaging-data-model.xls | Bin 0 -> 23552 bytes
.../imaging_dataset_config_validation.py | 163 +++++++++++++++++-
3 files changed, 231 insertions(+), 5 deletions(-)
create mode 100644 core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py
create mode 100644 core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py b/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py
new file mode 100644
index 00000000000..e1ed0ce1fa3
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/as/initialize-master-data.py
@@ -0,0 +1,73 @@
+#
+# Copyright 2014 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.
+#
+# MasterDataRegistrationTransaction Class
+from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
+from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
+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
+import sys
+
+helper = MasterDataRegistrationHelper(sys.path)
+api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
+sessionToken = api.loginAsSystem()
+props = CustomASServiceExecutionOptions().withParameter('xls', helper.listXlsByteArrays()) \
+ .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'IMAGING').withParameter('update_mode', 'UPDATE_IF_EXISTS') \
+ .withParameter('scripts', helper.getAllScripts())
+result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
+api.logout(sessionToken)
+print("======================== imaging-master-data xls ingestion result ========================")
+print(result)
+print("======================== imaging-data xls ingestion result ========================")
+
+
+
+# from ch.ethz.sis.openbis.generic.server.asapi.v3 import ApplicationServerApi
+# from ch.systemsx.cisd.openbis.generic.server import CommonServiceProvider
+# 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
+# import sys
+#
+# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNFixes
+# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNAnnotationsMigration
+# from ch.systemsx.cisd.openbis.generic.server.hotfix import ELNCollectionTypeMigration
+#
+# api = CommonServiceProvider.getApplicationContext().getBean(ApplicationServerApi.INTERNAL_SERVICE_NAME)
+# sessionToken = api.loginAsSystem()
+#
+# if ELNFixes.isELNInstalled():
+# ELNFixes.beforeUpgrade(sessionToken)
+# ELNAnnotationsMigration.beforeUpgrade(sessionToken)
+# ELNCollectionTypeMigration.beforeUpgrade(sessionToken)
+#
+# helper = MasterDataRegistrationHelper(sys.path)
+# props = CustomASServiceExecutionOptions().withParameter('xls', helper.getByteArray("common-data-model.xls"))\
+# .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'ELN-LIMS').withParameter('update_mode', 'UPDATE_IF_EXISTS')\
+# .withParameter('scripts', helper.getAllScripts())
+# result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
+#
+# if not ELNFixes.isMultiGroup():
+# props = CustomASServiceExecutionOptions().withParameter('xls', helper.getByteArray("single-group-data-model.xls"))\
+# .withParameter('method', 'import').withParameter('zip', False).withParameter('xls_name', 'ELN-LIMS').withParameter('update_mode', 'UPDATE_IF_EXISTS')\
+# .withParameter('scripts', helper.getAllScripts())
+# result = api.executeCustomASService(sessionToken, CustomASServiceCode("xls-import"), props)
+#
+# ELNCollectionTypeMigration.afterUpgrade()
+# api.logout(sessionToken)
+# print("======================== master-data xls ingestion result ========================")
+# print(result)
+# print("======================== master-data xls ingestion result ========================")
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls b/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/imaging-data-model.xls
new file mode 100644
index 0000000000000000000000000000000000000000..8f88765f4618a3462bf4118c977d56eb9f621c5d
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diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py b/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py
index 8f06d3e3744..6766c2ff211 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/as/master-data/scripts/imaging_dataset_config_validation.py
@@ -13,17 +13,170 @@
# limitations under the License.
#
+import json
+
+
+def assert_control(control_config):
+ if not control_config:
+ return True, ''
+ obligatory_tags = ['@type', 'label', 'type']
+ for tag in obligatory_tags:
+ if tag not in control_config:
+ return False, tag+': is missing!'
+ if control_config[tag] is None:
+ return False, tag+': can not be empty!'
+
+ list_tags = ['values', 'range', 'speeds', 'visibility']
+ for list_tag in list_tags:
+ if list_tag in control_config and control_config[list_tag] is not None and not isinstance(control_config[list_tag], list):
+ return False, list_tag+': must be a list or null!'
+
+ boolean_tags = ['playable', 'multiselect']
+ for boolean_tag in boolean_tags:
+ if boolean_tag in control_config and control_config[boolean_tag] is not None and not isinstance(control_config[boolean_tag], bool):
+ return False, boolean_tag+': must be a boolean or empty!'
+
+ if 'visibility' in control_config and control_config['visibility'] is not None:
+ visibility = control_config['visibility']
+ for vis in visibility:
+ tags = ['label', 'values']
+ all_tags = tags + ['range', 'unit']
+ for tag in ['label', 'values']:
+ if tag not in vis:
+ return False, 'visibility->'+tag+': is missing!'
+ if vis[tag] is None:
+ return False, 'visibility->'+tag+': can not be empty!'
+
+ for tag in ['values', 'range']:
+ if tag in vis and vis[tag] is not None and not isinstance(vis[tag], list):
+ return False, 'visibility->'+tag+': must be a list!'
+
+ if 'metadata' in control_config and control_config['metadata'] is not None and not isinstance(control_config['metadata'], dict):
+ return False, '->metadata: must be a dictionary or null!'
+
+ return True, ''
+
+
+def assert_config(json_config):
+ if 'config' in json_config:
+ config = json_config['config']
+ obligatory_tags = ['@type', 'adaptor', 'version', 'playable', 'exports', 'inputs']
+ for tag in obligatory_tags:
+ if tag not in config:
+ return False, 'config->' + tag + ': is missing!'
+ if config[tag] is None:
+ return False, 'config->' + tag + ': can not be empty!'
+
+ if config['adaptor'].strip() == '':
+ return False, 'config->adaptor: can not be blank!'
+
+ list_tags = ['speeds', 'resolutions', 'exports', 'inputs']
+ for list_tag in list_tags:
+ if list_tag in config and config[list_tag] is not None and not isinstance(config[list_tag], list):
+ return False, '\''+list_tag+'\' must be a list or null!'
+
+ if not isinstance(config['playable'], bool):
+ return False, 'config->playable: must be a boolean!'
+
+ for control in config['exports']:
+ result, err = assert_control(control)
+ if not result:
+ return result, 'config->exports->' + err
+
+ for control in config['inputs']:
+ result, err = assert_control(control)
+ if not result:
+ return result, 'config->inputs->' + err
+
+ if 'metadata' in config and config['metadata'] is not None and not isinstance(config['metadata'], dict):
+ return False, 'config->metadata: must be a dictionary or null!'
+ else:
+ return False, 'Missing \'config\' tag in configuration!'
+ return True, ''
+
+
+def assert_preview(preview_config):
+ obligatory_tags = ['@type', 'format', 'show']
+ for tag in obligatory_tags:
+ if tag not in config:
+ return False, tag + ': is missing!'
+ if config[tag] is None:
+ return False, tag + ': can not be empty!'
+
+ if not isinstance(preview_config['show'], bool):
+ return False, 'show: must be boolean!'
+
+ if not isinstance(preview_config['format'], str):
+ return False, 'format: must be string!'
+
+ if 'bytes' in preview_config and preview_config['bytes'] is not None and not isinstance(preview_config['bytes'], str):
+ return False, 'bytes: must be a base64 encoded string or null!'
+
+ if 'metadata' in preview_config and preview_config['metadata'] is not None and not isinstance(preview_config['metadata'], dict):
+ return False, 'metadata: must be a dictionary or null!'
+
+ if 'config' in preview_config and preview_config['config'] is not None and not isinstance(preview_config['config'], dict):
+ return False, 'config: must be a dictionary or null!'
+
+ return True, ''
+
+
+def assert_images(json_config):
+ if 'images' in json_config:
+ images = json_config['images']
+ if images is None:
+ return False, '\'images\' tag can not be null!'
+ if not isinstance(images, list):
+ return False, '\'images\' tag must be a list!'
+
+ for image in images:
+ obligatory_tags = ['@type']
+ for tag in obligatory_tags:
+ if tag not in image:
+ return False, 'images->' + tag + ': missing tag!'
+ if image[tag] is None:
+ return False, 'images->' + tag + ': can not be empty!'
+
+ if 'metadata' in image and image['metadata'] is not None and not isinstance(image['metadata'], dict):
+ return False, 'images->metadata: must be a dictionary or null!'
+
+ if 'previews' in image and image['previews'] is not None and not isinstance(image['previews'], list):
+ return False, 'images->previews: must be a list or null!'
+
+ for preview in image['previews']:
+ res, err = assert_preview(preview)
+ if not res:
+ return result, 'images->previews->' + err
+
+ else:
+ return False, 'Missing \'images\' tag in configuration!'
+ return True, ''
+
def get_rendered_property(entity, property):
- value = entity.property(property)
- if value is not None:
- return value.renderedValue()
+ properties = entity.externalDataPE().getProperties()
+ for prop in properties:
+ etpt = prop.getEntityTypePropertyType()
+ pt = etpt.getPropertyType()
+ code = pt.getCode()
+ if code == property:
+ return prop.tryGetUntypedValue()
+ return None
def validate(entity, is_new):
imaging_dataset_config = get_rendered_property(entity, "$IMAGING_DATA_CONFIG")
if imaging_dataset_config is None or imaging_dataset_config == "":
return "Imaging dataset config can not be empty!"
+ elif "test_validation_failure" in imaging_dataset_config:
+ return "Imaging dataset config validation failure!"
else:
- # TODO add deserialization and validation of particular fields
- pass
+
+ try:
+ config = json.loads(imaging_dataset_config)
+ except Exception as e:
+ return "Could not parse JSON: " + e
+
+ result, err = assert_config(config)
+ if not result:
+ return err
--
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