def test_viztrail_repository(self):
"""Test basic functionality of managing viztrails in the FS repository.
"""
repo = FileSystemViztrailRepository(VIZTRAIL_DIR, repos)
self.assertEquals(len(repo.list_viztrails()), 0)
# Create two viztrails
vt1 = repo.create_viztrail(ENGINEENV_DEFAULT, {'name': 'Name A'})
self.assertEquals(vt1.properties['name'], 'Name A')
self.assertTrue(PACKAGE_VIZUAL in vt1.command_repository)
self.assertTrue(PACKAGE_PYTHON in vt1.command_repository)
self.assertFalse(PACKAGE_MIMIR in vt1.command_repository)
vt2 = repo.create_viztrail(ENGINEENV_MIMIR, {'name': 'Name B'})
self.assertEquals(vt2.properties['name'], 'Name B')
self.assertTrue(PACKAGE_VIZUAL in vt2.command_repository)
self.assertTrue(PACKAGE_PYTHON in vt2.command_repository)
self.assertTrue(PACKAGE_MIMIR in vt2.command_repository)
self.assertEquals(len(repo.list_viztrails()), 2)
# Re-load the repository
repo = FileSystemViztrailRepository(VIZTRAIL_DIR, repos)
self.assertEquals(len(repo.list_viztrails()), 2)
vt1 = repo.get_viztrail(vt1.identifier)
self.assertEquals(vt1.properties['name'], 'Name A')
self.assertTrue(PACKAGE_VIZUAL in vt1.command_repository)
self.assertTrue(PACKAGE_PYTHON in vt1.command_repository)
self.assertFalse(PACKAGE_MIMIR in vt1.command_repository)
vt2 = repo.get_viztrail(vt2.identifier)
self.assertEquals(vt2.properties['name'], 'Name B')
self.assertTrue(PACKAGE_VIZUAL in vt2.command_repository)
self.assertTrue(PACKAGE_PYTHON in vt2.command_repository)
self.assertTrue(PACKAGE_MIMIR in vt2.command_repository)
# Delete the first viztrail
self.assertTrue(repo.delete_viztrail(vt1.identifier))
# Re-load the repository
repo = FileSystemViztrailRepository(VIZTRAIL_DIR, repos)
self.assertEquals(len(repo.list_viztrails()), 1)
self.assertIsNone(repo.get_viztrail(vt1.identifier))
self.assertIsNotNone(repo.get_viztrail(vt2.identifier))
vt2 = repo.list_viztrails()[0]
self.assertEquals(vt2.properties['name'], 'Name B')
self.assertTrue(PACKAGE_VIZUAL in vt2.command_repository)
self.assertTrue(PACKAGE_PYTHON in vt2.command_repository)
self.assertTrue(PACKAGE_MIMIR in vt2.command_repository)
self.assertFalse(repo.delete_viztrail(vt1.identifier))
def test_viztrail_branches(self):
"""Test basic functionality of creating a branch.
"""
repo = FileSystemViztrailRepository(VIZTRAIL_DIR, repos)
viztrail = repo.create_viztrail(ENGINEENV_DEFAULT, {'name': 'Name A'})
# Branching of an unknown viztrail will return None
self.assertIsNone(repo.create_branch('unknown', DEFAULT_BRANCH, {'name': 'My Branch'}))
# Branching of an empty branch raises a ValueError
with self.assertRaises(ValueError):
repo.create_branch(viztrail.identifier, DEFAULT_BRANCH, {'name': 'My Branch'})
# Re-load repository and repreat previous assertions
repo = FileSystemViztrailRepository(VIZTRAIL_DIR, repos)
self.assertIsNone(repo.create_branch('unknown', DEFAULT_BRANCH, {'name': 'My Branch'}))
with self.assertRaises(ValueError):
repo.create_branch(viztrail.identifier, DEFAULT_BRANCH, {'name': 'My Branch'})
# The master branch provenance does not contain any information
prov = repo.get_viztrail(viztrail.identifier).branches[DEFAULT_BRANCH].provenance
self.assertIsNone(prov.source_branch)
self.assertTrue(prov.workflow_version < 0)
self.assertTrue(prov.module_id < 0)
class TestFileSystemViztrailRepository(unittest.TestCase):
def setUp(self):
"""Create an empty work trails repository."""
# Clear VisTrails directory
if os.path.isdir(VIZTRAILS_DIRECTORY):
shutil.rmtree(VIZTRAILS_DIRECTORY)
# Setup project repository
self.db = FileSystemViztrailRepository(VIZTRAILS_DIRECTORY,
{ENV.identifier: ENV})
def tearDown(self):
"""Clean-up by dropping viztrails directory.
"""
shutil.rmtree(VIZTRAILS_DIRECTORY)
def test_append_module(self):
"""Test appending modules."""
# Create new viztrail.
vt = self.db.create_viztrail(ENV.identifier, {'name': 'My Project'})
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('abc'))
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=load_dataset('file', 'name'))
# The default branch should have two versions. The first versions contains
# one module and the second version contains two modules
self.assertEquals(len(vt.branches[DEFAULT_BRANCH].workflows), 2)
v1 = self.db.get_workflow(
viztrail_id=vt.identifier,
workflow_version=vt.branches[DEFAULT_BRANCH].workflows[0].version)
v2 = self.db.get_workflow(
viztrail_id=vt.identifier,
workflow_version=vt.branches[DEFAULT_BRANCH].workflows[1].version)
head = self.db.get_workflow(viztrail_id=vt.identifier,
branch_id=DEFAULT_BRANCH)
self.assertEquals(len(v1.modules), 1)
self.assertEquals(len(v2.modules), 2)
self.assertEquals(len(head.modules), 2)
# Ensure that all modules have non-negative identifier
for m in head.modules:
self.assertTrue(m.identifier >= 0)
self.assertEquals(head.modules[0].command.module_type, PACKAGE_PYTHON)
self.assertEquals(head.modules[1].command.module_type, PACKAGE_VIZUAL)
self.assertEquals(head.version, 1)
# Re-load the viztrails to ensure that all information has been persisted properly
self.db = FileSystemViztrailRepository(VIZTRAILS_DIRECTORY,
{ENV.identifier: ENV})
vt = self.db.get_viztrail(vt.identifier)
self.assertEquals(len(vt.branches[DEFAULT_BRANCH].workflows), 2)
v1 = self.db.get_workflow(
viztrail_id=vt.identifier,
workflow_version=vt.branches[DEFAULT_BRANCH].workflows[0].version)
v2 = self.db.get_workflow(
viztrail_id=vt.identifier,
workflow_version=vt.branches[DEFAULT_BRANCH].workflows[1].version)
head = self.db.get_workflow(viztrail_id=vt.identifier,
branch_id=DEFAULT_BRANCH)
self.assertEquals(len(v1.modules), 1)
self.assertEquals(len(v2.modules), 2)
self.assertEquals(len(head.modules), 2)
# Ensure that all modules have non-negative identifier
for m in head.modules:
self.assertTrue(m.identifier >= 0)
self.assertEquals(head.modules[0].command.module_type, PACKAGE_PYTHON)
self.assertEquals(head.modules[1].command.module_type, PACKAGE_VIZUAL)
self.assertEquals(head.version, 1)
# Append a third moduel to the head of the default branch
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('def'))
wf = self.db.get_workflow(viztrail_id=vt.identifier)
self.assertEquals(len(wf.modules), 3)
for m in wf.modules:
self.assertTrue(m.identifier >= 0)
self.assertEquals(m.stdout[0]['data'],
'SUCCESS ' + str(m.identifier))
self.assertEquals(wf.modules[0].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.modules[1].command.module_type, PACKAGE_VIZUAL)
self.assertEquals(wf.modules[2].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.version, 2)
# Append a module to the first version in the branch. The resulting new
# branch HEAD is expected to contain only two modules then.
self.db.append_workflow_module(viztrail_id=vt.identifier,
workflow_version=0,
command=python_cell('def'))
self.db = FileSystemViztrailRepository(VIZTRAILS_DIRECTORY,
{ENV.identifier: ENV})
vt = self.db.get_viztrail(vt.identifier)
wf = self.db.get_workflow(viztrail_id=vt.identifier)
self.assertEquals(len(wf.modules), 2)
for m in wf.modules:
self.assertTrue(m.identifier >= 0)
self.assertEquals(m.stdout[0]['data'],
'SUCCESS ' + str(m.identifier))
self.assertEquals(wf.modules[0].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.modules[1].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.version, 3)
def test_branching(self):
"""Test functionality to execute a workflow module."""
# Create new viztrail and ensure that it contains exactly one branch
vt = self.db.create_viztrail(ENV.identifier, {'name': 'My Project'})
self.assertEquals(len(vt.branches), 1)
self.assertTrue(DEFAULT_BRANCH in vt.branches)
self.assertEquals(vt.branches[DEFAULT_BRANCH].identifier,
DEFAULT_BRANCH)
# Append two modules to the defaukt branch
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('abc'))
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=load_dataset('file', 'name'))
# Create a branch at the end of the default branch. The new branch
# contains one workflow with two modules the version number is 2
newbranch = self.db.create_branch(viztrail_id=vt.identifier,
properties={'name': 'New Branch'})
self.assertEquals(len(newbranch.workflows), 1)
self.assertEquals(newbranch.workflows[-1].version, 2)
wf = vt.get_workflow(branch_id=newbranch.identifier)
self.assertEquals(wf.version, 2)
self.assertEquals(len(wf.modules), 2)
self.assertTrue(newbranch.identifier in vt.branches)
# Ensure that everything has been persisted properly
self.db = FileSystemViztrailRepository(VIZTRAILS_DIRECTORY,
{ENV.identifier: ENV})
vt = self.db.get_viztrail(vt.identifier)
newbranch = vt.branches[newbranch.identifier]
self.assertEquals(len(newbranch.workflows), 1)
self.assertEquals(newbranch.workflows[-1].version, 2)
wf = vt.get_workflow(branch_id=newbranch.identifier)
self.assertEquals(wf.version, 2)
self.assertEquals(len(wf.modules), 2)
self.assertTrue(newbranch.identifier in vt.branches)
self.assertEquals(newbranch.properties.get_properties()['name'],
'New Branch')
# Create a third branch from the start of the master branch
thirdbranch = self.db.create_branch(viztrail_id=vt.identifier,
properties={'name': 'Next Branch'},
module_id=0)
wf = vt.get_workflow(branch_id=thirdbranch.identifier)
self.assertEquals(wf.version, 3)
self.assertEquals(len(wf.modules), 1)
# Append modules at end of master and at beginning of thirdbranch
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('abc'))
self.db.append_workflow_module(viztrail_id=vt.identifier,
branch_id=thirdbranch.identifier,
command=python_cell('def'),
before_id=0)
master_head = vt.get_workflow()
self.assertEquals(len(master_head.modules), 3)
self.assertEquals(master_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(master_head.modules[1].command.module_type,
PACKAGE_VIZUAL)
self.assertEquals(master_head.modules[2].command.module_type,
PACKAGE_PYTHON)
b2_head = vt.get_workflow(branch_id=newbranch.identifier)
self.assertEquals(len(b2_head.modules), 2)
self.assertEquals(b2_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(b2_head.modules[1].command.module_type,
PACKAGE_VIZUAL)
b3_head = vt.get_workflow(branch_id=thirdbranch.identifier)
self.assertEquals(len(b3_head.modules), 2)
self.assertEquals(b3_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(b3_head.modules[1].command.module_type,
PACKAGE_PYTHON)
# Replace second module of third branch
self.db.replace_workflow_module(
viztrail_id=vt.identifier,
branch_id=thirdbranch.identifier,
module_id=b3_head.modules[1].identifier,
command=load_dataset('file', 'name'))
b3_head = vt.get_workflow(branch_id=thirdbranch.identifier)
self.assertEquals(len(b3_head.modules), 2)
self.assertEquals(b3_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(b3_head.modules[1].command.module_type,
PACKAGE_VIZUAL)
master_head = vt.get_workflow()
self.assertEquals(len(master_head.modules), 3)
self.assertEquals(master_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(master_head.modules[1].command.module_type,
PACKAGE_VIZUAL)
self.assertEquals(master_head.modules[2].command.module_type,
PACKAGE_PYTHON)
b2_head = vt.get_workflow(branch_id=newbranch.identifier)
self.assertEquals(len(b2_head.modules), 2)
self.assertEquals(b2_head.modules[0].command.module_type,
PACKAGE_PYTHON)
self.assertEquals(b2_head.modules[1].command.module_type,
PACKAGE_VIZUAL)
# Ensure there are exceptions raised when branching of an unknown branch
# or module
with self.assertRaises(ValueError):
self.db.create_branch(viztrail_id=vt.identifier,
source_branch='unknonw-branch',
properties={'name': 'New Branch'})
with self.assertRaises(ValueError):
self.db.create_branch(viztrail_id=vt.identifier,
properties={'name': 'New Branch'},
module_id=100)
with self.assertRaises(ValueError):
self.db.create_branch(viztrail_id=vt.identifier)
# Test branch provenance
self.assertEquals(newbranch.provenance.source_branch, DEFAULT_BRANCH)
self.assertEquals(newbranch.provenance.workflow_version, 1)
self.assertEquals(newbranch.provenance.module_id, 1)
self.assertEquals(thirdbranch.provenance.source_branch, DEFAULT_BRANCH)
self.assertEquals(thirdbranch.provenance.workflow_version, 1)
self.assertEquals(thirdbranch.provenance.module_id, 0)
def test_eval_command(self):
"""Test functionality to execute a workflow module."""
# Create new work trail, append a module and retrieve the resulting
# workflow from default branch HEAD.
vt = self.db.create_viztrail(ENV.identifier, {'name': 'My Project'})
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('abc'))
wf = vt.get_workflow()
self.assertEquals(wf.version, 0)
self.assertEquals(len(wf.modules), 1)
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('def'))
wf = vt.get_workflow(branch_id=DEFAULT_BRANCH)
self.assertEquals(wf.version, 1)
self.assertEquals(len(wf.modules), 2)
self.assertEquals(len(wf.modules[0].stdout), 1)
self.assertEquals(wf.modules[0].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.modules[0].command.command_identifier,
PYTHON_CODE)
self.assertEquals(wf.modules[0].command.arguments[PYTHON_SOURCE],
'abc')
self.assertEquals(len(wf.modules[1].stdout), 1)
self.assertEquals(wf.modules[1].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.modules[1].command.command_identifier,
PYTHON_CODE)
self.assertEquals(wf.modules[1].command.arguments[PYTHON_SOURCE],
'def')
self.db.replace_workflow_module(viztrail_id=vt.identifier,
module_id=0,
command=load_dataset('file', 'ds'))
wf = vt.get_workflow()
self.assertEquals(wf.version, 2)
self.assertEquals(len(wf.modules), 2)
self.assertEquals(len(wf.modules[0].stdout), 1)
self.assertEquals(wf.modules[0].command.module_type, PACKAGE_VIZUAL)
self.assertEquals(wf.modules[0].command.command_identifier,
VIZUAL_LOAD)
self.assertEquals(wf.modules[0].command.arguments[PARA_FILE]['fileid'],
'file')
self.assertEquals(wf.modules[0].command.arguments[PARA_NAME], 'ds')
self.assertEquals(len(wf.modules[1].stdout), 2)
self.assertEquals(wf.modules[1].command.module_type, PACKAGE_PYTHON)
self.assertEquals(wf.modules[1].command.command_identifier,
PYTHON_CODE)
self.assertEquals(wf.modules[1].command.arguments[PYTHON_SOURCE],
'def')
def test_workflow_life_cycle(self):
"""Test functionality to execute a workflow module."""
# Create new work trail.
vt = self.db.create_viztrail(ENV.identifier, {'name': 'My Project'})
# Append two modules
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=python_cell('abc'))
self.db.append_workflow_module(viztrail_id=vt.identifier,
command=load_dataset('file', 'name'))
# Create a branch at the end of the default branch
newbranch = self.db.create_branch(viztrail_id=vt.identifier,
properties={'name': 'New Branch'})
# Append modules at end ofnew branch
self.db.append_workflow_module(viztrail_id=vt.identifier,
branch_id=newbranch.identifier,
command=python_cell('xyz'))
self.db.append_workflow_module(viztrail_id=vt.identifier,
branch_id=newbranch.identifier,
command=load_dataset('file', 'myname'),
before_id=0)
# Ensure that all version files exist
self.check_files(vt.identifier, vt.branches[DEFAULT_BRANCH].workflows,
True)
new_versions = vt.branches[newbranch.identifier].workflows
self.check_files(vt.identifier, new_versions, True)
# Delete new branch. Ensure that only the master versions exist
self.assertTrue(
self.db.delete_branch(viztrail_id=vt.identifier,
branch_id=newbranch.identifier))
self.check_files(vt.identifier, vt.branches[DEFAULT_BRANCH].workflows,
True)
self.check_files(vt.identifier, new_versions, False)
# Deleting a non-existing branch should return False
self.assertFalse(
self.db.delete_branch(viztrail_id=vt.identifier,
branch_id=newbranch.identifier))
self.assertFalse(
self.db.delete_branch(viztrail_id=vt.identifier,
branch_id='unknown'))
# Deleting master branch should raise exception
with self.assertRaises(ValueError):
self.db.delete_branch(viztrail_id=vt.identifier,
branch_id=DEFAULT_BRANCH)
def test_viztrail_life_cycle(self):
"""Test API methods to create and delete work trails."""
# Create work trail and ensure that deleting it returns True
vt = self.db.create_viztrail(ENV.identifier, {'name': 'My Project'})
# Ensure that the viztrail has property name = 'My Project'
self.assertEquals(vt.properties.get_properties()['name'], 'My Project')
self.assertEquals(len(self.db.list_viztrails()), 1)
self.assertTrue(self.db.delete_viztrail(vt.identifier))
self.assertEquals(len(self.db.list_viztrails()), 0)
# Multiple deletes should return False
self.assertFalse(self.db.delete_viztrail(vt.identifier))
# Deleting an unknown work trail should return False
self.assertFalse(self.db.delete_viztrail('invalid id'))
self.assertFalse(self.db.delete_viztrail('f0f0f0f0f0f0f0f0f0f0f0f0'))
# Cannot create viztrail for unknown engine
with self.assertRaises(ValueError):
self.db.create_viztrail('UNKNOWN', {'name': 'My Project'})
def check_files(self, viztrail_id, versions, check_exists):
for wf_desc in versions:
filename = os.path.join(VIZTRAILS_DIRECTORY, viztrail_id,
str(wf_desc.version) + '.yaml')
self.assertEquals(os.path.isfile(filename), check_exists)