Issue 3770 WSI parser: sevral extension for file format

deploy/docker/cp-tools/research/wsi-parser/process_files.py

@@ -66,7 +66,27 @@
 FORCE_CATALOG_UPDATE = os.getenv('WSI_PARSING_FORCE_CATALOG_UPDATE', 'false') == 'true'
 CLOUD_STORAGE_ID = os.getenv('WSI_PARSING_STORAGE_ID', None)
 CATALOG_UPDATE_URL = os.getenv('WSI_PARSING_CATALOG_UPDATE_URL', None)
-OME_TIFF_TARGET_FORMAT_MASK = os.getenv('WSI_PARSING_OME_TIFF_TARGET_FORMAT_MASK', '*.qptiff')
+OME_TIFF_TARGET_FORMAT_MASK = os.getenv('WSI_PARSING_OME_TIFF_TARGET_FORMAT_MASK', '*.qptiff,*.tif')
+
+
+def parse_extension_mapping_property(format_to_extension_mapping_str):
+    result = {}
+    if not format_to_extension_mapping_str:
+        return result
+    for format in format_to_extension_mapping_str.split(";"):
+        try:
+            format, extensions = format.split("=")
+            for extension in extensions.split(","):
+                result[extension] = format
+        except ValueError as e:
+            # skip if problem
+            pass
+    return result
+
+
+EXTENSION_TO_FORMAT_MAPPING = parse_extension_mapping_property(
+    os.getenv('WSI_EXTENSION_TO_FORMAT_MAPPING', 'qptiff=.qptiff,.tif')
+)
 
 STAIN_METHOD_MAPPINGS = {
     'GENERAL': 'General',
@@ -99,6 +119,16 @@ def prepare_exception_tags_mapping():
 EXCEPTION_TAGS_MAPPING = prepare_exception_tags_mapping()
 
 
+def get_file_extension(file):
+    file_and_extension = os.path.splitext(file)
+    return file_and_extension[1] if file and len(file_and_extension) == 2 else None
+
+
+def is_file_has_format(file, format):
+    file_extension = get_file_extension(file)
+    return EXTENSION_TO_FORMAT_MAPPING.get(file_extension, None) == format
+
+
 class ImageDetails(object):
 
     def __init__(self, series_id, name, width, height, refractive_index, objective_id):
@@ -730,6 +760,11 @@ def map_to_metadata_dict(self, metadata):
 
     def add_qptiff_tags_from_filename(self, existing_tags):
         name_tags = WsiParsingUtils.get_basename_without_extension(self.file_path).split('_')
+        if len(name_tags) != 4:
+            self.log_processing_info(
+                'File name {} is not in format: <Study>_<Animal_id>_<Tissue>_<Stain>. '
+                'Skipping retrieving tas from file name.'.format(self.file_path))
+            return
         if not existing_tags.get(STUDY_NAME_CAT_ATTR_NAME):
             existing_tags[STUDY_NAME_CAT_ATTR_NAME] = {name_tags[0]}
         if not existing_tags.get(ANIMAL_ID_CAT_ATTR_NAME):
@@ -1310,10 +1345,11 @@ def process_file(self):
         target_series = target_image_details.id
         self.create_tmp_stat_file(target_image_details)
         target_tags_file = self.file_path
-        if self.file_path.endswith('.qptiff'):
+        is_qptiff = is_file_has_format(self.file_path, "qptiff")
+        if is_qptiff:
+            self.log_processing_info('File {} is recognized as QPTIFF'.format(self.file_path))
             target_tags_file = self.create_empty_vsi()
-        tags_processing_result = self.try_process_tags(target_tags_file, target_image_details,
-                                                       self.file_path.endswith('.qptiff'))
+        tags_processing_result = self.try_process_tags(target_tags_file, target_image_details, is_qptiff)
         if TAGS_PROCESSING_ONLY:
             return tags_processing_result
         elif self._is_same_series_selected(target_series):
@@ -1362,8 +1398,8 @@ def process_file(self):
     def try_process_tags(self, target_file_path, target_image_details, is_qptiff=False):
         tags_processing_result = 0
         try:
-            if WsiFileTagProcessor(target_file_path, self.xml_info_tree,
-                                   is_qptiff).process_tags(target_image_details) != 0:
+            wsi_file_tag_processor = WsiFileTagProcessor(target_file_path, self.xml_info_tree, is_qptiff)
+            if wsi_file_tag_processor.process_tags(target_image_details) != 0:
                 self.log_processing_info('Some errors occurred during file tagging')
                 tags_processing_result = 1
         except Exception as e: