add first tests

tests/test_cli.py

@@ -4,8 +4,52 @@
 # builtin
 import unittest
 
+import os
+import pandas as pd
+
 # local
-import alphamap.cli
+from alphamap.importing import read_file, \
+    extract_rawfile_unique_values
+
+THIS_FOLDER = os.path.dirname(__file__)
+TEST_FOLDER = os.path.join(
+    f"{os.path.dirname(THIS_FOLDER)}",
+    "nbs",
+    "testdata",
+)
+
+class TestAll(unittest.TestCase):
+
+    def test_read_file(self,):
+        file_with_missing_col = os.path.join(TEST_FOLDER,'test_not_all_columns_spectronaut.csv')
+        spectronaut_columns = ["PEP.AllOccurringProteinAccessions","EG.ModifiedSequence","R.FileName"]
+
+        try:
+            out = read_file(file_with_missing_col, spectronaut_columns)
+        except ValueError as e:
+            out = e
+        assert str(out) == "The list of specified column names cannot be extracted from the file." 
+
+    def test_extract_rawfile_unique_values(self, ):
+        data_Spectronaut_csv = os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv')
+        data_Spectronaut_tsv = os.path.join(TEST_FOLDER, 'test_spectronaut_input.tsv')
+        assert ['raw_01', 'raw_02'] == extract_rawfile_unique_values(data_Spectronaut_csv)
+        assert extract_rawfile_unique_values(data_Spectronaut_csv) == extract_rawfile_unique_values(data_Spectronaut_tsv)
+
+        data_MQ = os.path.join(TEST_FOLDER, 'test_maxquant_input.txt')
+        assert len(extract_rawfile_unique_values(data_MQ)) == 381
+
+        data_wrong = os.path.join(TEST_FOLDER, 'test_maxquant_imported.csv')
+        try:
+            out = extract_rawfile_unique_values(data_wrong)
+        except ValueError as e:
+            out = e
+        assert str(out) == "A column with the raw file names is not in the file." 
+
+        data_fragpipe_combined = os.path.join(TEST_FOLDER, 'combined_peptide.txt')
+        assert ['Y731F1', 'Y731F2', 'wt1', 'wt2'] == extract_rawfile_unique_values(data_fragpipe_combined)
+
+
 
 if __name__ == "__main__":
     unittest.main()