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_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.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_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_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])
used_syn101 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn101')
assert_is_not_none(used_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_is_not_none(used_syn102)
assert_equals(used_syn102['reference']['targetVersionNumber'], 2)
assert_true(used_syn102['wasExecuted'])
used_syn103 = _find_used(a, lambda res: res['reference']['targetId'] == 'syn103')
assert_is_not_none(used_syn103)
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_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_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_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.Code'}
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'])
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_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_command_line_client():
# Create a Project
output = run('synapse',
'--skip-checks',
'create',
'-name',
str(uuid.uuid4()),
'-description',
'test of command line client',
'Project')
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
# Create a File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'add',
'-name',
'BogusFileEntity',
'-description',
'Bogus data to test file upload',
'-parentid',
project_id,
filename)
file_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we stored the file in Synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert_equals(fh['concreteType'], 'org.sagebionetworks.repo.model.file.S3FileHandle')
# Get File from the command line
output = run('synapse',
'--skip-checks',
'get',
file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
assert_true(filecmp.cmp(filename, downloaded_filename))
# Update the File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'store',
'--id',
file_entity_id,
filename)
# Get the File again
output = run('synapse',
'--skip-checks',
'get',
file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
assert_true(filecmp.cmp(filename, downloaded_filename))
# Move the file to new folder
folder = syn.store(synapseclient.Folder(parentId=project_id))
output = run('synapse',
'mv',
'--id',
file_entity_id,
'--parentid',
folder.id)
movedFile = syn.get(file_entity_id, downloadFile=False)
assert_equals(movedFile.parentId, folder.id)
# Test Provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run('synapse',
'--skip-checks',
'set-provenance',
'-id',
file_entity_id,
'-name',
'TestActivity',
'-description',
'A very excellent provenance',
'-used',
file_entity_id,
'-executed',
repo_url)
output = run('synapse',
'--skip-checks',
'get-provenance',
'--id',
file_entity_id)
activity = json.loads(output)
assert_equals(activity['name'], 'TestActivity')
assert_equals(activity['description'], 'A very excellent provenance')
used = utils._find_used(activity, lambda used: 'reference' in used)
assert_equals(used['reference']['targetId'], file_entity_id)
used = utils._find_used(activity, lambda used: 'url' in used)
assert_equals(used['url'], repo_url)
assert_true(used['wasExecuted'])
# Note: Tests shouldn't have external dependencies
# but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/' \
'thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg' \
'/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
# Test external file handle
output = run('synapse',
'--skip-checks',
'add',
'-name',
'Singapore',
'-description',
'A nice picture of Singapore',
'-parentid',
project_id,
singapore_url)
exteral_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert_equals(fh['concreteType'], 'org.sagebionetworks.repo.model.file.ExternalFileHandle')
output = run('synapse',
'--skip-checks',
'get',
exteral_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
# Delete the Project
run('synapse', '--skip-checks', 'delete', project_id)
def test_command_line_client():
# Create a Project
output = run('synapse',
'--skip-checks',
'create',
'-name',
str(uuid.uuid4()),
'-description',
'test of command line client',
'Project')
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
# Create a File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'add',
'-name',
'BogusFileEntity',
'-description',
'Bogus data to test file upload',
'-parentid',
project_id,
filename)
file_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we stored the file in Synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert fh['concreteType'] == 'org.sagebionetworks.repo.model.file.S3FileHandle'
# Get File from the command line
output = run('synapse',
'--skip-checks',
'get',
file_entity_id)
downloaded_filename = parse(r'Creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Update the File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'update',
'-id',
file_entity_id,
filename)
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
# Get the File again
output = run('synapse',
'--skip-checks',
'get',
file_entity_id)
downloaded_filename = parse(r'Creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Create a deprecated Data object
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'add',
'-name',
'BogusData',
'-description',
'Bogus data to test file upload',
'-type',
'Data',
'-parentid',
project_id,
filename)
data_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Get the Data object back
output = run('synapse',
'--skip-checks',
'get',
data_entity_id)
downloaded_filename = parse(r'Creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Update the Data object
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse',
'--skip-checks',
'update',
'-id',
data_entity_id,
filename)
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
# Get the Data object back again
output = run('synapse',
'--skip-checks',
'get',
updated_entity_id)
downloaded_filename = parse(r'Creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Test query
output = run('synapse',
'--skip-checks',
'query',
'select id, name from entity where parentId=="%s"' % project_id)
assert 'BogusData' in output
assert data_entity_id in output
assert 'BogusFileEntity' in output
assert file_entity_id in output
# Test Provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run('synapse',
'--skip-checks',
'set-provenance',
'-id',
file_entity_id,
'-name',
'TestActivity',
'-description',
'A very excellent provenance',
'-used',
data_entity_id,
'-executed',
repo_url)
activity_id = parse(r'Set provenance record (\d+) on entity syn\d+', output)
output = run('synapse',
'--skip-checks',
'get-provenance',
'-id',
file_entity_id)
activity = json.loads(output)
assert activity['name'] == 'TestActivity'
assert activity['description'] == 'A very excellent provenance'
used = utils._find_used(activity, lambda used: 'reference' in used)
assert used['reference']['targetId'] == data_entity_id
used = utils._find_used(activity, lambda used: 'url' in used)
assert used['url'] == repo_url
assert used['wasExecuted'] == True
# Note: Tests shouldn't have external dependencies
# but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/' \
'thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg' \
'/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
# Test external file handle
output = run('synapse',
'--skip-checks',
'add',
'-name',
'Singapore',
'-description',
'A nice picture of Singapore',
'-type',
'File',
'-parentid',
project_id,
singapore_url)
exteral_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert fh['concreteType'] == 'org.sagebionetworks.repo.model.file.ExternalFileHandle'
output = run('synapse',
'--skip-checks',
'get',
exteral_entity_id)
downloaded_filename = parse(r'Creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
# Delete the Project
output = run('synapse',
'--skip-checks',
'delete',
project_id)
def test_command_line_client():
"""Test command line client"""
## Note:
## In Windows, quoting with single-quotes, as in -name 'My entity name'
## seems to cause problems in the call to subprocess.check_output. Make
## sure to use double-quotes.
## create project
output = run('synapse --skip-checks create -name "%s" -description "test of command line client" Project' % str(str(uuid.uuid4())))
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
## create file
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse --skip-checks add -name "BogusFileEntity" -description "Bogus data to test file upload" -parentid %s %s' % (project_id, filename,))
file_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## verify that we stored the file in synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert fh['concreteType'] == 'org.sagebionetworks.repo.model.file.S3FileHandle'
## get file
output = run('synapse --skip-checks get %s' % file_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## update file
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse --skip-checks update -id %s %s' % (file_entity_id, filename,))
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
## get file
output = run('synapse --skip-checks get %s' % file_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## create data
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse --skip-checks add -name "BogusData" -description "Bogus data to test file upload" -type Data -parentid %s %s' % (project_id, filename,))
data_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## get data
output = run('synapse --skip-checks get %s' % data_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## update data
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse --skip-checks update -id %s %s' % (data_entity_id, filename,))
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
## get data
output = run('synapse --skip-checks get %s' % data_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# query
output = run('synapse --skip-checks query "select id, name from entity where parentId==\\"%s\\""' % project_id)
assert 'BogusData' in output
assert data_entity_id in output
assert 'BogusFileEntity' in output
assert file_entity_id in output
# provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run('synapse --skip-checks set-provenance -id %s -name TestActivity -description "A very excellent provenance" -used %s -executed "%s"' % (file_entity_id, data_entity_id, repo_url,))
activity_id = parse(r'Set provenance record (\d+) on entity syn\d+', output)
output = run('synapse --skip-checks get-provenance -id %s' % (file_entity_id,))
activity = json.loads(output)
assert activity['name'] == 'TestActivity'
assert activity['description'] == 'A very excellent provenance'
used = utils._find_used(activity, lambda used: 'reference' in used)
assert used['reference']['targetId'] == data_entity_id
used = utils._find_used(activity, lambda used: 'url' in used)
assert used['url'] == repo_url
assert used['wasExecuted'] == True
## Tests shouldn't have external dependencies, but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
## test external file handle
output = run('synapse --skip-checks add -name "Singapore" -description "A nice picture of Singapore" -type File -parentid %s %s' % (project_id, singapore_url,))
exteral_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert fh['concreteType'] == 'org.sagebionetworks.repo.model.file.ExternalFileHandle'
output = run('synapse --skip-checks get %s' % exteral_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
## delete project
output = run('synapse --skip-checks delete %s' % project_id)
def test_command_line_client():
print("TESTING CMD LINE CLIENT")
# Create a Project
output = run('synapse', '--skip-checks', 'create', '-name',
str(uuid.uuid4()), '-description',
'test of command line client', 'Project')
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
# Create a File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse', '--skip-checks', 'add', '-name', 'BogusFileEntity',
'-description', 'Bogus data to test file upload', '-parentid',
project_id, filename)
file_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we stored the file in Synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert_equals(fh['concreteType'],
'org.sagebionetworks.repo.model.file.S3FileHandle')
# Get File from the command line
output = run('synapse', '--skip-checks', 'get', file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
assert_true(filecmp.cmp(filename, downloaded_filename))
# Update the File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse', '--skip-checks', 'store', '--id', file_entity_id,
filename)
# Get the File again
output = run('synapse', '--skip-checks', 'get', file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
assert_true(filecmp.cmp(filename, downloaded_filename))
# Store the same file and don't force a new version
# Get the existing file to determine it's current version
current_file = syn.get(file_entity_id, downloadFile=False)
current_version = current_file.versionNumber
# Store it without forcing version
output = run('synapse', '--skip-checks', 'store', '--noForceVersion',
'--id', file_entity_id, filename)
# Get the File again and check that the version did not change
new_file = syn.get(file_entity_id, downloadFile=False)
new_version = new_file.versionNumber
assert_equals(current_version, new_version)
# Move the file to new folder
folder = syn.store(synapseclient.Folder(parentId=project_id))
output = run('synapse', 'mv', '--id', file_entity_id, '--parentid',
folder.id)
movedFile = syn.get(file_entity_id, downloadFile=False)
assert_equals(movedFile.parentId, folder.id)
# Test Provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run('synapse', '--skip-checks', 'set-provenance', '-id',
file_entity_id, '-name', 'TestActivity', '-description',
'A very excellent provenance', '-used', file_entity_id,
'-executed', repo_url)
output = run('synapse', '--skip-checks', 'get-provenance', '--id',
file_entity_id)
activity = json.loads(output)
assert_equals(activity['name'], 'TestActivity')
assert_equals(activity['description'], 'A very excellent provenance')
used = utils._find_used(activity, lambda used: 'reference' in used)
assert_equals(used['reference']['targetId'], file_entity_id)
used = utils._find_used(activity, lambda used: 'url' in used)
assert_equals(used['url'], repo_url)
assert_true(used['wasExecuted'])
# Note: Tests shouldn't have external dependencies
# but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/' \
'thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg' \
'/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
# Test external file handle
output = run('synapse', '--skip-checks', 'add', '-name', 'Singapore',
'-description', 'A nice picture of Singapore', '-parentid',
project_id, singapore_url)
exteral_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert_equals(fh['concreteType'],
'org.sagebionetworks.repo.model.file.ExternalFileHandle')
output = run('synapse', '--skip-checks', 'get', exteral_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert_true(os.path.exists(downloaded_filename))
# Delete the Project
run('synapse', '--skip-checks', 'delete', project_id)
def test_command_line_client():
# Create a Project
output = run('synapse', '--skip-checks', 'create', '-name',
str(uuid.uuid4()), '-description',
'test of command line client', 'Project')
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
# Create a File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse', '--skip-checks', 'add', '-name', 'BogusFileEntity',
'-description', 'Bogus data to test file upload', '-parentid',
project_id, filename)
file_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we stored the file in Synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert fh[
'concreteType'] == 'org.sagebionetworks.repo.model.file.S3FileHandle'
# Get File from the command line
output = run('synapse', '--skip-checks', 'get', file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Update the File
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse', '--skip-checks', 'store', '--id', file_entity_id,
filename)
updated_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)', output)
# Get the File again
output = run('synapse', '--skip-checks', 'get', file_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# Test query
output = run(
'synapse', '--skip-checks', 'query',
'select id, name from entity where parentId=="%s"' % project_id)
assert 'BogusFileEntity' in output
assert file_entity_id in output
# Move the file to new folder
folder = syn.store(synapseclient.Folder(parentId=project_id))
output = run('synapse', 'mv', '--id', file_entity_id, '--parentid',
folder.id)
downloaded_filename = parse(r'Moved\s+(.*)', output)
movedFile = syn.get(file_entity_id, downloadFile=False)
assert movedFile.parentId == folder.id
# Test Provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run('synapse', '--skip-checks', 'set-provenance', '-id',
file_entity_id, '-name', 'TestActivity', '-description',
'A very excellent provenance', '-used', file_entity_id,
'-executed', repo_url)
activity_id = parse(r'Set provenance record (\d+) on entity syn\d+',
output)
output = run('synapse', '--skip-checks', 'get-provenance', '--id',
file_entity_id)
activity = json.loads(output)
assert activity['name'] == 'TestActivity'
assert activity['description'] == 'A very excellent provenance'
used = utils._find_used(activity, lambda used: 'reference' in used)
assert used['reference']['targetId'] == file_entity_id
used = utils._find_used(activity, lambda used: 'url' in used)
assert used['url'] == repo_url
assert used['wasExecuted'] == True
# Note: Tests shouldn't have external dependencies
# but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/' \
'thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg' \
'/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
# Test external file handle
output = run('synapse', '--skip-checks', 'add', '-name', 'Singapore',
'-description', 'A nice picture of Singapore', '-parentid',
project_id, singapore_url)
exteral_entity_id = parse(r'Created/Updated entity:\s+(syn\d+)\s+', output)
# Verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert fh[
'concreteType'] == 'org.sagebionetworks.repo.model.file.ExternalFileHandle'
output = run('synapse', '--skip-checks', 'get', exteral_entity_id)
downloaded_filename = parse(r'Downloaded file:\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
# Delete the Project
output = run('synapse', '--skip-checks', 'delete', project_id)
def test_command_line_client():
"""Test command line client"""
## Note:
## In Windows, quoting with single-quotes, as in -name 'My entity name'
## seems to cause problems in the call to subprocess.check_output. Make
## sure to use double-quotes.
## create project
output = run(
'synapse create -name "%s" -description "test of command line client" Project'
% str(str(uuid.uuid4())))
project_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
schedule_for_cleanup(project_id)
## create file
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run(
'synapse add -name "BogusFileEntity" -description "Bogus data to test file upload" -parentid %s %s'
% (
project_id,
filename,
))
file_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## verify that we stored the file in synapse
f1 = syn.get(file_entity_id)
fh = syn._getFileHandle(f1.dataFileHandleId)
assert fh[
'concreteType'] == 'org.sagebionetworks.repo.model.file.S3FileHandle'
## get file
output = run('synapse get %s' % file_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## update file
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse update -id %s %s' % (
file_entity_id,
filename,
))
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
## get file
output = run('synapse get %s' % file_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## create data
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run(
'synapse add -name "BogusData" -description "Bogus data to test file upload" -type Data -parentid %s %s'
% (
project_id,
filename,
))
data_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## get data
output = run('synapse get %s' % data_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
## update data
filename = utils.make_bogus_data_file()
schedule_for_cleanup(filename)
output = run('synapse update -id %s %s' % (
data_entity_id,
filename,
))
updated_entity_id = parse(r'Updated entity:\s+(syn\d+)', output)
## get data
output = run('synapse get %s' % data_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
assert filecmp.cmp(filename, downloaded_filename)
# query
output = run(
'synapse query "select id, name from entity where parentId==\\"%s\\""'
% project_id)
assert 'BogusData' in output
assert data_entity_id in output
assert 'BogusFileEntity' in output
assert file_entity_id in output
# provenance
repo_url = 'https://github.com/Sage-Bionetworks/synapsePythonClient'
output = run(
'synapse set-provenance -id %s -name TestActivity -description "A very excellent provenance" -used %s -executed "%s"'
% (
file_entity_id,
data_entity_id,
repo_url,
))
activity_id = parse(r'Set provenance record (\d+) on entity syn\d+',
output)
output = run('synapse get-provenance -id %s' % (file_entity_id, ))
activity = json.loads(output)
assert activity['name'] == 'TestActivity'
assert activity['description'] == 'A very excellent provenance'
used = utils._find_used(activity, lambda used: 'reference' in used)
assert used['reference']['targetId'] == data_entity_id
used = utils._find_used(activity, lambda used: 'url' in used)
assert used['url'] == repo_url
assert used['wasExecuted'] == True
## Tests shouldn't have external dependencies, but this is a pretty picture of Singapore
singapore_url = 'http://upload.wikimedia.org/wikipedia/commons/thumb/3/3e/1_singapore_city_skyline_dusk_panorama_2011.jpg/1280px-1_singapore_city_skyline_dusk_panorama_2011.jpg'
## test external file handle
output = run(
'synapse add -name "Singapore" -description "A nice picture of Singapore" -type File -parentid %s %s'
% (
project_id,
singapore_url,
))
exteral_entity_id = parse(r'Created entity:\s+(syn\d+)\s+', output)
## verify that we created an external file handle
f2 = syn.get(exteral_entity_id)
fh = syn._getFileHandle(f2.dataFileHandleId)
assert fh[
'concreteType'] == 'org.sagebionetworks.repo.model.file.ExternalFileHandle'
output = run('synapse get %s' % exteral_entity_id)
downloaded_filename = parse(r'creating\s+(.*)', output)
schedule_for_cleanup(downloaded_filename)
assert os.path.exists(downloaded_filename)
## delete project
output = run('synapse delete %s' % project_id)
