def test_private_getStringList():
act = Activity()
url_string = \
'https://github.com/Sage-Bionetworks/ampAdScripts/blob/master/Broad-Rush/migrateROSMAPGenotypesFeb2015.R'
act.used([{'wasExecuted': True,
'concreteType': 'org.sagebionetworks.repo.model.provenance.UsedURL',
'url': url_string}
])
assert_equals([url_string], act._getStringList())
def test_private_getStringList():
act = Activity()
url_string = \
'https://github.com/Sage-Bionetworks/ampAdScripts/blob/master/Broad-Rush/migrateROSMAPGenotypesFeb2015.R'
act.used([{
'wasExecuted': True,
'concreteType': 'org.sagebionetworks.repo.model.provenance.UsedURL',
'url': url_string
}])
assert_equals([url_string], act._getStringList())
def test_activity_creation_from_dict():
"""test that activities are created correctly from a dictionary"""
d = {
'name':
'Project Fuzz',
'description':
'hipster beard dataset',
'used': [{
'reference': {
'targetId': 'syn12345',
'versionNumber': 42
},
'wasExecuted': True
}]
}
a = Activity(data=d)
assert_equals(a['name'], 'Project Fuzz')
assert_equals(a['description'], 'hipster beard dataset')
usedEntities = a['used']
assert_equals(len(usedEntities), 1)
u = usedEntities[0]
assert_true(u['wasExecuted'])
assert_equals(u['reference']['targetId'], 'syn12345')
assert_equals(u['reference']['versionNumber'], 42)
def test_activity_creation_from_dict():
"""test that activities are created correctly from a dictionary"""
d = {
'name':
'Project Fuzz',
'description':
'hipster beard dataset',
'used': [{
'reference': {
'targetId': 'syn12345',
'versionNumber': 42
},
'wasExecuted': True
}]
}
a = Activity(data=d)
assert a['name'] == 'Project Fuzz'
assert a['description'] == 'hipster beard dataset'
usedEntities = a['used']
assert len(usedEntities) == 1
u = usedEntities[0]
assert u['wasExecuted'] == True
assert u['reference']['targetId'] == 'syn12345'
assert u['reference']['versionNumber'] == 42
def test_activity_used_url():
"""test activity creation with UsedURLs"""
u1 = "http://xkcd.com"
u2 = {"name": "The Onion", "url": "http://theonion.com"}
u3 = {
"name": "Seriously advanced code",
"url": "https://github.com/cbare/Pydoku/blob/ef88069f70823808f3462410e941326ae7ffbbe0/solver.py",
"wasExecuted": True,
}
u4 = {"name": "Heavy duty algorithm", "url": "https://github.com/cbare/Pydoku/blob/master/solver.py"}
a = Activity(name="Foobarbat", description="Apply foo to a bar and a bat", used=[u1, u2, u3], executed=[u3, u4])
a.executed(url="http://cran.r-project.org/web/packages/glmnet/index.html", name="glm.net")
a.used(url="http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day", name="earthquakes")
u = _find_used(a, lambda res: "url" in res and res["url"] == u1)
assert u is not None
assert u["url"] == u1
assert u["wasExecuted"] == False
u = _find_used(a, lambda res: "name" in res and res["name"] == "The Onion")
assert u is not None
assert u["url"] == "http://theonion.com"
assert u["wasExecuted"] == False
u = _find_used(a, lambda res: "name" in res and res["name"] == "Seriously advanced code")
assert u is not None
assert u["url"] == u3["url"]
assert u["wasExecuted"] == u3["wasExecuted"]
u = _find_used(a, lambda res: "name" in res and res["name"] == "Heavy duty algorithm")
assert u is not None
assert u["url"] == u4["url"]
assert u["wasExecuted"] == True
u = _find_used(a, lambda res: "name" in res and res["name"] == "glm.net")
assert u is not None
assert u["url"] == "http://cran.r-project.org/web/packages/glmnet/index.html"
assert u["wasExecuted"] == True
u = _find_used(a, lambda res: "name" in res and res["name"] == "earthquakes")
assert u is not None
assert u["url"] == "http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day"
assert u["wasExecuted"] == False
def test_activity_used_execute_methods():
"""test activity creation and used and execute methods"""
a = Activity(name='Fuzz', description='hipster beard dataset')
a.used({'id': 'syn101', 'versionNumber': 42, 'concreteType': 'org.sagebionetworks.repo.model.FileEntity'})
a.executed('syn102', targetVersion=1)
usedEntities = a['used']
len(usedEntities), 2
assert_equals(a['name'], 'Fuzz')
assert_equals(a['description'], 'hipster beard dataset')
used_syn101 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn101')
assert_equals(used_syn101['reference']['targetVersionNumber'], 42)
assert_false(used_syn101['wasExecuted'])
used_syn102 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn102')
assert_equals(used_syn102['reference']['targetVersionNumber'], 1)
assert_true(used_syn102['wasExecuted'])
def test_activity_used_execute_methods():
"""test activity creation and used and execute methods"""
a = Activity(name='Fuzz', description='hipster beard dataset')
a.used({'id':'syn101', 'versionNumber':42, 'concreteType': 'org.sagebionetworks.repo.model.Data'})
a.executed('syn102', targetVersion=1)
usedEntities = a['used']
len(usedEntities) == 2
assert a['name'] == 'Fuzz'
assert a['description'] == 'hipster beard dataset'
## ??? are activities supposed to come back in order? Let's not count on it
used_syn101 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn101')
assert used_syn101['reference']['targetVersionNumber'] == 42
assert used_syn101['wasExecuted'] == False
used_syn102 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn102')
assert used_syn102['reference']['targetVersionNumber'] == 1
assert used_syn102['wasExecuted'] == True
def test_activity_used_execute_methods():
"""test activity creation and used and execute methods"""
a = Activity(name="Fuzz", description="hipster beard dataset")
a.used({"id": "syn101", "versionNumber": 42, "concreteType": "org.sagebionetworks.repo.model.FileEntity"})
a.executed("syn102", targetVersion=1)
usedEntities = a["used"]
len(usedEntities) == 2
assert a["name"] == "Fuzz"
assert a["description"] == "hipster beard dataset"
## ??? are activities supposed to come back in order? Let's not count on it
used_syn101 = _find_used(a, lambda res: res["reference"]["targetId"] == "syn101")
assert used_syn101["reference"]["targetVersionNumber"] == 42
assert used_syn101["wasExecuted"] == False
used_syn102 = _find_used(a, lambda res: res["reference"]["targetId"] == "syn102")
assert used_syn102["reference"]["targetVersionNumber"] == 1
assert used_syn102["wasExecuted"] == True
def test_activity_used_url():
"""test activity creation with UsedURLs"""
u1 = 'http://xkcd.com'
u2 = {'name': 'The Onion', 'url': 'http://theonion.com'}
u3 = {'name': 'Seriously advanced code',
'url': 'https://github.com/cbare/Pydoku/blob/ef88069f70823808f3462410e941326ae7ffbbe0/solver.py',
'wasExecuted': True}
u4 = {'name': 'Heavy duty algorithm', 'url': 'https://github.com/cbare/Pydoku/blob/master/solver.py'}
a = Activity(name='Foobarbat', description='Apply foo to a bar and a bat', used=[u1, u2, u3], executed=[u3, u4])
a.executed(url='http://cran.r-project.org/web/packages/glmnet/index.html', name='glm.net')
a.used(url='http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day', name='earthquakes')
u = _find_used(a, lambda res: 'url' in res and res['url'] == u1)
assert_is_not_none(u)
assert_equals(u['url'], u1)
assert_false(u['wasExecuted'])
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'The Onion')
assert_is_not_none(u)
assert_equals(u['url'], 'http://theonion.com')
assert_false(u['wasExecuted'])
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'Seriously advanced code')
assert_is_not_none(u)
assert_equals(u['url'], u3['url'])
assert_equals(u['wasExecuted'], u3['wasExecuted'])
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'Heavy duty algorithm')
assert_is_not_none(u)
assert_equals(u['url'], u4['url'])
assert_true(u['wasExecuted'])
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'glm.net')
assert_is_not_none(u)
assert_equals(u['url'], 'http://cran.r-project.org/web/packages/glmnet/index.html')
assert_true(u['wasExecuted'])
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'earthquakes')
assert_is_not_none(u)
assert_equals(u['url'], 'http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day')
assert_false(u['wasExecuted'])
def test_provenance():
# Create a Data Entity
fname = utils.make_bogus_data_file()
schedule_for_cleanup(fname)
data_entity = syn.createEntity(Data(parent=project['id']))
data_entity = syn.uploadFile(data_entity, fname)
# Create a Code Entity
fd, path = tempfile.mkstemp(suffix=".py")
os.write(fd, """
## Chris's fabulous random data generator
############################################################
import random
random.seed(12345)
data = [random.gauss(mu=0.0, sigma=1.0) for i in range(100)]
""")
os.close(fd)
schedule_for_cleanup(path)
code_entity = syn.createEntity(Code(parent=project['id']))
code_entity = syn.uploadFile(code_entity, path)
# Create a new Activity asserting that the Code Entity was 'used'
activity = Activity(name='random.gauss', description='Generate some random numbers')
activity.used(code_entity, wasExecuted=True)
activity.used({'name':'Superhack', 'url':'https://github.com/joe_coder/Superhack'}, wasExecuted=True)
activity = syn.setProvenance(data_entity, activity)
# Retrieve and verify the saved Provenance record
retrieved_activity = syn.getProvenance(data_entity)
assert retrieved_activity == activity
# Test Activity update
new_description = 'Generate random numbers like a gangsta'
retrieved_activity['description'] = new_description
updated_activity = syn.updateActivity(retrieved_activity)
assert updated_activity['name'] == retrieved_activity['name']
assert updated_activity['description'] == new_description
# Test delete
syn.deleteProvenance(data_entity)
assert_raises(SynapseHTTPError, syn.getProvenance, data_entity['id'])
def test_activity_used_execute_methods():
"""test activity creation and used and execute methods"""
a = Activity(name='Fuzz', description='hipster beard dataset')
a.used({
'id': 'syn101',
'versionNumber': 42,
'concreteType': 'org.sagebionetworks.repo.model.FileEntity'
})
a.executed('syn102', targetVersion=1)
usedEntities = a['used']
len(usedEntities) == 2
assert a['name'] == 'Fuzz'
assert a['description'] == 'hipster beard dataset'
## ??? are activities supposed to come back in order? Let's not count on it
used_syn101 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn101')
assert used_syn101['reference']['targetVersionNumber'] == 42
assert used_syn101['wasExecuted'] == False
used_syn102 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn102')
assert used_syn102['reference']['targetVersionNumber'] == 1
assert used_syn102['wasExecuted'] == True
def test_activity_used_url():
"""test activity creation with UsedURLs"""
u1 = 'http://xkcd.com'
u2 = {'name': 'The Onion', 'url': 'http://theonion.com'}
u3 = {
'name': 'Seriously advanced code',
'url':
'https://github.com/cbare/Pydoku/blob/ef88069f70823808f3462410e941326ae7ffbbe0/solver.py',
'wasExecuted': True
}
u4 = {
'name': 'Heavy duty algorithm',
'url': 'https://github.com/cbare/Pydoku/blob/master/solver.py'
}
a = Activity(name='Foobarbat',
description='Apply foo to a bar and a bat',
used=[u1, u2, u3],
executed=[u3, u4])
a.executed(url='http://cran.r-project.org/web/packages/glmnet/index.html',
name='glm.net')
a.used(url='http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day',
name='earthquakes')
u = _find_used(a, lambda res: 'url' in res and res['url'] == u1)
assert u is not None
assert u['url'] == u1
assert u['wasExecuted'] == False
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'The Onion')
assert u is not None
assert u['url'] == 'http://theonion.com'
assert u['wasExecuted'] == False
u = _find_used(
a,
lambda res: 'name' in res and res['name'] == 'Seriously advanced code')
assert u is not None
assert u['url'] == u3['url']
assert u['wasExecuted'] == u3['wasExecuted']
u = _find_used(
a, lambda res: 'name' in res and res['name'] == 'Heavy duty algorithm')
assert u is not None
assert u['url'] == u4['url']
assert u['wasExecuted'] == True
u = _find_used(a, lambda res: 'name' in res and res['name'] == 'glm.net')
assert u is not None
assert u[
'url'] == 'http://cran.r-project.org/web/packages/glmnet/index.html'
assert u['wasExecuted'] == True
u = _find_used(a,
lambda res: 'name' in res and res['name'] == 'earthquakes')
assert u is not None
assert u[
'url'] == 'http://earthquake.usgs.gov/earthquakes/feed/geojson/2.5/day'
assert u['wasExecuted'] == False
def test_activity_parameter_errors():
"""Test error handling in Activity.used()"""
a = Activity(name='Foobarbat', description='Apply foo to a bar and a bat')
assert_raises(SynapseMalformedEntityError,
a.used, ['syn12345', 'http://google.com'],
url='http://amazon.com')
assert_raises(SynapseMalformedEntityError,
a.used,
'syn12345',
url='http://amazon.com')
assert_raises(SynapseMalformedEntityError,
a.used,
'http://amazon.com',
targetVersion=1)
def test_provenance():
# Create a Data Entity
fname = utils.make_bogus_data_file()
schedule_for_cleanup(fname)
data_entity = syn.createEntity(Data(parent=project['id']))
data_entity = syn.uploadFile(data_entity, fname)
# Create a Code Entity
fd, path = tempfile.mkstemp(suffix=".py")
os.write(
fd, """
## Chris's fabulous random data generator
############################################################
import random
random.seed(12345)
data = [random.gauss(mu=0.0, sigma=1.0) for i in range(100)]
""")
os.close(fd)
schedule_for_cleanup(path)
code_entity = syn.createEntity(Code(parent=project['id']))
code_entity = syn.uploadFile(code_entity, path)
# Create a new Activity asserting that the Code Entity was 'used'
activity = Activity(name='random.gauss',
description='Generate some random numbers')
activity.used(code_entity, wasExecuted=True)
activity.used(
{
'name': 'Superhack',
'url': 'https://github.com/joe_coder/Superhack'
},
wasExecuted=True)
activity = syn.setProvenance(data_entity, activity)
# Retrieve and verify the saved Provenance record
retrieved_activity = syn.getProvenance(data_entity)
assert retrieved_activity == activity
# Test Activity update
new_description = 'Generate random numbers like a gangsta'
retrieved_activity['description'] = new_description
updated_activity = syn.updateActivity(retrieved_activity)
assert updated_activity['name'] == retrieved_activity['name']
assert updated_activity['description'] == new_description
# Test delete
syn.deleteProvenance(data_entity)
assert_raises(SynapseHTTPError, syn.getProvenance, data_entity['id'])
def test_activity_creation_by_constructor():
"""test activity creation adding used entities by the constructor"""
ue1 = {
'reference': {
'targetId': 'syn101',
'targetVersionNumber': 42
},
'wasExecuted': False
}
ue2 = {
'id': 'syn102',
'versionNumber': 2,
'concreteType': 'org.sagebionetworks.repo.model.FileEntity'
}
ue3 = 'syn103'
a = Activity(name='Fuzz',
description='hipster beard dataset',
used=[ue1, ue3],
executed=[ue2])
# print(a['used'])
used_syn101 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn101')
assert used_syn101 is not None
assert used_syn101['reference']['targetVersionNumber'] == 42
assert used_syn101['wasExecuted'] == False
used_syn102 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn102')
assert used_syn102 is not None
assert used_syn102['reference']['targetVersionNumber'] == 2
assert used_syn102['wasExecuted'] == True
used_syn103 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn103')
assert used_syn103 is not None
def test_activity_used_execute_methods():
"""test activity creation and used and execute methods"""
a = Activity(name='Fuzz', description='hipster beard dataset')
a.used({
'id': 'syn101',
'versionNumber': 42,
'concreteType': 'org.sagebionetworks.repo.model.FileEntity'
})
a.executed('syn102', targetVersion=1)
usedEntities = a['used']
len(usedEntities), 2
assert_equals(a['name'], 'Fuzz')
assert_equals(a['description'], 'hipster beard dataset')
used_syn101 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn101')
assert_equals(used_syn101['reference']['targetVersionNumber'], 42)
assert_false(used_syn101['wasExecuted'])
used_syn102 = _find_used(
a, lambda res: res['reference']['targetId'] == 'syn102')
assert_equals(used_syn102['reference']['targetVersionNumber'], 1)
assert_true(used_syn102['wasExecuted'])
