metameq 2026.1.1__tar.gz → 2026.1.2__tar.gz

{metameq-2026.1.1/metameq.egg-info → metameq-2026.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: metameq
-Version: 2026.1.1
+Version: 2026.1.2
 Summary: Qiita-compliant metadata generation and validation tool
 Home-page: https://github.com/AmandaBirmingham/metameq
 Author: Amanda Birmingham

{metameq-2026.1.1 → metameq-2026.1.2}/environment.yml

@@ -10,5 +10,6 @@ dependencies:
   - pyyaml
   - flake8
   - pep8
+  - pytest
   - pip:
     - cerberus

{metameq-2026.1.1 → metameq-2026.1.2}/metameq/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-01-28T14:30:42-0800",
+ "date": "2026-01-31T12:28:01-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "b60757af0c4b7b16d71119971565d9991779f6d2",
- "version": "2026.01.1"
+ "full-revisionid": "889941fbd7d28889867e3f4b6edba2d50dbc5956",
+ "version": "2026.01.2"
 }
 '''  # END VERSION_JSON
 

{metameq-2026.1.1 → metameq-2026.1.2}/metameq/src/metadata_configurator.py

@@ -4,7 +4,8 @@ from metameq.src.util import extract_config_dict, extract_stds_config, \
     METADATA_FIELDS_KEY, STUDY_SPECIFIC_METADATA_KEY, \
     HOST_TYPE_SPECIFIC_METADATA_KEY, \
     SAMPLE_TYPE_SPECIFIC_METADATA_KEY, ALIAS_KEY, BASE_TYPE_KEY, \
-    DEFAULT_KEY, ALLOWED_KEY, ANYOF_KEY, TYPE_KEY
+    DEFAULT_KEY, ALLOWED_KEY, ANYOF_KEY, TYPE_KEY, \
+    SAMPLE_TYPE_KEY, QIITA_SAMPLE_TYPE
 
 
 def combine_stds_and_study_config(
@@ -89,6 +90,15 @@ def flatten_nested_stds_dict(
         if curr_host_type_sub_host_dict:
             wip_host_types_dict.update(curr_host_type_sub_host_dict)
 
+        # resolve aliases and base types for this host's sample types
+        # This happens AFTER recursion so children inherit unresolved aliases,
+        # ensuring correct bottom-up resolution order
+        if SAMPLE_TYPE_SPECIFIC_METADATA_KEY in curr_host_type_wip_flat_dict:
+            curr_host_type_wip_flat_dict[SAMPLE_TYPE_SPECIFIC_METADATA_KEY] = \
+                _resolve_sample_type_aliases_and_bases(
+                    curr_host_type_wip_flat_dict[SAMPLE_TYPE_SPECIFIC_METADATA_KEY],
+                    curr_host_type_wip_flat_dict.get(METADATA_FIELDS_KEY, {}))
+
         # assign the flattened wip dict for the current host type to the result
         # (which now contains flat records for the hosts lower down than
         # this, if there are any)
@@ -270,8 +280,11 @@ def _combine_base_and_added_host_type(
         _combine_base_and_added_sample_type_specific_metadata(
             host_type_wip_nested_dict,
             host_type_add_dict)
+
     # if we got back a non-empty dictionary of sample types,
     # add it to the wip for this host type dict
+    # Note: resolution of aliases/base types happens in flatten_nested_stds_dict
+    # AFTER recursion, to ensure correct bottom-up resolution order
     if curr_host_wip_sample_types_dict:
         host_type_wip_nested_dict[
             SAMPLE_TYPE_SPECIFIC_METADATA_KEY] = \
@@ -450,6 +463,130 @@ def _id_sample_type_definition(sample_type_name: str, sample_type_dict: Dict[str
                          "the same sample type dict")
 
 
+def _construct_sample_type_metadata_fields_dict(
+        sample_type: str,
+        host_sample_types_config_dict: Dict[str, Any],
+        a_host_type_metadata_fields_dict: Dict[str, Any]) -> Dict[str, Any]:
+    """Construct metadata fields dictionary for a specific host+sample type, resolving aliases and base types.
+
+    Parameters
+    ----------
+    sample_type : str
+        The sample type to process.
+    host_sample_types_config_dict : Dict[str, Any]
+        Dictionary containing config for *all* sample types in
+        the host type in question.
+    a_host_type_metadata_fields_dict : Dict[str, Any]
+        Dictionary containing metadata fields for the host type in question.
+
+    Returns
+    -------
+    Dict[str, Any]
+        The constructed metadata fields dictionary for this host-and-sample-type combination.
+
+    Raises
+    ------
+    ValueError
+        If there are invalid alias chains or base type configurations.
+    """
+    sample_type_for_metadata = sample_type
+
+    # get dict associated with the naive sample type
+    sample_type_specific_dict = \
+        host_sample_types_config_dict[sample_type]
+
+    # if naive sample type contains an alias
+    sample_type_alias = sample_type_specific_dict.get(ALIAS_KEY)
+    if sample_type_alias:
+        # change the sample type to the alias sample type
+        # and use the alias's sample type dict
+        sample_type_for_metadata = sample_type_alias
+        sample_type_specific_dict = \
+            host_sample_types_config_dict[sample_type_alias]
+        if METADATA_FIELDS_KEY not in sample_type_specific_dict:
+            raise ValueError(f"May not chain aliases "
+                             f"('{sample_type}' to '{sample_type_alias}')")
+    # endif sample type is an alias
+
+    # if the sample type has a base type
+    sample_type_base = sample_type_specific_dict.get(BASE_TYPE_KEY)
+    if sample_type_base:
+        # get the base's sample type dict and add this sample type's
+        # info on top of it
+        base_sample_dict = host_sample_types_config_dict[sample_type_base]
+        if list(base_sample_dict.keys()) != [METADATA_FIELDS_KEY]:
+            raise ValueError(f"Base sample type '{sample_type_base}' "
+                             f"must only have metadata fields")
+        sample_type_specific_dict_metadata = update_wip_metadata_dict(
+            deepcopy_dict(base_sample_dict[METADATA_FIELDS_KEY]),
+            sample_type_specific_dict.get(METADATA_FIELDS_KEY, {}))
+        sample_type_specific_dict = deepcopy_dict(sample_type_specific_dict)
+        sample_type_specific_dict[METADATA_FIELDS_KEY] = \
+            sample_type_specific_dict_metadata
+    # endif sample type has a base type
+
+    # add the sample-type-specific info generated above on top of the host info
+    sample_type_metadata_dict = update_wip_metadata_dict(
+        deepcopy_dict(a_host_type_metadata_fields_dict),
+        sample_type_specific_dict.get(METADATA_FIELDS_KEY, {}))
+
+    # set sample_type, and qiita_sample_type if it is not already set
+    sample_type_definition = {
+        ALLOWED_KEY: [sample_type_for_metadata],
+        DEFAULT_KEY: sample_type_for_metadata,
+        TYPE_KEY: "string"
+    }
+    sample_type_metadata_dict = update_wip_metadata_dict(
+        sample_type_metadata_dict, {SAMPLE_TYPE_KEY: sample_type_definition})
+    if QIITA_SAMPLE_TYPE not in sample_type_metadata_dict:
+        sample_type_metadata_dict = update_wip_metadata_dict(
+            sample_type_metadata_dict, {QIITA_SAMPLE_TYPE: sample_type_definition})
+    # end if qiita_sample_type not already set
+
+    return sample_type_metadata_dict
+
+
+def _resolve_sample_type_aliases_and_bases(
+        sample_types_dict: Dict[str, Any],
+        host_metadata_fields_dict: Dict[str, Any]) -> Dict[str, Any]:
+    """Resolve aliases and base types in sample type definitions.
+
+    For each sample type in the input dictionary:
+    1. If it's an alias, follow the alias and resolve the target's metadata
+    2. If it has a base_type, inherit metadata fields from the base
+    3. Merge sample-type metadata fields with host-level metadata fields
+    4. Add sample_type and qiita_sample_type fields
+
+    Parameters
+    ----------
+    sample_types_dict : Dict[str, Any]
+        Dictionary of sample type configurations (from sample_type_specific_metadata).
+    host_metadata_fields_dict : Dict[str, Any]
+        Host-level metadata fields to merge into each sample type.
+
+    Returns
+    -------
+    Dict[str, Any]
+        Dictionary with all sample types resolved.
+
+    Raises
+    ------
+    ValueError
+        If chained aliases are detected or base type has invalid structure.
+    """
+    result = {}
+
+    for sample_type_name in sample_types_dict.keys():
+        resolved_metadata = _construct_sample_type_metadata_fields_dict(
+            sample_type_name, sample_types_dict, host_metadata_fields_dict)
+
+        result[sample_type_name] = {
+            METADATA_FIELDS_KEY: resolved_metadata
+        }
+
+    return result
+
+
 def build_full_flat_config_dict(
         study_specific_config_dict: Optional[Dict[str, Any]] = None,
         software_config_dict: Optional[Dict[str, Any]] = None,
@@ -503,6 +640,14 @@ def build_full_flat_config_dict(
         full_nested_hosts_dict, None)
     software_plus_study_flat_config_dict[HOST_TYPE_SPECIFIC_METADATA_KEY] = \
         full_flat_hosts_dict
+
+    # drop the STUDY_SPECIFIC_METADATA_KEY from the final output dict (because
+    # its contents have already been incorporated into the
+    # HOST_TYPE_SPECIFIC_METADATA_KEY section); note we keep all the other
+    # top-level keys from the study-specific config dict
+    if STUDY_SPECIFIC_METADATA_KEY in software_plus_study_flat_config_dict:
+        del software_plus_study_flat_config_dict[STUDY_SPECIFIC_METADATA_KEY]
+
     # this is just a renaming to indicate that, having overwritten any original
     # HOST_TYPE_SPECIFIC_METADATA_KEY in the software_plus_study_flat_config_dict
     # with the complete and flattened combination of software+study+standards, it is now

{metameq-2026.1.1 → metameq-2026.1.2}/metameq/src/metadata_extender.py

@@ -42,7 +42,7 @@ pandas.set_option("future.no_silent_downcasting", True)
 def get_reserved_cols(
         raw_metadata_df: pandas.DataFrame,
         study_specific_config_dict: Dict[str, Any],
-        study_specific_transformers_dict: Optional[Dict[str, Any]] = None) -> List[str]:
+        stds_fp: Optional[str] = None) -> List[str]:
     """Get a list of all reserved column names for all host+sample type combinations in the metadata.
 
     Note that 'reserved' is not the same as 'required'.  Some column names (e.g.,
@@ -55,8 +55,9 @@ def get_reserved_cols(
         The input metadata DataFrame.
     study_specific_config_dict : Dict[str, Any]
         Study-specific flat-host-type config dictionary.
-    study_specific_transformers_dict : Optional[Dict[str, Any]], default=None
-        Dictionary of custom transformers for this study (only).
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
 
     Returns
     -------
@@ -90,10 +91,10 @@ def get_reserved_cols(
 
     # extend the metadata_df to get all the required columns for all host+sample type combinations;
     # we don't really care about the contents of these columns, just their names.
-    # (I doubt it is necessary to pass the actual study_specific_transformers_dict; could probably just use None)
+    # (Likewise, it is not necessary to pass the actual study_specific_transformers_dict so
+    # just use None)
     metadata_df, _ = extend_metadata_df(
-        temp_df, study_specific_config_dict,
-        study_specific_transformers_dict)
+        temp_df, study_specific_config_dict, None, None, stds_fp)
 
     return sorted(metadata_df.columns.to_list())
 
@@ -119,7 +120,7 @@ def id_missing_cols(a_df: pandas.DataFrame) -> List[str]:
 def find_standard_cols(
         a_df: pandas.DataFrame,
         study_specific_config_dict: Dict[str, Any],
-        study_specific_transformers_dict: Optional[Dict[str, Any]] = None,
+        stds_fp: Optional[str] = None,
         suppress_missing_name_err: bool = False) -> List[str]:
     """Find all the standard columns in the metadata DataFrame.
 
@@ -129,8 +130,9 @@ def find_standard_cols(
         The metadata DataFrame to analyze.
     study_specific_config_dict : Dict[str, Any]
         Study-specific flat-host-type config dictionary.
-    study_specific_transformers_dict : Optional[Dict[str, Any]], default=None
-        Dictionary of custom transformers for this study (only).
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
     suppress_missing_name_err : bool, default=False
         Whether to suppress errors about missing sample name.
 
@@ -156,8 +158,7 @@ def find_standard_cols(
     # get the intersection of the reserved standard columns and
     # the columns in the input dataframe
     standard_cols = get_reserved_cols(
-        a_df, study_specific_config_dict,
-        study_specific_transformers_dict=study_specific_transformers_dict)
+        a_df, study_specific_config_dict, stds_fp)
 
     standard_cols_set = (set(standard_cols) - set(INTERNAL_COL_KEYS))
 
@@ -167,7 +168,7 @@ def find_standard_cols(
 def find_nonstandard_cols(
         a_df: pandas.DataFrame,
         study_specific_config_dict: Dict[str, Any],
-        study_specific_transformers_dict: Optional[Dict[str, Any]] = None) -> List[str]:
+        stds_fp: Optional[str] = None) -> List[str]:
     """Find any non-standard columns in the metadata DataFrame.
 
     Parameters
@@ -176,8 +177,9 @@ def find_nonstandard_cols(
         The metadata DataFrame to analyze.
     study_specific_config_dict : Dict[str, Any]
         Study-specific flat-host-type config dictionary.
-    study_specific_transformers_dict : Optional[Dict[str, Any]], default=None
-        Dictionary of custom transformers for this study (only).
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
 
     Returns
     -------
@@ -195,15 +197,15 @@ def find_nonstandard_cols(
 
     # get the columns in
     standard_cols = get_reserved_cols(
-        a_df, study_specific_config_dict,
-        study_specific_transformers_dict=study_specific_transformers_dict)
+        a_df, study_specific_config_dict, stds_fp)
 
     return list(set(a_df.columns) - set(standard_cols))
 
 
 def get_extended_metadata_from_df_and_yaml(
         raw_metadata_df: pandas.DataFrame,
-        study_specific_config_fp: Optional[str]) -> Tuple[pandas.DataFrame, pandas.DataFrame]:
+        study_specific_config_fp: Optional[str],
+        stds_fp: Optional[str] = None) -> Tuple[pandas.DataFrame, pandas.DataFrame]:
     """Extend metadata using configuration from a study-specific YAML config file.
 
     Parameters
@@ -212,6 +214,9 @@ def get_extended_metadata_from_df_and_yaml(
         The raw metadata DataFrame to extend.
     study_specific_config_fp : Optional[str]
         Path to the study-specific configuration YAML file.
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
 
     Returns
     -------
@@ -226,7 +231,8 @@ def get_extended_metadata_from_df_and_yaml(
 
     # extend the metadata DataFrame using the study-specific flat-host-type config dictionary
     metadata_df, validation_msgs_df = \
-        extend_metadata_df(raw_metadata_df, study_specific_config_dict)
+        extend_metadata_df(raw_metadata_df, study_specific_config_dict,
+                           None, None, stds_fp)
 
     return metadata_df, validation_msgs_df
 
@@ -257,7 +263,8 @@ def write_extended_metadata(
         out_name_base: str,
         sep: str = "\t",
         remove_internals: bool = True,
-        suppress_empty_fails: bool = False) -> pandas.DataFrame:
+        suppress_empty_fails: bool = False,
+        stds_fp: Optional[str] = None) -> pandas.DataFrame:
     """Write extended metadata to files starting from input file paths to metadata and config.
 
     Parameters
@@ -276,6 +283,9 @@ def write_extended_metadata(
         Whether to remove internal columns.
     suppress_empty_fails : bool, default=False
         Whether to suppress empty failure files.
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
 
     Returns
     -------
@@ -310,7 +320,8 @@ def write_extended_metadata(
         raw_metadata_df, study_specific_config_dict,
         out_dir, out_name_base, sep=sep,
         remove_internals=remove_internals,
-        suppress_empty_fails=suppress_empty_fails)
+        suppress_empty_fails=suppress_empty_fails,
+        stds_fp=stds_fp)
 
     # for good measure, return the extended metadata DataFrame
     return extended_df
@@ -351,7 +362,8 @@ def write_extended_metadata_from_df(
         sep: str = "\t",
         remove_internals: bool = True,
         suppress_empty_fails: bool = False,
-        internal_col_names: Optional[List[str]] = None) -> pandas.DataFrame:
+        internal_col_names: Optional[List[str]] = None,
+        stds_fp: Optional[str] = None) -> pandas.DataFrame:
     """Write extended metadata to files starting from a metadata DataFrame and config dictionary.
 
     Parameters
@@ -374,6 +386,9 @@ def write_extended_metadata_from_df(
         Whether to suppress empty failure files.
     internal_col_names : Optional[List[str]], default=None
         List of internal column names.
+    stds_fp : Optional[str], default=None
+        Path to standards dictionary file. If None, the default standards
+        config pulled from the standards.yml file will be used.
 
     Returns
     -------
@@ -383,7 +398,7 @@ def write_extended_metadata_from_df(
     # extend the metadata DataFrame using the study-specific flat-host-type config dictionary
     metadata_df, validation_msgs_df = extend_metadata_df(
         raw_metadata_df, study_specific_config_dict,
-        study_specific_transformers_dict)
+        study_specific_transformers_dict, None, stds_fp)
 
     # write the metadata and validation results to files
     write_metadata_results(
@@ -814,12 +829,6 @@ def _generate_metadata_for_a_sample_type_in_a_host_type(
             - The updated metadata DataFrame with sample-type-specific elements added
             - A list of validation messages
     """
-    # copy the metadata fields dict from the host type config to be the
-    # basis of the work-in-progress metadata dict--these are the default fields
-    # that will be overwritten, if necessary, by sample type-specific fields
-    wip_metadata_fields_dict = deepcopy_dict(
-        a_host_type_config_dict.get(METADATA_FIELDS_KEY, {}))
-
     # get the config section for *all* sample types within this host type
     host_sample_types_config_dict = \
         a_host_type_config_dict[SAMPLE_TYPE_SPECIFIC_METADATA_KEY]
@@ -837,20 +846,17 @@ def _generate_metadata_for_a_sample_type_in_a_host_type(
         update_metadata_df_field(
             sample_type_df, QC_NOTE_KEY, "invalid sample_type")
     else:
-        # resolve any aliases and base types for the sample type and combine its
-        # specific metadata fields with the host type's metadata fields
-        # to get the full set of config info for this host+sample type
+        # Get the already-resolved metadata fields dict for this sample type.
+        # The config is pre-resolved: aliases/base types are merged and
+        # host metadata is combined.
+        sample_type_config = host_sample_types_config_dict[a_sample_type]
         full_sample_type_metadata_fields_dict = \
-            _construct_sample_type_metadata_fields_dict(
-                a_sample_type, host_sample_types_config_dict, wip_metadata_fields_dict)
+            sample_type_config.get(METADATA_FIELDS_KEY, {})
 
         # update the metadata df with the sample type specific metadata fields
-        # TODO: this is taking in wip_metadata_fields_dict instead of full_sample_type_metadata_fields_dict,
-        # which only works because the code underlying _construct_sample_type_metadata_fields_dict
-        # is *modifying* wip_metadata_fields_dict in place. This should be corrected, but that
-        # needs to wait until there are tests to make sure doing so doesn't break anything.
         sample_type_df = _update_metadata_from_dict(
-            sample_type_df, wip_metadata_fields_dict, dict_is_metadata_fields=True,
+            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])
 
         # for fields that are required but not yet filled, replace the placeholder with