From b04d88934a67b16e62274eacb12e57732e7e3d27 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Thu, 8 Aug 2019 13:50:25 +0200
Subject: [PATCH] added all sorts of entity types
---
pybis/src/python/pybis/definitions.py | 98 +++++++++++++++++++++++++--
pybis/src/python/pybis/sample_type.py | 54 ---------------
2 files changed, 92 insertions(+), 60 deletions(-)
delete mode 100644 pybis/src/python/pybis/sample_type.py
diff --git a/pybis/src/python/pybis/definitions.py b/pybis/src/python/pybis/definitions.py
index cabfa20ea61..baa0cf8f57c 100644
--- a/pybis/src/python/pybis/definitions.py
+++ b/pybis/src/python/pybis/definitions.py
@@ -54,10 +54,22 @@ def openbis_definitions(entity):
"multi": "parents children components tags attachments".split(),
},
"sampleType": {
- "attrs_new": "code autoGeneratedCode generatedCodePrefix subcodeUnique description listable showContainer showParents showParentMetadata".split(),
- "attrs_up": "autoGeneratedCode generatedCodePrefix subcodeUnique description listable showContainer showParents showParentMetadata".split(),
- "attrs": "code autoGeneratedCode generatedCodePrefix subcodeUnique description listable showContainer showParents showParentMetadata".split(),
-
+ "attrs_new": "code description autoGeneratedCode generatedCodePrefix subcodeUnique listable showContainer showParents showParentMetadata".split(),
+ "attrs_up": "description autoGeneratedCode generatedCodePrefix subcodeUnique listable showContainer showParents showParentMetadata".split(),
+ "attrs": "permId code description autoGeneratedCode generatedCodePrefix subcodeUnique listable showContainer showParents showParentMetadata modificationDate".split(),
+ "default_attribute_values": {
+ "autoGeneratedCode" : False,
+ "generatedCodePrefix" : "S",
+ "subcodeUnique" : False,
+ "description" : "",
+ "listable" : True,
+ "showContainer" : False,
+ "showParents" : True,
+ "showParentMetadata" : False
+ },
+ "search": {
+ "@type": "as.dto.sample.search.SampleTypeSearchCriteria"
+ },
"create": {
"@type": "as.dto.sample.create.SampleTypeCreation"
},
@@ -67,11 +79,78 @@ def openbis_definitions(entity):
"delete": {
"@type": "as.dto.sample.delete.SampleTypeDeletionOptions"
},
+ "identifier": "typeId",
+ },
+ "materialType": {
+ "attrs_new": "code description validationPluginId".split(),
+ "attrs_up": "description validationPluginId".split(),
+ "attrs": "permId code description validationPlugin".split(),
+ "search": {
+ "@type": "as.dto.material.search.MaterialTypeSearchCriteria"
+ },
+ "fetch": {
+ "@type": "as.dto.material.fetchoptions.MaterialTypeFetchOptions"
+ },
+ "create": {
+ "@type": "as.dto.material.create.MaterialTypeCreation"
+ },
+ "update": {
+ "@type": "as.dto.material.update.MaterialTypeUpdate"
+ },
+ "delete": {
+ "@type": "as.dto.material.delete.MaterialTypeDeletionOptions"
+ },
+ "identifier": "typeId",
+ },
+ "dataSetType": {
+ "attrs_new": "code description mainDataSetPattern mainDataSetPath disallowDeletion validationPluginId".split(),
+ "attrs_up": "description mainDataSetPattern mainDataSetPath disallowDeletion validationPluginId".split(),
+ "attrs": "permId code description mainDataSetPattern mainDataSetPath disallowDeletion modificationDate validationPlugin".split(),
+ "search": {
+ "@type": "as.dto.dataset.search.DataSetTypeSearchCriteria"
+ },
+ "fetch": {
+ "@type": "as.dto.dataset.fetchoptions.DataSetTypeFetchOptions"
+ },
+ "create": {
+ "@type": "as.dto.dataset.create.DataSetTypeCreation"
+ },
+ "update": {
+ "@type": "as.dto.dataset.update.DataSetTypeUpdate"
+ },
+ "delete": {
+ "@type": "as.dto.dataset.delete.DataSetTypeDeletionOptions"
+ },
+ "identifier": "typeId",
+ },
+ "experimentType": {
+ "attrs_new": "code description modificationDate validationPluginId".split(),
+ "attrs_up": "description modificationDate validationPluginId".split(),
+ "attrs": "permId code description modificationDate validationPlugin".split(),
+ "search": {
+ "@type": "as.dto.experiment.search.ExperimentTypeSearchCriteria"
+ },
+ "fetch": {
+ "@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions"
+ },
+ "create": {
+ "@type": "as.dto.experiment.create.ExperimentTypeCreation"
+ },
+ "update": {
+ "@type": "as.dto.experiment.create.ExperimentTypeUpdate"
+ },
+ "delete": {
+ "@type": "as.dto.experiment.delete.ExperimentTypeDeletionOptions"
+ },
+ "identifier": "typeId",
},
"propertyType": {
"attrs": "code label description managedInternally internalNameSpace dataType vocabulary materialType schema transformation semanticAnnotations registrator registrationDate".split(),
"attrs_new": "code label description managedInternally internalNameSpace dataType vocabularyId materialTypeId schema transformation metaData".split(),
"attrs_up": "label description schema transformation metaData".split(),
+ "search": {
+ "@type": "as.dto.property.search.PropertyTypeSearchCriteria"
+ },
"create": {
"@type": "as.dto.property.create.PropertyTypeCreation"
},
@@ -81,6 +160,11 @@ def openbis_definitions(entity):
"delete": {
"@type": "as.dto.property.delete.PropertyTypeDeletionOptions"
},
+ "dataType": [
+ "INTEGER", "VARCHAR", "MULTILINE_VARCHAR",
+ "REAL", "TIMESTAMP", "BOOLEAN", "CONTROLLEDVOCABULARY",
+ "MATERIAL", "HYPERLINK", "XML"
+ ],
"identifier": "typeId",
},
"SemanticAnnotation": {
@@ -200,6 +284,7 @@ def openbis_definitions(entity):
"users": "userIds",
"description": "description",
"vocabulary": "vocabularyId",
+ "validationPlugin": "validationPluginId",
},
"ids2type": {
'spaceId': {'permId': {'@type': 'as.dto.space.id.SpacePermId'}},
@@ -314,7 +399,7 @@ def get_fetchoption_for_entity(entity):
return {}
def get_type_for_entity(entity, action):
- if action not in "create update delete fetch".split():
+ if action not in "create update delete search".split():
raise ValueError('unknown action: {}'.format(action))
definition = openbis_definitions(entity)
@@ -327,8 +412,9 @@ def get_type_for_entity(entity, action):
"create": "Creation",
"update": "Update",
"delete": "DeletionOptions",
- "fetch" : "FetchOptions"
+ "search": "SearchCriteria",
}
+
return {
"@type": "as.dto.{}.{}.{}{}"
.format(entity.lower(), action, cap_entity, noun[action])
diff --git a/pybis/src/python/pybis/sample_type.py b/pybis/src/python/pybis/sample_type.py
deleted file mode 100644
index b64b584700c..00000000000
--- a/pybis/src/python/pybis/sample_type.py
+++ /dev/null
@@ -1,54 +0,0 @@
-from .property_assignment import PropertyAssignments
-from .semantic_annotation import SemanticAnnotation
-from .attribute import AttrHolder
-#from .entity_type import EntityType
-from .openbis_object import OpenBisObject
-
-class SampleType(
- OpenBisObject,
- entity='sampleType',
- single_item_method_name='get_sample_type'
-):
- """ Helper class for sample types, adding functionality.
- """
- def __init_old__(self, openbis_obj, data=None, **kwargs):
-
- # call __init__ of EntityType parent class
- super().__init__(openbis_obj, data)
-
- self.__dict__['a'] = AttrHolder(openbis_obj, 'SampleType')
- if data is not None:
- self._set_data(data)
-
- self.__dict__['openbis'] = openbis_obj
-
- defaults = {
- "autoGeneratedCode" : False,
- "generatedCodePrefix" : "S",
- "subcodeUnique" : False,
- "description" : "",
- "listable" : True,
- "showContainer" : False,
- "showParents" : True,
- "showParentMetadata" : False
- }
-
-
- def _set_data(self, data):
- # assign the attribute data to self.a by calling it
- # (invoking the AttrHolder.__call__ function)
- self.a(data)
- self.__dict__['data'] = data
-
-
- def add_semantic_annotation(self, **kwargs):
- semantic_annotation = SemanticAnnotation(
- openbis_obj=self.openbis, isNew=True,
- entityType=self.code, **kwargs
- )
- semantic_annotation.save()
- return semantic_annotation
-
- def get_semantic_annotations(self):
- return self.openbis.search_semantic_annotations(entityType=self.code)
-
--
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