diff --git a/.gitignore b/.gitignore
index f8f1a114a0b60291dbc4c43af79b374d066e2dd2..4c9cc242ca00f1f359b8d6017dbba6b13dbec9b4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ __pycache__
.cache
.vagrant
.env
+*.tar
src/python/OBis/build/
src/python/OBis/dist/
src/python/PyBis/build/
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 72cba1d2680bdd173b8311828f7d868b77c73d05..348f84ec4aac44605c0014b95980e3305ee3b3b5 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -643,8 +643,8 @@ class Openbis:
'new_space(name, description)',
'new_project(space, code, description)',
'new_experiment(type, code, project, props={})',
- 'new_sample(type, space, project, experiment)',
- 'new_object(type, space, project, experiment)', # 'new_sample(type, space, project, experiment)' alias
+ 'new_sample(type, space, project, experiment, parents)',
+ 'new_object(type, space, project, experiment, parents)', # 'new_sample(type, space, project, experiment)' alias
'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)',
@@ -1167,12 +1167,13 @@ class Openbis:
data = resp[id]
)
- def new_experiment(self, type, code, props=None, **kwargs):
+ def new_experiment(self, type, code, project, props=None, **kwargs):
""" Creates a new experiment of a given experiment type.
"""
return Experiment(
openbis_obj = self,
type = self.get_experiment_type(type),
+ project = project,
data = None,
props = props,
code = code,
@@ -2950,7 +2951,12 @@ class AttrHolder():
new_sample.space = 'MATERIALS'
new_sample.parents = ['/MATERIALS/YEAST747']
"""
- if name in ["parents", "children", "components"]:
+ if name in ["parents", "parent", "children", "child", "components"]:
+ if name == "parent":
+ name = "parents"
+ if name == "child":
+ name = "children"
+
if not isinstance(value, list):
value = [value]
objs = []
@@ -3029,9 +3035,9 @@ class AttrHolder():
raise KeyError("you can not modify the {}".format(name))
elif name == "code":
try:
- if self._type.data['autoGeneratedCode']:
- raise KeyError("for this {}Type you can not set a code".format(self.entity))
- except AttributeError:
+ if self._type['autoGeneratedCode']:
+ raise KeyError("This {}Type has auto-generated code. You cannot set a code".format(self.entity))
+ except KeyError:
pass
self.__dict__['_code'] = value
@@ -3415,6 +3421,14 @@ class Space(OpenBisObject):
get_objects = get_samples #Alias
+ def get_sample(self, sample_code):
+ if is_identifier(sample_code) or is_permid(sample_code):
+ return self.openbis.get_sample(sample_code)
+ else:
+ # we assume we just got the code
+ return self.openbis.get_sample('/{}/{}'.format(self.code,sample_code) )
+
+
def get_projects(self, **kwargs):
return self.openbis.get_projects(space=self.code, **kwargs)
@@ -3597,7 +3611,7 @@ class Experiment(OpenBisObject):
"""
"""
- def __init__(self, openbis_obj, type, data=None, props=None, code=None, **kwargs):
+ def __init__(self, openbis_obj, type, project=None, data=None, props=None, code=None, **kwargs):
self.__dict__['openbis'] = openbis_obj
self.__dict__['type'] = type
self.__dict__['p'] = PropertyHolder(openbis_obj, type)
@@ -3606,6 +3620,9 @@ class Experiment(OpenBisObject):
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])
@@ -3639,7 +3656,9 @@ class Experiment(OpenBisObject):
# the list of possible methods/attributes displayed
# when invoking TAB-completition
return [
- 'props', 'space', 'project',
+ 'code', 'permId', 'identifier',
+ 'type', 'project',
+ 'props.',
'project', 'tags', 'attachments', 'data',
'get_datasets()', 'get_samples()',
'set_tags()', 'add_tags()', 'del_tags()',
@@ -3821,6 +3840,13 @@ class Project(OpenBisObject):
def get_samples(self, **kwargs):
return self.openbis.get_samples(project=self.permId, **kwargs)
+ def get_sample(self, sample_code):
+ if is_identifier(sample_code) or is_permid(sample_code):
+ return self.openbis.get_sample(sample_code)
+ else:
+ # we assume we just got the code
+ return self.openbis.get_sample(project=self, code=sample_code)
+
get_objects = get_samples # Alias
def get_experiments(self):
diff --git a/src/python/PyBis/setup.py b/src/python/PyBis/setup.py
index 45887cf516fef476037cfcb361dccd285e04f108..70a2255cd572c894f5f99b862ae910009f6b6636 100644
--- a/src/python/PyBis/setup.py
+++ b/src/python/PyBis/setup.py
@@ -9,7 +9,7 @@ from setuptools import setup
setup(
name='PyBIS',
- version= '1.3',
+ version= '1.4',
description='openBIS connection and interaction, optimized for using with Jupyter',
url='https://sissource.ethz.ch/sispub/pybis/',
author='Swen Vermeul | ID SIS | ETH Zürich',
diff --git a/src/python/PyBis/tests/conftest.py b/src/python/PyBis/tests/conftest.py
index ca95953bdc1d6e384c52dc736ab18644b8568564..dca56d7cb7850eebccadf61c860fda60706c20cd 100644
--- a/src/python/PyBis/tests/conftest.py
+++ b/src/python/PyBis/tests/conftest.py
@@ -22,12 +22,7 @@ def space():
o = Openbis(url=openbis_url, verify_certificates=False)
o.login(admin_username, admin_password)
- timestamp = time.strftime('%a_%y%m%d_%H%M%S').upper()
- space_name = 'test_space_' + timestamp
- space = o.new_space(code=space_name)
- space.save()
- space_exists = o.get_space(code=space_name)
+ space_exists = o.get_space(code='DEFAULT')
yield space_exists
- space.delete("testing on {}".format(timestamp))
o.logout()
diff --git a/src/python/PyBis/tests/test_experiment.py b/src/python/PyBis/tests/test_experiment.py
new file mode 100644
index 0000000000000000000000000000000000000000..10ba05ef05618db415a6034a04d1d98a914245e0
--- /dev/null
+++ b/src/python/PyBis/tests/test_experiment.py
@@ -0,0 +1,45 @@
+import json
+import random
+import re
+
+import pytest
+import time
+from pybis import DataSet
+from pybis import Openbis
+
+
+def test_create_delete_project(space):
+ o=space.openbis
+ timestamp = time.strftime('%a_%y%m%d_%H%M%S').upper()
+ new_code='test_experiment_'+timestamp
+
+ with pytest.raises(TypeError):
+ # experiments must be assigned to a project
+ e_new = o.new_experiment(
+ code=new_code,
+ type='DEFAULT_EXPERIMENT',
+ )
+
+ e_new = o.new_experiment(
+ code=new_code,
+ project='DEFAULT',
+ type='DEFAULT_EXPERIMENT',
+ )
+ assert e_new.project is not None
+ assert e_new.permId is None
+
+ e_new.save()
+
+ assert e_new.permId is not None
+ assert e_new.code == new_code.upper()
+ assert e_new.identifier == '/DEFAULT/DEFAULT/'+new_code.upper()
+
+ e_exists = o.get_experiment('/DEFAULT/DEFAULT/'+new_code.upper())
+ assert e_exists is not None
+
+ e_new.delete('delete test experiment '+new_code.upper())
+
+ with pytest.raises(ValueError):
+ e_no_longer_exists = o.get_experiment('/DEFAULT/DEFAULT/'+new_code.upper())
+
+
diff --git a/src/python/PyBis/tests/test_openbis.py b/src/python/PyBis/tests/test_openbis.py
index 21c09b70100358a3b8b711e3e093943cc6adb4f3..02f65ba1732c9e9890d9156f79e6597dd1d3cc14 100644
--- a/src/python/PyBis/tests/test_openbis.py
+++ b/src/python/PyBis/tests/test_openbis.py
@@ -22,17 +22,6 @@ def test_wrong_login(openbis_instance):
assert new_instance.token is None
assert new_instance.is_session_active() is False
-def test_create_delete_space(openbis_instance):
- space_name = 'test_space_' + time.strftime('%a_%y%m%d_%H%M%S').upper()
- space = openbis_instance.new_space(code=space_name)
- space.save()
- space_exists = openbis_instance.get_space(code=space_name)
- assert space_exists is not None
-
- space.delete()
- with pytest.raises(ValueError):
- space_not_exists = openbis_instance.get_space(code=space_name)
-
def test_cached_token(openbis_instance):
openbis_instance.save_token()
@@ -46,64 +35,6 @@ def test_cached_token(openbis_instance):
assert openbis_instance._get_cached_token() is None
-def test_create_sample(openbis_instance):
- # given
- sample_code = 'test_create_' + time.strftime('%a_%y%m%d_%H%M%S').upper()
- sample_type = 'UNKNOWN'
- space = 'DEFAULT'
- # when
- sample = openbis_instance.new_sample(code=sample_code, type=sample_type, space=space)
- # then
- assert sample is not None
- assert sample.space == space
- assert sample.code == sample_code
-
-
-def test_get_sample_by_id(openbis_instance):
- # given
- sample_code = 'test_get_by_id_' + time.strftime('%a_%y%m%d_%H%M%S').upper()
- sample = openbis_instance.new_sample(code=sample_code, type='UNKNOWN', space='DEFAULT')
- sample.save()
- # when
- persisted_sample = openbis_instance.get_sample('/DEFAULT/' + sample_code)
- # then
- assert persisted_sample is not None
- assert persisted_sample.permId is not None
-
-def test_get_sample_by_permid(openbis_instance):
- # given
- sample_code = 'test_get_by_permId_' + time.strftime('%a_%y%m%d_%H%M%S').upper()
- sample = openbis_instance.new_sample(code=sample_code, type='UNKNOWN', space='DEFAULT')
- sample.save()
- persisted_sample = openbis_instance.get_sample('/DEFAULT/' + sample_code)
- permId = persisted_sample.permId
- # when
- sample_by_permId = openbis_instance.get_sample(permId)
- # then
- assert sample_by_permId is not None
- assert sample_by_permId.permId == permId
-
-
-def test_get_sample_parents(openbis_instance):
- id = '/TEST/TEST-SAMPLE-2'
- sample = openbis_instance.get_sample(id)
- assert sample is not None
- assert sample.parents is not None
- assert sample.parents[0]['identifier']['identifier'] == '/TEST/TEST-SAMPLE-2-PARENT'
- parents = sample.get_parents()
- assert isinstance(parents, list)
- assert parents[0].ident == '/TEST/TEST-SAMPLE-2-PARENT'
-
-
-def test_get_sample_children(openbis_instance):
- id = '/TEST/TEST-SAMPLE-2'
- sample = openbis_instance.get_sample(id)
- assert sample is not None
- assert sample.children is not None
- assert sample.children[0]['identifier']['identifier'] == '/TEST/TEST-SAMPLE-2-CHILD-1'
- children = sample.get_children()
- assert isinstance(children, list)
- assert children[0].ident == '/TEST/TEST-SAMPLE-2-CHILD-1'
def test_get_dataset_parents(openbis_instance):
diff --git a/src/python/PyBis/tests/test_sample.py b/src/python/PyBis/tests/test_sample.py
new file mode 100644
index 0000000000000000000000000000000000000000..037bf018be8ac06d5658a5592ca59546be46d226
--- /dev/null
+++ b/src/python/PyBis/tests/test_sample.py
@@ -0,0 +1,71 @@
+import json
+import random
+import re
+
+import pytest
+import time
+from pybis import DataSet
+from pybis import Openbis
+
+def test_create_delete_sample(space):
+ o=space.openbis
+
+ sample_type = 'UNKNOWN'
+ sample = o.new_sample(code='illegal sample name with spaces', type=sample_type, space=space)
+ with pytest.raises(ValueError):
+ sample.save()
+ assert "should not have been created" is None
+
+ timestamp = time.strftime('%a_%y%m%d_%H%M%S').upper()
+ sample_code = 'test_sample_'+timestamp
+ sample = o.new_sample(code=sample_code, type=sample_type, space=space)
+ assert sample is not None
+ assert sample.space == space
+ assert sample.code == sample_code
+
+ assert sample.permId is None
+ sample.save()
+
+ # now there should appear a permId
+ assert sample.permId is not None
+
+ # get it by permId
+ sample_by_permId = o.get_sample(sample.permId)
+ assert sample_by_permId is not None
+
+ sample_by_permId = space.get_sample(sample.permId)
+ assert sample_by_permId is not None
+
+
+ # get it by identifier
+ sample_by_identifier = o.get_sample(sample.identifier)
+ assert sample_by_identifier is not None
+
+ sample_by_identifier = space.get_sample(sample.identifier)
+ assert sample_by_identifier is not None
+
+ sample.delete('sample creation test on '+timestamp)
+
+
+def test_parent_child(space):
+ o=space.openbis
+ sample_type = 'UNKNOWN'
+ timestamp = time.strftime('%a_%y%m%d_%H%M%S').upper()
+ parent_code = 'parent_sample_{}'.format(timestamp)
+ sample_parent = o.new_sample(code=parent_code, type=sample_type, space=space)
+ sample_parent.save()
+
+ child_code='child_sample_{}'.format(timestamp)
+ sample_child = o.new_sample(code=child_code, type=sample_type, space=space, parent=sample_parent)
+ sample_child.save()
+ time.sleep(5)
+
+ ex_sample_parents = sample_child.get_parents()
+ ex_sample_parent = ex_sample_parents[0]
+ assert ex_sample_parent.identifier == '/DEFAULT/{}'.format(parent_code).upper()
+
+ ex_sample_children = ex_sample_parent.get_children()
+ ex_sample_child = ex_sample_children[0]
+ assert ex_sample_child.identifier == '/DEFAULT/{}'.format(child_code).upper()
+
+
diff --git a/src/vagrant/jupyter-bis/README.md b/src/vagrant/jupyter-bis/README.md
index 23a1d760d47f843adac11aa195c7d8d0c2b63c89..acb88a17cedb0b9b24acb06d8481a6ae9e5e0b5e 100644
--- a/src/vagrant/jupyter-bis/README.md
+++ b/src/vagrant/jupyter-bis/README.md
@@ -67,6 +67,18 @@ ame` ``
10. copy the output and add it to /etc/hosts: `sudo vi /etc/hosts` so that Java is happy
11. `exit` -- log off the virtual machine
+## upgrading openBIS
+
+Before upgrading, make sure your openBIS instance is not running.
+
+1. download [latest openBIS Sprint release](https://wiki-bsse.ethz.ch/display/bis/Sprint+Releases)
+2. make sure your OS is not automatically unzipping it
+3. move *.gz file from ~/Download to pybis/src/vagrant/jupyter-bis
+4. cd pybis/src/vagrant/jupyter-bis
+5. vagrant ssh
+6. sudo su - openbis
+7. cp /vagrant/openBIS-installation-standard-technologies-S267.0-r39027.tar.gz ~/servers
+8. bin/upgrade.sh
## start openBIS and JupyterHub