metameq 2026.2.2__tar.gz → 2026.2.3__tar.gz

{metameq-2026.2.2/metameq.egg-info → metameq-2026.2.3}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: metameq
-Version: 2026.2.2
+Version: 2026.2.3
 Summary: Qiita-compliant metadata generation and validation tool
 Home-page: https://github.com/AmandaBirmingham/metameq
 Author: Amanda Birmingham
 Author-email: abirmingham@ucsd.edu
 License: BSD-3-Clause
 Requires-Dist: click>=8.0.0
+Requires-Dist: openpyxl>=3.0.0
 Requires-Dist: pandas>=1.3.0
 Requires-Dist: PyYAML>=5.4.0
 Requires-Dist: Cerberus>=1.3.4

{metameq-2026.2.2 → metameq-2026.2.3}/README.md

@@ -106,7 +106,7 @@ from metameq import (
 )
 
 # Load your raw metadata into a DataFrame
-raw_metadata_df = pd.read_csv("my_samples.csv")
+raw_metadata_df = pd.read_csv("my_samples.csv", dtype=str)
 
 # Ensure required columns exist
 raw_metadata_df[HOSTTYPE_SHORTHAND_KEY] = "human"

{metameq-2026.2.2 → metameq-2026.2.3}/environment.yml

@@ -6,6 +6,7 @@ dependencies:
   - python
   - click
   - pandas
+  - openpyxl
   - pip
   - pyyaml
   - flake8

{metameq-2026.2.2 → metameq-2026.2.3}/metameq/__init__.py

@@ -9,7 +9,7 @@ from metameq.src.metadata_extender import \
     write_extended_metadata, write_extended_metadata_from_df, \
     get_reserved_cols, get_extended_metadata_from_df_and_yaml, \
     write_metadata_results, id_missing_cols, find_standard_cols, \
-    find_nonstandard_cols, get_qc_failures
+    find_nonstandard_cols, get_qc_failures, extend_metadata_df
 from metameq.src.metadata_merger import merge_sample_and_subject_metadata, \
     merge_many_to_one_metadata, merge_one_to_one_metadata, \
     find_common_col_names, find_common_df_cols
@@ -36,7 +36,8 @@ __all__ = ["HOSTTYPE_SHORTHAND_KEY", "SAMPLETYPE_SHORTHAND_KEY",
            "find_nonstandard_cols", "get_qc_failures",
            "format_a_datetime", "standardize_input_sex",
            "set_life_stage_from_age_yrs", "transform_input_sex_to_std_sex",
-           "transform_age_to_life_stage", "transform_date_to_formatted_date"]
+           "transform_age_to_life_stage", "transform_date_to_formatted_date",
+           "extend_metadata_df"]
 
 from . import _version
 __version__ = _version.get_versions()['version']

{metameq-2026.2.2 → metameq-2026.2.3}/metameq/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-02-02T16:43:52-0800",
+ "date": "2026-02-03T15:03:32-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "4fe1396e1007820dc7a4bdb58708fff0df6b9a57",
- "version": "2026.02.2"
+ "full-revisionid": "89687d23015566a7583179a69f92c2e1d1adcf61",
+ "version": "2026.02.3"
 }
 '''  # END VERSION_JSON
 

{metameq-2026.2.2 → metameq-2026.2.3}/metameq/src/metadata_extender.py

@@ -301,13 +301,13 @@ def write_extended_metadata(
     # extract the extension from the raw_metadata_fp file path
     extension = os.path.splitext(raw_metadata_fp)[1]
     if extension == ".csv":
-        raw_metadata_df = load_df_with_best_fit_encoding(raw_metadata_fp, ",")
+        raw_metadata_df = load_df_with_best_fit_encoding(raw_metadata_fp, ",", str)
     elif extension == ".txt":
-        raw_metadata_df = load_df_with_best_fit_encoding(raw_metadata_fp, "\t")
+        raw_metadata_df = load_df_with_best_fit_encoding(raw_metadata_fp, "\t", str)
     elif extension == ".xlsx":
         # NB: this loads (only) the first sheet of the input excel file.
         # If needed, can expand with pandas.read_excel sheet_name parameter.
-        raw_metadata_df = pandas.read_excel(raw_metadata_fp)
+        raw_metadata_df = pandas.read_excel(raw_metadata_fp, dtype=str)
     else:
         raise ValueError("Unrecognized input file extension; "
                          "must be .csv, .txt, or .xlsx")

{metameq-2026.2.2 → metameq-2026.2.3}/metameq/tests/test_metadata_extender.py

@@ -475,7 +475,7 @@ class TestMetadataExtender(TestCase):
 
             # Verify metadata file contents - includes failed row when remove_internals=False
             result_df = pandas.read_csv(
-                metadata_files[0], sep="\t", keep_default_na=False)
+                metadata_files[0], sep="\t", dtype=str, keep_default_na=False)
             assert_frame_equal(metadata_df, result_df)
 
             # Find the validation errors file (uses comma separator)
@@ -484,7 +484,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(validation_files))
 
             # Verify validation errors file contents
-            result_validation_df = pandas.read_csv(validation_files[0], sep=",")
+            result_validation_df = pandas.read_csv(validation_files[0], sep=",", dtype=str, keep_default_na=False)
             assert_frame_equal(validation_msgs_df, result_validation_df)
 
             # No fails file should be created when remove_internals=False
@@ -513,7 +513,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(metadata_files))
 
             # Verify metadata has internal cols removed and no failures
-            result_df = pandas.read_csv(metadata_files[0], sep="\t")
+            result_df = pandas.read_csv(metadata_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample3"],
                 "field_a": ["a1", "a3"]
@@ -526,7 +526,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(fails_files))
 
             # Verify fails file contains the failed row
-            fails_df = pandas.read_csv(fails_files[0], sep=",")
+            fails_df = pandas.read_csv(fails_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_fails_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample2"],
                 "field_a": ["a2"],
@@ -593,7 +593,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(metadata_files))
 
             # Verify custom internal cols are removed
-            result_df = pandas.read_csv(metadata_files[0], sep="\t")
+            result_df = pandas.read_csv(metadata_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "field_a": ["a1", "a2"]
@@ -3334,7 +3334,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(output_files))
 
             # Read and verify contents (keep_default_na=False preserves empty strings)
-            result_df = pandas.read_csv(output_files[0], sep="\t", keep_default_na=False)
+            result_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_df = input_df
             assert_frame_equal(expected_df, result_df)
 
@@ -3358,7 +3358,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(output_files))
 
             # Verify main output has internal cols removed and no failures
-            result_df = pandas.read_csv(output_files[0], sep="\t")
+            result_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample3"],
                 "field_a": ["a1", "a3"]
@@ -3370,7 +3370,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(fails_files))
 
             # Verify fails file contains the failed row
-            fails_df = pandas.read_csv(fails_files[0], sep=",")
+            fails_df = pandas.read_csv(fails_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_fails_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample2"],
                 "field_a": ["a2"],
@@ -3447,7 +3447,7 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(output_files))
 
             # Read and verify contents (keep_default_na=False preserves empty strings)
-            result_df = pandas.read_csv(output_files[0], sep=",", keep_default_na=False)
+            result_df = pandas.read_csv(output_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_df = input_df
             assert_frame_equal(expected_df, result_df)
 
@@ -3469,14 +3469,14 @@ class TestMetadataExtender(TestCase):
             # Main output file should have only headers (empty data)
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            result_df = pandas.read_csv(output_files[0], sep="\t")
+            result_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             self.assertTrue(result_df.empty)
             self.assertEqual([SAMPLE_NAME_KEY, "field_a"], list(result_df.columns))
 
             # Fails file should have both rows
             fails_files = glob.glob(os.path.join(tmpdir, "*_test_output_fails.csv"))
             self.assertEqual(1, len(fails_files))
-            fails_df = pandas.read_csv(fails_files[0], sep=",")
+            fails_df = pandas.read_csv(fails_files[0], sep=",", dtype=str, keep_default_na=False)
             self.assertEqual(2, len(fails_df))
 
     # Tests for get_extended_metadata_from_df_and_yaml
@@ -3621,7 +3621,7 @@ class TestMetadataExtender(TestCase):
             # Verify main output file was created (internal cols removed by default)
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
@@ -3694,7 +3694,7 @@ class TestMetadataExtender(TestCase):
             # Verify main output file excludes failure rows
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample3"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
@@ -3709,7 +3709,7 @@ class TestMetadataExtender(TestCase):
             # Verify fails file contains the failed row
             fails_files = glob.glob(os.path.join(tmpdir, "*_test_output_fails.csv"))
             self.assertEqual(1, len(fails_files))
-            fails_df = pandas.read_csv(fails_files[0], sep=",")
+            fails_df = pandas.read_csv(fails_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_fails_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample2"],
                 "body_product": ["not provided"],
@@ -3780,7 +3780,7 @@ class TestMetadataExtender(TestCase):
             validation_files = glob.glob(
                 os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
             self.assertEqual(1, len(validation_files))
-            validation_df = pandas.read_csv(validation_files[0], sep=",")
+            validation_df = pandas.read_csv(validation_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_validation_df = pandas.DataFrame({
                 "sample_name": ["sample1"],
                 "field_name": ["restricted_field"],
@@ -3821,7 +3821,7 @@ class TestMetadataExtender(TestCase):
             # Verify main output file includes internal columns
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t", keep_default_na=False)
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1"],
                 "body_product": ["UBERON:feces"],
@@ -3844,6 +3844,7 @@ class TestMetadataExtender(TestCase):
 
     TEST_METADATA_CSV_FP = path.join(TEST_DIR, "data/test_metadata.csv")
     TEST_METADATA_TXT_FP = path.join(TEST_DIR, "data/test_metadata.txt")
+    TEST_METADATA_XLSX_FP = path.join(TEST_DIR, "data/test_metadata.xlsx")
     TEST_METADATA_WITH_ERRORS_FP = path.join(
         TEST_DIR, "data/test_metadata_with_errors.csv")
     TEST_STUDY_CONFIG_WITH_VALIDATION_FP = path.join(
@@ -3862,6 +3863,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -3876,12 +3878,13 @@ class TestMetadataExtender(TestCase):
             # Verify main output file was created (internal cols removed by default)
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -3914,6 +3917,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -3928,12 +3932,13 @@ class TestMetadataExtender(TestCase):
             # Verify main output file was created
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -3942,6 +3947,60 @@ class TestMetadataExtender(TestCase):
             })
             assert_frame_equal(expected_output_df, output_df)
 
+    def test_write_extended_metadata_xlsx_input(self):
+        """Test writing extended metadata from an Excel XLSX input file."""
+        with tempfile.TemporaryDirectory() as tmpdir:
+            result_df = write_extended_metadata(
+                self.TEST_METADATA_XLSX_FP, self.TEST_STUDY_CONFIG_FP,
+                tmpdir, "test_output", stds_fp=self.TEST_STDS_FP)
+
+            # Verify returned DataFrame
+            expected_result_df = pandas.DataFrame({
+                SAMPLE_NAME_KEY: ["sample1", "sample2"],
+                "body_product": ["UBERON:feces", "UBERON:feces"],
+                "body_site": ["gut", "gut"],
+                "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
+                "host_common_name": ["human", "human"],
+                QIITA_SAMPLE_TYPE: ["stool", "stool"],
+                SAMPLE_TYPE_KEY: ["stool", "stool"],
+                "study_custom_field": ["custom_value", "custom_value"],
+                "study_stool_field": ["stool_custom", "stool_custom"],
+                HOSTTYPE_SHORTHAND_KEY: ["human", "human"],
+                SAMPLETYPE_SHORTHAND_KEY: ["stool", "stool"],
+                QC_NOTE_KEY: ["", ""]
+            })
+            assert_frame_equal(expected_result_df, result_df)
+
+            # Verify main output file was created
+            output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
+            self.assertEqual(1, len(output_files))
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
+            expected_output_df = pandas.DataFrame({
+                SAMPLE_NAME_KEY: ["sample1", "sample2"],
+                "body_product": ["UBERON:feces", "UBERON:feces"],
+                "body_site": ["gut", "gut"],
+                "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
+                "host_common_name": ["human", "human"],
+                QIITA_SAMPLE_TYPE: ["stool", "stool"],
+                SAMPLE_TYPE_KEY: ["stool", "stool"],
+                "study_custom_field": ["custom_value", "custom_value"],
+                "study_stool_field": ["stool_custom", "stool_custom"]
+            })
+            assert_frame_equal(expected_output_df, output_df)
+
+            # Verify empty fails file was created
+            fails_files = glob.glob(os.path.join(tmpdir, "*_test_output_fails.csv"))
+            self.assertEqual(1, len(fails_files))
+            self.assertEqual(0, os.path.getsize(fails_files[0]))
+
+            # Verify empty validation errors file was created
+            validation_files = glob.glob(
+                os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
+            self.assertEqual(1, len(validation_files))
+            self.assertEqual(0, os.path.getsize(validation_files[0]))
+
     def test_write_extended_metadata_with_validation_errors(self):
         """Test writing extended metadata when validation errors occur."""
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -3956,6 +4015,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 "restricted_field": ["invalid_value", "allowed_value"],
@@ -3969,12 +4029,13 @@ class TestMetadataExtender(TestCase):
             # Verify main output file was created
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 "restricted_field": ["invalid_value", "allowed_value"],
@@ -3986,7 +4047,7 @@ class TestMetadataExtender(TestCase):
             validation_files = glob.glob(
                 os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
             self.assertEqual(1, len(validation_files))
-            validation_df = pandas.read_csv(validation_files[0], sep=",")
+            validation_df = pandas.read_csv(validation_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_validation_df = pandas.DataFrame({
                 "sample_name": ["sample1"],
                 "field_name": ["restricted_field"],
@@ -4021,6 +4082,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4035,12 +4097,13 @@ class TestMetadataExtender(TestCase):
             # Verify output file has .csv extension
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.csv"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep=",")
+            output_df = pandas.read_csv(output_files[0], sep=",", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4063,6 +4126,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4077,12 +4141,13 @@ class TestMetadataExtender(TestCase):
             # Verify main output file includes internal columns
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t", keep_default_na=False)
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4112,6 +4177,7 @@ class TestMetadataExtender(TestCase):
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4126,12 +4192,13 @@ class TestMetadataExtender(TestCase):
             # Verify main output file was created
             output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
             self.assertEqual(1, len(output_files))
-            output_df = pandas.read_csv(output_files[0], sep="\t")
+            output_df = pandas.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             expected_output_df = pandas.DataFrame({
                 SAMPLE_NAME_KEY: ["sample1", "sample2"],
                 "body_product": ["UBERON:feces", "UBERON:feces"],
                 "body_site": ["gut", "gut"],
                 "description": ["human sample", "human sample"],
+                "dna_extracted": ["TRUE", "FALSE"],
                 "host_common_name": ["human", "human"],
                 QIITA_SAMPLE_TYPE: ["stool", "stool"],
                 SAMPLE_TYPE_KEY: ["stool", "stool"],
@@ -4149,6 +4216,64 @@ class TestMetadataExtender(TestCase):
                 os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
             self.assertEqual(0, len(validation_files))
 
+    def test_write_extended_metadata_preserves_string_booleans(self):
+        """Test that TRUE/FALSE string values are not converted to booleans.
+
+        This tests for a bug where loading a CSV without dtype=str causes
+        pandas to convert 'TRUE'/'FALSE' strings to boolean True/False,
+        which then fail validation against allowed string values.
+        """
+        with tempfile.TemporaryDirectory() as tmpdir:
+            # Create a CSV file with TRUE/FALSE string values
+            csv_content = (
+                "sample_name,hosttype_shorthand,sampletype_shorthand,dna_extracted\n"
+                "sample1,human,stool,TRUE\n"
+                "sample2,human,stool,FALSE\n"
+            )
+            csv_fp = path.join(tmpdir, "test_bool_strings.csv")
+            with open(csv_fp, "w") as f:
+                f.write(csv_content)
+
+            # Create a config that defines TRUE/FALSE as allowed string values
+            config_content = """
+default: "not provided"
+leave_requireds_blank: false
+overwrite_non_nans: false
+study_specific_metadata:
+  host_type_specific_metadata:
+    human:
+      default: "not provided"
+      leave_requireds_blank: false
+      overwrite_non_nans: false
+      sample_type_specific_metadata:
+        stool:
+          metadata_fields:
+            dna_extracted:
+              type: string
+              allowed:
+                - "TRUE"
+                - "FALSE"
+"""
+            config_fp = path.join(tmpdir, "test_bool_config.yml")
+            with open(config_fp, "w") as f:
+                f.write(config_content)
+
+            # Call write_extended_metadata
+            result_df = write_extended_metadata(
+                csv_fp, config_fp, tmpdir, "test_output",
+                stds_fp=self.TEST_STDS_FP)
+
+            # Verify the dna_extracted values are preserved as strings
+            self.assertEqual("TRUE", result_df.loc[0, "dna_extracted"])
+            self.assertEqual("FALSE", result_df.loc[1, "dna_extracted"])
+
+            # Verify no validation errors occurred
+            validation_files = glob.glob(
+                os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
+            self.assertEqual(1, len(validation_files))
+            # The validation errors file should be empty (0 bytes)
+            self.assertEqual(0, os.path.getsize(validation_files[0]))
+
     # Integration tests
 
     TEST_PROJECT1_METADATA_FP = path.join(TEST_DIR, "data/test_project1_input_metadata.csv")
@@ -4171,9 +4296,6 @@ class TestMetadataExtender(TestCase):
 
         # Load input metadata CSV
         input_df = pandas.read_csv(self.TEST_PROJECT1_METADATA_FP, dtype=str)
-        # for the columns "plating_notes" and "notes", fill NaN with empty string
-        input_df["plating_notes"] = input_df["plating_notes"].fillna("")
-        input_df["notes"] = input_df["notes"].fillna("")
 
         # Load study config
         study_config = _get_study_specific_config(self.TEST_PROJECT1_CONFIG_FP)
@@ -4219,6 +4341,58 @@ class TestMetadataExtender(TestCase):
             self.assertEqual(1, len(validation_files))
             self.assertEqual(0, os.path.getsize(validation_files[0]))
 
+    def test_write_extended_metadata_project1_integration(self):
+        """Integration test for write_extended_metadata using project1 test data files."""
+
+        def write_mismatched_debug_files(expected_content, actual_content, file_name):
+            """Write debug files to Desktop for unmatched content."""
+            debug_dir = path.join(path.expanduser("~"), "Desktop")
+            with open(path.join(debug_dir, f"UNMATCHED_1_{file_name}"), 'w') as debug_expected_file:
+                debug_expected_file.write(expected_content)
+            with open(path.join(debug_dir, f"UNMATCHED_2_{file_name}"), 'w') as debug_actual_file:
+                debug_actual_file.write(actual_content)
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            write_extended_metadata(
+                self.TEST_PROJECT1_METADATA_FP, self.TEST_PROJECT1_CONFIG_FP,
+                tmpdir, "test_output", remove_internals=True)
+
+            # Compare main output file directly to expected file
+            output_files = glob.glob(os.path.join(tmpdir, "*_test_output.txt"))
+            self.assertEqual(1, len(output_files))
+            with open(output_files[0], 'r') as actual_file:
+                actual_content = actual_file.read()
+            with open(self.TEST_PROJECT1_EXPECTED_OUTPUT_FP, 'r') as expected_file:
+                expected_content = expected_file.read()
+            try:
+                self.assertEqual(expected_content, actual_content)
+            except AssertionError:
+                write_mismatched_debug_files(
+                    expected_content, actual_content,
+                    "project1_output.txt")
+                raise
+
+            # Compare fails file directly to expected file
+            fails_files = glob.glob(os.path.join(tmpdir, "*_test_output_fails.csv"))
+            self.assertEqual(1, len(fails_files))
+            with open(fails_files[0], 'r') as actual_file:
+                actual_fails_content = actual_file.read()
+            with open(self.TEST_PROJECT1_EXPECTED_FAILS_FP, 'r') as expected_file:
+                expected_fails_content = expected_file.read()
+            try:
+                self.assertEqual(expected_fails_content, actual_fails_content)
+            except AssertionError:
+                write_mismatched_debug_files(
+                    expected_fails_content, actual_fails_content,
+                    "project1_fails.csv")
+                raise
+
+            # Verify validation errors file is empty
+            validation_files = glob.glob(
+                os.path.join(tmpdir, "*_test_output_validation_errors.csv"))
+            self.assertEqual(1, len(validation_files))
+            self.assertEqual(0, os.path.getsize(validation_files[0]))
+
     # Tests for _get_specified_column_name
 
     def test__get_specified_column_name_finds_column(self):

{metameq-2026.2.2 → metameq-2026.2.3}/metameq/tests/test_metadata_validator.py

@@ -547,7 +547,7 @@ class TestOutputValidationMsgs(TestCase):
             output_files = glob.glob(os.path.join(tmp_dir, "*_test_validation_errors.txt"))
             self.assertEqual(1, len(output_files))
 
-            result_df = pd.read_csv(output_files[0], sep="\t")
+            result_df = pd.read_csv(output_files[0], sep="\t", dtype=str, keep_default_na=False)
             pd.testing.assert_frame_equal(validation_msgs_df, result_df)
 
     def test_output_validation_msgs_non_empty_df_comma_separator(self):
@@ -564,7 +564,7 @@ class TestOutputValidationMsgs(TestCase):
             output_files = glob.glob(os.path.join(tmp_dir, "*_test_validation_errors.csv"))
             self.assertEqual(1, len(output_files))
 
-            result_df = pd.read_csv(output_files[0], sep=",")
+            result_df = pd.read_csv(output_files[0], sep=",", dtype=str, keep_default_na=False)
             pd.testing.assert_frame_equal(validation_msgs_df, result_df)
 
     def test_output_validation_msgs_empty_df_creates_empty_file(self):

{metameq-2026.2.2 → metameq-2026.2.3/metameq.egg-info}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: metameq
-Version: 2026.2.2
+Version: 2026.2.3
 Summary: Qiita-compliant metadata generation and validation tool
 Home-page: https://github.com/AmandaBirmingham/metameq
 Author: Amanda Birmingham
 Author-email: abirmingham@ucsd.edu
 License: BSD-3-Clause
 Requires-Dist: click>=8.0.0
+Requires-Dist: openpyxl>=3.0.0
 Requires-Dist: pandas>=1.3.0
 Requires-Dist: PyYAML>=5.4.0
 Requires-Dist: Cerberus>=1.3.4

{metameq-2026.2.2 → metameq-2026.2.3}/metameq.egg-info/requires.txt

@@ -1,4 +1,5 @@
 click>=8.0.0
+openpyxl>=3.0.0
 pandas>=1.3.0
 PyYAML>=5.4.0
 Cerberus>=1.3.4

{metameq-2026.2.2 → metameq-2026.2.3}/setup.py

@@ -25,6 +25,7 @@ setup(name='metameq',
       # NB: if changing here, also change the environment.yml
       install_requires=[
           'click>=8.0.0',
+          'openpyxl>=3.0.0',
           'pandas>=1.3.0',
           'PyYAML>=5.4.0',
           'Cerberus>=1.3.4',