def test_overwrite_obj(tmpdir):
jobdb = str(tmpdir.join("db"))
j = dep.open_job_db(jobdb)
j.add_template(
dep.Template([dep.ForEach("in", {"A": "a"})], [], "transform"))
# add the object, which results in a rule execution
id1 = j.add_obj("public", 1, {"A": "a", "mut": {"$value": "1"}})
objs = j.find_objs("public", {"A": "a"})
assert len(objs) == 1
j.refresh_rules()
assert len(j.get_pending()) == 1
assert len(j.get_all_executions()) == 0
rule_exec_id1 = j.get_pending()[0].id
# add object with same "key" which should result in the old rule execution being replaced
id2 = j.add_obj("public", 2, {"A": "a", "mut": {"$value": "2"}})
objs = j.find_objs("public", {"A": "a"})
assert len(objs) == 1
j.refresh_rules()
assert len(j.get_pending()) == 1
# there should still only be a single rule, but it should be a new rule with the new input
rule_exec_id2 = j.get_pending()[0].id
assert id1 != id2
assert rule_exec_id1 != rule_exec_id2
# now, try with a different key to make sure it's not that all objects overwrite one another
id1 = j.add_obj("public", 1, {"B": "b", "mut": {"$filename": "1"}})
objs = j.find_objs("public", {"B": "b"})
assert len(objs) == 1
id2 = j.add_obj("public", 2, {"B": "b", "mut": {"$filename": "2"}})
objs = j.find_objs("public", {"B": "b"})
assert len(objs) == 1
assert id1 != id2
def to_template(jinja2_env: Environment, rule: Rule,
config: Dict[str, Union[str, Dict[str, str]]]) -> Template:
queries, predicates = convert_input_spec_to_queries(
jinja2_env, rule, config)
return dep.Template(
queries,
predicates,
rule.name,
output_matches_expectation=rule.output_matches_expectation)
def test_stuff(tmpdir):
jobdb = str(tmpdir.join("db"))
templates = [
dep.Template([dep.ForEach("contexts", dict(type="contexts"))], [],
"MakeContexts"),
dep.Template([
dep.ForEach("avana_lib",
dict(type="crispr_dataset", library="Avana")),
dep.ForAll("gecko_libs", dict(library="Gecko"))
], [], "AvanaGeckoMerge"),
dep.Template([
dep.ForEach("dataset", dict(type="crispr_dataset")),
dep.ForEach("context", dict(type="context"))
], [], "CalculateEnrichment"),
dep.Template([
dep.ForEach("dataset", dict(type="crispr_dataset")),
dep.ForEach("parameters", dict(type="atlantis_params"))
], [], "RunAtlantis")
]
j = dep.open_job_db(jobdb)
for t in templates:
j.add_template(t)
def execute(execution_id, transform, inputs):
if transform == "MakeContexts":
j.record_completed(2, execution_id, dep.STATUS_COMPLETED, [
dict(name="a", type="context"),
dict(name="b", type="context")
])
j.add_obj("public", 1, dict(type="contexts"))
j.add_obj("public", 1, dict(type="atlantis_params", parameters="p1"))
j.add_obj("public", 1, dict(type="atlantis_params", parameters="p2"))
j.add_obj("public", 1, dict(type="crispr_dataset", library="Avana"))
j.add_obj("public", 1, dict(type="crispr_dataset", library="Gecko"))
j.refresh_rules()
for pending in j.get_pending():
execute(pending.id, pending.transform, pending.inputs)
print(j.to_dot(True))
def debugrun(state_dir, depfile, target, override_vars, config_file):
db_path = os.path.join(state_dir, "db.sqlite3")
print("opening", db_path)
j = dep.open_job_db(db_path)
rules = read_rules(state_dir, depfile, config_file)
for var, value in override_vars.items():
rules.set_var(var, value)
rule = rules.get_rule(target)
queries, predicates = convert_input_spec_to_queries(
rules.jinja2_env, rule, rules.vars)
for q in queries:
t = dep.Template([q], [], rule.name)
applications = j.query_template(t)
log.info("{} matches for {}".format(len(applications), q))
applications = j.query_template(
dep.Template(queries, predicates, rule.name))
log.info("{} matches for entire rule".format(len(applications)))
def test_foreach(tmpdir):
jobdb = str(tmpdir.join("db"))
templates = [
dep.Template([dep.ForEach("contexts", dict(type="contexts"))], [],
"MakeContexts")
]
j = dep.open_job_db(jobdb)
for t in templates:
j.add_template(t)
j.add_obj("public", 1, dict(type="contexts", name="a"))
j.refresh_rules()
assert len(j.get_pending()) == 1
j.add_obj("public", 1, dict(type="contexts", name="b"))
j.refresh_rules()
assert len(j.get_pending()) == 2