From a7c0a01ec496e77bbc66d2c08098cef24a9afa4c Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Wed, 23 Oct 2019 17:23:55 +0200
Subject: [PATCH] added new_experiment_type() and new_material_type()
---
pybis/src/python/pybis/pybis.py | 171 ++++++++++++++++++++++----------
1 file changed, 119 insertions(+), 52 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index fc2273f781e..db5733c542f 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -28,7 +28,7 @@ from tabulate import tabulate
from . import data_set as pbds
from .utils import parse_jackson, check_datatype, split_identifier, format_timestamp, is_identifier, is_permid, nvl, VERBOSE
-from .utils import extract_attr, extract_permid, extract_code,extract_deletion,extract_identifier,extract_nested_identifier,extract_nested_permid,extract_property_assignments,extract_role_assignments,extract_person, extract_person_details,extract_id,extract_userId
+from .utils import extract_attr, extract_permid, extract_code,extract_deletion,extract_identifier,extract_nested_identifier,extract_nested_permid, extract_nested_permids, extract_property_assignments,extract_role_assignments,extract_person, extract_person_details,extract_id,extract_userId
from .entity_type import EntityType, SampleType, DataSetType, MaterialType, ExperimentType
from .vocabulary import Vocabulary, VocabularyTerm
from .openbis_object import OpenBisObject
@@ -682,74 +682,81 @@ class Openbis:
def __dir__(self):
return [
- 'url', 'port', 'hostname',
- 'login(username, password, save_token=True)', 'logout()', 'is_session_active()', 'token', 'is_token_valid("")',
+ 'url', 'port', 'hostname', 'token',
+ 'login()',
+ 'logout()',
+ 'is_session_active()',
+ 'is_token_valid()',
"get_server_information()",
- "get_dataset('permId')",
+ "get_dataset()",
"get_datasets()",
- "get_dataset_type('type')",
+ "get_dataset_type()",
"get_dataset_types()",
"get_datastores()",
- "gen_code(entity, prefix)",
+ "gen_code()",
"get_deletions()",
- "get_experiment('permId', withAttachments=False)",
+ "get_experiment()",
"get_experiments()",
- "get_experiment_type('type')",
+ "get_experiment_type()",
"get_experiment_types()",
- "get_collection('permId', withAttachments=False)",
+ "get_collection()",
"get_collections()",
- "get_collection_type('type')",
+ "get_collection_type()",
"get_collection_types()",
- "get_external_data_management_system(permId)",
- "get_material_type('type')",
+ "get_external_data_management_system()",
+ "get_material_type()",
"get_material_types()",
- "get_project('project')",
- "get_projects(space=None, code=None)",
- "get_sample('id')",
- "get_object('id')", # "get_sample('id')" alias
+ "get_project()",
+ "get_projects()",
+ "get_sample()",
+ "get_object()",
"get_samples()",
- "get_objects()", # "get_samples()" alias
- "get_sample_type('type')",
- "get_object_type('type')", # "get_sample_type(type))" alias
+ "get_objects()",
+ "get_sample_type()",
+ "get_object_type()",
"get_sample_types()",
- "get_object_types()", # "get_sample_types()" alias
+ "get_object_types()",
"get_property_types()",
"get_property_type()",
"new_property_type()",
"get_semantic_annotations()",
- "get_semantic_annotation(permId, only_data = False)",
- "get_space(code)",
+ "get_semantic_annotation()",
+ "get_space()",
"get_spaces()",
"get_tags()",
- "get_tag(tagId)",
- "new_tag(code, description)",
+ "get_tag()",
+ "new_tag()",
"get_terms()",
"get_term()",
"get_vocabularies()",
"get_vocabulary()",
- "new_person(userId, space)",
+ "new_person()",
"get_persons()",
- "get_person(userId)",
+ "get_person()",
"get_groups()",
- "get_group(code)",
+ "get_group()",
"get_role_assignments()",
- "get_role_assignment(techId)",
+ "get_role_assignment()",
"get_plugins()",
- "get_plugin(code)",
- "new_plugin(code)",
- "new_group(code, description, userIds)",
- 'new_space(name, description)',
- 'new_project(space, code, description, attachments)',
- 'new_experiment(type, code, project, props={})',
- 'new_collection(type, code, project, props={})',
- 'new_sample(type, space, project, experiment, parents)',
- 'new_object(type, space, project, experiment, parents)', # 'new_sample(type, space, project, experiment)' alias
+ "get_plugin()",
+ "new_plugin()",
+ "new_group()",
+ 'new_space()',
+ 'new_project()',
+ 'new_experiment()',
+ 'new_collection()',
+ 'new_sample()',
+ 'new_object()',
'new_sample_type()',
'new_object_type()',
- 'new_dataset(type, parent, experiment, sample, files=[], folder, props={})',
- 'new_semantic_annotation(entityType, propertyType)',
- 'update_sample(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)',
- 'update_object(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)', # 'update_sample(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)' alias
+ 'new_dataset()',
+ 'new_dataset_type()',
+ 'new_experiment_type()',
+ 'new_collection_type()',
+ 'new_material_type()',
+ 'new_semantic_annotation()',
+ 'update_sample()',
+ 'update_object()',
]
def _repr_html_(self):
@@ -2708,6 +2715,8 @@ class Openbis:
df = DataFrame(objects)
df['registrationDate'] = df['registrationDate'].map(format_timestamp)
df['registrator'] = df['registrator'].map(extract_person)
+ df['vocabulary'] = df['vocabulary'].map(extract_code)
+ df['semanticAnnotations'] = df['semanticAnnotations'].map(extract_nested_permids)
return Things(
openbis_obj = self,
@@ -2835,6 +2844,8 @@ class Openbis:
entity_types = DataFrame(objects)
entity_types['permId'] = entity_types['permId'].map(extract_permid)
entity_types['modificationDate'] = entity_types['modificationDate'].map(format_timestamp)
+ entity_types['validationPlugin'] = entity_types['validationPlugin'].map(extract_nested_permid
+ )
single_item_method = getattr(self, cls._single_item_method_name)
return Things(
@@ -3358,21 +3369,77 @@ class Openbis:
new_object = new_sample # Alias
- def new_sample_type(self,
- code,
- **kwargs
- ):
- return SampleType(self, code=code, **kwargs)
-
+ def new_sample_type(self,
+ code,
+ generatedCodePrefix,
+ autoGeneratedCode=False,
+ listable=True,
+ showContainer=False,
+ showParents=True,
+ showParentMetadata=False,
+ validationPlugin=None):
+ """Creates a new sample type.
+ """
+
+ return SampleType(self,
+ code=code,
+ generatedCodePrefix = generatedCodePrefix,
+ autoGeneratedCode = autoGeneratedCode,
+ listable = listable,
+ showContainer = showContainer,
+ showParents = showParents,
+ showParentMetadata = showParentMetadata,
+ validationPlugin = validationPlugin,
+ )
new_object_type = new_sample_type
def new_dataset_type(self,
- code,
- **kwargs
- ):
- return DataSetType(self, code=code, **kwargs)
+ code,
+ description=None,
+ mainDataSetPattern=None,
+ mainDataSetPath=None,
+ disallowDeletion=False,
+ validationPlugin=None,
+ ):
+ """Creates a new dataSet type.
+ """
- new_object_type = new_sample_type
+ return DataSetType(self,
+ code=code,
+ description=description,
+ mainDataSetPattern=mainDataSetPattern,
+ mainDataSetPath=mainDataSetPath,
+ disallowDeletion=disallowDeletion,
+ validationPlugin=validationPlugin,
+ )
+
+ def new_experiment_type(self,
+ code,
+ description=None,
+ validationPlugin=None,
+ ):
+ """Creates a new experiment type (collection type)
+ """
+ return ExperimentType(self,
+ code=code,
+ description=description,
+ validationPlugin=validationPlugin,
+ )
+ new_collection_type = new_experiment_type
+
+
+ def new_material_type(self,
+ code,
+ description=None,
+ validationPlugin=None,
+ ):
+ """Creates a new material type.
+ """
+ return MaterialType(self,
+ code=code,
+ description=description,
+ validationPlugin=validationPlugin,
+ )
def new_dataset(self, type=None, kind='PHYSICAL_DATA', files=None, props=None, folder=None, **kwargs):
""" Creates a new dataset of a given sample type.
--
GitLab