Simplify output dir and file naming

input_files/campaignDescriptor1_LI.yaml

@@ -2,7 +2,7 @@
 input_file_directory: '//fs101/5505/Data'
 
 # Path to directory where raw data is copied and converted to HDF5 format for local analysis.
-output_file_directory: '../output_files/'
+output_file_directory: '../data/'
 
 # Project metadata for data lineage and provenance
 project:  'Photoenhanced uptake of NO2 driven by Fe(III)-carboxylate'

input_files/campaignDescriptor2_TBR.yaml

@@ -2,7 +2,7 @@
 input_file_directory: '//fs101/5505/People/Juan/TypicalBeamTime'
 
 # Path to directory where raw data is copied and converted to HDF5 format for local analysis.
-output_file_directory: '../output_files/'
+output_file_directory: '../data/'
 
 # Project metadata for data lineage and provenance
 project: 'Beamtime May 2024, Ice Napp'  

input_files/campaignDescriptor3_NG.yaml

@@ -2,7 +2,7 @@
 input_file_directory: '//fs03/Iron_Sulphate'
 
 # Path to directory where raw data is copied and converted to HDF5 format for local analysis.
-output_file_directory: '../output_files/'
+output_file_directory: '../data/'
 
 # Project metadata for data lineage and provenance
 project: 'Fe SOA project' 

instruments/readers/g5505_text_reader.py

@@ -19,19 +19,94 @@ import yaml
 import h5py
 import argparse
 import logging
-# Import project modules
-#root_dir = os.path.abspath(os.curdir)
-#sys.path.append(root_dir)
-
-
-#try:
-#    from dima.utils import g5505_utils as utils
-#except ModuleNotFoundError:
-#    import utils.g5505_utils as utils
-#    import src.hdf5_ops as hdf5_ops
+import warnings
 import utils.g5505_utils as utils
 
 
+def detect_table_header_line(filepath, table_header_list, encoding_list, separator_list, verbose=False):
+    """
+    Detects the table header line in the file and returns:
+    - header_line_idx (int)
+    - column_names (List[str])
+    - tb_idx used
+    - preamble_lines (List[str])
+    Returns (-1, [], None, []) if not found.
+    """
+    preamble_lines = []
+    header_line_idx = -1
+    column_names = []
+    tb_idx = None
+
+    with open(filepath, 'rb') as f:
+        for line_number, line in enumerate(f):
+            decoded_line = line.decode(encoding_list[0])  # assume consistent encoding initially
+            for idx, tb in enumerate(table_header_list):
+                if tb in decoded_line:
+                    tb_idx = idx
+                    list_of_substrings = decoded_line.split(separator_list[idx].replace('\\t', '\t'))
+                    counts = collections.Counter(list_of_substrings)
+                    column_names = [f"{i}_{name.strip()}" if counts[name] > 1 else name.strip()
+                                    for i, name in enumerate(list_of_substrings)]
+                    header_line_idx = line_number
+                    if verbose:
+                        print(f"[Detected header] Line {line_number}: {column_names}")
+                    return header_line_idx, column_names, tb_idx, preamble_lines
+            preamble_lines.append(' '.join(decoded_line.split()))
+    
+    warnings.warn("Table header was not detected using known patterns. Will attempt inference mode.")
+    return -1, [], None, preamble_lines
+
+def load_file_reader_parameters(filename: str, instruments_dir: str) -> tuple:
+    """
+    Load file reader configuration parameters based on the file and instrument directory.
+
+    Returns:
+        - config_dict: Full configuration dictionary
+        - file_encoding
+        - separator
+        - table_header
+        - timestamp_variables
+        - datetime_format
+        - description_dict
+    """
+    config_path = os.path.abspath(os.path.join(instruments_dir, 'readers', 'config_text_reader.yaml'))
+
+    try:
+        with open(config_path, 'r') as stream:
+            config_dict = yaml.load(stream, Loader=yaml.FullLoader)
+    except yaml.YAMLError as exc:
+        print(f"[YAML Load Error] {exc}")
+        return {}, '', '', '', [], [], {}
+
+    # Defaults
+    file_encoding = config_dict.get('default', {}).get('file_encoding', 'utf-8')
+    separator = config_dict.get('default', {}).get('separator', ',')
+    table_header = config_dict.get('default', {}).get('table_header', 'infer')
+    timestamp_variables = []
+    datetime_format = []
+    description_dict = {}
+
+    for instFolder in config_dict.keys():
+        if instFolder in filename.split(os.sep):
+            file_encoding = config_dict[instFolder].get('file_encoding', file_encoding)
+            separator = config_dict[instFolder].get('separator', separator)
+            table_header = config_dict[instFolder].get('table_header', table_header)
+            timestamp_variables = config_dict[instFolder].get('timestamp', [])
+            datetime_format = config_dict[instFolder].get('datetime_format', [])
+
+            link_to_description = config_dict[instFolder].get('link_to_description', '').replace('/', os.sep)
+            if link_to_description:
+                path = os.path.join(instruments_dir, link_to_description)
+                try:
+                    with open(path, 'r') as stream:
+                        description_dict = yaml.load(stream, Loader=yaml.FullLoader)
+                except (FileNotFoundError, yaml.YAMLError) as exc:
+                    print(f"[Description Load Error] {exc}")
+
+    return (config_dict, file_encoding, separator, table_header,
+            timestamp_variables, datetime_format, description_dict)
+
+
 def read_txt_files_as_dict(filename: str, instruments_dir: str = None, work_with_copy: bool = True):
 
     filename = os.path.normpath(filename)
@@ -41,56 +116,16 @@ def read_txt_files_as_dict(filename: str, instruments_dir: str = None, work_with
         module_dir = os.path.dirname(__file__)
         instruments_dir = os.path.join(module_dir, '..')
 
-    # Normalize the path (resolves any '..' in the path)
-    instrument_configs_path = os.path.abspath(os.path.join(instruments_dir,'readers','config_text_reader.yaml'))
-
-    print(instrument_configs_path)
-
-    with open(instrument_configs_path,'r') as stream:
-        try:
-            config_dict = yaml.load(stream, Loader=yaml.FullLoader)
-        except yaml.YAMLError as exc:
-            print(exc)
-    # Verify if file can be read by available intrument configurations.
-    #if not any(key in filename.replace(os.sep,'/') for key in config_dict.keys()):
-    #    return {}
-
-
-    #TODO: this may be prone to error if assumed folder structure is non compliant 
-    file_encoding = config_dict['default']['file_encoding'] #'utf-8'
-    separator = config_dict['default']['separator']
-    table_header = config_dict['default']['table_header']
-    timestamp_variables = []
-    datetime_format = []
-    tb_idx = 0
-    column_names = ''
-    description_dict = {}
-
-    for instFolder in config_dict.keys():
-        
-        if instFolder in filename.split(os.sep):
-            
-            file_encoding = config_dict[instFolder].get('file_encoding',file_encoding)
-            separator = config_dict[instFolder].get('separator',separator)
-            table_header = config_dict[instFolder].get('table_header',table_header)
-            timestamp_variables = config_dict[instFolder].get('timestamp',[])
-            datetime_format = config_dict[instFolder].get('datetime_format',[])
-
-            
-            link_to_description = config_dict[instFolder].get('link_to_description', '').replace('/', os.sep) 
-
-            if link_to_description:
-                path = os.path.join(instruments_dir, link_to_description)                
-                try:
-                    with open(path, 'r') as stream:
-                        description_dict = yaml.load(stream, Loader=yaml.FullLoader)
-                except (FileNotFoundError, yaml.YAMLError) as exc:
-                    print(exc)
-    #if 'None' in table_header:
-    #    return {}
+    (config_dict,
+    file_encoding,
+    separator,
+    table_header,
+    timestamp_variables,
+    datetime_format,
+    description_dict) = load_file_reader_parameters(filename, instruments_dir)
 
     # Read header as a dictionary and detect where data table starts
-    header_dict = {}
+    header_dict = {'actris_level': 0, 'processing_date':utils.created_at(), 'processing_script' : os.path.relpath(thisFilePath,dimaPath)}
     data_start = False    
     # Work with copy of the file for safety
     if work_with_copy:
@@ -109,58 +144,20 @@ def read_txt_files_as_dict(filename: str, instruments_dir: str = None, work_with
     table_preamble = []
     line_number = 0
     if 'infer' not in table_header:
+        header_line_idx, column_names, tb_idx, table_preamble = detect_table_header_line(
+            tmp_filename, table_header, file_encoding, separator)
 
-        with open(tmp_filename,'rb') as f:
-            
-            for line_number, line in enumerate(f):   
-                decoded_line = line.decode(file_encoding[tb_idx])
-                
-
-                for tb_idx, tb in enumerate(table_header):
-                    print(tb)
-                    if tb in decoded_line:                    
-                        break
-                
-                if tb in decoded_line:   
-                    
-                    list_of_substrings = decoded_line.split(separator[tb_idx].replace('\\t','\t'))  
-
-                    # Count occurrences of each substring
-                    substring_counts = collections.Counter(list_of_substrings)
-                    data_start = True  
-                    # Generate column names with appended index only for repeated substrings
-                    column_names = [f"{i}_{name.strip()}" if substring_counts[name] > 1 else name.strip() for i, name in enumerate(list_of_substrings)]           
-
-                    #column_names = [str(i)+'_'+name.strip() for i, name in enumerate(list_of_substrings)]
-                    #column_names = []
-                    #for i, name in enumerate(list_of_substrings):
-                    #    column_names.append(str(i)+'_'+name) 
-
-                    #print(line_number, len(column_names ),'\n')
-                    break
-                else:
-                    print('Table header was not detected.')
-                # Subdivide line into words, and join them by single space. 
-                # I asumme this can produce a cleaner line that contains no weird separator characters \t \r or extra spaces and so on.
-                list_of_substrings = decoded_line.split()
-                # TODO: ideally we should use a multilinear string but the yalm parser is not recognizing \n as special character
-                #line = ' '.join(list_of_substrings+['\n'])
-                #line = ' '.join(list_of_substrings)     
-                table_preamble.append(' '.join([item for item in list_of_substrings]))# += new_line  
+        if header_line_idx == -1:
+            table_header = ['infer']  # fallback to pandas' inference
 
   
     # TODO: it does not work with separator as none :(. fix for RGA
     
     try:
-        print(column_names)
         if not 'infer' in table_header:            
-            #print(table_header)
-            #print(file_encoding[tb_idx])
-            
             df = pd.read_csv(tmp_filename, 
                             delimiter = separator[tb_idx].replace('\\t','\t'), 
-                            header=line_number, 
-                            #encoding='latin-1',
+                            header=header_line_idx, 
                             encoding = file_encoding[tb_idx],
                             names=column_names,
                             skip_blank_lines=True)

instruments/readers/structured_file_reader.py

@@ -32,7 +32,7 @@ def read_structured_file_as_dict(path_to_file):
     _, path_head = os.path.split(path_to_file)
 
     file_dict['name'] = path_head
-    file_dict['attributes_dict'] = {}
+    file_dict['attributes_dict'] = {'actris_level': 0, 'processing_date': utils.created_at(), 'processing_script' : os.path.relpath(thisFilePath,dimaPath)}
     file_dict['datasets'] = []
 
     try:

instruments/readers/xps_ibw_reader.py

@@ -1,10 +1,27 @@
-import os
 import sys
+import os
+
+try:
+    thisFilePath = os.path.abspath(__file__)
+except NameError:
+    print("Error: __file__ is not available. Ensure the script is being run from a file.")
+    print("[Notice] Path to DIMA package may not be resolved properly.")
+    thisFilePath = os.getcwd()  # Use current directory or specify a default
+
+dimaPath = os.path.normpath(os.path.join(thisFilePath, "..",'..','..'))  # Move up to project root
+
+if dimaPath not in sys.path:  # Avoid duplicate entries
+    sys.path.insert(0,dimaPath)
+
+
+
 import h5py
 
 from igor2.binarywave import load as loadibw
 import logging
 import argparse
+import utils.g5505_utils as utils
+
 
 def read_xps_ibw_file_as_dict(filename):
     """
@@ -49,7 +66,7 @@ def read_xps_ibw_file_as_dict(filename):
 
     # Group name and attributes
     file_dict['name'] = path_head
-    file_dict['attributes_dict'] = {}
+    file_dict['attributes_dict'] =  {'actris_level': 0, 'processing_date':utils.created_at(), 'processing_script' : os.path.relpath(thisFilePath,dimaPath)}
  
     # Convert notes of bytes class to string class and split string into a list of elements separated by '\r'. 
     notes_list = file_obj['wave']['note'].decode("utf-8").split('\r')
@@ -85,22 +102,11 @@ def read_xps_ibw_file_as_dict(filename):
 
 if __name__ == "__main__":
 
-
-    try:
-        thisFilePath = os.path.abspath(__file__)
-    except NameError:
-        print("Error: __file__ is not available. Ensure the script is being run from a file.")
-        print("[Notice] Path to DIMA package may not be resolved properly.")
-        thisFilePath = os.getcwd()  # Use current directory or specify a default
-
-    dimaPath = os.path.normpath(os.path.join(thisFilePath, "..",'..','..'))  # Move up to project root
-
-    if dimaPath not in sys.path:  # Avoid duplicate entries
-        sys.path.insert(0,dimaPath)
-
     from src.hdf5_ops import save_file_dict_to_hdf5
     from utils.g5505_utils import created_at
 
+
+
     # Set up argument parsing
     parser = argparse.ArgumentParser(description="Data ingestion process to HDF5 files.")
     parser.add_argument('dst_file_path', type=str, help="Path to the target HDF5 file.")

notebooks/demo_data_integration.ipynb

@@ -49,15 +49,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "#output_filename_path = 'output_files/unified_file_smog_chamber_2024-04-07_UTC-OFST_+0200_NG.h5'\n",
-    "yaml_config_file_path = '../input_files/data_integr_config_file_TBR.yaml'\n",
+    "number, initials = 1, 'LI' # Set as either 2, 'TBR' or 3, 'NG'\n",
+    "campaign_descriptor_path = f'../input_files/campaignDescriptor{number}_{initials}.yaml'\n",
     "\n",
-    "#path_to_input_directory = 'output_files/kinetic_flowtube_study_2022-01-31_LuciaI'\n",
-    "#path_to_hdf5_file = hdf5_lib.create_hdf5_file_from_filesystem_path(path_to_input_directory)\n"
+    "print(campaign_descriptor_path)\n"
    ]
   },
   {
@@ -76,7 +75,7 @@
    "outputs": [],
    "source": [
     "\n",
-    "hdf5_file_path = data_integration.run_pipeline(yaml_config_file_path)"
+    "hdf5_file_path = data_integration.run_pipeline(campaign_descriptor_path)"
    ]
   },
   {
@@ -146,7 +145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +159,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "multiphase_chemistry_env",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -174,7 +173,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

pipelines/data_integration.py

@@ -38,12 +38,19 @@ def _generate_datetime_dict(datetime_steps):
     """ Generate the datetime augment dictionary from datetime steps. """
     datetime_augment_dict = {}
     for datetime_step in datetime_steps:
-        #tmp = datetime.strptime(datetime_step, '%Y-%m-%d %H-%M-%S')
         datetime_augment_dict[datetime_step] = [
-            datetime_step.strftime('%Y-%m-%d'), datetime_step.strftime('%Y_%m_%d'), datetime_step.strftime('%Y.%m.%d'), datetime_step.strftime('%Y%m%d')
+            datetime_step.strftime('%Y-%m-%d'), datetime_step.strftime('%Y_%m_%d'),
+            datetime_step.strftime('%Y.%m.%d'), datetime_step.strftime('%Y%m%d')
         ]
     return datetime_augment_dict
 
+def _generate_output_path_fragment(filename_prefix, integration_mode, dataset_startdate, dataset_enddate, index=None):
+    """Generate consistent directory or file name fragment based on mode."""
+    if integration_mode == 'collection':
+        return f'collection_{index}_{filename_prefix}_{dataset_enddate}' 
+    else:
+        return f'{filename_prefix}_{dataset_enddate}'
+
 def load_config_and_setup_logging(yaml_config_file_path, log_dir):
     """Load YAML configuration file, set up logging, and validate required keys and datetime_steps."""
     
@@ -189,17 +196,6 @@ def copy_subtree_and_create_hdf5(src, dst, select_dir_keywords, select_file_keyw
 
 
 def run_pipeline(path_to_config_yamlFile, log_dir='logs/'):
-
-    """Integrates data sources specified by the input configuration file into HDF5 files.
-
-    Parameters:
-        yaml_config_file_path (str): Path to the YAML configuration file.
-        log_dir (str): Directory to save the log file.
-
-    Returns:
-        list: List of Paths to the created HDF5 file(s).
-    """
-   
     config_dict = load_config_and_setup_logging(path_to_config_yamlFile, log_dir)
 
     path_to_input_dir = config_dict['input_file_directory']
@@ -213,22 +209,27 @@ def run_pipeline(path_to_config_yamlFile, log_dir='logs/'):
     dataset_startdate = config_dict['dataset_startdate']
     dataset_enddate = config_dict['dataset_enddate']
 
-    # Determine mode and process accordingly
-    output_filename_path = []
-    campaign_name_template = lambda filename_prefix, suffix: '_'.join([filename_prefix, suffix])
-    date_str = f'{dataset_startdate}_{dataset_enddate}'    
+    integration_mode = config_dict.get('integration_mode', 'single_experiment')
+    filename_prefix = config_dict['filename_prefix']
+
+    output_filename_path = []
+
+    # Determine top-level campaign folder path
+    top_level_foldername = _generate_output_path_fragment(
+        filename_prefix, integration_mode, dataset_startdate, dataset_enddate, index=1
+    )
 
-    # Create path to new raw datafolder and standardize with forward slashes
     path_to_rawdata_folder = os.path.join(
-        path_to_output_dir, 'collection_' + campaign_name_template(config_dict['filename_prefix'], date_str), "").replace(os.sep, '/')
+        path_to_output_dir, top_level_foldername, ""
+    ).replace(os.sep, '/')
 
     # Process individual datetime steps if available, regardless of mode    
     if config_dict.get('datetime_steps_dict', {}):
-        # Single experiment mode
         for datetime_step, file_keywords in config_dict['datetime_steps_dict'].items():
-            date_str = datetime_step.strftime('%Y-%m-%d')
-            single_campaign_name = campaign_name_template(config_dict['filename_prefix'], date_str)
-            path_to_rawdata_subfolder = os.path.join(path_to_rawdata_folder, single_campaign_name, "")
+            single_date_str = datetime_step.strftime('%Y%m%d')
+            subfolder_name = f"{filename_prefix}_{single_date_str}"
+            subfolder_name = f"experimental_step_{single_date_str}"
+            path_to_rawdata_subfolder = os.path.join(path_to_rawdata_folder, subfolder_name, "")
 
             path_to_integrated_stepwise_hdf5_file = copy_subtree_and_create_hdf5(
                 path_to_input_dir, path_to_rawdata_subfolder, select_dir_keywords, 
@@ -236,11 +237,12 @@ def run_pipeline(path_to_config_yamlFile, log_dir='logs/'):
 
             output_filename_path.append(path_to_integrated_stepwise_hdf5_file)
 
-        # Collection mode processing if specified
-        if 'collection' in config_dict.get('integration_mode', 'single_experiment'):
+        # Collection mode post-processing
+        if integration_mode == 'collection':
             path_to_filenames_dict = {path_to_rawdata_folder: [os.path.basename(path) for path in output_filename_path]} if output_filename_path else {}
-            #hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path_new(path_to_rawdata_folder, path_to_filenames_dict, [], root_metadata_dict)
-            hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path(path_to_rawdata_folder, path_to_filenames_dict, [], root_metadata_dict)
+            hdf5_path = hdf5_lib.create_hdf5_file_from_filesystem_path(
+                path_to_rawdata_folder, path_to_filenames_dict, [], root_metadata_dict
+            )
             output_filename_path.append(hdf5_path)
     else:
         path_to_integrated_stepwise_hdf5_file = copy_subtree_and_create_hdf5(
@@ -250,24 +252,16 @@ def run_pipeline(path_to_config_yamlFile, log_dir='logs/'):
 
     return output_filename_path
 
-
 if __name__ == "__main__":
-
     if len(sys.argv) < 2:
         print("Usage: python data_integration.py <function_name> <function_args>")
         sys.exit(1)
 
-    # Extract the function name from the command line arguments
     function_name = sys.argv[1]
 
-    # Handle function execution based on the provided function name
     if function_name == 'run':
-
         if len(sys.argv) != 3:
             print("Usage: python data_integration.py run <path_to_config_yamlFile>")
             sys.exit(1)
-        # Extract path to configuration file, specifying the data integration task    
         path_to_config_yamlFile = sys.argv[2]
         run_pipeline(path_to_config_yamlFile)
-
-

src/hdf5_ops.py

@@ -19,17 +19,10 @@ import pandas as pd
 import numpy as np
 import logging
 import datetime
-
-import h5py
-
 import yaml
 import json
 import copy
 
-#try:
-#    from dima.utils import g5505_utils as utils
-#    from dima.src import hdf5_writer as hdf5_lib
-#except ModuleNotFoundError:
 import utils.g5505_utils as utils
 import src.hdf5_writer as hdf5_lib
 

utils/g5505_utils.py

@@ -217,49 +217,49 @@ def convert_string_to_bytes(input_list: list):
 
 def convert_attrdict_to_np_structured_array(attr_value: dict):
     """
-    Converts a dictionary of attributes into a numpy structured array for HDF5 
-    compound type compatibility.
-
-    Each dictionary key is mapped to a field in the structured array, with the 
-    data type (S) determined by the longest string representation of the values. 
-    If the dictionary is empty, the function returns 'missing'.
+    Converts a dictionary of attributes into a NumPy structured array with byte-encoded fields.
+    Handles UTF-8 encoding to avoid UnicodeEncodeError with non-ASCII characters.
 
     Parameters
     ----------
     attr_value : dict
-        Dictionary containing the attributes to be converted. Example:
-        attr_value = {
-            'name': 'Temperature',
-            'unit': 'Celsius',
-            'value': 23.5,
-            'timestamp': '2023-09-26 10:00'
-        }
+        Dictionary with scalar values (int, float, str).
 
     Returns
     -------
     new_attr_value : ndarray 
-        Numpy structured array with UTF-8 encoded fields. Returns np.array(['missing'], dtype=[str]) if 
-        the input dictionary is empty.
+        1-row structured array with fixed-size byte fields (dtype='S').
     """
-    if not isinstance(attr_value,dict):
-        raise ValueError(f'Input paremeter {attr_value} must be a dictionary of scalar values.')
+    if not isinstance(attr_value, dict):
+        raise ValueError(f"Input must be a dictionary, got {type(attr_value)}")
+
+    if not attr_value:
+        return np.array(['missing'], dtype=[('value', 'S16')])  # placeholder
 
     dtype = []
     values_list = []
-    max_length = max(len(str(attr_value[key])) for key in attr_value.keys())
-    for key, val in attr_value.items():
-        # Verify if 'rename_as' is still used in metadata revision
-        if key != 'rename_as' and isinstance(val, (int, float, str)):
-            dtype.append((key, f'S{max_length}'))
-            values_list.append(attr_value[key])  
-        else:
-            print(f"Skipping unsupported type for key {key}: {type(val)}")
-    if values_list:
-        new_attr_value = np.array([tuple(values_list)], dtype=dtype)
-    else:
-        new_attr_value = np.array(['missing'], dtype=[str])
 
-    return new_attr_value
+    max_str_len = max(len(str(v)) for v in attr_value.values())
+    byte_len = max_str_len * 4  # UTF-8 worst-case
+
+    for key, val in attr_value.items():
+        if key == 'rename_as':
+            continue
+        if isinstance(val, (int, float, str)):
+            dtype.append((key, f'S{byte_len}'))
+            try:
+                encoded_val = str(val).encode('utf-8')  # explicit UTF-8
+                values_list.append(encoded_val)
+            except UnicodeEncodeError as e:
+                logging.error(f"Failed to encode {key}={val}: {e}")
+                raise
+        else:
+            logging.warning(f"Skipping unsupported type for key {key}: {type(val)}")
+
+    if values_list:
+        return np.array([tuple(values_list)], dtype=dtype)
+    else:
+        return np.array(['missing'], dtype=[('value', 'S16')])
 
 
 def infer_units(column_name):