metameq 2026.2.1__tar.gz → 2026.2.2__tar.gz

{metameq-2026.2.1/metameq.egg-info → metameq-2026.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: metameq
-Version: 2026.2.1
+Version: 2026.2.2
 Summary: Qiita-compliant metadata generation and validation tool
 Home-page: https://github.com/AmandaBirmingham/metameq
 Author: Amanda Birmingham

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-02-01T21:32:06-0800",
+ "date": "2026-02-02T16:43:52-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "87171fd73f555e2c03a15fa36ed9b5a912b824e9",
- "version": "2026.02.1"
+ "full-revisionid": "4fe1396e1007820dc7a4bdb58708fff0df6b9a57",
+ "version": "2026.02.2"
 }
 '''  # END VERSION_JSON
 

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/src/metadata_configurator.py

@@ -5,7 +5,7 @@ from metameq.src.util import extract_config_dict, extract_stds_config, \
     HOST_TYPE_SPECIFIC_METADATA_KEY, \
     SAMPLE_TYPE_SPECIFIC_METADATA_KEY, ALIAS_KEY, BASE_TYPE_KEY, \
     DEFAULT_KEY, ALLOWED_KEY, ANYOF_KEY, TYPE_KEY, \
-    SAMPLE_TYPE_KEY, QIITA_SAMPLE_TYPE
+    SAMPLE_TYPE_KEY, QIITA_SAMPLE_TYPE, GLOBAL_SETTINGS_KEYS
 
 
 def combine_stds_and_study_config(
@@ -257,11 +257,12 @@ def _combine_base_and_added_host_type(
     host_type_wip_nested_dict = \
         deepcopy_dict(host_type_base_dict)
 
-    # look for a default key in the add dict for this host; if
-    # it exists, add it to the wip dict (ok to overwrite existing)
-    if DEFAULT_KEY in host_type_add_dict:
-        host_type_wip_nested_dict[DEFAULT_KEY] = \
-            host_type_add_dict.get(DEFAULT_KEY)
+    # look for global settings in the add dict for this host; if
+    # any exists, add it to the wip dict (ok to overwrite existing)
+    for curr_global_setting_key in GLOBAL_SETTINGS_KEYS:
+        if curr_global_setting_key in host_type_add_dict:
+            host_type_wip_nested_dict[curr_global_setting_key] = \
+                host_type_add_dict.get(curr_global_setting_key)
 
     # combine add metadata fields with the wip metadata fields
     # for the current host type and assign to wip if not empty
@@ -636,6 +637,10 @@ def build_full_flat_config_dict(
         # since the software config doesn't include any host type specific info
         full_nested_hosts_dict = extract_stds_config(stds_fp)
 
+    full_nested_hosts_dict = _push_global_settings_into_top_host(
+            full_nested_hosts_dict,
+            software_plus_study_flat_config_dict)
+
     full_flat_hosts_dict = flatten_nested_stds_dict(
         full_nested_hosts_dict, None)
     software_plus_study_flat_config_dict[HOST_TYPE_SPECIFIC_METADATA_KEY] = \
@@ -655,3 +660,45 @@ def build_full_flat_config_dict(
     full_flat_config_dict = software_plus_study_flat_config_dict
 
     return full_flat_config_dict
+
+
+def _push_global_settings_into_top_host(
+        a_full_nested_hosts_dict: Dict[str, Any],
+        a_software_plus_study_flat_config_dict: Dict[str, Any]) -> Dict[str, Any]:
+    """Push global settings from flat config into top-level host in nested hosts dict.
+
+    Parameters
+    ----------
+    a_full_nested_hosts_dict : Dict[str, Any]
+        Nested hosts dictionary to update.
+    a_software_plus_study_flat_config_dict : Dict[str, Any]
+        Flat configuration dictionary containing global settings.
+
+    Returns
+    -------
+    Dict[str, Any]
+        Updated nested hosts dictionary with global settings added to top-level host.
+
+    Raises
+    ------
+    ValueError
+        If there is not exactly one top-level host in the nested hosts dictionary.
+    """
+    result = deepcopy_dict(a_full_nested_hosts_dict)
+
+    # get the top level host(s) in full_nested_hosts_dict
+    # (should be only one because it is nested)
+    top_level_host_keys = list(a_full_nested_hosts_dict[HOST_TYPE_SPECIFIC_METADATA_KEY].keys())
+    if len(top_level_host_keys) != 1:
+        raise ValueError(f"Expected exactly one top-level key in "
+                         f"full_nested_hosts_dict but found: {top_level_host_keys}")
+    top_level_host_key = top_level_host_keys[0]
+
+    # check for each top-level setting from the software+study dictionary
+    # and add it under the top level host key in a_full_nested_hosts_dict
+    for curr_setting_key in GLOBAL_SETTINGS_KEYS:
+        if curr_setting_key in a_software_plus_study_flat_config_dict:
+            result[HOST_TYPE_SPECIFIC_METADATA_KEY][top_level_host_key][curr_setting_key] = \
+                a_software_plus_study_flat_config_dict[curr_setting_key]
+
+    return result

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/src/metadata_extender.py

@@ -6,7 +6,7 @@ from pathlib import Path
 from datetime import datetime
 from typing import List, Dict, Optional, Tuple, Any
 from metameq.src.util import extract_config_dict, \
-    deepcopy_dict, validate_required_columns_exist, get_extension, \
+    validate_required_columns_exist, get_extension, \
     load_df_with_best_fit_encoding, update_metadata_df_field, \
     HOSTTYPE_SHORTHAND_KEY, SAMPLETYPE_SHORTHAND_KEY, \
     QC_NOTE_KEY, METADATA_FIELDS_KEY, HOST_TYPE_SPECIFIC_METADATA_KEY, \
@@ -451,7 +451,7 @@ def extend_metadata_df(
     full_flat_config_dict = build_full_flat_config_dict(
         study_specific_config_dict, software_config_dict, stds_fp)
 
-    needed_cols = [(HOSTTYPE_SHORTHAND_KEY, HOSTTYPE_COL_OPTIONS_KEY), 
+    needed_cols = [(HOSTTYPE_SHORTHAND_KEY, HOSTTYPE_COL_OPTIONS_KEY),
                    (SAMPLETYPE_SHORTHAND_KEY, SAMPLETYPE_COL_OPTIONS_KEY)]
     for curr_key, curr_options_key in needed_cols:
         if curr_key not in raw_metadata_df.columns:
@@ -485,7 +485,7 @@ def _get_specified_column_name(
         The metadata DataFrame to check.
     config_dict : Dict[str, Any], default=None
         Configuration dictionary. If provided, may contain a list of possible
-        column names under the key specified by col_options_key. 
+        column names under the key specified by col_options_key.
         If None, defaults to values from the main config.yml file.
     Returns
     -------
@@ -503,7 +503,8 @@ def _get_specified_column_name(
                 found_name = col_name
                 break
 
-    return found_name 
+    return found_name
+
 
 def write_metadata_results(
         metadata_df: pandas.DataFrame,
@@ -738,12 +739,6 @@ def _generate_metadata_for_host_types(
             - The processed DataFrame with specific metadata added to each sample of each host type
             - A list of validation messages
     """
-    # gather global settings
-    settings_dict = {DEFAULT_KEY: full_flat_config_dict.get(DEFAULT_KEY),
-                     LEAVE_REQUIREDS_BLANK_KEY:
-                         full_flat_config_dict.get(LEAVE_REQUIREDS_BLANK_KEY),
-                     OVERWRITE_NON_NANS_KEY:
-                         full_flat_config_dict.get(OVERWRITE_NON_NANS_KEY)}
 
     validation_msgs = []
     host_type_dfs = []
@@ -751,7 +746,7 @@ def _generate_metadata_for_host_types(
     host_type_shorthands = pandas.unique(metadata_df[HOSTTYPE_SHORTHAND_KEY])
     for curr_host_type_shorthand in host_type_shorthands:
         concatted_dfs, curr_validation_msgs = _generate_metadata_for_a_host_type(
-                metadata_df, curr_host_type_shorthand, settings_dict, full_flat_config_dict)
+                metadata_df, curr_host_type_shorthand, full_flat_config_dict)
 
         host_type_dfs.append(concatted_dfs)
         validation_msgs.extend(curr_validation_msgs)
@@ -767,7 +762,7 @@ def _generate_metadata_for_host_types(
     # NB: passing in the same dict twice here is not a mistake, just a
     # convenience since we don't have a more specific dict at this point.
     output_df = _fill_na_if_default(
-        output_df, settings_dict, settings_dict)
+        output_df, full_flat_config_dict)
 
     # TODO: this is setting a value in the output; should it be centralized
     #  so it is easy to find?
@@ -779,7 +774,6 @@ def _generate_metadata_for_host_types(
 def _generate_metadata_for_a_host_type(
         metadata_df: pandas.DataFrame,
         a_host_type: str,
-        settings_dict: Dict[str, Any],
         full_flat_config_dict: Dict[str, Any]) -> Tuple[pandas.DataFrame, List[str]]:
     """Generate metadata df for samples with a specific host type.
 
@@ -790,8 +784,6 @@ def _generate_metadata_for_a_host_type(
         the columns in REQUIRED_RAW_METADATA_FIELDS.
     a_host_type : str
         The specific host type for which to process samples.
-    settings_dict : Dict[str, Any]
-        Dictionary containing global settings for default/nan/etc.
     full_flat_config_dict : Dict[str, Any]
         Fully combined flat-host-type config dictionary.
 
@@ -814,16 +806,11 @@ def _generate_metadata_for_a_host_type(
         # for these samples but do not error out; move on to the next host type
         update_metadata_df_field(
             host_type_df, QC_NOTE_KEY, "invalid host_type")
-        # host_type_df[QC_NOTE_KEY] = "invalid host_type"
         concatted_df = host_type_df
     else:
         # gather host-type-specific settings and overwrite the global settings with them, if any
         a_host_type_config_dict = \
             full_flat_config_dict[HOST_TYPE_SPECIFIC_METADATA_KEY][a_host_type]
-        global_plus_host_settings_dict = deepcopy_dict(settings_dict)
-        # if this host type has a default value for empty fields, use it; otherwise, use the global default
-        global_plus_host_settings_dict[DEFAULT_KEY] = a_host_type_config_dict.get(
-            DEFAULT_KEY, global_plus_host_settings_dict[DEFAULT_KEY])
 
         dfs_to_concat = []
         # loop through each sample type in the metadata for this host type
@@ -833,8 +820,7 @@ def _generate_metadata_for_a_host_type(
             # generate the specific metadata for this sample type *in this host type*
             curr_sample_type_df, curr_validation_msgs = \
                 _generate_metadata_for_a_sample_type_in_a_host_type(
-                    host_type_df, curr_sample_type, global_plus_host_settings_dict,
-                    a_host_type_config_dict)
+                    host_type_df, curr_sample_type, a_host_type_config_dict)
 
             dfs_to_concat.append(curr_sample_type_df)
             validation_msgs.extend(curr_validation_msgs)
@@ -851,7 +837,6 @@ def _generate_metadata_for_a_host_type(
 def _generate_metadata_for_a_sample_type_in_a_host_type(
         host_type_metadata_df: pandas.DataFrame,
         a_sample_type: str,
-        global_plus_host_settings_dict: Dict[str, Any],
         a_host_type_config_dict: Dict[str, Any]) -> Tuple[pandas.DataFrame, List[str]]:
     """Generate metadata df for samples with a specific sample type within a specific host type.
 
@@ -861,8 +846,6 @@ def _generate_metadata_for_a_sample_type_in_a_host_type(
         DataFrame containing metadata samples for a specific host type.
     a_sample_type : str
         The sample type to process.
-    global_plus_host_settings_dict : Dict[str, Any]
-        Dictionary containing default/nan/etc settings for current context.
     a_host_type_config_dict : Dict[str, Any]
         Dictionary containing config for this host type.
 
@@ -901,19 +884,19 @@ def _generate_metadata_for_a_sample_type_in_a_host_type(
         sample_type_df = _update_metadata_from_dict(
             sample_type_df, full_sample_type_metadata_fields_dict,
             dict_is_metadata_fields=True,
-            overwrite_non_nans=global_plus_host_settings_dict[OVERWRITE_NON_NANS_KEY])
+            overwrite_non_nans=a_host_type_config_dict[OVERWRITE_NON_NANS_KEY])
 
         # for fields that are required but not yet filled, replace the placeholder with
         # either an indicator that it should be blank or else
         # fill with NA (replaced with default just below), based on config setting
-        leave_reqs_blank = global_plus_host_settings_dict[LEAVE_REQUIREDS_BLANK_KEY]
+        leave_reqs_blank = a_host_type_config_dict[LEAVE_REQUIREDS_BLANK_KEY]
         reqs_val = LEAVE_BLANK_VAL if leave_reqs_blank else np.nan
         sample_type_df.replace(
             to_replace=REQ_PLACEHOLDER, value=reqs_val, inplace=True)
 
         # fill NAs with appropriate default value if any is set
         sample_type_df = _fill_na_if_default(
-            sample_type_df, full_sample_type_metadata_fields_dict, global_plus_host_settings_dict)
+            sample_type_df, a_host_type_config_dict)
 
         # validate the metadata df based on the specific requirements
         # for this host+sample type
@@ -1095,7 +1078,6 @@ def _update_metadata_from_metadata_fields_dict(
 # fill NAs with default value if any is set
 def _fill_na_if_default(
         metadata_df: pandas.DataFrame,
-        specific_dict: Dict[str, Any],
         settings_dict: Dict[str, Any]) -> pandas.DataFrame:
     """Fill NaN values in metadata df with default values if available.
 
@@ -1103,24 +1085,20 @@ def _fill_na_if_default(
     ----------
     metadata_df : pandas.DataFrame
         The metadata DataFrame to process.
-    specific_dict : Dict[str, Any]
-        Dictionary containing context-specific settings. Will be used first as a source of default values.
     settings_dict : Dict[str, Any]
-        Dictionary containing global settings. Will be used as a
-          source of default values if specific_dict does not contain a DEFAULT_KEY.
+        Dictionary containing settings.
 
     Returns
     -------
     pandas.DataFrame
         The updated DataFrame with NaN values filled. Unchanged if no default values are set.
     """
-    default_val = specific_dict.get(DEFAULT_KEY, settings_dict[DEFAULT_KEY])
+    default_val = settings_dict.get(DEFAULT_KEY)
     if default_val:
         # TODO: this is setting a value in the output; should it be
         #  centralized so it is easy to find?
         metadata_df = \
             metadata_df.fillna(default_val)
-#             metadata_df.astype("string").fillna(default_val)
 
     return metadata_df
 

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/src/util.py

@@ -51,6 +51,13 @@ REQUIRED_RAW_METADATA_FIELDS = [SAMPLE_NAME_KEY,
                                 SAMPLETYPE_SHORTHAND_KEY]
 
 
+GLOBAL_SETTINGS_KEYS = [
+    DEFAULT_KEY,
+    LEAVE_REQUIREDS_BLANK_KEY,
+    OVERWRITE_NON_NANS_KEY
+]
+
+
 def extract_config_dict(
         config_fp: Union[str, None]) -> dict:
     """Extract configuration dictionary from a YAML file.

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/tests/test_metadata_configurator.py

@@ -17,7 +17,8 @@ from metameq.src.metadata_configurator import \
     _id_sample_type_definition, \
     update_wip_metadata_dict, \
     build_full_flat_config_dict, \
-    _resolve_sample_type_aliases_and_bases
+    _resolve_sample_type_aliases_and_bases, \
+    _push_global_settings_into_top_host
 
 
 class TestMetadataConfigurator(TestCase):
@@ -3847,6 +3848,9 @@ class TestMetadataConfigurator(TestCase):
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 # base: top level in test_standards.yml, no default
                 "base": {
+                    DEFAULT_KEY: "software_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         # sample_name defined at base level
                         "sample_name": {
@@ -3865,6 +3869,8 @@ class TestMetadataConfigurator(TestCase):
                 "host_associated": {
                     # default defined at host_associated level
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         # description defined at host_associated level
                         "description": {
@@ -3919,6 +3925,8 @@ class TestMetadataConfigurator(TestCase):
                 "human": {
                     # default inherited from host_associated
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         # custom_field added from study_specific_metadata
                         "custom_field": {
@@ -4037,6 +4045,8 @@ class TestMetadataConfigurator(TestCase):
                 "mouse": {
                     # default inherited from host_associated
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         # description inherited from host_associated (not overridden)
                         "description": {
@@ -4103,6 +4113,7 @@ class TestMetadataConfigurator(TestCase):
                 }
             }
         }
+
         self.assertEqual(expected, result)
 
     def test_build_full_flat_config_dict_without_study_config(self):
@@ -4130,6 +4141,9 @@ class TestMetadataConfigurator(TestCase):
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 # base: top level, no default, just sample_name/sample_type
                 "base": {
+                    DEFAULT_KEY: "software_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "sample_name": {
                             REQUIRED_KEY: True,
@@ -4145,6 +4159,8 @@ class TestMetadataConfigurator(TestCase):
                 # host_associated: inherits from base, adds default and description
                 "host_associated": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4194,6 +4210,8 @@ class TestMetadataConfigurator(TestCase):
                 # human: inherits from host_associated, overrides description
                 "human": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "human sample",
@@ -4291,6 +4309,8 @@ class TestMetadataConfigurator(TestCase):
                 # mouse: inherits from host_associated, keeps parent description
                 "mouse": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4395,6 +4415,12 @@ class TestMetadataConfigurator(TestCase):
             # Flattened host types
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "base": {
+                    # default from study_config overrides software_config
+                    DEFAULT_KEY: "study_default",
+                    # leave_requireds_blank from study_config overrides software_config
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    # overwrite_non_nans from software_config (not overridden by study)
+                    OVERWRITE_NON_NANS_KEY: True,
                     METADATA_FIELDS_KEY: {
                         "sample_name": {
                             REQUIRED_KEY: True,
@@ -4409,6 +4435,10 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "host_associated": {
                     DEFAULT_KEY: "not provided",
+                    # leave_requireds_blank from study_config overrides software_config
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    # overwrite_non_nans from software_config (not overridden by study)
+                    OVERWRITE_NON_NANS_KEY: True,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4457,6 +4487,10 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "human": {
                     DEFAULT_KEY: "not provided",
+                    # leave_requireds_blank from study_config overrides software_config
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    # overwrite_non_nans from software_config (not overridden by study)
+                    OVERWRITE_NON_NANS_KEY: True,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "human sample",
@@ -4553,6 +4587,10 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "mouse": {
                     DEFAULT_KEY: "not provided",
+                    # leave_requireds_blank from study_config overrides software_config
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    # overwrite_non_nans from software_config (not overridden by study)
+                    OVERWRITE_NON_NANS_KEY: True,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4649,6 +4687,9 @@ class TestMetadataConfigurator(TestCase):
             # Flattened host types
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "base": {
+                    DEFAULT_KEY: "not applicable",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "sample_name": {
                             REQUIRED_KEY: True,
@@ -4663,6 +4704,8 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "host_associated": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4711,6 +4754,8 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "human": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "human sample",
@@ -4807,6 +4852,8 @@ class TestMetadataConfigurator(TestCase):
                 },
                 "mouse": {
                     DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "description": {
                             DEFAULT_KEY: "host associated sample",
@@ -4867,4 +4914,140 @@ class TestMetadataConfigurator(TestCase):
                 }
             }
         }
+
+        self.assertEqual(expected, result)
+
+    # Tests for _push_global_settings_into_top_host
+
+    def test__push_global_settings_into_top_host_single_setting(self):
+        """Test pushing a single global setting into the top-level host."""
+        nested_hosts_dict = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+        flat_config_dict = {
+            DEFAULT_KEY: "custom_default"
+        }
+
+        expected = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    DEFAULT_KEY: "custom_default",
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+
+        result = _push_global_settings_into_top_host(
+            nested_hosts_dict, flat_config_dict)
+
+        self.assertEqual(expected, result)
+        # Original should be unchanged
+        self.assertNotIn(
+            DEFAULT_KEY,
+            nested_hosts_dict[HOST_TYPE_SPECIFIC_METADATA_KEY]["base"])
+
+    def test__push_global_settings_into_top_host_multiple_settings(self):
+        """Test pushing multiple global settings into the top-level host."""
+        nested_hosts_dict = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+        flat_config_dict = {
+            DEFAULT_KEY: "custom_default",
+            LEAVE_REQUIREDS_BLANK_KEY: True,
+            OVERWRITE_NON_NANS_KEY: True
+        }
+
+        expected = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    DEFAULT_KEY: "custom_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,
+                    OVERWRITE_NON_NANS_KEY: True,
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+
+        result = _push_global_settings_into_top_host(
+            nested_hosts_dict, flat_config_dict)
+
         self.assertEqual(expected, result)
+
+    def test__push_global_settings_into_top_host_no_settings(self):
+        """Test that function returns copy when no global settings present."""
+        nested_hosts_dict = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+        flat_config_dict = {
+            "some_other_key": "value"
+        }
+
+        expected = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "base": {
+                    METADATA_FIELDS_KEY: {
+                        "field1": {TYPE_KEY: "string"}
+                    }
+                }
+            }
+        }
+
+        result = _push_global_settings_into_top_host(
+            nested_hosts_dict, flat_config_dict)
+
+        self.assertEqual(expected, result)
+
+    def test__push_global_settings_into_top_host_raises_on_zero_hosts(self):
+        """Test that ValueError is raised when no top-level hosts exist."""
+        nested_hosts_dict = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {}
+        }
+        flat_config_dict = {
+            DEFAULT_KEY: "custom_default"
+        }
+
+        with self.assertRaisesRegex(
+                ValueError,
+                r"Expected exactly one top-level key.*found: \[\]"):
+            _push_global_settings_into_top_host(
+                nested_hosts_dict, flat_config_dict)
+
+    def test__push_global_settings_into_top_host_raises_on_multiple_hosts(self):
+        """Test that ValueError is raised when multiple top-level hosts exist."""
+        nested_hosts_dict = {
+            HOST_TYPE_SPECIFIC_METADATA_KEY: {
+                "host1": {METADATA_FIELDS_KEY: {}},
+                "host2": {METADATA_FIELDS_KEY: {}}
+            }
+        }
+        flat_config_dict = {
+            DEFAULT_KEY: "custom_default"
+        }
+
+        with self.assertRaisesRegex(
+                ValueError,
+                r"Expected exactly one top-level key"):
+            _push_global_settings_into_top_host(
+                nested_hosts_dict, flat_config_dict)

{metameq-2026.2.1 → metameq-2026.2.2}/metameq/tests/test_metadata_extender.py

@@ -748,16 +748,15 @@ class TestMetadataExtender(TestCase):
 
     # Tests for _fill_na_if_default
 
-    def test__fill_na_if_default_specific_overrides_settings(self):
+    def test__fill_na_if_default_has_default_in_settings(self):
         """Test that specific_dict default takes precedence over settings_dict."""
         input_df = pandas.DataFrame({
             "field1": ["value1", np.nan, "value3"],
             "field2": [np.nan, "value2", np.nan]
         })
-        specific_dict = {DEFAULT_KEY: "filled"}
-        settings_dict = {DEFAULT_KEY: "unused"}
+        settings_dict = {DEFAULT_KEY: "filled"}
 
-        result = _fill_na_if_default(input_df, specific_dict, settings_dict)
+        result = _fill_na_if_default(input_df, settings_dict)
 
         expected = pandas.DataFrame({
             "field1": ["value1", "filled", "value3"],
@@ -765,18 +764,19 @@ class TestMetadataExtender(TestCase):
         })
         assert_frame_equal(expected, result)
 
-    def test__fill_na_if_default_uses_settings_when_specific_missing(self):
-        """Test that settings_dict default is used when specific_dict has no default."""
+    def test__fill_na_if_default_no_default_in_settings(self):
+        """Test that NaN values are unchanged when no default is in settings."""
         input_df = pandas.DataFrame({
-            "field1": [np.nan]
+            "field1": ["value1", np.nan, "value3"],
+            "field2": [np.nan, "value2", np.nan]
         })
-        specific_dict = {}
-        settings_dict = {DEFAULT_KEY: "settings_default"}
+        settings_dict = {}
 
-        result = _fill_na_if_default(input_df, specific_dict, settings_dict)
+        result = _fill_na_if_default(input_df, settings_dict)
 
         expected = pandas.DataFrame({
-            "field1": ["settings_default"]
+            "field1": ["value1", np.nan, "value3"],
+            "field2": [np.nan, "value2", np.nan]
         })
         assert_frame_equal(expected, result)
 
@@ -1273,14 +1273,13 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool", "stool"],
             QC_NOTE_KEY: ["", ""]
         })
-        global_plus_host_settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
+
         # Config is pre-resolved: sample type's metadata_fields already includes
         # host fields merged in, plus sample_type and qiita_sample_type
         host_type_config_dict = {
+            OVERWRITE_NON_NANS_KEY: False,
+            LEAVE_REQUIREDS_BLANK_KEY: False,
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {
                 "host_field": {
                     DEFAULT_KEY: "host_default",
@@ -1314,7 +1313,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1", "sample2"],
@@ -1337,12 +1336,11 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["unknown_type"],
             QC_NOTE_KEY: [""]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: False,
             LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1352,7 +1350,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "unknown_type", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "unknown_type", host_type_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1"],
@@ -1371,12 +1369,11 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool", "blood", "stool"],
             QC_NOTE_KEY: ["", "", ""]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: False,
             LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1394,7 +1391,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         # Should only have the two stool samples
         self.assertEqual(2, len(result_df))
@@ -1409,12 +1406,11 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool"],
             QC_NOTE_KEY: [""]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: False,
             LEAVE_REQUIREDS_BLANK_KEY: True,
-            DEFAULT_KEY: "not provided"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1429,7 +1425,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         self.assertEqual(LEAVE_BLANK_VAL, result_df["required_field"].iloc[0])
 
@@ -1441,12 +1437,11 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool"],
             QC_NOTE_KEY: [""]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: False,
             LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "global_default",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1461,7 +1456,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         # When leave_requireds_blank is False, NaN values get filled with global default
         self.assertEqual("global_default", result_df["required_field"].iloc[0])
@@ -1475,12 +1470,11 @@ class TestMetadataExtender(TestCase):
             QC_NOTE_KEY: [""],
             "existing_field": ["original_value"]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: True,
             LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1495,7 +1489,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         self.assertEqual("new_value", result_df["existing_field"].iloc[0])
 
@@ -1508,12 +1502,11 @@ class TestMetadataExtender(TestCase):
             QC_NOTE_KEY: [""],
             "existing_field": ["original_value"]
         })
-        global_plus_host_settings_dict = {
+
+        host_type_config_dict = {
             OVERWRITE_NON_NANS_KEY: False,
             LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
-        host_type_config_dict = {
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "stool": {
@@ -1528,7 +1521,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "stool", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "stool", host_type_config_dict)
 
         self.assertEqual("original_value", result_df["existing_field"].iloc[0])
 
@@ -1540,14 +1533,13 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["feces"],
             QC_NOTE_KEY: [""]
         })
-        global_plus_host_settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "not provided"
-        }
+
         # Config is pre-resolved: alias "feces" has its own metadata_fields
         # that is a copy of "stool"'s resolved fields with sample_type="stool"
         host_type_config_dict = {
+            OVERWRITE_NON_NANS_KEY: False,
+            LEAVE_REQUIREDS_BLANK_KEY: False,
+            DEFAULT_KEY: "not provided",
             METADATA_FIELDS_KEY: {},
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                 "feces": {
@@ -1590,7 +1582,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_sample_type_in_a_host_type(
-            input_df, "feces", global_plus_host_settings_dict, host_type_config_dict)
+            input_df, "feces", host_type_config_dict)
 
         self.assertEqual("stool_value", result_df["stool_field"].iloc[0])
         # sample_type should be set to the resolved type "stool"
@@ -1606,17 +1598,15 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool", "stool"],
             QC_NOTE_KEY: ["", ""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
+
         # Config is pre-resolved: sample type's metadata_fields includes
         # host fields merged in, plus sample_type and qiita_sample_type
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
                     DEFAULT_KEY: "human_default",
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "host_field": {
                             DEFAULT_KEY: "host_value",
@@ -1652,7 +1642,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "human", settings_dict, full_flat_config_dict)
+            input_df, "human", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1", "sample2"],
@@ -1675,14 +1665,13 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool"],
             QC_NOTE_KEY: [""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
+
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    DEFAULT_KEY: "global_default",
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {}
                 }
@@ -1690,7 +1679,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "unknown_host", settings_dict, full_flat_config_dict)
+            input_df, "unknown_host", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1"],
@@ -1709,14 +1698,13 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["unknown_sample"],
             QC_NOTE_KEY: [""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
+
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    DEFAULT_KEY: "global_default",
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -1728,7 +1716,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "human", settings_dict, full_flat_config_dict)
+            input_df, "human", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1"],
@@ -1747,16 +1735,15 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool", "stool", "stool"],
             QC_NOTE_KEY: ["", "", ""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
+
         # Config is pre-resolved: sample type's metadata_fields includes
         # host fields merged in, plus sample_type and qiita_sample_type
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    DEFAULT_KEY: "global_default",
                     METADATA_FIELDS_KEY: {
                         "human_field": {
                             DEFAULT_KEY: "human_value",
@@ -1785,6 +1772,9 @@ class TestMetadataExtender(TestCase):
                     }
                 },
                 "mouse": {
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    DEFAULT_KEY: "global_default",
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {}
                 }
@@ -1792,7 +1782,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "human", settings_dict, full_flat_config_dict)
+            input_df, "human", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1", "sample3"],
@@ -1813,17 +1803,15 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool"],
             QC_NOTE_KEY: [""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
+
         # Config is pre-resolved: sample type's metadata_fields includes
         # host fields merged in, plus sample_type and qiita_sample_type
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
                     DEFAULT_KEY: "human_specific_default",
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -1850,7 +1838,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "human", settings_dict, full_flat_config_dict)
+            input_df, "human", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1"],
@@ -1871,17 +1859,14 @@ class TestMetadataExtender(TestCase):
             SAMPLETYPE_SHORTHAND_KEY: ["stool"],
             QC_NOTE_KEY: [""]
         })
-        settings_dict = {
-            OVERWRITE_NON_NANS_KEY: False,
-            LEAVE_REQUIREDS_BLANK_KEY: False,
-            DEFAULT_KEY: "global_default"
-        }
         # Config is pre-resolved: sample type's metadata_fields includes
         # host fields merged in, plus sample_type and qiita_sample_type
         full_flat_config_dict = {
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
-                    # No DEFAULT_KEY here
+                    OVERWRITE_NON_NANS_KEY: False,
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    DEFAULT_KEY: "global_default",
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -1908,7 +1893,7 @@ class TestMetadataExtender(TestCase):
         }
 
         result_df, validation_msgs = _generate_metadata_for_a_host_type(
-            input_df, "human", settings_dict, full_flat_config_dict)
+            input_df, "human", full_flat_config_dict)
 
         expected_df = pandas.DataFrame({
             SAMPLE_NAME_KEY: ["sample1"],
@@ -1939,6 +1924,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "global_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "host_field": {
                             DEFAULT_KEY: "host_value",
@@ -2005,6 +1993,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "global_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "human_field": {
                             DEFAULT_KEY: "human_value",
@@ -2051,6 +2042,9 @@ class TestMetadataExtender(TestCase):
                     }
                 },
                 "mouse": {
+                    DEFAULT_KEY: "global_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "mouse_field": {
                             DEFAULT_KEY: "mouse_value",
@@ -2182,6 +2176,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "global_default",
+                    LEAVE_REQUIREDS_BLANK_KEY: True,  # This causes required fields to get LEAVE_BLANK_VAL
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -2506,6 +2503,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {
                         "host_field": {
                             DEFAULT_KEY: "host_value",
@@ -2580,6 +2580,9 @@ class TestMetadataExtender(TestCase):
             },
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -2639,6 +2642,9 @@ class TestMetadataExtender(TestCase):
             },
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -2687,6 +2693,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {}
                 }
@@ -2721,6 +2730,9 @@ class TestMetadataExtender(TestCase):
             OVERWRITE_NON_NANS_KEY: False,
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -2781,6 +2793,9 @@ class TestMetadataExtender(TestCase):
             },
             HOST_TYPE_SPECIFIC_METADATA_KEY: {
                 "human": {
+                    DEFAULT_KEY: "not provided",
+                    LEAVE_REQUIREDS_BLANK_KEY: False,
+                    OVERWRITE_NON_NANS_KEY: False,
                     METADATA_FIELDS_KEY: {},
                     SAMPLE_TYPE_SPECIFIC_METADATA_KEY: {
                         "stool": {
@@ -4142,6 +4157,7 @@ class TestMetadataExtender(TestCase):
         TEST_DIR, "data/test_project1_output_metadata.txt")
     TEST_PROJECT1_EXPECTED_FAILS_FP = path.join(
         TEST_DIR, "data/test_project1_output_fails.csv")
+
     def test_write_extended_metadata_from_df_project1_integration(self):
         """Integration test using project1 test data files."""
 
@@ -4153,7 +4169,6 @@ class TestMetadataExtender(TestCase):
             with open(path.join(debug_dir, f"UNMATCHED_2_{file_name}"), 'w') as debug_actual_file:
                 debug_actual_file.write(actual_content)
 
-
         # 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

{metameq-2026.2.1 → metameq-2026.2.2/metameq.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: metameq
-Version: 2026.2.1
+Version: 2026.2.2
 Summary: Qiita-compliant metadata generation and validation tool
 Home-page: https://github.com/AmandaBirmingham/metameq
 Author: Amanda Birmingham