def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
[
SQLManager.instance().get_session().add(
FooBase(name="foo " + str(i))) for i in range(10000)
]
SQLManager.instance().get_session().commit()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
s_root_path = PathFinder.get_module_path()
self.__s_path_to_example_definition_file_finishing = os.path.join(s_root_path, "test/resource/wopfile/example_def_file.yml")
self.__s_path_to_example_definition_file_that_end_with_error = os.path.join(s_root_path, "test/resource/wopfile/example_def_file_toolwrapper_never_ready.yml")
self.__wm = WorkflowManager()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
s_root_path = PathFinder.get_module_path()
self.__s_path_to_example_definition_file_finishing = os.path.join(s_root_path, "test/resource/wopfile/example_def_file1.yml")
self.__s_path_to_example_definition_file_that_end_with_error = os.path.join(s_root_path, "test/resource/wopfile/example_def_file5_never_ready.yml")
self.__wm = WorkflowManager()
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
[
SQLManager.instance().get_session().add(
FooBase(name="foo " + str(i))) for i in range(10000)
]
SQLManager.instance().get_session().commit()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
session = SQLManager.instance().get_session()
session.get_or_create(Type, defaults={"id": 1}, name="input")
session.get_or_create(Type, defaults={"id": 2}, name="output")
session.commit()
self.__s_root_path = PathFinder.get_module_path()
self.__parser = Parser()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
session = SQLManager.instance().get_session()
session.get_or_create(Type, defaults={"id": 1}, name="input")
session.get_or_create(Type, defaults={"id": 2}, name="output")
session.commit()
self.__s_root_path = PathFinder.get_module_path()
self.__parser = Parser()
def setUp(self):
self.test_path = PathManager.get_test_path() # Get tests path
OptionManager.initial_test_setup() # Set tests arguments
self.db_url = OptionManager.instance()["--database"]
self.db = self.db_url[10:]
self.example_dir_path = os.path.join(PathManager.get_package_path(),
"data/example")
self.wopfile = os.path.join(self.example_dir_path, "Wopfile.yml")
self.working_directory = os.path.join(PathManager.get_package_path(),
"data/example")
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
self.test_path = PathManager.get_test_path()
self.__s_path_to_example_definition_file_finishing = os.path.join(
self.test_path, "resource/wopfile/example_def_file1.yml")
self.__s_path_to_example_definition_file_that_end_with_error = os.path.join(
self.test_path, "resource/wopfile/example_def_file5_never_ready.yml")
self.__workflow_manager = WorkflowManager()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
self.__local_session = SQLManager.instance().get_session()
SQLManager()
self.__t1 = ConcurrentCommitingThread()
self.__t2 = ConcurrentCommitingThread()
self.__t3 = ConcurrentCommitingThread()
self.__t4 = ConcurrentRollBackingThread()
self.__t5 = ConcurrentRollBackingThread()
self.__t6 = ConcurrentRollBackingThread()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
self.__local_session = SQLManager.instance().get_session()
SQLManager()
self.__t1 = ConcurrentCommitingThread()
self.__t2 = ConcurrentCommitingThread()
self.__t3 = ConcurrentCommitingThread()
self.__t4 = ConcurrentRollBackingThread()
self.__t5 = ConcurrentRollBackingThread()
self.__t6 = ConcurrentRollBackingThread()
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
s_path_to_example_existing_file = os.path.join(self.s_root_path, "test/resource/input_files/example_existing_file.txt")
s_path_to_example_existing_file2 = os.path.join(self.s_root_path, "test/resource/input_files/example_existing_file2.txt")
s_path_to_example_not_existing_file = os.path.join(self.s_root_path, "test/resource/input_files/example_not_existing_file.txt")
self.__io_file_existing = IOFilePut(name="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing2 = IOFilePut(name="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing3 = IOFilePut(name="existing_file2", path=s_path_to_example_existing_file)
self.__io_file_existing4 = IOFilePut(name="existing_file", path=s_path_to_example_existing_file2)
self.__io_file_not_existing = IOFilePut(name="not_existing_file", path=s_path_to_example_not_existing_file)
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
session = SQLManager.instance().get_session()
session.get_or_create(TypeInputOrOutput,
defaults={"is_input": True},
is_input=True)
session.get_or_create(TypeInputOrOutput,
defaults={"is_input": False},
is_input=False)
session.commit()
self.__test_path = PathManager.get_test_path()
# self.__test_path = PathManager.get_package_path()
self.__parser = Parser()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
session = SQLManager.instance().get_session()
session.get_or_create(Type, defaults={"id": 1}, name="input")
session.get_or_create(Type, defaults={"id": 2}, name="output")
session.commit()
self.__session = SQLManager.instance().get_session()
self.__reader = Reader()
self.__s_root_path = PathFinder.get_module_path()
# The good -------------------------------:
self.__s_example_definition_file = os.path.join(
self.__s_root_path, "test/resource/wopfile/example_def_file.yml")
self.__s_example_definition_file2 = os.path.join(
self.__s_root_path, "test/resource/wopfile/example_def_file3.yml")
# The ugly (malformed file) --------------------:
self.__s_example_definition_file_duplicate_rule = os.path.join(
self.__s_root_path,
"test/resource/wopfile/example_def_file_duplicate_rule.yml")
self.__list_f_to_exception_init = [
os.path.join(self.__s_root_path, s_path) for s_path in [
"test/resource/wopfile/example_def_file_wrong_yaml.yml",
"test/resource/wopfile/example_def_file_duplicate_rule.yml",
"test/resource/wopfile/example_def_file_wrong_grammar.yml",
"test/resource/wopfile/example_def_file_wrong_grammar2.yml",
"test/resource/wopfile/example_def_file_wrong_grammar3.yml",
"test/resource/wopfile/example_def_file_wrong_grammar4.yml"
]
]
# The bad (invalid file) ----------------------:
self.__list_s_to_exception_read = [
os.path.join(self.__s_root_path, s_path) for s_path in [
"test/resource/wopfile/example_def_file_wrong_content.yml",
"test/resource/wopfile/example_def_file_wrong_content2.yml",
"test/resource/wopfile/example_def_file_wrong_content3.yml",
"test/resource/wopfile/example_def_file_wrong_content4.yml",
"test/resource/wopfile/example_def_file_wrong_content5.yml",
"test/resource/wopfile/example_def_file_wrong_class_name.yml",
"test/resource/wopfile/example_def_file_wrong_rule.yml",
]
]
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
self.__local_session = SQLManager.instance().get_session()
SQLManager()
self.__t1 = ConcurrentCommitingThread()
self.__t2 = ConcurrentCommitingThread()
self.__t3 = ConcurrentCommitingThread()
self.__t4 = ConcurrentRollBackingThread()
self.__t5 = ConcurrentRollBackingThread()
self.__t6 = ConcurrentRollBackingThread()
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
session = SQLManager.instance().get_session()
session.get_or_create(TypeInputOrOutput, defaults={"is_input": True}, is_input=True)
session.get_or_create(TypeInputOrOutput, defaults={"is_input": False}, is_input=False)
session.commit()
self.__session = SQLManager.instance().get_session()
self.__reader = Reader()
self.__testdir_path = PathManager.get_test_path()
# The good -------------------------------:
self.__example_def_file1_path = os.path.join(self.__testdir_path, "resource/wopfile/example_def_file1.yml")
self.__example_def_file3_path = os.path.join(self.__testdir_path, "resource/wopfile/example_def_file3.yml")
# The ugly (malformed file) --------------------:
self.__s_example_definition_file_duplicate_rule = os.path.join(self.__testdir_path, "resource/wopfile/example_def_file_duplicate_rule.yml")
self.__list_f_to_exception_init = [
os.path.join(self.__testdir_path, s_path) for s_path in [
"resource/wopfile/example_def_file_wrong_yaml.yml",
"resource/wopfile/example_def_file_duplicate_rule.yml",
"resource/wopfile/example_def_file_wrong_grammar.yml",
"resource/wopfile/example_def_file_wrong_grammar2.yml",
"resource/wopfile/example_def_file_wrong_grammar3.yml",
"resource/wopfile/example_def_file_wrong_grammar4.yml"
]
]
# The bad (invalid file) ----------------------:
self.__list_s_to_exception_read = [
os.path.join(self.__testdir_path, s_path) for s_path in [
"resource/wopfile/example_def_file1.yml",
"resource/wopfile/example_def_file_wrong_content2.yml",
"resource/wopfile/example_def_file_wrong_content3.yml",
"resource/wopfile/example_def_file_wrong_content4.yml",
"resource/wopfile/example_def_file_wrong_content5.yml",
"resource/wopfile/example_def_file_wrong_class_name.yml",
"resource/wopfile/example_def_file_wrong_rule.yml",
]
]
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
session = SQLManager.instance().get_session()
session.get_or_create(Type, defaults={"id": 1}, name="input")
session.get_or_create(Type, defaults={"id": 2}, name="output")
session.commit()
self.__session = SQLManager.instance().get_session()
self.__reader = Reader()
self.__s_root_path = PathFinder.get_module_path()
# The good -------------------------------:
self.__s_example_definition_file = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file1.yml")
self.__s_example_definition_file2 = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file3.yml")
# The ugly (malformed file) --------------------:
self.__s_example_definition_file_duplicate_rule = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file_duplicate_rule.yml")
self.__list_f_to_exception_init = [
os.path.join(self.__s_root_path, s_path) for s_path in [
"test/resource/wopfile/example_def_file_wrong_yaml.yml",
"test/resource/wopfile/example_def_file_duplicate_rule.yml",
"test/resource/wopfile/example_def_file_wrong_grammar.yml",
"test/resource/wopfile/example_def_file_wrong_grammar2.yml",
"test/resource/wopfile/example_def_file_wrong_grammar3.yml",
"test/resource/wopfile/example_def_file_wrong_grammar4.yml"
]
]
# The bad (invalid file) ----------------------:
self.__list_s_to_exception_read = [
os.path.join(self.__s_root_path, s_path) for s_path in [
"test/resource/wopfile/example_def_file1.yml",
"test/resource/wopfile/example_def_file_wrong_content2.yml",
"test/resource/wopfile/example_def_file_wrong_content3.yml",
"test/resource/wopfile/example_def_file_wrong_content4.yml",
"test/resource/wopfile/example_def_file_wrong_content5.yml",
"test/resource/wopfile/example_def_file_wrong_class_name.yml",
"test/resource/wopfile/example_def_file_wrong_rule.yml",
]
]
def setUp(self):
self.s_root_path = PathFinder.get_module_path()
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
self.__local_session = SQLManager.instance().get_session()
try:
for i in range(10):
self.__local_session.add(FooBase(name="testIODB " + str(i)))
self.__local_session.commit()
except Exception as e:
self.__local_session.rollback()
self.__local_session.close()
raise e
self.__io_base_existing = IODbPut(model="FooBase", tablename="FooBase")
self.__io_base_existing.set_table(FooBase)
self.__io_base_existing2 = IODbPut(model="FooBase", tablename="FooBase")
self.__io_base_existing2.set_table(FooBase)
self.__io_base_existing3 = IODbPut(model="FooBase2", tablename="FooBase2")
self.__io_base_existing3.set_table(FooBase2)
def setUp(self):
self.test_path = PathManager.get_test_path() # Get tests path
OptionManager.initial_test_setup() # Set tests arguments
self.__db_url = OptionManager.instance()["--database"]
self.__example_def_file1 = os.path.join(
self.test_path, "resource/wopfile/example_def_file1.yml")
self.__example_def_file1_only_database = \
os.path.join(self.test_path, "resource/wopfile/example_def_file1_only_database.yml")
self.__example_def_file2_only_files = os.path.join(
self.test_path,
"resource/wopfile/example_def_file2_only_files.yml")
self.__example_def_file4 = os.path.join(
self.test_path, "resource/wopfile/example_def_file4.yml")
self.__example_def_file5_never_ready = os.path.join(
self.test_path,
"resource/wopfile/example_def_file5_never_ready.yml")
self.__example_def_file_input_not_ready = os.path.join(
self.test_path,
"resource/wopfile/example_def_file_input_not_ready.yml")
def setUp(self):
self.test_path = PathManager.get_test_path()
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
self.__local_session = SQLManager.instance().get_session()
try:
for i in range(10):
self.__local_session.add(FooBase(name="testIODB " + str(i)))
self.__local_session.commit()
except Exception as e:
self.__local_session.rollback()
self.__local_session.close()
raise e
self.__io_base_existing = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
self.__io_base_existing.set_table(FooBase)
self.__io_base_existing2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
self.__io_base_existing2.set_table(FooBase)
self.__io_base_existing3 = TableInputOutputInformation(model_py_path="FooBase2", table_key="FooBase2", table_name="FooBase2")
self.__io_base_existing3.set_table(FooBase2)
def setUp(self):
self.test_path = PathManager.get_test_path() # Get tests path
OptionManager.initial_test_setup() # Set tests arguments
s_path_to_example_existing_file = os.path.join(
self.test_path, "resource/input_files/example_existing_file.txt")
s_path_to_example_existing_file2 = os.path.join(
self.test_path, "resource/input_files/example_existing_file2.txt")
s_path_to_example_not_existing_file = os.path.join(
self.test_path,
"resource/input_files/example_not_existing_file.txt")
self.__io_file_existing = FileInputOutputInformation(
file_key="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing2 = FileInputOutputInformation(
file_key="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing3 = FileInputOutputInformation(
file_key="existing_file2", path=s_path_to_example_existing_file)
self.__io_file_existing4 = FileInputOutputInformation(
file_key="existing_file", path=s_path_to_example_existing_file2)
self.__io_file_not_existing = FileInputOutputInformation(
file_key="not_existing_file",
path=s_path_to_example_not_existing_file)
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
s_path_to_example_existing_file = os.path.join(
self.s_root_path,
"test/resource/input_files/example_existing_file.txt")
s_path_to_example_existing_file2 = os.path.join(
self.s_root_path,
"test/resource/input_files/example_existing_file2.txt")
s_path_to_example_not_existing_file = os.path.join(
self.s_root_path,
"test/resource/input_files/example_not_existing_file.txt")
self.__io_file_existing = IOFilePut(
name="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing2 = IOFilePut(
name="existing_file", path=s_path_to_example_existing_file)
self.__io_file_existing3 = IOFilePut(
name="existing_file2", path=s_path_to_example_existing_file)
self.__io_file_existing4 = IOFilePut(
name="existing_file", path=s_path_to_example_existing_file2)
self.__io_file_not_existing = IOFilePut(
name="not_existing_file", path=s_path_to_example_not_existing_file)
def setUp(self):
self.s_root_path = PathFinder.get_module_path()
OptionManager.initial_test_setup()
print(OptionManager.instance()["--log"])
SQLManager.instance().create_all()
self.__local_session = SQLManager.instance().get_session()
try:
for i in range(10):
self.__local_session.add(FooBase(name="testIODB " + str(i)))
self.__local_session.commit()
except Exception as e:
self.__local_session.rollback()
self.__local_session.close()
raise e
self.__io_base_existing = IODbPut(model="FooBase", tablename="FooBase")
self.__io_base_existing.set_table(FooBase)
self.__io_base_existing2 = IODbPut(model="FooBase",
tablename="FooBase")
self.__io_base_existing2.set_table(FooBase)
self.__io_base_existing3 = IODbPut(model="FooBase2",
tablename="FooBase2")
self.__io_base_existing3.set_table(FooBase2)
def test_parse(self):
OptionManager.initial_test_setup()
# The good --------------------------:
input_entry = Type(name="input")
output_entry = Type(name="output")
f1 = IOFilePut(name="input1", path="test/resource/input_files/input_File1.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="test/output/output_File1.txt")
f2.type = output_entry
f3 = IOFilePut(name="input1", path="test/output/output_File1.txt")
f3.type = input_entry
f3bis = IOFilePut(name="input1", path="test/output/output_File1.txt")
f3bis.type = input_entry
f4 = IOFilePut(name="output1", path="test/output/output_File2.txt")
f4.type = output_entry
f5 = IOFilePut(name="output1", path="test/output/output_File3.txt")
f5.type = output_entry
f6 = IOFilePut(name="output2", path="test/output/output_File4.txt")
f6.type = output_entry
f7 = IOFilePut(name="input1", path="test/output/output_File3.txt")
f7.type = input_entry
f8 = IOFilePut(name="input2", path="test/output/output_File2.txt")
f8.type = input_entry
f9 = IOFilePut(name="output1", path="test/output/output_File5.txt")
f9.type = output_entry
f10 = IOFilePut(name="input1", path="test/output/output_File4.txt")
f10.type = input_entry
f11 = IOFilePut(name="output1", path="test/output/output_File6.txt")
f11.type = output_entry
f12 = IOFilePut(name="input1", path="test/output/output_File1.txt")
f12.type = input_entry
f13 = IOFilePut(name="input2", path="test/output/output_File5.txt")
f13.type = input_entry
f14 = IOFilePut(name="input3", path="test/output/output_File6.txt")
f14.type = input_entry
f15 = IOFilePut(name="output1", path="test/output/output_File7.txt")
f15.type = output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.type = output_entry
t1bis = IODbPut(model="FooBase", tablename="FooBase")
t1bis.type = input_entry
t2 = IODbPut(model="FooBase2", tablename="FooBase2")
t2.type = output_entry
t2bis = IODbPut(model="FooBase2", tablename="FooBase2")
t2bis.type = input_entry
tw1 = FooWrapper4(rule_name="rule1")
tw1.files.extend([f1, f2])
tw2 = FooWrapper5(rule_name="rule2")
tw2.files.extend([f3, f4])
tw2.tables.extend([t1])
tw3 = FooWrapper6(rule_name="rule3")
tw3.files.extend([f3bis, f5, f6])
tw4 = FooWrapper7(rule_name="rule4")
tw4.tables.extend([t1bis, t2])
tw5 = FooWrapper8(rule_name="rule5")
tw5.files.extend([f8, f7, f9])
tw6 = FooWrapper9(rule_name="rule6")
tw6.files.extend([f10, f11])
tw6.tables.extend([t2bis])
tw7 = FooWrapper10(rule_name="rule7")
tw7.files.extend([f12, f13, f14, f15])
set_toolwrappers = set([tw1, tw2, tw3, tw4, tw5, tw6, tw7])
OptionManager.instance()["--dot"] = None
dag_expected = DAG(set_toolwrappers)
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file.yml")
dag_obtained = self.__parser.parse()
self.assertEqual(dag_expected, dag_obtained)
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file_not_a_dag.yml")
with self.assertRaises(WopMarsException):
self.__parser.parse()
# Verify the dot file ----------------:
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file.yml")
#dot_path = os.path.join(self.__s_root_path, "test_bak.dot")
#OptionManager.instance()["--dot"] = dot_path
self.__parser.parse()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
# first
# / \
# second third
# \ /
# fourth
#
self.__session = SQLManager.instance().get_session()
input_entry = Type(name="input")
output_entry = Type(name="output")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file3.txt")
f2.type = output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file4.txt")
f2.type = output_entry
self.__toolwrapper_third = FooWrapper2(rule_name="rule3")
self.__toolwrapper_third.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file3.txt")
f1.type = input_entry
f2 = IOFilePut(name="input2", path="file4.txt")
f2.type = input_entry
f3 = IOFilePut(name="output1", path="file5.txt")
f3.type = output_entry
self.__toolwrapper_fourth = FooWrapper8(rule_name="rule4")
self.__toolwrapper_fourth.files.extend([f1, f2, f3])
list_tool = [
self.__toolwrapper_first, self.__toolwrapper_second,
self.__toolwrapper_third, self.__toolwrapper_fourth
]
self.__set_tool = set(list_tool)
SQLManager.instance().get_session().add_all(list_tool)
SQLManager.instance().get_session().commit()
def setUp(self):
OptionManager.initial_test_setup()
SQLManager.instance().create_all()
# first
# / \
# second third
# \ /
# fourth
#
self.__session = SQLManager.instance().get_session()
input_entry = Type(name="input")
output_entry = Type(name="output")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file3.txt")
f2.type = output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="file4.txt")
f2.type = output_entry
self.__toolwrapper_third = FooWrapper2(rule_name="rule3")
self.__toolwrapper_third.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file3.txt")
f1.type = input_entry
f2 = IOFilePut(name="input2", path="file4.txt")
f2.type = input_entry
f3 = IOFilePut(name="output1", path="file5.txt")
f3.type = output_entry
self.__toolwrapper_fourth = FooWrapper8(rule_name="rule4")
self.__toolwrapper_fourth.files.extend([f1, f2, f3])
list_tool = [self.__toolwrapper_first,
self.__toolwrapper_second,
self.__toolwrapper_third,
self.__toolwrapper_fourth]
self.__set_tool = set(list_tool)
SQLManager.instance().get_session().add_all(list_tool)
SQLManager.instance().get_session().commit()
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
SQLManager.instance().create_all()
set_tw_to_add = set()
self.__session = SQLManager.instance().get_session()
self.input_entry = Type(name="input")
self.output_entry = Type(name="output")
### Toolwrappers for __eq__ test_bak
opt1 = Option(name="param1", value="1")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper1 = ToolWrapper(rule_name="rule1")
self.__toolwrapper1.files.extend([f1, f2])
self.__toolwrapper1.options.append(opt1)
opt1 = Option(name="param1", value="1")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper2 = ToolWrapper(rule_name="rule2")
self.__toolwrapper2.files.extend([f1, f2])
self.__toolwrapper2.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper3 = ToolWrapper(rule_name="rule3")
self.__toolwrapper3.files.extend([f1, f2])
self.__toolwrapper3.options.append(opt1)
### ToolWrappers for content_respected
opt1 = Option(name="param1", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t1.type = self.input_entry
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
t2.type = self.output_entry
self.__foowrapper_right_content = FooWrapper3(rule_name="rule1")
self.__foowrapper_right_content.files.extend([f1, f2])
self.__foowrapper_right_content.tables.extend([t1, t2])
self.__foowrapper_right_content.options.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content1 = FooWrapper3(rule_name="rule2")
self.__foowrapper_wrong_content1.files.extend([f1, f2])
self.__foowrapper_wrong_content1.tables.extend([t1, t2])
self.__foowrapper_wrong_content1.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
f3 = IOFilePut(name="input2", path="file2.txt")
f3.type = self.input_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content2 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content2.files.extend([f1, f2, f3])
self.__foowrapper_wrong_content2.tables.extend([t1, t2])
self.__foowrapper_wrong_content2.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content3 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content3.files.extend([f1, f2])
self.__foowrapper_wrong_content3.tables.extend([t1, t2])
self.__foowrapper_wrong_content3.options.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content4 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content4.files.extend([f1, f2])
self.__foowrapper_wrong_content4.tables.extend([t1, t2])
self.__foowrapper_wrong_content4.options.append(opt1)
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content5 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content5.files.extend([f1, f2])
self.__foowrapper_wrong_content5.tables.extend([t1, t2])
### TooLWrappers for follows
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file3.txt")
f2.type = self.output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.files.extend([f1, f2])
### ToolWrappers for are_input_ready
s_root_path = PathFinder.get_module_path()
s_path_to_example_file_that_exists = os.path.join(s_root_path, "test/resource/input_files/input_file1.txt")
f1 = IOFilePut(name="input1", path=s_path_to_example_file_that_exists)
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_ready.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="/not/existent/file")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_not_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_not_ready.files.extend([f1, f2])
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables)
self.__session = SQLManager.instance().get_session()
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
SQLManager.instance().create_all()
set_tw_to_add = set()
self.__session = SQLManager.instance().get_session()
self.input_entry = Type(name="input")
self.output_entry = Type(name="output")
### Toolwrappers for __eq__ test_bak
opt1 = Option(name="param1", value="1")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper1 = ToolWrapper(rule_name="rule1")
self.__toolwrapper1.files.extend([f1, f2])
self.__toolwrapper1.options.append(opt1)
opt1 = Option(name="param1", value="1")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper2 = ToolWrapper(rule_name="rule2")
self.__toolwrapper2.files.extend([f1, f2])
self.__toolwrapper2.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper3 = ToolWrapper(rule_name="rule3")
self.__toolwrapper3.files.extend([f1, f2])
self.__toolwrapper3.options.append(opt1)
### ToolWrappers for content_respected
opt1 = Option(name="param1", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t1.type = self.input_entry
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
t2.type = self.output_entry
self.__foowrapper_right_content = FooWrapper3(rule_name="rule1")
self.__foowrapper_right_content.files.extend([f1, f2])
self.__foowrapper_right_content.tables.extend([t1, t2])
self.__foowrapper_right_content.options.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content1 = FooWrapper3(rule_name="rule2")
self.__foowrapper_wrong_content1.files.extend([f1, f2])
self.__foowrapper_wrong_content1.tables.extend([t1, t2])
self.__foowrapper_wrong_content1.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
f3 = IOFilePut(name="input2", path="file2.txt")
f3.type = self.input_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content2 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content2.files.extend([f1, f2, f3])
self.__foowrapper_wrong_content2.tables.extend([t1, t2])
self.__foowrapper_wrong_content2.options.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content3 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content3.files.extend([f1, f2])
self.__foowrapper_wrong_content3.tables.extend([t1, t2])
self.__foowrapper_wrong_content3.options.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content4 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content4.files.extend([f1, f2])
self.__foowrapper_wrong_content4.tables.extend([t1, t2])
self.__foowrapper_wrong_content4.options.append(opt1)
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.set_table(FooBase)
t1.table = t1
t2 = IODbPut(model="FooBase", tablename="FooBase")
t2.set_table(FooBase)
t2.table = t2
self.__foowrapper_wrong_content5 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content5.files.extend([f1, f2])
self.__foowrapper_wrong_content5.tables.extend([t1, t2])
### TooLWrappers for follows
f1 = IOFilePut(name="input1", path="file1.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="file2.txt")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file3.txt")
f2.type = self.output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.files.extend([f1, f2])
### ToolWrappers for are_input_ready
s_root_path = PathFinder.get_module_path()
s_path_to_example_file_that_exists = os.path.join(
s_root_path, "test/resource/input_files/input_File1.txt")
f1 = IOFilePut(name="input1", path=s_path_to_example_file_that_exists)
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_ready.files.extend([f1, f2])
f1 = IOFilePut(name="input1", path="/not/existent/file")
f1.type = self.input_entry
f2 = IOFilePut(name="output1", path="file2.txt")
f2.type = self.output_entry
self.__toolwrapper_not_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_not_ready.files.extend([f1, f2])
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
SQLManager.instance().create_all()
self.__session = SQLManager.instance().get_session()
def test_parse(self):
OptionManager.initial_test_setup()
# The good --------------------------:
input_entry = TypeInputOrOutput(is_input=True)
output_entry = TypeInputOrOutput(is_input=False)
f1 = FileInputOutputInformation(
file_key="input1", path="resource/input_files/input_file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = input_entry
f2 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file1.txt")
f2.relation_file_or_tableioinfo_to_typeio = output_entry
f3 = FileInputOutputInformation(file_key="input1",
path="outdir/output_file1.txt")
f3.relation_file_or_tableioinfo_to_typeio = input_entry
f3bis = FileInputOutputInformation(file_key="input1",
path="outdir/output_file1.txt")
f3bis.relation_file_or_tableioinfo_to_typeio = input_entry
f4 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file2.txt")
f4.relation_file_or_tableioinfo_to_typeio = output_entry
f5 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file3.txt")
f5.relation_file_or_tableioinfo_to_typeio = output_entry
f6 = FileInputOutputInformation(file_key="output2",
path="outdir/output_file4.txt")
f6.relation_file_or_tableioinfo_to_typeio = output_entry
f7 = FileInputOutputInformation(file_key="input1",
path="outdir/output_file3.txt")
f7.relation_file_or_tableioinfo_to_typeio = input_entry
f8 = FileInputOutputInformation(file_key="input2",
path="outdir/output_file2.txt")
f8.relation_file_or_tableioinfo_to_typeio = input_entry
f9 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file5.txt")
f9.relation_file_or_tableioinfo_to_typeio = output_entry
f10 = FileInputOutputInformation(file_key="input1",
path="outdir/output_file4.txt")
f10.relation_file_or_tableioinfo_to_typeio = input_entry
f11 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file6.txt")
f11.relation_file_or_tableioinfo_to_typeio = output_entry
f12 = FileInputOutputInformation(file_key="input1",
path="outdir/output_file1.txt")
f12.relation_file_or_tableioinfo_to_typeio = input_entry
f13 = FileInputOutputInformation(file_key="input2",
path="outdir/output_file5.txt")
f13.relation_file_or_tableioinfo_to_typeio = input_entry
f14 = FileInputOutputInformation(file_key="input3",
path="outdir/output_file6.txt")
f14.relation_file_or_tableioinfo_to_typeio = input_entry
f15 = FileInputOutputInformation(file_key="output1",
path="outdir/output_file7.txt")
f15.relation_file_or_tableioinfo_to_typeio = output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase",
table_key="FooBase",
table_name="FooBase")
t1.relation_file_or_tableioinfo_to_typeio = output_entry
t1bis = TableInputOutputInformation(model_py_path="FooBase",
table_key="FooBase",
table_name="FooBase")
t1bis.relation_file_or_tableioinfo_to_typeio = input_entry
t2 = TableInputOutputInformation(model_py_path="FooBase2",
table_key="FooBase2",
table_name="FooBase2")
t2.relation_file_or_tableioinfo_to_typeio = output_entry
t2bis = TableInputOutputInformation(model_py_path="FooBase2",
table_key="FooBase2",
table_name="FooBase2")
t2bis.relation_file_or_tableioinfo_to_typeio = input_entry
tw1 = FooWrapper4(rule_name="rule1")
tw1.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
tw2 = FooWrapper5(rule_name="rule2")
tw2.relation_toolwrapper_to_fileioinfo.extend([f3, f4])
tw2.relation_toolwrapper_to_tableioinfo.extend([t1])
tw3 = FooWrapper6(rule_name="rule3")
tw3.relation_toolwrapper_to_fileioinfo.extend([f3bis, f5, f6])
tw4 = FooWrapper7(rule_name="rule4")
tw4.relation_toolwrapper_to_tableioinfo.extend([t1bis, t2])
tw5 = FooWrapper8(rule_name="rule5")
tw5.relation_toolwrapper_to_fileioinfo.extend([f8, f7, f9])
tw6 = FooWrapper9(rule_name="rule6")
tw6.relation_toolwrapper_to_fileioinfo.extend([f10, f11])
tw6.relation_toolwrapper_to_tableioinfo.extend([t2bis])
tw7 = FooWrapper10(rule_name="rule7")
tw7.relation_toolwrapper_to_fileioinfo.extend([f12, f13, f14, f15])
set_toolwrappers = set([tw1, tw2, tw3, tw4, tw5, tw6, tw7])
OptionManager.instance()["--dot"] = None
dag_expected = DAG(set_toolwrappers)
OptionManager.instance()["--wopfile"] = os.path.join(
self.__test_path, "resource/wopfile/example_def_file1.yml")
dag_obtained = self.__parser.parse()
self.assertEqual(dag_expected, dag_obtained)
OptionManager.instance()["--wopfile"] = os.path.join(
self.__test_path,
"resource/wopfile/example_def_file_not_a_dag.yml")
with self.assertRaises(WopMarsException):
self.__parser.parse()
# Verify the dot file ----------------:
OptionManager.instance()["--wopfile"] = os.path.join(
self.__test_path, "resource/wopfile/example_def_file1.yml")
#dot_path = os.path.join(self.__package_path, "test_bak.dot")
#OptionManager.instance()["--dot"] = dot_path
self.__parser.parse()
def setUp(self):
OptionManager.initial_test_setup()
self.s_root_path = PathFinder.get_module_path()
SQLManager.instance().create_all()
self.__session = SQLManager.instance().get_session()
def setUp(self):
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
# first
# / \
# second third
# \ /
# fourth
#
self.__session = SQLManager.instance().get_session()
input_entry = TypeInputOrOutput(is_input=True)
output_entry = TypeInputOrOutput(is_input=False)
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
f1 = FileInputOutputInformation(file_key="input1", path="file2.txt")
f1.relation_file_or_tableioinfo_to_typeio = input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file3.txt")
f2.relation_file_or_tableioinfo_to_typeio = output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
f1 = FileInputOutputInformation(file_key="input1", path="file2.txt")
f1.relation_file_or_tableioinfo_to_typeio = input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file4.txt")
f2.relation_file_or_tableioinfo_to_typeio = output_entry
self.__toolwrapper_third = FooWrapper2(rule_name="rule3")
self.__toolwrapper_third.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
f1 = FileInputOutputInformation(file_key="input1", path="file3.txt")
f1.relation_file_or_tableioinfo_to_typeio = input_entry
f2 = FileInputOutputInformation(file_key="input2", path="file4.txt")
f2.relation_file_or_tableioinfo_to_typeio = input_entry
f3 = FileInputOutputInformation(file_key="output1", path="file5.txt")
f3.relation_file_or_tableioinfo_to_typeio = output_entry
self.__toolwrapper_fourth = FooWrapper8(rule_name="rule4")
self.__toolwrapper_fourth.relation_toolwrapper_to_fileioinfo.extend([f1, f2, f3])
list_tool = [self.__toolwrapper_first,
self.__toolwrapper_second,
self.__toolwrapper_third,
self.__toolwrapper_fourth]
self.__set_tool = set(list_tool)
SQLManager.instance().get_session().add_all(list_tool)
SQLManager.instance().get_session().commit()
def test_parse(self):
OptionManager.initial_test_setup()
# The good --------------------------:
input_entry = Type(name="input")
output_entry = Type(name="output")
f1 = IOFilePut(name="input1", path="test/resource/input_files/input_file1.txt")
f1.type = input_entry
f2 = IOFilePut(name="output1", path="test/output/output_file1.txt")
f2.type = output_entry
f3 = IOFilePut(name="input1", path="test/output/output_file1.txt")
f3.type = input_entry
f3bis = IOFilePut(name="input1", path="test/output/output_file1.txt")
f3bis.type = input_entry
f4 = IOFilePut(name="output1", path="test/output/output_file2.txt")
f4.type = output_entry
f5 = IOFilePut(name="output1", path="test/output/output_file3.txt")
f5.type = output_entry
f6 = IOFilePut(name="output2", path="test/output/output_file4.txt")
f6.type = output_entry
f7 = IOFilePut(name="input1", path="test/output/output_file3.txt")
f7.type = input_entry
f8 = IOFilePut(name="input2", path="test/output/output_file2.txt")
f8.type = input_entry
f9 = IOFilePut(name="output1", path="test/output/output_file5.txt")
f9.type = output_entry
f10 = IOFilePut(name="input1", path="test/output/output_file4.txt")
f10.type = input_entry
f11 = IOFilePut(name="output1", path="test/output/output_file6.txt")
f11.type = output_entry
f12 = IOFilePut(name="input1", path="test/output/output_file1.txt")
f12.type = input_entry
f13 = IOFilePut(name="input2", path="test/output/output_file5.txt")
f13.type = input_entry
f14 = IOFilePut(name="input3", path="test/output/output_file6.txt")
f14.type = input_entry
f15 = IOFilePut(name="output1", path="test/output/output_file7.txt")
f15.type = output_entry
t1 = IODbPut(model="FooBase", tablename="FooBase")
t1.type = output_entry
t1bis = IODbPut(model="FooBase", tablename="FooBase")
t1bis.type = input_entry
t2 = IODbPut(model="FooBase2", tablename="FooBase2")
t2.type = output_entry
t2bis = IODbPut(model="FooBase2", tablename="FooBase2")
t2bis.type = input_entry
tw1 = FooWrapper4(rule_name="rule1")
tw1.files.extend([f1, f2])
tw2 = FooWrapper5(rule_name="rule2")
tw2.files.extend([f3, f4])
tw2.tables.extend([t1])
tw3 = FooWrapper6(rule_name="rule3")
tw3.files.extend([f3bis, f5, f6])
tw4 = FooWrapper7(rule_name="rule4")
tw4.tables.extend([t1bis, t2])
tw5 = FooWrapper8(rule_name="rule5")
tw5.files.extend([f8, f7, f9])
tw6 = FooWrapper9(rule_name="rule6")
tw6.files.extend([f10, f11])
tw6.tables.extend([t2bis])
tw7 = FooWrapper10(rule_name="rule7")
tw7.files.extend([f12, f13, f14, f15])
set_toolwrappers = set([tw1, tw2, tw3, tw4, tw5, tw6, tw7])
OptionManager.instance()["--dot"] = None
dag_expected = DAG(set_toolwrappers)
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file1.yml")
dag_obtained = self.__parser.parse()
self.assertEqual(dag_expected, dag_obtained)
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file_not_a_dag.yml")
with self.assertRaises(WopMarsException):
self.__parser.parse()
# Verify the dot file ----------------:
OptionManager.instance()["--wopfile"] = os.path.join(self.__s_root_path, "test/resource/wopfile/example_def_file1.yml")
#dot_path = os.path.join(self.__s_root_path, "test_bak.dot")
#OptionManager.instance()["--dot"] = dot_path
self.__parser.parse()
def setUp(self):
self.test_path = PathManager.get_test_path()
OptionManager.initial_test_setup() # Set tests arguments
SQLManager.instance().create_all() # Create database with tables
set_tw_to_add = set()
self.__session = SQLManager.instance().get_session()
self.input_entry = TypeInputOrOutput(is_input=True)
self.output_entry = TypeInputOrOutput(is_input=False)
# Toolwrappers for __eq__ test_bak
opt1 = Option(name="param1", value="1")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper1 = ToolWrapper(rule_name="rule1")
self.__toolwrapper1.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__toolwrapper1.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param1", value="1")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper2 = ToolWrapper(rule_name="rule2")
self.__toolwrapper2.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__toolwrapper2.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper3 = ToolWrapper(rule_name="rule3")
self.__toolwrapper3.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__toolwrapper3.relation_toolwrapper_to_option.append(opt1)
# ToolWrappers for content_respected
opt1 = Option(name="param1", value="2")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t1.relation_file_or_tableioinfo_to_typeio = self.input_entry
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
t2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__foowrapper_right_content = FooWrapper3(rule_name="rule1")
self.__foowrapper_right_content.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__foowrapper_right_content.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
self.__foowrapper_right_content.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
self.__foowrapper_wrong_content1 = FooWrapper3(rule_name="rule2")
self.__foowrapper_wrong_content1.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__foowrapper_wrong_content1.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
self.__foowrapper_wrong_content1.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
f3 = FileInputOutputInformation(file_key="input2", path="file2.txt")
f3.relation_file_or_tableioinfo_to_typeio = self.input_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
self.__foowrapper_wrong_content2 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content2.relation_toolwrapper_to_fileioinfo.extend([f1, f2, f3])
self.__foowrapper_wrong_content2.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
self.__foowrapper_wrong_content2.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param2", value="2")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
self.__foowrapper_wrong_content3 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content3.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__foowrapper_wrong_content3.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
self.__foowrapper_wrong_content3.relation_toolwrapper_to_option.append(opt1)
opt1 = Option(name="param1", value="String")
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
self.__foowrapper_wrong_content4 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content4.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__foowrapper_wrong_content4.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
self.__foowrapper_wrong_content4.relation_toolwrapper_to_option.append(opt1)
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
t1 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t1.set_table(FooBase)
t1.model_declarative_meta = FooBase
t1.table = t1
t2 = TableInputOutputInformation(model_py_path="FooBase", table_key="FooBase", table_name="FooBase")
# t2.set_table(FooBase)
t2.model_declarative_meta = FooBase
t2.table = t2
self.__foowrapper_wrong_content5 = FooWrapper3(rule_name="rule3")
self.__foowrapper_wrong_content5.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
self.__foowrapper_wrong_content5.relation_toolwrapper_to_tableioinfo.extend([t1, t2])
# TooLWrappers for follows
f1 = FileInputOutputInformation(file_key="input1", path="file1.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper_first = FooWrapper2(rule_name="rule1")
self.__toolwrapper_first.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
f1 = FileInputOutputInformation(file_key="input1", path="file2.txt")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file3.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper_second = FooWrapper2(rule_name="rule2")
self.__toolwrapper_second.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
# ToolWrappers for are_input_ready
s_path_to_example_file_that_exists = os.path.join(self.test_path, "resource/input_files/input_file1.txt")
f1 = FileInputOutputInformation(file_key="input1", path=s_path_to_example_file_that_exists)
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_ready.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
f1 = FileInputOutputInformation(file_key="input1", path="/not/existent/file")
f1.relation_file_or_tableioinfo_to_typeio = self.input_entry
f2 = FileInputOutputInformation(file_key="output1", path="file2.txt")
f2.relation_file_or_tableioinfo_to_typeio = self.output_entry
self.__toolwrapper_not_ready = FooWrapper2(rule_name="rule2")
self.__toolwrapper_not_ready.relation_toolwrapper_to_fileioinfo.extend([f1, f2])
