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Rename host_subject_id to host_subject_name for v1.1.0 schema #92

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Rename host_subject_id to host_subject_name for v1.1.0 schema #92

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10 changes: 5 additions & 5 deletions src/pmotools/pmo_builder/metatable_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ def specimen_info_table_to_pmo(
has_travel_out_six_month_col: str = None,
host_age_col: str = None,
host_sex_col: str = None,
host_subject_id: str = None,
host_subject_name_col: str = None,
lat_lon_col: str = None,
parasite_density_col: str = None,
parasite_density_method_col: str = None,
Expand Down Expand Up @@ -281,8 +281,8 @@ def specimen_info_table_to_pmo(
:type host_age_col: str, optional
:param host_sex_col: if the specimen is from a person, the sex of that person
:type host_sex_col: str, optional
:param host_subject_id: ID for the individual a specimen was collected from
:type host_subject_id: str, optional
:param host_subject_name_col: identifier for the individual a specimen was collected from
:type host_subject_name_col: str, optional
:param lat_lon_col: latitude and longitude of the collection site
:type lat_lon_col: str, optional
:param parasite_density_col: the parasite density in parasites per microliter
Expand Down Expand Up @@ -353,7 +353,7 @@ def specimen_info_table_to_pmo(
geo_admin3_col: "geo_admin3",
host_age_col: "host_age",
host_sex_col: "host_sex",
host_subject_id: "host_subject_id",
host_subject_name_col: "host_subject_name",
lat_lon_col: "lat_lon",
specimen_accession_col: "specimen_accession",
specimen_type_col: "specimen_type",
Expand Down Expand Up @@ -392,7 +392,7 @@ def specimen_info_table_to_pmo(
geo_admin3_col,
host_age_col,
host_sex_col,
host_subject_id,
host_subject_name_col,
lat_lon_col,
specimen_accession_col,
specimen_type_col,
Expand Down
16 changes: 8 additions & 8 deletions tests/test_pmo_builder/test_metatable_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1028,7 +1028,7 @@ def test_specimen_info_table_to_pmo_with_host_fields(self):
"project_name": ["project1", "project2", "project3"],
"host_age": [25, None, 30],
"host_sex": ["M", "F", ""],
"host_subject_id": ["SUB001", "", "SUB003"],
"host_subject_name": ["SUB001", "", "SUB003"],
"gravid": [True, None, False],
"gravidity": [2, None, 0],
}
Expand All @@ -1044,33 +1044,33 @@ def test_specimen_info_table_to_pmo_with_host_fields(self):
project_name_col="project_name",
host_age_col="host_age",
host_sex_col="host_sex",
host_subject_id="host_subject_id",
host_subject_name_col="host_subject_name",
gravid_col="gravid",
gravidity_col="gravidity",
)

# sample1: all fields have values
self.assertEqual(result[0]["host_age"], 25)
self.assertEqual(result[0]["host_sex"], "M")
self.assertEqual(result[0]["host_subject_id"], "SUB001")
self.assertEqual(result[0]["host_subject_name"], "SUB001")
self.assertEqual(result[0]["gravid"], True)
self.assertEqual(result[0]["gravidity"], 2)

# sample2: host_age is None, host_subject_id is empty string, gravid is None, gravidity is None
# Should remove: host_age, host_subject_id, gravid, gravidity
# sample2: host_age is None, host_subject_name is empty string, gravid is None, gravidity is None
# Should remove: host_age, host_subject_name, gravid, gravidity
# Should keep: host_sex
self.assertNotIn("host_age", result[1])
self.assertEqual(result[1]["host_sex"], "F")
self.assertNotIn("host_subject_id", result[1])
self.assertNotIn("host_subject_name", result[1])
self.assertNotIn("gravid", result[1])
self.assertNotIn("gravidity", result[1])

# sample3: host_sex is empty string
# Should remove: host_sex
# Should keep: host_age, host_subject_id, gravid, gravidity
# Should keep: host_age, host_subject_name, gravid, gravidity
self.assertEqual(result[2]["host_age"], 30)
self.assertNotIn("host_sex", result[2])
self.assertEqual(result[2]["host_subject_id"], "SUB003")
self.assertEqual(result[2]["host_subject_name"], "SUB003")
self.assertEqual(result[2]["gravid"], False)
self.assertEqual(result[2]["gravidity"], 0)

Expand Down
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