def setUp(self) -> None:
"""Test up the test cases with the third basic example."""
msdf1 = read_sssom_table(f"{data_dir}/basic.tsv")
msdf2 = read_sssom_table(f"{data_dir}/basic2.tsv")
msdf3 = read_sssom_table(f"{data_dir}/basic3.tsv")
self.msdf = msdf1
self.msdfs = [msdf1, msdf2, msdf3]
def test_merge(self):
"""Test merging two tables."""
msdf1 = read_sssom_table(data_dir / "basic.tsv")
msdf2 = read_sssom_table(data_dir / "basic2.tsv")
merged_msdf = merge_msdf(msdf1, msdf2)
self.assertEqual(71, len(merged_msdf.df))
def test_merge_no_reconcile(self):
"""Test merging two tables without reconciliation."""
msdf1 = read_sssom_table(data_dir / "basic4.tsv")
msdf2 = read_sssom_table(data_dir / "basic5.tsv")
merged_msdf = merge_msdf(msdf1, msdf2, reconcile=False)
self.assertEqual(53, len(msdf1.df))
self.assertEqual(53, len(msdf2.df))
self.assertEqual(len(merged_msdf.df), (len(msdf1.df) + len(msdf2.df)))
def test_read_sssom_table(self):
"""Test read SSSOM method to validate import of all columns."""
input_path = os.path.join(test_data_dir, "basic3.tsv")
msdf = read_sssom_table(input_path)
imported_df = pd.read_csv(input_path, comment="#", sep="\t")
imported_df = sort_df_rows_columns(imported_df)
self.assertEqual(set(imported_df.columns), set(msdf.df.columns))
list_cols = [
"subject_match_field",
"object_match_field",
"match_string",
"match_type",
]
for idx, row in msdf.df.iterrows():
for k, v in row.iteritems():
if v == "":
self.assertTrue(math.isnan(imported_df.iloc[idx][k]))
else:
if k not in list_cols:
if v is np.nan:
self.assertTrue(imported_df.iloc[idx][k] is v)
else:
self.assertEqual(imported_df.iloc[idx][k], v)
elif k == "match_type":
self.assertEqual(imported_df.iloc[idx][k], v)
else:
self.assertEqual(imported_df.iloc[idx][k], v)
def test_parse_sssom_dataframe_url(self):
"""Test parsing a TSV from a URL."""
msdf = read_sssom_table(self.df_url)
output_path = os.path.join(test_out_dir, "test_parse_sssom_dataframe_url.tsv")
with open(output_path, "w") as file:
write_table(msdf, file)
self.assertEqual(
len(msdf.df),
141,
f"{self.df_url} has the wrong number of mappings.",
)
def test_piped_element_to_list(self):
"""Test for multi-valued element (piped in SSSOM tables) to list."""
input_path = os.path.join(test_data_dir, "basic.tsv")
msdf = read_sssom_table(input_path)
df = msdf.df
msdf.df = df[df["match_type"].str.contains("\\|", na=False)].reset_index()
old_match_type = msdf.df["match_type"]
msdoc = to_mapping_set_document(msdf)
new_msdf = to_mapping_set_dataframe(msdoc)
new_match_type = new_msdf.df["match_type"]
self.assertTrue(old_match_type.equals(new_match_type))
def test_write_sssom_dataframe(self):
"""Test writing as a dataframe."""
tmp_path = os.path.join(test_out_dir, "test_write_sssom_dataframe.tsv")
with open(tmp_path, "w") as tmp_file:
write_table(self.msdf, tmp_file)
msdf = read_sssom_table(tmp_path)
self.assertEqual(
len(msdf.df),
self.mapping_count,
f"{tmp_file} has the wrong number of mappings.",
)
def test_parse_sssom_dataframe(self):
"""Test parsing a TSV."""
input_path = f"{test_data_dir}/basic.tsv"
msdf = read_sssom_table(input_path)
output_path = os.path.join(test_out_dir, "test_parse_sssom_dataframe.tsv")
with open(output_path, "w") as file:
write_table(msdf, file)
self.assertEqual(
len(msdf.df),
141,
f"{input_path} has the wrong number of mappings.",
)
def test_reconcile_prefix(self):
"""Test curie reconciliation is performing as expected."""
msdf = read_sssom_table(data_dir / "basic3.tsv")
with open(prefix_recon_yaml) as pref_rec:
prefix_reconciliation = yaml.safe_load(pref_rec)
recon_msdf = reconcile_prefix_and_data(msdf, prefix_reconciliation)
prefix_expansion = prefix_reconciliation[
"prefix_expansion_reconciliation"]
for pfx, exp in prefix_expansion.items():
if pfx in recon_msdf.prefix_map.keys():
self.assertEqual(recon_msdf.prefix_map[pfx], exp)
def setUp(self) -> None:
"""Test up the test cases with the third basic example."""
self.msdf = read_sssom_table(f"{data_dir}/basic6.tsv")
def setUp(self) -> None:
"""Set up the test case with the COB mappings et and OWL graph."""
self.mset = read_sssom_table(data_dir / "cob-to-external.tsv")
g = Graph()
g.parse(os.path.join(data_dir, "cob.owl"), format="xml")
self.graph = g
def setUp(self) -> None:
"""Test up the test case with the third basic example."""
self.msdf = read_sssom_table(data_dir / "basic3.tsv")
def setUp(self) -> None:
"""Set up the test case with two tables."""
self.msdf = read_sssom_table(data_dir / "basic.tsv")
self.cob = read_sssom_table(data_dir / "cob-to-external.tsv")
def setUp(self) -> None:
"""Set up the test case by reading the basic SSSOM example."""
self.mset = read_sssom_table(data_dir / "basic.tsv")
def setUp(self) -> None:
"""Set up the test case with a basic SSSOM example."""
self.msdf = read_sssom_table(f"{test_data_dir}/basic.tsv")
# self.msdf = read_sssom_table(f"{test_data_dir}/basic-simple.tsv")
self.mapping_count = 141 # 141 for basic.tsv