#17 - Validate unit test

Author: patkyn

Diff for: tests/test_validate_dwca.py

@@ -0,0 +1,76 @@
+from io import BytesIO
+from zipfile import ZipFile
+import zipfile
+from pathlib import Path
+from dwcahandler import DwcaHandler
+import logging
+import pytest
+
+input_folder = "./input_files/dwca"
+
+
+def make_zip_from_folder_contents(folder: str):
+    zip_buffer = BytesIO()
+    with ZipFile(file=zip_buffer, mode="w", compression=zipfile.ZIP_DEFLATED, allowZip64=True) as zf:
+        for path in Path(folder).rglob("*"):
+            zf.write(path, arcname=path.name)
+        zf.close()
+    return zip_buffer
+
+
+class TestValidateDwca:
+
+    def test_validate_dwca(self):
+        """
+        Test for read and extract dwca. Validate core content
+        """
+        simple_dwca = make_zip_from_folder_contents(f"{input_folder}/dwca-sample1")
+        keys_lookup = {'occurrence': 'occurrenceID'}
+        dwca_result = DwcaHandler.validate_dwca(dwca_file=simple_dwca, keys_lookup=keys_lookup)
+        assert dwca_result
+
+    def test_validate_dwca2(self):
+        """
+        Test for read and extract dwca. Validate core content
+        """
+        simple_dwca = make_zip_from_folder_contents(f"{input_folder}/dwca-sample2")
+        keys_lookup = {'occurrence': 'occurrenceID'}
+        dwca_result = DwcaHandler.validate_dwca(dwca_file=simple_dwca, keys_lookup=keys_lookup)
+        assert dwca_result
+
+    def test_empty_keys(self, caplog):
+        """
+        Test for read and extract dwca. Validate core content with empty keys
+        """
+        caplog.set_level(logging.INFO)
+        simple_dwca = make_zip_from_folder_contents(f"{input_folder}/dwca-sample3")
+        keys_lookup = {'occurrence': 'occurrenceID'}
+        dwca_result = DwcaHandler.validate_dwca(dwca_file=simple_dwca, keys_lookup=keys_lookup)
+        assert not dwca_result
+        assert "Empty values found in ['occurrenceID']. Total rows affected: 1" in caplog.messages
+        assert "Empty values found in dataframe row: [0]" in caplog.messages
+
+    def test_duplicate_key(self, caplog):
+        """
+        Test for read and extract dwca. Validate core content with duplicate keys
+        """
+        caplog.set_level(logging.INFO)
+        simple_dwca = make_zip_from_folder_contents(f"{input_folder}/dwca-sample4")
+        keys_lookup = {'occurrence': 'catalogNumber'}
+        dwca_result = DwcaHandler.validate_dwca(dwca_file=simple_dwca, keys_lookup=keys_lookup)
+        assert not dwca_result
+        assert "Duplicate ['catalogNumber'] found. Total rows affected: 3" in caplog.messages
+        assert "Duplicate values: ['014800' '014823']" in caplog.messages
+
+    def test_duplicate_columns_in_dwca(self):
+        """
+        Test for read and extract dwca. Validate duplicate columns specified in metadata of dwca
+        """
+        simple_dwca = make_zip_from_folder_contents(f"{input_folder}/dwca-sample5")
+        keys_lookup = {'occurrence': 'catalogNumber'}
+
+        with pytest.raises(ValueError) as exc_info:
+            DwcaHandler.validate_dwca(dwca_file=simple_dwca, keys_lookup=keys_lookup)
+
+        assert "Duplicate columns ['catalogNumber'] specified in the " \
+                   "metadata for occurrence.csv" in str(exc_info.value)