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-rw-r--r--gn3/db/sample_data.py32
-rw-r--r--tests/unit/db/test_sample_data.py21
2 files changed, 53 insertions, 0 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index ccb03f2..06c3cc5 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -11,6 +11,38 @@ _MAP = {
}
+def __extract_actions(original_data: str,
+ updated_data: str,
+ csv_header: str) -> dict:
+ original_data = original_data.strip().split(",")
+ updated_data = updated_data.strip().split(",")
+ csv_header = csv_header.strip().split(",")
+ result = {
+ "delete": {"data": [], "csv_header": []},
+ "insert": {"data": [], "csv_header": []},
+ "update": {"data": [], "csv_header": []},
+ }
+ for _o, _u, _h in zip(original_data, updated_data, csv_header):
+ if _o == _u: # No change
+ continue
+ elif _o and _u == "x": # Deletion
+ result["delete"]["data"].append(_o)
+ result["delete"]["csv_header"].append(_h)
+ elif _o == "x" and _u: # Insert
+ result["insert"]["data"].append(_u)
+ result["insert"]["csv_header"].append(_h)
+ elif _o and _u: # Update
+ result["update"]["data"].append(_u)
+ result["update"]["csv_header"].append(_h)
+ for key, val in result.items():
+ if not val["data"]:
+ result[key] = None
+ else:
+ result[key]["data"] = ",".join(result[key]["data"])
+ result[key]["csv_header"] = ",".join(result[key]["csv_header"])
+ return result
+
+
def get_trait_csv_sample_data(conn: Any,
trait_name: int, phenotype_id: int) -> str:
"""Fetch a trait and return it as a csv string"""
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index 4c03dbd..4015ba5 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -2,6 +2,7 @@ import pytest
from gn3.db.sample_data import insert_sample_data
from gn3.db.sample_data import delete_sample_data
+from gn3.db.sample_data import __extract_actions
@pytest.mark.unit_test
@@ -73,3 +74,23 @@ def test_delete_sample_data(mocker):
(strain_id, "Sex", inbredset_id)),
]
cursor.execute.assert_has_calls(calls, any_order=False)
+
+
+@pytest.mark.unit_test
+def test_extract_actions():
+ assert (__extract_actions(original_data="BXD1,18,x,0,x",
+ updated_data="BXD1,x,2,1,F",
+ csv_header="Strain Name,Value,SE,Count,Sex") ==
+ {
+ "delete": {"data": "18", "csv_header": "Value"},
+ "insert": {"data": "2,F", "csv_header": "SE,Sex"},
+ "update": {"data": "1", "csv_header": "Count"},
+ })
+ assert(__extract_actions(original_data="BXD1,18,x,0,x",
+ updated_data="BXD1,19,2,1,F",
+ csv_header="Strain Name,Value,SE,Count,Sex") ==
+ {
+ "delete": None,
+ "insert": {"data": "2,F", "csv_header": "SE,Sex"},
+ "update": {"data": "19,1", "csv_header": "Value,Count"},
+ })