def setUp(self, is_instance_mock):
is_instance_mock.return_value = True
alchemist = Mock(spec=AlchemyHandler)
engine = Mock(spec=Engine)
graph = Mock(spec=Graph)
session = Mock(spec=Session)
mapper = Mock(spec=DeclarativeMeta)
key = Mock(spec=Column)
proxy = Mock()
type(alchemist).engine = PropertyMock(return_value=engine)
type(alchemist).graph = PropertyMock(return_value=graph)
type(alchemist).session = PropertyMock(return_value=session)
type(alchemist).mapper = PropertyMock(return_value=mapper)
type(alchemist).connected = PropertyMock(return_value=True)
engine.execute.return_value = proxy
proxy.fetchall.return_value = []
self.mock_isinstance = is_instance_mock
self.mock_alchemist = alchemist
self.mock_engine = engine
self.mock_graph = graph
self.mock_session = session
self.mock_mapper = mapper
self.mock_key = key
self.db_filter = Filter(alchemist=alchemist, key=key)
self.assertEqual(self.db_filter.engine, self.mock_engine)
self.assertEqual(self.db_filter.graph, self.mock_graph)
def get_cds_seqrecords(alchemist, values, data_cache=None, nucleotide=False,
verbose=False):
if data_cache is None:
data_cache = {}
cds_list = parse_feature_data(alchemist, values=values)
db_filter = Filter(alchemist)
db_filter.key = 'gene.GeneID'
if verbose:
print("...Converting SQL data...")
seqrecords = []
for cds in cds_list:
parent_genome = data_cache.get(cds.genome_id)
if parent_genome is None:
parent_genome = get_single_genome(alchemist, cds.genome_id,
data_cache=data_cache)
cds.genome_length = parent_genome.length
cds.set_seqfeature()
db_filter.values = [cds.id]
gene_domains = db_filter.select(CDD_DATA_COLUMNS)
record = flat_files.cds_to_seqrecord(cds, parent_genome,
gene_domains=gene_domains)
seqrecords.append(record)
return seqrecords
def main(unparsed_args_list):
"""Run main get_gb_records pipeline."""
# Parse command line arguments
args = parse_args(unparsed_args_list)
# Filters input: phage.Status=draft AND phage.HostGenus=Mycobacterium
# Args structure: [['phage.Status=draft'], ['phage.HostGenus=Mycobacterium']]
filters = args.filters
ncbi_cred_dict = ncbi.get_ncbi_creds(args.ncbi_credentials_file)
output_folder = basic.set_path(args.output_folder, kind="dir", expect=True)
working_dir = pathlib.Path(RESULTS_FOLDER)
working_path = basic.make_new_dir(output_folder, working_dir, attempt=50)
if working_path is None:
print(f"Invalid working directory '{working_dir}'")
sys.exit(1)
# Verify database connection and schema compatibility.
print("Connecting to the MySQL database...")
alchemist = AlchemyHandler(database=args.database)
alchemist.connect(pipeline=True)
engine = alchemist.engine
mysqldb.check_schema_compatibility(engine, "the get_gb_records pipeline")
# Get SQLAlchemy metadata Table object
# table_obj.primary_key.columns is a
# SQLAlchemy ColumnCollection iterable object
# Set primary key = 'phage.PhageID'
alchemist.build_metadata()
table = querying.get_table(alchemist.metadata, TARGET_TABLE)
for column in table.primary_key.columns:
primary_key = column
# Create filter object and then add command line filter strings
db_filter = Filter(alchemist=alchemist, key=primary_key)
db_filter.values = []
# Attempt to add filters and exit if needed.
add_filters(db_filter, filters)
# Performs the query
db_filter.update()
# db_filter.values now contains list of PhageIDs that pass the filters.
# Get the accessions associated with these PhageIDs.
keep_set = set(db_filter.values)
# Create data sets
print("Retrieving accessions from the database...")
query = construct_accession_query(keep_set)
list_of_dicts = mysqldb_basic.query_dict_list(engine, query)
id_acc_dict = get_id_acc_dict(list_of_dicts)
acc_id_dict = get_acc_id_dict(id_acc_dict)
engine.dispose()
if len(acc_id_dict.keys()) > 0:
get_data(working_path, acc_id_dict, ncbi_cred_dict)
else:
print("There are no records to retrieve.")
def setUp(self):
self.review_test_dir = self.test_dir.joinpath("review_test_dir")
self.alchemist = AlchemyHandler()
self.alchemist.username = USER
self.alchemist.password = PWD
self.alchemist.database = DB
self.alchemist.connect(ask_database=True, login_attempts=0)
self.db_filter = Filter(alchemist=self.alchemist)
self.db_filter.add(review.BASE_CONDITIONALS)
self.db_filter.key = "gene.PhamID"
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username = "******"
alchemist.password = "******"
alchemist.database = "test_db"
alchemist.connect()
alchemist.build_graph()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
phageid = self.alchemist.get_column("phage.PhageID")
self.phageid = phageid
def build_filter(alchemist, key, filters, values=None, verbose=False):
"""Applies MySQL WHERE clause filters using a Filter.
:param alchemist: A connected and fully built AlchemyHandler object.
:type alchemist: AlchemyHandler
:param table: MySQL table name.
:type table: str
:param filters: A list of lists with filter values, grouped by ORs.
:type filters: list[list[str]]
:param groups: A list of supported MySQL column names.
:type groups: list[str]
:returns: filter-Loaded Filter object.
:rtype: Filter
"""
db_filter = Filter(alchemist=alchemist)
db_filter.key = key
db_filter.values = values
if filters != "":
try:
db_filter.add(filters)
except:
print("Please check your syntax for the conditional string: "
f"{filters}")
exit(1)
db_filter.parenthesize()
return db_filter
def setUp(self, IsInstance):
IsInstance.return_value = True
alchemist = Mock()
engine = Mock()
graph = Mock()
key = Mock()
alchemist.engine.return_value = engine
alchemist.graph.return_value = graph
alchemist.connected.return_value = True
self.mock_isinstance = IsInstance
self.mock_alchemist = alchemist
self.mock_engine = engine
self.mock_graph = graph
self.mock_key = key
self.db_filter = Filter(alchemist=alchemist, key=key)
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username=user
alchemist.password=pwd
alchemist.database=db
alchemist.connect()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
self.phage = self.alchemist.metadata.tables["phage"]
self.gene = self.alchemist.metadata.tables["gene"]
self.trna = self.alchemist.metadata.tables["trna"]
self.PhageID = self.phage.c.PhageID
self.Cluster = self.phage.c.Cluster
self.Subcluster = self.phage.c.Subcluster
self.Notes = self.gene.c.Notes
def setUp(self):
self.alchemist = AlchemyHandler()
self.alchemist.username=USER
self.alchemist.password=PWD
self.alchemist.database=DB
self.alchemist.connect(ask_database=True, login_attempts=0)
self.alchemist.build_graph()
self.db_filter = Filter(alchemist=self.alchemist)
self.export_test_dir = self.test_dir.joinpath("export_test_dir")
def get_acc_id_dict(alchemist):
"""Test helper function to retrieve accessions of database entries.
"""
db_filter = Filter(alchemist=alchemist)
db_filter.key = "phage.PhageID"
db_filter.values = db_filter.build_values()
groups = db_filter.group("phage.Accession")
return groups
class TestFilter(unittest.TestCase):
@patch("pdm_utils.classes.filter.isinstance")
def setUp(self, is_instance_mock):
is_instance_mock.return_value = True
alchemist = Mock(spec=AlchemyHandler)
engine = Mock(spec=Engine)
graph = Mock(spec=Graph)
session = Mock(spec=Session)
mapper = Mock(spec=DeclarativeMeta)
key = Mock(spec=Column)
proxy = Mock()
type(alchemist).engine = PropertyMock(return_value=engine)
type(alchemist).graph = PropertyMock(return_value=graph)
type(alchemist).session = PropertyMock(return_value=session)
type(alchemist).mapper = PropertyMock(return_value=mapper)
type(alchemist).connected = PropertyMock(return_value=True)
engine.execute.return_value = proxy
proxy.fetchall.return_value = []
self.mock_isinstance = is_instance_mock
self.mock_alchemist = alchemist
self.mock_engine = engine
self.mock_graph = graph
self.mock_session = session
self.mock_mapper = mapper
self.mock_key = key
self.db_filter = Filter(alchemist=alchemist, key=key)
self.assertEqual(self.db_filter.engine, self.mock_engine)
self.assertEqual(self.db_filter.graph, self.mock_graph)
def test_updated_1(self):
"""Verify that the upload property portrays Filter._upload.
"""
self.db_filter._updated = True
self.assertTrue(self.db_filter.updated)
def test_updated_2(self):
"""Verify that upload property is immutable.
"""
with self.assertRaises(AttributeError):
self.db_filter.updated = True
def test_values_valid_1(self):
"""Verify that the values_valid property portrays Filter._values_valid.
"""
self.db_filter._values_valid = True
self.assertTrue(self.db_filter.values_valid)
def test_values_valid_2(self):
"""Verify that the values_valid property is immutable.
"""
with self.assertRaises(AttributeError):
self.db_filter.values_valid = True
def test_connected_1(self):
"""Verify that the connected property portrays Filter._connected.
"""
self.db_filter._connected = True
self.assertTrue(self.db_filter.connected)
def test_connected_2(self):
"""Verify that the connected property is immutable.
"""
with self.assertRaises(AttributeError):
self.db_filter.connected = True
def test_engine_1(self):
"""Verify that the engine property portrays Filter._engine.
"""
self.db_filter._engine = self.mock_engine
self.assertEqual(self.db_filter.engine, self.mock_engine)
def test_graph_1(self):
"""Verify that the graph property portrays Filter._graph.
"""
self.db_filter._graph = self.mock_graph
self.assertEqual(self.db_filter.graph, self.mock_graph)
def test_session_1(self):
"""Verify that the session property portrays Filter._session.
"""
self.db_filter._session = self.mock_session
self.assertEqual(self.db_filter.session, self.mock_session)
def test_mapper_1(self):
"""Verify that the mapper property portrays Filter._mapper.
"""
self.db_filter._mapper = self.mock_mapper
self.assertEqual(self.db_filter.mapper, self.mock_mapper)
def test_values_1(self):
"""Verify that the values property portrays Filter._values.
"""
self.db_filter._values = ["Test1", "Test2"]
self.assertEqual(self.db_filter.values, ["Test1", "Test2"])
def test_values_2(self):
"""Verify that the values property can set Filter._values.
"""
self.db_filter.values = ["Test1", "Test2"]
self.assertEqual(self.db_filter.values, ["Test1", "Test2"])
def test_values_3(self):
"""Verify that the values property modifies the values_valid property.
"""
self.db_filter.values = ["Test1", "Test2"]
self.assertFalse(self.db_filter.values_valid)
def test_values_2(self):
"""Verify that the values property raises TypeError on invalid input.
"""
with self.assertRaises(TypeError):
self.db_filter.values = "Hello"
def test_key_1(self):
"""Verify that the key property modifies the Filter._key
"""
self.db_filter.key = self.mock_key
self.assertEqual(self.db_filter.key, self.mock_key)
def test_key_2(self):
"""Verify that the key property raises TypeError on invalid input.
"""
with self.assertRaises(TypeError):
self.db_filter.key = Mock()
@patch("pdm_utils.classes.filter.AlchemyHandler")
def test_connect_1(self, alchemyhandler_mock):
"""Verfiy that connect() returns when Filter is already connected.
"""
alchemyhandler_mock.return_value = self.mock_alchemist
self.db_filter._connected = True
self.db_filter.connect()
alchemyhandler_mock.assert_not_called()
@patch("pdm_utils.classes.filter.AlchemyHandler")
def test_connect_2(self, alchemyhandler_mock):
"""Verify that the Filter creates an AlchemyHandler.
"""
alchemyhandler_mock.return_value = self.mock_alchemist
self.db_filter._connected = False
self.db_filter.connect()
alchemyhandler_mock.assert_called()
@patch("pdm_utils.classes.filter.AlchemyHandler")
def test_connect_3(self, alchemyhandler_mock):
"""Verify that the Filter uses an AlchemyHandler to connect.
"""
alchemyhandler_mock.return_value = self.mock_alchemist
self.db_filter._connected = False
self.db_filter.connect()
self.mock_alchemist.connect.assert_called()
@patch("pdm_utils.classes.filter.isinstance")
def test_link_1(self, isinstance_mock):
"""Verify link() calls isinstance().
"""
self.db_filter.link(self.mock_alchemist)
isinstance_mock.assert_called()
def test_link_2(self):
"""Verify link() raises TypeError upon bad alchemist input.
"""
with self.assertRaises(TypeError):
self.db_filter.link("Bad input")
def test_link_3(self):
"""Verify function structure of link().
"""
type(self.mock_alchemist).connected = PropertyMock(return_value=False)
type(self.mock_alchemist).graph = PropertyMock(return_value=None)
self.db_filter.link(self.mock_alchemist)
self.mock_alchemist.connect.assert_called()
@patch("pdm_utils.classes.filter.Filter.connect")
def test_check_1(self, connect_mock):
"""Verify that the Filter will connect if not connected.
"""
self.db_filter._connected = False
self.db_filter.check()
connect_mock.assert_called()
@patch("pdm_utils.classes.filter.isinstance")
def test_check_2(self, is_instance_mock):
"""Verify that the Filter calls isinstance() with correct paremeters.
"""
is_instance_mock.return_value = True
self.db_filter.check()
is_instance_mock.assert_any_call(self.mock_engine, Engine)
is_instance_mock.assert_any_call(self.mock_graph, Graph)
is_instance_mock.assert_any_call(self.mock_key, Column)
def test_check_3(self):
"""Verify that the Filter raises AttributeError with an invalid engine.
"""
self.db_filter._engine = "Not a valid engine"
with self.assertRaises(AttributeError):
self.db_filter.check()
def test_check_4(self):
"""Verify that the Filter raises AttributeError with an invalid graph.
"""
self.db_filter._graph = "Not a valid graph"
with self.assertRaises(AttributeError):
self.db_filter.check()
def test_check_5(self):
"""Verify that the Filter raises AttibuteError with an invalid key.
"""
self.db_filter._key = "Not a valid key"
with self.assertRaises(AttributeError):
self.db_filter.check()
@patch("pdm_utils.classes.filter.q.build_distinct")
@patch("pdm_utils.classes.filter.isinstance")
def test_build_values_1(self, is_instance_mock, build_distinct_mock):
"""Verify that build_distinct() is called with correct parameters.
"""
is_instance_mock.return_value = True
self.db_filter.build_values(where="Not a list")
build_distinct_mock.assert_called_with(self.mock_graph,
self.mock_key,
where="Not a list",
add_in=self.mock_key)
@patch("pdm_utils.classes.filter.Filter.check")
def test_transpose_1(self, check_mock):
"""Verify that transpose() returns without values.
"""
self.db_filter.transpose("gene.Notes")
check_mock.assert_called()
@patch("pdm_utils.classes.filter.Filter.check")
def test_mass_transpose_1(self, check_mock):
"""Verify that mass_tranpose() returns without values.
"""
self.db_filter.mass_transpose("Column")
check_mock.assert_called()
@patch("pdm_utils.classes.filter.q.build_distinct")
@patch("pdm_utils.classes.filter.Filter.check")
def test_retrieve_1(self, check_mock, build_distinct_mock):
"""Verify that retrieve() returns without values.
"""
self.db_filter.retrieve("Column")
check_mock.assert_called()
build_distinct_mock.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_refresh_1(self, build_values_mock, check_mock):
"""Verify that refresh() returns without values.
"""
self.db_filter.refresh()
check_mock.assert_called()
build_values_mock.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_refresh_2(self, build_values_mock, check_mock):
"""Verify that refresh() calls build_values() and conserves values.
"""
build_values_mock.return_value = ["Phage"]
self.db_filter._values_valid = False
self.db_filter.refresh()
check_mock.assert_called()
build_values_mock.assert_called()
self.assertTrue(self.db_filter.values_valid)
self.assertEqual(self.db_filter.values, ["Phage"])
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_1(self, build_values_mock, Refresh, check_mock):
"""Verify update() returns without values.
"""
self.db_filter.update()
check_mock.assert_called()
Refresh.assert_not_called()
build_values_mock.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_2(self, build_values_mock, Refresh, check_mock):
"""Verify update() refreshes values before updating.
"""
self.db_filter._values_valid = False
self.db_filter.update()
check_mock.assert_called()
Refresh.assert_called()
build_values_mock.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_3(self, build_values_mock, Refresh, check_mock):
"""Verify function structure of update().
"""
self.db_filter._values_valid = False
self.db_filter._updated = False
self.db_filter.update()
check_mock.assert_called()
Refresh.assert_called()
build_values_mock.assert_called()
self.assertTrue(self.db_filter._values_valid)
self.assertTrue(self.db_filter._values_valid)
@patch("pdm_utils.classes.filter.q.first_column")
@patch("pdm_utils.classes.filter.q.build_select")
@patch("pdm_utils.classes.filter.Filter.get_column")
def test_sort_1(self, get_column_mock, build_select_mock,
first_column_mock):
"""Verify function structure of sort().
"""
self.db_filter._values_valid = False
first_column_mock.return_value = ["Phage"]
self.db_filter.sort("column")
get_column_mock.assert_called()
build_select_mock.assert_called()
first_column_mock.assert_called()
self.assertTrue(self.db_filter._values_valid)
self.assertEqual(self.db_filter.values, ["Phage"])
def test_sort_2(self):
"""Verify that sort() raises TypeError at bad ORDER BY input.
"""
with self.assertRaises(TypeError):
self.db_filter.sort(None)
def test_reset_1(self):
"""Verify that reset() clears filters.
"""
self.db_filter._filters = [{"Expression": "Some Whereclause"}]
self.db_filter.reset()
self.assertEqual(self.db_filter.filters, [])
def test_reset_2(self):
"""Verify that reset() clears values.
"""
self.db_filter._values = ["Phage1", "Phage2", "Phage3"]
self.db_filter.reset()
self.assertEqual(self.db_filter.values, [])
def test_reset_3(self):
"""Verify that reset() sets values_valid Filter property.
"""
self.db_filter._values_valid = False
self.db_filter.reset()
self.assertTrue(self.db_filter.values_valid)
def test_reset_4(self):
"""Verify that reset() sets updated Filter property.
"""
self.db_filter._updated = False
self.db_filter.reset()
self.assertTrue(self.db_filter.updated)
def test_reset_5(self):
"""Verify that reset sets on_index property.
"""
self.db_filter._on_index = 5
self.db_filter.reset()
self.assertEqual(self.db_filter.or_index, -1)
def test_hits_1(self):
"""Verify that hits() accurately portrays no values.
"""
self.assertEqual(self.db_filter.hits(), 0)
def test_hits_2(self):
"""Verify that hits() accurately portrays a number of values.
"""
self.db_filter._values = ["Phage1", "Phage2", "Phage3"]
self.assertEqual(self.db_filter.hits(), 3)
def test_copy_1(self):
"""Verify that copy() reflects a Filter's updated property.
"""
self.db_filter._updated = False
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.updated, self.db_filter.updated)
def test_copy_2(self):
"""Verify that copy() reflects a Filter's values_valid property.
"""
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.values_valid, self.db_filter.values_valid)
def test_copy_3(self):
"""Verify that copy() reflects a Filter's filters property.
"""
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.filters, self.db_filter.filters)
def test_copy_4(self):
"""Verify that copy() reflects a Filter's engine property.
"""
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.engine, self.db_filter.engine)
def test_copy_5(self):
"""Verify that copy() reflects a Filter's graph property.
"""
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.graph, self.db_filter.graph)
def test_copy_6(self):
"""Verify that copy() reflects a Fitler's key property.
"""
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.key, self.db_filter.key)
def test_copy_7(self):
"""Verify that copy() reflects a Filter's values property.
"""
self.db_filter._values = ["Values"]
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.values, self.db_filter.values)
def test_copy_8(self):
"""Verify that copy() reflects a Filter's connected property.
"""
self.db_filter._connected = True
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter._connected, self.db_filter._connected)
def test_copy_filters_1(self):
"""Verify that copy_filters() replicates filters.
"""
self.db_filter._filters = [{
"Filter1": "Filter1",
"Filter2": "Filter2",
"Filter3": "Filter3"
}]
filters_copy = self.db_filter.copy_filters()
self.assertEqual(filters_copy, self.db_filter._filters)
def test_copy_filters_2(self):
"""Verify that copy_filters() creates new address for copied filters.
"""
self.db_filter._filters = [{
"Filter1": "Filter1",
"Filter2": "Filter2",
"Filter3": "Filter3"
}]
filters_copy = self.db_filter.copy_filters()
self.db_filter._filters[0].update({"Filter2": "filter2"})
self.assertNotEqual(filters_copy, self.db_filter._filters)
class TestFilter(unittest.TestCase):
@patch("pdm_utils.classes.filter.isinstance")
def setUp(self, IsInstance):
IsInstance.return_value = True
alchemist = Mock()
engine = Mock()
graph = Mock()
key = Mock()
alchemist.engine.return_value = engine
alchemist.graph.return_value = graph
alchemist.connected.return_value = True
self.mock_isinstance = IsInstance
self.mock_alchemist = alchemist
self.mock_engine = engine
self.mock_graph = graph
self.mock_key = key
self.db_filter = Filter(alchemist=alchemist, key=key)
def test_constructor_1(self):
db_filter = Filter()
def test_constructor_2(self):
self.mock_isinstance.assert_any_call(self.mock_alchemist,
AlchemyHandler)
self.mock_isinstance.assert_any_call(self.mock_key, Column)
def test_values_1(self):
self.db_filter.values = ["Test1", "Test2"]
self.assertFalse(self.db_filter.values_valid)
def test_values_2(self):
with self.assertRaises(TypeError):
self.db_filter.values = "Hello"
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.q.build_distinct")
def test_transpose_2(self, BuildDistinct, Check):
empty_values = self.db_filter.transpose("gene.Notes")
self.assertEqual(empty_values, [])
BuildDistinct.assert_not_called()
Check.assert_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.transpose")
def test_retrieve_1(self, Transpose, Check):
empty_data = self.db_filter.retrieve("Error")
self.assertEqual(empty_data, {})
Transpose.assert_not_called()
Check.assert_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_refresh_1(self, BuildValues, Check):
self.db_filter.refresh()
Check.assert_called()
BuildValues.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_refresh_2(self, BuildValues, Check):
BuildValues.return_value = ["Phage"]
self.db_filter._values_valid = False
self.db_filter.refresh()
Check.assert_called()
BuildValues.assert_called()
self.assertTrue(self.db_filter.values_valid)
self.assertEqual(self.db_filter.values, ["Phage"])
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_1(self, BuildValues, Refresh, Check):
self.db_filter.update()
Check.assert_called()
Refresh.assert_not_called()
BuildValues.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_2(self, BuildValues, Refresh, Check):
self.db_filter._values_valid = False
self.db_filter.update()
Check.assert_called()
Refresh.assert_called()
BuildValues.assert_not_called()
@patch("pdm_utils.classes.filter.Filter.check")
@patch("pdm_utils.classes.filter.Filter.refresh")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_update_3(self, BuildValues, Refresh, Check):
self.db_filter._values_valid = False
self.db_filter._updated = False
self.db_filter.update()
Check.assert_called()
Refresh.assert_called()
BuildValues.assert_called()
self.assertTrue(self.db_filter._values_valid)
self.assertTrue(self.db_filter._values_valid)
@patch("pdm_utils.classes.filter.isinstance")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_sort_1(self, BuildValues, IsInstance):
IsInstance.return_value = True
BuildValues.return_value = ["Phage"]
self.db_filter._values_valid = False
self.db_filter.sort("column")
IsInstance.assert_called()
BuildValues.assert_called()
self.assertTrue(self.db_filter._values_valid)
self.assertEqual(self.db_filter.values, ["Phage"])
@patch("pdm_utils.classes.filter.isinstance")
@patch("pdm_utils.classes.filter.Filter.build_values")
def test_sort_1(self, BuildValues, IsInstance):
IsInstance.return_value = False
with self.assertRaises(TypeError):
self.db_filter.sort()
def test_reset_1(self):
self.db_filter._filters = {"Expression": "Some Whereclause"}
self.db_filter.reset()
self.assertEqual(self.db_filter.filters, {})
def test_reset_2(self):
self.db_filter._values = ["Phage1", "Phage2", "Phage3"]
self.db_filter.reset()
self.assertEqual(self.db_filter.values, [])
def test_reset_3(self):
self.db_filter._values_valid = False
self.db_filter.reset()
self.assertTrue(self.db_filter.values_valid)
def test_reset_4(self):
self.db_filter._updated = False
self.db_filter.reset()
self.assertTrue(self.db_filter.updated)
def test_hits_1(self):
self.assertEqual(self.db_filter.hits(), 0)
def test_hits_2(self):
self.db_filter._values = ["Phage1", "Phage2", "Phage3"]
self.assertEqual(self.db_filter.hits(), 3)
def test_copy_1(self):
self.db_filter._updated = False
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.updated, self.db_filter.updated)
def test_copy_2(self):
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.values_valid, self.db_filter.values_valid)
def test_copy_3(self):
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.filters, self.db_filter.filters)
def test_copy_4(self):
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.engine, self.db_filter.engine)
def test_copy_5(self):
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.graph, self.db_filter.graph)
def test_copy_6(self):
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.key, self.db_filter.key)
def test_copy_7(self):
self.db_filter._values = ["Values"]
copy_filter = self.db_filter.copy()
self.assertEqual(copy_filter.values, self.db_filter.values)
def test_copy_filters_1(self):
self.db_filter._filters = {
"Filter1": ["Filter1"],
"Filter2": ["Filter2"],
"Filter3": ["Filter3"]
}
filters_copy = self.db_filter.copy_filters()
self.assertEqual(filters_copy, self.db_filter._filters)
def test_copy_filters_2(self):
self.db_filter._filters = {
"Filter1": ["Filter1"],
"Filter2": ["Filter2"],
"Filter3": ["Filter3"]
}
filters_copy = self.db_filter.copy_filters()
self.db_filter._filters.update({"Filter2": []})
self.assertNotEqual(filters_copy, self.db_filter._filters)
class TestFilter(unittest.TestCase):
@classmethod
def setUpClass(self):
test_db_utils.create_filled_test_db()
@classmethod
def tearDownClass(self):
test_db_utils.remove_db()
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username=user
alchemist.password=pwd
alchemist.database=db
alchemist.connect()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
self.phage = self.alchemist.metadata.tables["phage"]
self.gene = self.alchemist.metadata.tables["gene"]
self.trna = self.alchemist.metadata.tables["trna"]
self.PhageID = self.phage.c.PhageID
self.Cluster = self.phage.c.Cluster
self.Subcluster = self.phage.c.Subcluster
self.Notes = self.gene.c.Notes
def tearDown(self):
self.alchemist.clear()
def test_and__1(self):
"""Verify that and_() creates a dictionary key as expected.
"""
self.db_filter.and_("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
def test_and__2(self):
"""Verify that and_() stores BinaryExpression data as expected.
"""
self.db_filter.and_("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue(isinstance(or_block, dict))
where_clauses = or_block["phage.PhageID=Myrna"]
self.assertTrue(isinstance(where_clauses, BinaryExpression))
def test_and_3(self):
"""Verify that and_() recognizes previous and_() data.
"""
self.db_filter.and_("phage.PhageID = Myrna")
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
or_block = self.db_filter.filters[0]
self.assertEqual(len(or_block), 2)
def test_remove_1(self):
"""Verify that remove() removes dictionary entry after depleted.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.remove("phage.PhageID=Myrna")
self.assertEqual(self.db_filter.filters, [{}])
def test_remove_2(self):
"""Verify that remove() conserves dictionary entry if not depleted.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
self.db_filter.remove("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
where_clauses = or_block["phage.PhageID=D29"]
self.assertEqual(where_clauses.right.value, "D29")
def test_add_1(self):
"""Verify that add() creates a dictionary key as expected.
"""
self.db_filter.add("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
def test_add_2(self):
"""Verify that add() creates multiple keys as expected.
"""
self.db_filter.add("phage.PhageID=Myrna AND phage.PhageID = Trixie")
or_block = self.db_filter.filters[0]
self.assertTrue(len(or_block) == 2)
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
self.assertTrue("phage.PhageID=Trixie" in or_block.keys())
def test_add_3(self):
"""Verify that add() creates multiple or blocks as expected.
"""
self.db_filter.add("phage.PhageID=Myrna OR phage.PhageID = Trixie")
self.assertTrue(len(self.db_filter.filters) == 2)
first_or_block = self.db_filter.filters[0]
second_or_block = self.db_filter.filters[1]
self.assertTrue("phage.PhageID=Myrna" in first_or_block.keys())
self.assertFalse("phage.PhageID=Trixie" in first_or_block.keys())
self.assertFalse("phage.PhageID=Myrna" in second_or_block.keys())
self.assertTrue("phage.PhageID=Trixie" in second_or_block.keys())
def test_get_column_1(self):
"""Verify that get_column() converts string column input.
"""
self.db_filter.key = self.Cluster
column = self.db_filter.get_column("phage.PhageID")
self.assertEqual(column, self.PhageID)
def test_get_column_2(self):
"""Verify that get_column() conserves Column input.
"""
self.db_filter.key = self.Cluster
column = self.db_filter.get_column(self.PhageID)
self.assertEqual(column, self.PhageID)
def test_get_column_3(self):
"""Verify that get_column() raises TypeError.
get_column() should raise TypeError when column input is
neither a string or a Column.
"""
self.db_filter.key = self.Cluster
with self.assertRaises(TypeError):
self.db_filter.get_column(None)
def test_build_where_clauses_1(self):
"""Verify that build_where_clauses() forms list of expected length.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
self.assertEqual(len(queries[0]), 2)
def test_build_where_clauses_2(self):
"""Verify that build_where_clauses() forms list of BinaryExpressions.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
for query in queries:
self.assertTrue(isinstance(query, BooleanClauseList))
def test_build_values_1(self):
"""Verify that build_values() does not exclude values as expected.
"""
self.db_filter.key = self.PhageID
values = self.db_filter.build_values()
self.assertTrue("Myrna" in values)
self.assertTrue("D29" in values)
self.assertTrue("Alice" in values)
self.assertTrue("Trixie" in values)
def test_build_values_2(self):
"""Verify that build_values() utilizes WHERE clauses as expected.
"""
self.db_filter.key = self.PhageID
where_clause = (self.Cluster == "A")
values = self.db_filter.build_values(where=where_clause)
self.assertTrue("D29" in values)
self.assertTrue("Trixie" in values)
self.assertFalse("Myrna" in values)
self.assertFalse("Alice" in values)
def test_build_values_3(self):
"""Verify that build_values() creates DISTINCT values as expected.
"""
self.db_filter.key = self.Cluster
where_clause = (self.Subcluster == "A2")
values = self.db_filter.build_values(where=where_clause)
self.assertEqual(len(values), 1)
self.assertEqual(values, ["A"])
def test_build_values_4(self):
"""Verify that build_values() recognizes bytes-type column data.
"""
self.db_filter.key = self.Notes
values = self.db_filter.build_values()
self.assertTrue(isinstance(values[0], str))
def test_query_1(self):
"""Verify that query() creates instances as expected.
"""
self.db_filter.key = "phage.PhageID"
self.db_filter.values = ["Trixie", "D29"]
self.db_filter.refresh()
instances = self.db_filter.query("phage")
instance_ids = []
for instance in instances:
instance_ids.append(instance.PhageID)
self.assertTrue("Trixie" in instance_ids)
self.assertTrue("D29" in instance_ids)
self.assertFalse("Myrna" in instance_ids)
def test_query_2(self):
"""Verify that query() creates instances as expected.
"""
self.db_filter.key = "phage.PhageID"
self.db_filter.values = ["Trixie", "D29"]
self.db_filter.refresh()
instances = self.db_filter.query("gene")
instance_ids = set()
for instance in instances:
instance_ids.add(instance.phage.PhageID)
instance_ids = list(instance_ids)
self.assertTrue("Trixie" in instance_ids)
self.assertTrue("D29" in instance_ids)
self.assertFalse("Myrna" in instance_ids)
def test_transpose_1(self):
"""Verify that transpose() utilizes Filter values as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
clusters = self.db_filter.transpose("phage.Cluster")
self.assertEqual(clusters, ["C"])
def test_transpose_2(self):
"""Verify that transpose() can optionally create dict return value.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
clusters_dict = self.db_filter.transpose(self.Cluster, return_dict=True)
self.assertEqual(clusters_dict["Cluster"], ["C"])
def test_transpose_3(self):
"""Verify that transpose() can alter Filter properties as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
self.db_filter.transpose("phage.Cluster", set_values=True)
self.assertEqual(self.db_filter.key, self.Cluster)
self.assertEqual(self.db_filter.values, ["C"])
def test_transpose_4(self):
"""Verify that transpose() filter parameter functions as expected.
"""
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.key = self.PhageID
self.db_filter.add("gene.GeneID = Myrna_CDS_28")
values = self.db_filter.transpose("gene.GeneID", filter=True)
self.assertEqual(len(values), 1)
self.assertEqual(values[0], "Myrna_CDS_28")
def test_mass_transpose_1(self):
"""Verify that mass_tranpose() returns DISTINCT values as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
myrna_data = self.db_filter.mass_transpose(["phage.HostGenus",
"phage.Cluster",
"gene.Notes"])
self.assertTrue(len(myrna_data) == 3 )
self.assertTrue(isinstance(myrna_data, dict))
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
def test_mass_transpose_2(self):
"""Verify that mass_tranpose() utilizes all values as expected.
"""
self.db_filter.values = ["Myrna", "Trixie"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
data = self.db_filter.mass_transpose(["phage.HostGenus",
"phage.Cluster",
"gene.Notes"])
self.assertTrue(len(data) == 3)
self.assertTrue(isinstance(data, dict))
self.assertEqual(data["HostGenus"], ["Mycobacterium"])
self.assertEqual(data["Cluster"], ["C", "A"])
def test_retrieve_1(self):
"""Verify that retrieve() separates data as expected.
"""
self.db_filter.values = ["Myrna", "Trixie"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
data = self.db_filter.retrieve(["phage.HostGenus",
"phage.Cluster"])
myrna_data = data["Myrna"]
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
trixie_data = data["Trixie"]
self.assertEqual(trixie_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(trixie_data["Cluster"], ["A"])
def test_retrieve_2(self):
"""Verify that retrieve() separates data as expected.
"""
self.db_filter.values = ["A", "C"]
self.db_filter.key = self.Cluster
self.db_filter.refresh()
data = self.db_filter.retrieve(["phage.Cluster", "phage.PhageID"])
a_data = data["A"]
self.assertEqual(a_data["Cluster"], ["A"])
self.assertTrue("Trixie" in a_data["PhageID"])
self.assertFalse("Myrna" in a_data["PhageID"])
c_data = data["C"]
self.assertEqual(c_data["Cluster"], ["C"])
self.assertFalse("Trixie" in c_data["PhageID"])
self.assertTrue("Myrna" in c_data["PhageID"])
def test_refresh_1(self):
"""Verify that refresh() eliminates invalid data.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Sheetz"]
self.db_filter.refresh()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertFalse("Sheetz" in self.db_filter.values)
def test_update_1(self):
"""Verify that update() filters out values.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.update()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertFalse("D29" in self.db_filter.values)
def test_sort_1(self):
"""Verify that sort() orders values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.sort(self.PhageID)
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
def test_sort_2(self):
"""Verify that sort() orders values with multiple sort columns.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Alice"]
self.db_filter.sort([self.Cluster, self.PhageID])
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertTrue("Alice" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
self.assertEqual(self.db_filter.values[1], "Alice")
def test_group_1(self):
"""Verify that group() creates separate groups as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group(self.PhageID)
self.assertTrue("Myrna" in group_results.keys())
self.assertTrue("Myrna" in group_results["Myrna"])
self.assertTrue("D29" in group_results.keys())
self.assertTrue("D29" in group_results["D29"])
def test_group_2(self):
"""Verify that group() recognizes similarities in values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group("phage.HostGenus")
self.assertTrue("Mycobacterium" in group_results.keys())
self.assertTrue("Myrna" in group_results["Mycobacterium"])
self.assertTrue("D29" in group_results["Mycobacterium"])
def test_group_3(self):
"""Verify that group() recognizes differences in values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Trixie"]
group_results = self.db_filter.group("phage.Cluster")
self.assertTrue("A" in group_results.keys())
self.assertTrue("C" in group_results.keys())
self.assertTrue("Myrna" in group_results["C"])
self.assertTrue("D29" in group_results["A"])
self.assertTrue("Trixie" in group_results["A"])
def test_constructor_1(self):
db_filter = Filter(alchemist=self.alchemist)
def execute_review(alchemist, folder_path, folder_name,
review=True, values=[],
filters="", groups=[], sort=[],
g_reports=False, s_report=False,
verbose=False):
"""Executes the entirety of the pham review pipeline.
:param alchemist: A connected and fully built AlchemyHandler object.
:type alchemist: AlchemyHandler
:param folder_path: Path to a valid dir for new dir creation.
:type folder_path: Path
:param folder_name: A name for the export folder.
:type folder_name: str
:param csv_title: Title for an appended csv file prefix.
:type csv_title: str
:param review: A boolean to toggle filtering of phams by pham discrepancies.
:type review: bool
:param values: List of values to filter database results.
:type values: list[str]
:param filters: A list of lists with filter values, grouped by ORs.
:type filters: list[list[str]]
:param groups: A list of supported MySQL column names to group by.
:type groups: list[str]
:param sort: A list of supported MySQL column names to sort by.
:param g_reports: A boolean to toggle export of additional pham information.
:type g_reports: bool
:param verbose: A boolean value to toggle progress print statements.
:type verbose: bool
"""
db_filter = Filter(alchemist=alchemist)
db_filter.key = ("gene.PhamID")
if values:
db_filter.values = values
if verbose:
print(f"Identified {len(values)} phams to review...")
if filters != "":
try:
db_filter.add(filters)
except:
print("Please check your syntax for the conditional string:\n"
f"{filters}")
sys.exit(1)
finally:
db_filter.update()
db_filter._filters = []
db_filter._updated = False
db_filter._or_index = -1
db_filter.add(BASE_CONDITIONALS)
db_filter.update()
if not db_filter.values:
print("Current settings produced no database hits.")
sys.exit(1)
if review:
review_phams(db_filter, verbose=verbose)
if sort:
db_filter.sort(sort)
if verbose:
print("Creating export folder...")
export_path = folder_path.joinpath(folder_name)
export_path = basic.make_new_dir(folder_path, export_path, attempt=50)
conditionals_map = {}
export_db.build_groups_map(db_filter, export_path, conditionals_map,
groups=groups,
verbose=verbose)
if verbose:
print("Prepared query and path structure, beginning review export...")
original_phams = db_filter.values
total_g_data = {}
for mapped_path in conditionals_map.keys():
conditionals = conditionals_map[mapped_path]
db_filter.values = original_phams
db_filter.values = db_filter.build_values(where=conditionals)
pf_data = get_pf_data(alchemist, db_filter, verbose=verbose)
write_report(pf_data, mapped_path, PF_HEADER,
csv_name=f"FunctionReport",
verbose=verbose)
if g_reports:
execute_g_report_export(alchemist, db_filter, mapped_path,
total_g_data=total_g_data,
verbose=verbose)
if s_report:
execute_s_report_export(alchemist, db_filter, conditionals,
mapped_path,
verbose=verbose)
class TestFilter(unittest.TestCase):
@classmethod
def setUpClass(self):
setup_test_db()
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username = "******"
alchemist.password = "******"
alchemist.database = "test_db"
alchemist.connect()
alchemist.build_graph()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
phageid = self.alchemist.get_column("phage.PhageID")
self.phageid = phageid
def test_constructor_1(self):
db_filter = Filter(alchemist=self.alchemist)
def test_constructor_2(self):
self.assertTrue(isinstance(self.db_filter.graph, Graph))
self.assertTrue(isinstance(self.db_filter.engine, Engine))
def test_add_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.assertTrue("phage.PhageID=" in self.db_filter.filters.keys())
def test_add_2(self):
self.db_filter.add("phage.PhageID=Myrna")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertTrue(isinstance(where_clauses, list))
self.assertTrue(isinstance(where_clauses[0], BinaryExpression))
def test_add_3(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertEqual(len(where_clauses), 2)
def test_remove_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.remove("phage.PhageID=Myrna")
self.assertEqual(self.db_filter.filters, {})
def test_remove_2(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
self.db_filter.remove("phage.PhageID=Myrna")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertTrue(len(where_clauses) == 1)
self.assertEqual(where_clauses[0].right.value, "D29")
def test_build_where_clauses_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
self.assertEqual(len(queries), 2)
def test_build_where_clauses_2(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
for query in queries:
self.assertTrue(isinstance(query, BinaryExpression))
def test_build_values_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
values = self.db_filter.build_values()
self.assertTrue("Myrna" in values)
self.assertTrue("D29" in values)
def test_transpose_1(self):
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.phageid
self.db_filter.refresh()
host_genera = self.db_filter.transpose("phage.HostGenus")
self.assertEqual(host_genera, ["Mycobacterium"])
def test_retrieve_1(self):
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.phageid
self.db_filter.refresh()
myrna_data = self.db_filter.retrieve(
["phage.HostGenus", "phage.Cluster", "gene.Notes"])
self.assertTrue(len(myrna_data) == 3)
self.assertTrue(isinstance(myrna_data, dict))
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
def test_refresh_2(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29", "Sheetz"]
self.db_filter.refresh()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertFalse("Sheetz" in self.db_filter.values)
def test_update_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.update()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertFalse("D29" in self.db_filter.values)
def test_sort_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.sort(self.phageid)
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
def test_group_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group(self.phageid)
self.assertTrue("Myrna" in group_results.keys())
self.assertTrue("Myrna" in group_results["Myrna"])
self.assertTrue("D29" in group_results.keys())
self.assertTrue("D29" in group_results.keys())
def test_group_2(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group("phage.HostGenus")
self.assertTrue("Mycobacterium" in group_results.keys())
self.assertTrue("Myrna" in group_results["Mycobacterium"])
self.assertTrue("D29" in group_results["Mycobacterium"])
@classmethod
def tearDownClass(self):
teardown_test_db()
def main(unparsed_args_list):
"""Run main freeze database pipeline."""
args = parse_args(unparsed_args_list)
ref_database = args.database
reset = args.reset
new_database = args.new_database_name
prefix = args.prefix
# Filters input: phage.Status=draft AND phage.HostGenus=Mycobacterium
# Args structure: [['phage.Status=draft'], ['phage.HostGenus=Mycobacterium']]
filters = args.filters
# Create config object with data obtained from file and/or defaults.
config = configfile.build_complete_config(args.config_file)
mysql_creds = config["mysql"]
# Verify database connection and schema compatibility.
print("Connecting to the MySQL database...")
alchemist1 = AlchemyHandler(database=ref_database,
username=mysql_creds["user"],
password=mysql_creds["password"])
alchemist1.connect(pipeline=True)
engine1 = alchemist1.engine
mysqldb.check_schema_compatibility(engine1, "the freeze pipeline")
# Get SQLAlchemy metadata Table object
# table_obj.primary_key.columns is a
# SQLAlchemy ColumnCollection iterable object
# Set primary key = 'phage.PhageID'
alchemist1.build_metadata()
table = querying.get_table(alchemist1.metadata, TARGET_TABLE)
for column in table.primary_key.columns:
primary_key = column
# Create filter object and then add command line filter strings
db_filter = Filter(alchemist=alchemist1, key=primary_key)
db_filter.values = []
# Attempt to add filters and exit if needed.
add_filters(db_filter, filters)
# Performs the query
db_filter.update()
# db_filter.values now contains list of PhageIDs that pass the filters.
# Get the number of genomes that will be retained and build the
# MYSQL DELETE statement.
keep_set = set(db_filter.values)
delete_stmt = construct_delete_stmt(TARGET_TABLE, primary_key, keep_set)
count_query = construct_count_query(TARGET_TABLE, primary_key, keep_set)
phage_count = mysqldb_basic.scalar(alchemist1.engine, count_query)
# Determine the name of the new database.
if new_database is None:
if prefix is None:
prefix = get_prefix()
new_database = f"{prefix}_{phage_count}"
# Create the new database, but prevent overwriting of current database.
if engine1.url.database != new_database:
result = mysqldb_basic.drop_create_db(engine1, new_database)
else:
print(
"Error: names of the reference and frozen databases are the same.")
print("No database will be created.")
result = 1
# Copy database.
if result == 0:
print(f"Reference database: {ref_database}")
print(f"New database: {new_database}")
result = mysqldb_basic.copy_db(engine1, new_database)
if result == 0:
print(f"Deleting genomes...")
alchemist2 = AlchemyHandler(database=new_database,
username=engine1.url.username,
password=engine1.url.password)
alchemist2.connect(pipeline=True)
engine2 = alchemist2.engine
engine2.execute(delete_stmt)
if reset:
engine2.execute(RESET_VERSION)
# Close up all connections in the connection pool.
engine2.dispose()
else:
print("Unable to copy the database.")
# Close up all connections in the connection pool.
engine1.dispose()
else:
print(f"Error creating new database: {new_database}.")
print("Freeze database script completed.")
def test_constructor_1(self):
db_filter = Filter()
class TestPhamReview(unittest.TestCase):
@classmethod
def setUpClass(self):
test_db_utils.create_filled_test_db()
self.test_dir = Path(TEST_DIR)
if self.test_dir.is_dir():
shutil.rmtree(TEST_DIR)
self.test_dir.mkdir()
@classmethod
def tearDownClass(self):
test_db_utils.remove_db()
shutil.rmtree(TEST_DIR)
def setUp(self):
self.review_test_dir = self.test_dir.joinpath("review_test_dir")
self.alchemist = AlchemyHandler()
self.alchemist.username = USER
self.alchemist.password = PWD
self.alchemist.database = DB
self.alchemist.connect(ask_database=True, login_attempts=0)
self.db_filter = Filter(alchemist=self.alchemist)
self.db_filter.add(review.BASE_CONDITIONALS)
self.db_filter.key = "gene.PhamID"
def tearDown(self):
if self.review_test_dir.is_dir():
shutil.rmtree(str(self.review_test_dir))
def test_execute_review_1(self):
"""Verify execute_review() creates new directory as expected.
"""
review.execute_review(self.alchemist, self.test_dir,
self.review_test_dir.name)
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_review_2(self):
"""Verify execute_review() filter parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
filters=("phage.Cluster='A' "
"AND phage.Subcluster='A2'"))
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_review_3(self):
"""Verify execute_review() group parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
groups=["phage.Cluster"])
self.assertTrue(self.review_test_dir.is_dir())
clusterA_dir = self.review_test_dir.joinpath("A")
self.assertTrue(clusterA_dir.is_dir())
def test_execute_review_4(self):
"""Verify execute_review() sort parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
sort=["gene.Name"])
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_review_5(self):
"""Verify execute_review() review parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
review=False)
self.assertTrue(self.review_test_dir.is_dir())
def test_execute_review_6(self):
"""Verify execute_review() g_reports parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
g_reports=True)
self.assertTrue(self.review_test_dir.is_dir())
gene_report_dir = self.review_test_dir.joinpath("GeneReports")
self.assertTrue(gene_report_dir.is_dir())
def test_execute_review_7(self):
"""Verify execute_review() s_report parameter functions as expected.
"""
review.execute_review(self.alchemist,
self.test_dir,
self.review_test_dir.name,
s_report=True)
self.assertTrue(self.review_test_dir.is_dir())
summary_report_file = self.review_test_dir.joinpath(
"SummaryReport.txt")
self.assertTrue(summary_report_file.is_file())
def test_review_phams_1(self):
"""Verify review_phams() correctly identifies disrepencies.
"""
self.db_filter.values = self.db_filter.build_values(
where=self.db_filter.build_where_clauses())
review.review_phams(self.db_filter)
self.assertFalse(39854 in self.db_filter.values)
self.assertTrue(40481 in self.db_filter.values)
def test_get_pf_data_1(self):
"""Verify get_pf_data() retrieves and returns data as expected.
"""
self.db_filter.values = [40481]
pf_data = review.get_pf_data(self.alchemist, self.db_filter)
self.assertTrue(isinstance(pf_data, list))
for header in review.PF_HEADER:
with self.subTest(header=header):
self.assertTrue(header in pf_data[0].keys())
self.assertFalse(isinstance(pf_data[0][header], list))
def test_get_g_data_1(self):
"""Verify get_g_data() retreives and retrusn data as expected.
"""
self.db_filter.values = [40481]
g_data = review.get_g_data(self.alchemist, self.db_filter, 40481)
self.assertTrue(isinstance(g_data, list))
for header in review.PG_HEADER:
with self.subTest(header=header):
self.assertTrue(header in g_data[0].keys())
self.assertFalse(isinstance(g_data[0][header], list))
def execute_resubmit(alchemist,
revisions_data_dicts,
folder_path,
folder_name,
filters="",
groups=[],
verbose=False):
"""Executes the entirety of the genbank resubmit pipeline.
:param alchemist: A connected and fully built AlchemyHandler object.
:type alchemist: AlchemyHandler
:param revisions_data_dicts: Data dictionaries containing pham/notes data.
:type revisions_data_dicts: list[dict]
:param folder_path: Path to a valid dir for new dir creation.
:type folder_path: Path
:param folder_name: A name for the export folder.
:type folder_name: str
:param verbose: A boolean value to toggle progress print statements.
:type verbose: bool
"""
db_filter = Filter(alchemist=alchemist)
db_filter.key = "gene.PhamID"
db_filter.add(BASE_CONDITIONALS)
if filters != "":
try:
db_filter.add(filters)
except:
print("Please check your syntax for the conditional string:\n"
f"{filters}")
resubmit_columns = db_filter.get_columns(RESUBMIT_COLUMNS)
phams = []
for data_dict in revisions_data_dicts:
phams.append(data_dict["Pham"])
db_filter.values = phams
if verbose:
print("Creating export folder...")
export_path = folder_path.joinpath(folder_name)
export_path = basic.make_new_dir(folder_path, export_path, attempt=50)
conditionals_map = {}
export_db.build_groups_map(db_filter,
export_path,
conditionals_map,
groups=groups,
verbose=verbose)
if verbose:
print("Prepared query and path structure, beginning review export...")
for mapped_path in conditionals_map.keys():
if verbose:
print("Retreiving phage data for pham revisions...")
export_dicts = []
for data_dict in revisions_data_dicts:
if verbose:
print(f"...Retrieving data for pham {data_dict['Pham']}...")
conditionals = conditionals_map[mapped_path]
final_call = data_dict["Final Call"]
if final_call == "Hypothetical Protein":
final_call = ""
conditionals.append(
querying.build_where_clause(alchemist.graph,
f"gene.Notes!={final_call}"))
query = querying.build_select(alchemist.graph,
resubmit_columns,
where=conditionals)
results = querying.execute(alchemist.engine,
query,
in_column=db_filter.key,
values=[data_dict["Pham"]])
for result in results:
format_resubmit_data(result, data_dict["Final Call"])
export_dicts.append(result)
if not export_dicts:
if verbose:
print("'{mapped_path.name}' data selected for resubmision "
"matches selected call; no resubmision exported...")
mapped_path.rmdir()
continue
export_dicts = sorted(export_dicts,
key=lambda export_dict: export_dict["Phage"])
if verbose:
print(f"Writing {CSV_NAME} in {mapped_path.name}...")
file_path = mapped_path.joinpath(CSV_NAME)
basic.export_data_dict(export_dicts,
file_path,
RESUBMIT_HEADER,
include_headers=True)
def execute_export(alchemist,
output_path,
output_name,
values=[],
verbose=False,
csv_export=False,
ffile_export=None,
db_export=False,
table="phage",
filters=[],
groups=[]):
"""Executes the entirety of the file export pipeline.
:param sql_handle:
Input a valid SQLAlchemy Engine object.
:type sql_handle: Engine:
:param export_path:
Input a valid path to place export folder.
:type export_path: Path
:param folder_name:
Input a name for the export folder.
:type folder_name: str
:param phage_filter_list:
Input a list of phageIDs.
:type phage_filter_list: List[str]
:param verbose:
Input a boolean value for verbose option.
:type verbose: boolean
:param csv_export:
Input a boolean value to toggle csv_export.
:type csv_export: boolean
:param ffile_export:
Input a SeqIO supported file format to toggle ffile_export.
:type ffile_export: str
:param db_export:
Input a boolean value to toggle db_export.
:type db_export: boolean
:param filters:
Input a list of lists with filter values
:type filters: List[List[str]]
:param groups:
Input a list of supported group values.
:type groups: List[str]
"""
if verbose:
print("Retrieving database version...")
db_version = mysqldb.get_version_table_data(alchemist.engine)
if verbose:
print("Creating export folder...")
export_path = output_path.joinpath(output_name)
export_path = basic.make_new_dir(output_path, export_path, attempt=50)
if db_export:
if verbose:
print("Writing SQL database file...")
write_database(alchemist, db_version["Version"], export_path)
elif csv_export or ffile_export != None:
table_obj = alchemist.get_table(table)
for column in table_obj.primary_key.columns:
primary_key = column
db_filter = Filter(alchemist=alchemist, key=primary_key)
db_filter.values = values
for or_filters in filters:
for filter in or_filters:
db_filter.add(filter)
db_filter.update()
if filters and not db_filter.values:
return
values_map = {}
if groups:
build_groups_map(db_filter,
export_path,
groups=groups,
values_map=values_map,
verbose=verbose)
else:
values_map.update({export_path: db_filter.values})
for export_path in values_map.keys():
values = values_map[export_path]
if csv_export:
execute_csv_export(alchemist,
export_path,
table=table,
values=values,
verbose=verbose)
elif ffile_export != None:
execute_ffx_export(alchemist,
export_path,
ffile_export,
db_version,
table=table,
values=values,
verbose=verbose)