def review_flagged_outputs():
"""Finds common ComponentRuns for a group of flagged outputs.
Returns a list of ComponentRuns and occurrence counts in the
group of flagged outputs, sorted by descending count and then
alphabetically."""
store = Store(_db_uri)
return store.review_flagged_outputs()
class TestStore(unittest.TestCase):
def setUp(self):
self.store = Store("test")
def testComponent(self):
self.store.create_component("test_component", "test_description",
"shreya")
component = self.store.get_component("test_component")
self.assertEqual(component.name, "test_component")
# Retrieve components with owner
components = self.store.get_components(owner="shreya")
self.assertEqual(1, len(components))
def testCompleteComponentRun(self):
# Create component
self.store.create_component("test_component", "test_description",
"shreya")
# Create component run
cr = self.store.initialize_empty_component_run("test_component")
cr.set_start_timestamp()
cr.set_end_timestamp()
cr.add_input(IOPointer("inp"))
cr.add_output(IOPointer("out"))
self.store.commit_component_run(cr)
# Test retrieval
component_runs = self.store.get_history("test_component", limit=None)
self.assertEqual(1, len(component_runs))
self.assertEqual(component_runs[0], cr)
def testLogComponentRunWithoutComponentCreated(self):
# Create a ComponentRun
cr = self.store.initialize_empty_component_run("test_component_new")
cr.set_start_timestamp()
cr.set_end_timestamp()
cr.add_input(IOPointer("inp"))
cr.add_output(IOPointer("out"))
self.store.commit_component_run(cr)
# Test retrieval
component_runs = self.store.get_history("test_component_new",
limit=None)
self.assertEqual(1, len(component_runs))
self.assertEqual(component_runs[0], cr)
def testIncompleteComponentRun(self):
# Create component
self.store.create_component("test_component", "test_description",
"shreya")
# Create incomplete component run
cr = self.store.initialize_empty_component_run("test_component")
with self.assertRaises(RuntimeError):
self.store.commit_component_run(cr)
def testTags(self):
# Create component without tags
self.store.create_component("test_component", "test_description",
"shreya")
# Add tags
self.store.add_tags_to_component("test_component", ["tag1", "tag2"])
# Test retrieval
component = self.store.get_component("test_component")
tags = [t.name for t in component.tags]
self.assertEqual(component.name, "test_component")
self.assertEqual(set(tags), set(["tag1", "tag2"]))
def testDuplicateTags(self):
# Create component without tags
self.store.create_component("test_component", "test_description",
"shreya")
# Add duplicate tags
self.store.add_tags_to_component("test_component", ["tag1", "tag1"])
# Test retrieval
component = self.store.get_component("test_component")
tags = [t.name for t in component.tags]
self.assertEqual(component.name, "test_component")
self.assertEqual(tags, ["tag1"])
def testIOPointer(self):
# Test there is no IOPointer
with self.assertRaises(RuntimeError):
self.store.get_io_pointer("iop", create=False)
# Create IOPointer
iop = self.store.get_io_pointer("iop")
iop2 = self.store.get_io_pointer("iop")
self.assertEqual(iop, iop2)
def testIOPointers(self):
# Create new IOPointers from scratch
iop_names = [f"iop_{i}" for i in range(100)]
iops = self.store.get_io_pointers(iop_names)
iops2 = self.store.get_io_pointers(iop_names)
self.assertEqual(set(iops), set(iops2))
def testKVIOPointer(self):
iop_name = "name"
iop_value = "value"
iop = self.store.get_io_pointer(iop_name, iop_value)
iop2 = self.store.get_io_pointer(iop_name, iop_value)
self.assertEqual(iop, iop2)
def testSetDependenciesFromInputs(self):
# Create IO pointers
inp = self.store.get_io_pointer("inp")
out = self.store.get_io_pointer("out")
another_out = self.store.get_io_pointer("another_out")
# Create two component runs that have the same output
self.store.create_component("test_component", "test_description",
"shreya")
for idx in range(2):
cr = self.store.initialize_empty_component_run("test_component")
cr.set_start_timestamp()
cr.set_end_timestamp()
cr.add_input(inp)
cr.add_output(out)
self.store.commit_component_run(cr)
# Create another two component runs that have the same output
self.store.create_component("test_component", "test_description",
"shreya")
for idx in range(2):
cr = self.store.initialize_empty_component_run("test_component")
cr.set_start_timestamp()
cr.set_end_timestamp()
cr.add_input(inp)
cr.add_output(another_out)
self.store.commit_component_run(cr)
# Create new component run that depends on "out" pointer
cr = self.store.initialize_empty_component_run("test_component")
cr.set_start_timestamp()
cr.set_end_timestamp()
cr.add_inputs([out, another_out])
self.store.set_dependencies_from_inputs(cr)
self.store.commit_component_run(cr)
# Retrieve latest component run and check dependencies
component_runs = self.store.get_history("test_component", limit=None)
self.assertTrue(component_runs[1] in component_runs[0].dependencies)
self.assertTrue(component_runs[3] in component_runs[0].dependencies)
def _set_up_computation(self):
# Create dag of computation
# Create component and IOPointers
for i in range(1, 5):
self.store.create_component(f"test_component_{i}",
"test_description", "shreya")
iop = [self.store.get_io_pointer(f"iop_{i}") for i in range(1, 5)]
# Create component runs
cr1 = self.store.initialize_empty_component_run("test_component_1")
cr1.set_start_timestamp()
cr1.set_end_timestamp()
cr1.add_output(iop[0])
self.store.set_dependencies_from_inputs(cr1)
self.store.commit_component_run(cr1)
cr2 = self.store.initialize_empty_component_run("test_component_2")
cr2.set_start_timestamp()
cr2.set_end_timestamp()
cr2.add_output(iop[0])
self.store.set_dependencies_from_inputs(cr2)
self.store.commit_component_run(cr2)
cr3 = self.store.initialize_empty_component_run("test_component_3")
cr3.set_start_timestamp()
cr3.set_end_timestamp()
cr3.add_input(iop[0])
cr3.add_outputs([iop[1], iop[2]])
self.store.set_dependencies_from_inputs(cr3)
self.store.commit_component_run(cr3)
cr4 = self.store.initialize_empty_component_run("test_component_4")
cr4.set_start_timestamp()
cr4.set_end_timestamp()
cr4.add_input(iop[2])
cr4.add_output(iop[3])
self.store.set_dependencies_from_inputs(cr4)
self.store.commit_component_run(cr4)
def testTrace(self):
self._set_up_computation()
# Call trace functionality
trace = self.store.trace("iop_4")
level_id = [(level, cr.id) for level, cr in trace]
self.assertEqual(level_id, [(0, 4), (1, 3), (2, 2)])
def testEmptyTrace(self):
with self.assertRaises(RuntimeError):
self.store.trace("some_weird_pointer")
with self.assertRaises(RuntimeError):
self.store.web_trace("some_weird_pointer")
def testWebTrace(self):
self._set_up_computation()
# Call web trace functionality. The ordering is nondeterministic.
expected_res = [{
"id":
"componentrun_4",
"label":
"test_component_4",
"hasCaret":
True,
"isExpanded":
True,
"stale": [],
"childNodes": [
{
"id": "iopointer_iop_4",
"label": "iop_4",
"hasCaret": False,
"parent": "componentrun_4",
},
{
"id":
"componentrun_3",
"label":
"test_component_3",
"hasCaret":
True,
"isExpanded":
True,
"stale": [],
"childNodes": [
{
"id": "iopointer_iop_2",
"label": "iop_2",
"hasCaret": False,
"parent": "componentrun_3",
},
{
"id": "iopointer_iop_3",
"label": "iop_3",
"hasCaret": False,
"parent": "componentrun_3",
},
{
"id":
"componentrun_2",
"label":
"test_component_2",
"hasCaret":
True,
"isExpanded":
True,
"stale": [],
"childNodes": [{
"id": "iopointer_iop_1",
"label": "iop_1",
"hasCaret": False,
"parent": "componentrun_2",
}],
},
],
},
],
}]
web_trace = self.store.web_trace("iop_4")
self.assertEqual(web_trace, expected_res)
def testBasicFlaggedOutputs(self):
# Create components and iopointers
self.store.create_component("test_component_A", "test_description",
"shreya")
self.store.create_component("test_component_B", "test_description",
"shreya")
iop = [self.store.get_io_pointer(f"iop_{i}") for i in range(1, 5)]
# Create component runs
# First pipeline
cr_A1 = self.store.initialize_empty_component_run("test_component_A")
cr_A1.set_start_timestamp()
cr_A1.set_end_timestamp()
cr_A1.add_outputs([iop[0], iop[1]])
self.store.set_dependencies_from_inputs(cr_A1)
self.store.commit_component_run(cr_A1)
cr_B1 = self.store.initialize_empty_component_run("test_component_B")
cr_B1.set_start_timestamp()
cr_B1.set_end_timestamp()
cr_B1.add_input(iop[0])
cr_B1.add_output(iop[2])
self.store.set_dependencies_from_inputs(cr_B1)
self.store.commit_component_run(cr_B1)
# Second pipeline, which builds off iop2
cr_B2 = self.store.initialize_empty_component_run("test_component_B")
cr_B2.set_start_timestamp()
cr_B2.set_end_timestamp()
cr_B2.add_input(iop[1])
cr_B2.add_output(iop[3])
self.store.set_dependencies_from_inputs(cr_B2)
self.store.commit_component_run(cr_B2)
# Flag iop_3 and iop_4
self.store.set_io_pointer_flag("iop_3", True)
self.store.set_io_pointer_flag("iop_4", True)
# Run diagnose. It should output
# [component_A, component_B, component_B]'s corresponding run IDs
_, res = self.store.review_flagged_outputs()
res = [(cr.id, count) for cr, count in res]
expected_res = [(1, 2), (3, 1), (2, 1)]
self.assertEqual(res, expected_res)
def testManyFlaggedOutputs(self):
# Create components and iopointers
self.store.create_component("test_component_A", "test_description",
"shreya")
self.store.create_component("test_component_B", "test_description",
"shreya")
self.store.create_component("test_component_C", "test_description",
"shreya")
iop = [self.store.get_io_pointer(f"iop_{i}") for i in range(1, 8)]
# Create component runs
# First pipeline
cr_A1 = self.store.initialize_empty_component_run("test_component_A")
cr_A1.set_start_timestamp()
cr_A1.set_end_timestamp()
cr_A1.add_outputs([iop[0], iop[1]])
self.store.set_dependencies_from_inputs(cr_A1)
self.store.commit_component_run(cr_A1)
cr_B1 = self.store.initialize_empty_component_run("test_component_B")
cr_B1.set_start_timestamp()
cr_B1.set_end_timestamp()
cr_B1.add_input(iop[0])
cr_B1.add_output(iop[2])
self.store.set_dependencies_from_inputs(cr_B1)
self.store.commit_component_run(cr_B1)
cr_C1 = self.store.initialize_empty_component_run("test_component_C")
cr_C1.set_start_timestamp()
cr_C1.set_end_timestamp()
cr_C1.add_inputs([iop[1], iop[2]])
cr_C1.add_output(iop[3])
self.store.set_dependencies_from_inputs(cr_C1)
self.store.commit_component_run(cr_C1)
# Second pipeline
cr_C2 = self.store.initialize_empty_component_run("test_component_C")
cr_C2.set_start_timestamp()
cr_C2.set_end_timestamp()
cr_C2.add_inputs([iop[1], iop[2]])
cr_C2.add_output(iop[4])
self.store.set_dependencies_from_inputs(cr_C2)
self.store.commit_component_run(cr_C2)
# Third pipeline
cr_C3 = self.store.initialize_empty_component_run("test_component_C")
cr_C3.set_start_timestamp()
cr_C3.set_end_timestamp()
cr_C3.add_inputs([iop[1], iop[2]])
cr_C3.add_output(iop[5])
self.store.set_dependencies_from_inputs(cr_C3)
self.store.commit_component_run(cr_C3)
# Fourth pipeline
cr_C4 = self.store.initialize_empty_component_run("test_component_C")
cr_C4.set_start_timestamp()
cr_C4.set_end_timestamp()
cr_C4.add_inputs([iop[1], iop[2]])
cr_C4.add_output(iop[6])
self.store.set_dependencies_from_inputs(cr_C4)
self.store.commit_component_run(cr_C4)
# Flag
self.store.set_io_pointer_flag("iop_4", True)
self.store.set_io_pointer_flag("iop_5", True)
self.store.set_io_pointer_flag("iop_6", True)
self.store.set_io_pointer_flag("iop_7", True)
_, res = self.store.review_flagged_outputs()
res = [(cr.component_name, cr.id, count) for cr, count in res]
expected_res = [
("test_component_B", 2, 4),
("test_component_A", 1, 4),
("test_component_C", 6, 1),
("test_component_C", 5, 1),
("test_component_C", 4, 1),
("test_component_C", 3, 1),
]
self.assertEqual(res, expected_res)