From eb01d7a24bda19b91963d766ff2f973b1374615c Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 6 Aug 2019 17:06:23 +0200
Subject: [PATCH] added new_plugin and new_sample_type methods, implemented
new_plugin
---
pybis/src/python/pybis/pybis.py | 55 +++++++++++++++------------------
1 file changed, 25 insertions(+), 30 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index de03652df68..78c6795065a 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -628,7 +628,8 @@ class Openbis:
"get_role_assignments()",
"get_role_assignment(techId)",
"get_plugins()",
- "get_plugin(name)",
+ "get_plugin(code)",
+ "new_plugin(code)",
"new_group(code, description, userIds)",
'new_space(name, description)',
'new_project(space, code, description, attachments)',
@@ -636,6 +637,8 @@ class Openbis:
'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
+ '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)',
@@ -2506,28 +2509,17 @@ class Openbis:
else:
return Plugin(self, data=resp[permId])
- def new_plugin(self, pluginType= "MANAGED_PROPERTY", pluginKind = "JYTHON", **kwargs):
- """ Note: not functional yet. Creates a new Plugin in openBIS. The attribute pluginKind must be one of
- the following:
- DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION;
-
- Usage::
- o.new_plugin(
- name = 'name of plugin',
- description = '...',
- pluginType = "ENTITY_VALIDATION",
- script = "def a():\n pass",
- available = True,
- entityKind = None
- )
- """
-
- if pluginType not in [
- 'DYNAMIC_PROPERTY', 'MANAGED_PROPERTY', 'ENTITY_VALIDATION'
- ]:
- raise ValueError(
- "pluginType must be one of the following: DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION")
- return Plugin(self, pluginType=pluginType, pluginKind=pluginKind, **kwargs)
+ def new_plugin(self, name, pluginType, **kwargs):
+ """ Creates a new Plugin in openBIS.
+
+ name -- name of the plugin
+ description --
+ pluginType -- DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION
+ entityKind -- MATERIAL, EXPERIMENT, SAMPLE, DATA_SET
+ script -- string of the script itself
+ available --
+ """
+ return Plugin(self, name=name, pluginType=pluginType, **kwargs)
def new_property_type(self, code, dataType, **kwargs):
@@ -2537,7 +2529,10 @@ class Openbis:
"MATERIAL", "HYPERLINK", "XML"
]
if dataType not in allowed_dataTypes:
- raise ValueError("please use one of these dataTypes: {}".format(allowed_dataTypes))
+ raise ValueError(
+ "please use one of these dataTypes: {}"
+ .format(allowed_dataTypes)
+ )
return PropertyType(openbis_obj=self, code=code, dataType=dataType, **kwargs)
def get_property_type(self, code, only_data=False):
@@ -2712,14 +2707,12 @@ class Openbis:
optional_attributes = []
search_request = {
- "@type": "as.dto.{}.search.{}TypeSearchCriteria".format(
- entity.lower(), entity
- )
+ "@type": "as.dto.{}.search.{}TypeSearchCriteria"
+ .format(entity.lower(), entity)
}
fetch_options = {
- "@type": "as.dto.{}.fetchoptions.{}TypeFetchOptions".format(
- entity.lower(), entity
- )
+ "@type": "as.dto.{}.fetchoptions.{}TypeFetchOptions"
+ .format(entity.lower(), entity)
}
fetch_options['from'] = start_with
fetch_options['count'] = count
@@ -3181,6 +3174,8 @@ class Openbis:
"""
return SampleType(self, code=code, **kwargs)
+ new_object_type = new_sample_type
+
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.
--
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