From cf45dc89bd2c21624c69088a99277af312b9327d Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 29 Sep 2017 17:52:20 +0200
Subject: [PATCH] added more meaningful autocompletion hints for the Openbis
object itself
---
src/python/PyBis/pybis/pybis.py | 61 +++++++++++++++++++++++++++------
1 file changed, 50 insertions(+), 11 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 28eb55e159d..c4002e20d75 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -603,6 +603,40 @@ class Openbis:
if self.token is None:
self.token = self._get_cached_token()
+ def __dir__(self):
+ return [
+ 'url', 'port', 'hostname',
+ 'login()', 'logout()', 'is_session_active()', 'token', 'is_token_valid("")',
+ "get_dataset('permId')",
+ "get_datasets()",
+ "get_dataset_type('raw_data')",
+ "get_dataset_types()",
+ "get_datastores()",
+ "get_deletions()",
+ "get_experiment('permId', withAttachments=False)",
+ "get_experiments()",
+ "get_experiment_type('type')",
+ "get_experiment_types()",
+ "get_external_data_management_system('permId')",
+ "get_material_type('type')",
+ "get_material_types()",
+ "get_project('project')",
+ "get_projects(space=None, code=None)",
+ "get_sample('id')",
+ "get_samples()",
+ "get_sample_type('type'))",
+ "get_sample_types()",
+ "get_space('spaceId')",
+ "get_spaces()",
+ "get_tags()",
+ "get_terms()",
+ 'new_space(name, description)',
+ 'new_project(space, code, description)',
+ 'new_experiment(type, code, project, props={})',
+ 'new_sample(type, space, project, experiment)',
+ 'new_dataset(type, parent, experiment, sample, files=[], folder, props={})',
+ ]
+
@property
def spaces(self):
return self.get_spaces()
@@ -1666,9 +1700,9 @@ class Openbis:
else:
return Sample(self, self.get_sample_type(resp[sample_ident]["type"]["code"]), resp[sample_ident])
- def get_external_data_management_system(self, perm_id, only_data=False):
+ def get_external_data_management_system(self, permId, only_data=False):
"""Retrieve metadata for the external data management system.
- :param perm_id: A permId for an external DMS.
+ :param permId: A permId for an external DMS.
:param only_data: Return the result data as a hash-map, not an object.
"""
@@ -1678,7 +1712,7 @@ class Openbis:
self.token,
[{
"@type": "as.dto.externaldms.id.ExternalDmsPermId",
- "permId": perm_id
+ "permId": permId
}],
{},
],
@@ -1688,7 +1722,7 @@ class Openbis:
parse_jackson(resp)
if resp is None or len(resp) == 0:
- raise ValueError('no such external DMS found: ' + perm_id)
+ raise ValueError('no such external DMS found: ' + permId)
else:
for ident in resp:
if only_data:
@@ -1696,7 +1730,7 @@ class Openbis:
else:
return ExternalDMS(self, resp[ident])
- def new_space(self, name, description=None):
+ def new_space(self, code, description=None):
""" Creates a new space in the openBIS instance.
"""
request = {
@@ -1704,14 +1738,14 @@ class Openbis:
"params": [
self.token,
[{
- "code": name,
+ "code": code,
"description": description,
"@type": "as.dto.space.create.SpaceCreation"
}]
],
}
resp = self._post_request(self.as_v3, request)
- return self.get_space(name)
+ return self.get_space(code)
def new_analysis(self, name, description=None, sample=None, dss_code=None, result_files=None,
notebook_files=None, parents=None):
@@ -3065,7 +3099,7 @@ class AttrHolder():
def __repr__(self):
- headers = ['property', 'value']
+ headers = ['attribute', 'value']
lines = []
for attr in self._allowed_attrs:
if attr == 'attachments':
@@ -3113,7 +3147,7 @@ class Sample():
'props', 'get_parents()', 'get_children()',
'add_parents()', 'add_children()', 'del_parents()', 'del_children()',
'get_datasets()', 'get_experiment()',
- 'space', 'project', 'experiment', 'project', 'tags',
+ 'space', 'project', 'experiment', 'tags',
'set_tags()', 'add_tags()', 'del_tags()',
'add_attachment()', 'get_attachments()', 'download_attachments()',
'save()', 'delete()'
@@ -3214,8 +3248,13 @@ class Space(OpenBisObject):
"""all the available methods and attributes that should be displayed
when using the autocompletion feature (TAB) in Jupyter
"""
- return ['code', 'permId', 'description', 'registrator', 'registrationDate',
- 'modificationDate', 'get_projects()', 'new_project()', 'get_samples()', 'delete()']
+ return [
+ 'code', 'permId', 'description', 'registrator', 'registrationDate', 'modificationDate',
+ 'get_projects()',
+ "new_project(code='', description='')",
+ 'get_samples()',
+ 'delete()'
+ ]
def __str__(self):
return self.data.get('code', None)
--
GitLab