From 282912731356e1cb414070e197e57fb18626eeb0 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Thu, 22 Aug 2019 14:02:43 +0200
Subject: [PATCH] added abstraction class OpenBisObject
---
pybis/src/python/pybis/experiment.py | 68 +++-------------------------
pybis/src/python/pybis/project.py | 12 -----
pybis/src/python/pybis/space.py | 12 -----
3 files changed, 6 insertions(+), 86 deletions(-)
diff --git a/pybis/src/python/pybis/experiment.py b/pybis/src/python/pybis/experiment.py
index 6cd6eca92fd..8a97b290441 100644
--- a/pybis/src/python/pybis/experiment.py
+++ b/pybis/src/python/pybis/experiment.py
@@ -4,40 +4,14 @@ from .openbis_object import OpenBisObject
from .definitions import openbis_definitions
from .utils import VERBOSE
-class Experiment(OpenBisObject):
- """
+class Experiment(
+ OpenBisObject,
+ entity='experiment',
+ single_item_method_name='get_experiment'
+):
+ """Handling experiment (collection) entities in openBIS
"""
- def __init__(self, openbis_obj, type, project=None, data=None, props=None, code=None, **kwargs):
- self.__dict__['openbis'] = openbis_obj
- self.__dict__['type'] = type
- ph = PropertyHolder(openbis_obj, type)
- self.__dict__['p'] = ph
- self.__dict__['props'] = ph
- self.__dict__['a'] = AttrHolder(openbis_obj, 'Experiment', type)
-
- if data is not None:
- self._set_data(data)
-
- if project is not None:
- setattr(self, 'project', project)
-
- if props is not None:
- for key in props:
- setattr(self.p, key, props[key])
-
- if code is not None:
- self.code = code
-
- if kwargs is not None:
- defs = openbis_definitions('Experiment')
- for key in kwargs:
- if key in defs['attrs']:
- setattr(self, key, kwargs[key])
- else:
- raise ValueError("{attr} is not a known attribute for an Experiment".format(attr=key))
-
-
def _set_data(self, data):
# assign the attribute data to self.a by calling it
# (invoking the AttrHolder.__call__ function)
@@ -94,36 +68,6 @@ class Experiment(OpenBisObject):
set_props = set_properties
- def save(self):
- for prop_name, prop in self.props._property_names.items():
- if prop['mandatory']:
- if getattr(self.props, prop_name) is None or getattr(self.props, prop_name) == "":
- raise ValueError("Property '{}' is mandatory and must not be None".format(prop_name))
-
- if self.is_new:
- request = self._new_attrs()
- props = self.p._all_props()
- request["params"][1][0]["properties"] = props
- resp = self.openbis._post_request(self.openbis.as_v3, request)
-
- if VERBOSE: print("Experiment successfully created.")
- new_exp_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
- self._set_data(new_exp_data)
- return self
- else:
- request = self._up_attrs()
- props = self.p._all_props()
- request["params"][1][0]["properties"] = props
- self.openbis._post_request(self.openbis.as_v3, request)
- if VERBOSE: print("Experiment successfully updated.")
- new_exp_data = self.openbis.get_experiment(self.permId, only_data=True)
- self._set_data(new_exp_data)
-
- def delete(self, reason):
- if self.permId is None:
- return None
- self.openbis.delete_entity(entity='Experiment', id=self.permId, reason=reason)
- if VERBOSE: print("Experiment {} successfully deleted.".format(self.permId))
def get_datasets(self, **kwargs):
if self.permId is None:
diff --git a/pybis/src/python/pybis/project.py b/pybis/src/python/pybis/project.py
index 6e4644103a4..1d022b4dbed 100644
--- a/pybis/src/python/pybis/project.py
+++ b/pybis/src/python/pybis/project.py
@@ -9,18 +9,6 @@ class Project(
single_item_method_name='get_project'
):
- def __init__(self, openbis_obj, data=None, **kwargs):
- self.__dict__['openbis'] = openbis_obj
- self.__dict__['a'] = AttrHolder(openbis_obj, 'project')
-
- if data is not None:
- self.a(data)
- self.__dict__['data'] = data
-
- if kwargs is not None:
- for key in kwargs:
- setattr(self, key, kwargs[key])
-
def _modifiable_attrs(self):
return
diff --git a/pybis/src/python/pybis/space.py b/pybis/src/python/pybis/space.py
index 9b7ad2f1e8d..c88a7748848 100644
--- a/pybis/src/python/pybis/space.py
+++ b/pybis/src/python/pybis/space.py
@@ -11,18 +11,6 @@ class Space(
""" managing openBIS spaces
"""
- def __init__(self, openbis_obj, data=None, **kwargs):
- self.__dict__['openbis'] = openbis_obj
- self.__dict__['a'] = AttrHolder(openbis_obj, 'space' )
-
- if data is not None:
- self.a(data)
- self.__dict__['data'] = data
-
- if kwargs is not None:
- for key in kwargs:
- setattr(self, key, kwargs[key])
-
def __dir__(self):
"""all the available methods and attributes that should be displayed
when using the autocompletion feature (TAB) in Jupyter
--
GitLab