def apply_filters(alchemist, table, 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, key=table)
db_filter.key = table
db_filter.values = values
try:
db_filter.add(filters)
except:
print("Please check your syntax for the conditional string: "
f"{filters}")
exit(1)
return db_filter
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()
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_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):
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 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)