Merge branch 'dev_batch_runner' into 'staging'

BatchRunner file parsing

See merge request rhodes/model_server!95

model_server/clients/batch_runner.py

@@ -144,7 +144,6 @@ class FileBatchRunnerClient(HttpClient):
                         matching_files.append(f.name)
                 return matching_files
 
-            files += _append_files_by_pattern(where_local, inp.get('pattern'))
             is_multiposition = inp.get('multiposition', False)
             where_remote = Path(self.remote_paths['input']) / inp['directory']
 
@@ -153,20 +152,27 @@ class FileBatchRunnerClient(HttpClient):
                 for subdir in where_local.iterdir():
                     if not subdir.is_dir():
                         continue
+                    if (sdp := inp.get('subdirectory_pattern')) is not None:
+                        if sdp.upper() not in subdir.name.upper():
+                            continue
                     matches = _append_files_by_pattern(subdir, inp.get('pattern'))
                     files += [f'{subdir}/{f}' for f in matches]
+            else:
+                files += _append_files_by_pattern(where_local, inp.get('pattern'))
 
-            def _get_file_info(filename):
+            def _get_file_info(fpath_str):
                 info = {
-                    'remote_path': (where_remote / filename).as_posix(),
-                    'local_path': where_local / filename,
+                    'remote_path': (where_remote / fpath_str).as_posix(),
+                    'local_path': where_local / fpath_str,
                     'is_multiposition': is_multiposition,
                 }
+                filename = Path(fpath_str).name
                 if (coord_regex := inp.get('coord_regex')) is not None:
                     for coord_k, coord_v in re.search(coord_regex, filename).groupdict().items():
-                        if coord_k.lower() not in ['well', 'position', 'time']:
-                            raise InvalidStackCoordinateKeyError(f'Cannot interpret coordinate {coord_k}')
-                        info[f'coord_{coord_k.lower()}'] = int(coord_v)
+                        if coord_k.lower() in ['well', 'position', 'time', 'date']:
+                            info[f'coord_{coord_k.lower()}'] = int(coord_v)
+                        else:
+                            info[f'coord_{coord_k.lower()}'] = coord_v
                 return info
             paths = paths + [_get_file_info(f) for f in files]
         if max_count is not None: