bug(medcat): CU-869bj8g9k Fix hardcoded requirement for spacy model download

medcat-v2/medcat/tokenizing/spacy_impl/utils.py

@@ -35,4 +35,17 @@ def ensure_spacy_model(model_name: str) -> None:
     cmd = f"{sys.executable} -m spacy download {model_name}"
     logger.info("Installing the spacy model %s using the CLI command "
                 "'%s'", model_name, cmd)
-    subprocess.run(cmd.split(" "), check=True)
+    try:
+        subprocess.run(
+            cmd.split(" "), check=True, capture_output=True, text=True)
+    except subprocess.CalledProcessError as err:
+        if ("requests.exceptions.ConnectionError" in err.stderr and
+                "Failed to resolve" in err.stderr):
+            logger.warning(
+                "Unable to ensure the existing of spacy model '%s'. "
+                "Internet seems to be unavailable. If the model "
+                "does not provide its own implementation (it should), "
+                "subsequent usage may prove problematic. Underlying error:\n"
+                "%s", model_name, err.stderr, exc_info=err)
+        else:
+            raise err

medcat-v2/medcat/utils/legacy/conversion_all.py

@@ -7,9 +7,11 @@
 from medcat.components.types import CoreComponentType
 from medcat.storage.serialisers import AvailableSerialisers
 from medcat.components.linking.no_action_linker import NoActionLinker
+from medcat.utils.config_utils import temp_changed_config
 
 from medcat.utils.legacy.convert_cdb import get_cdb_from_old
 from medcat.utils.legacy.convert_config import get_config_from_old
+from medcat.utils.legacy.convert_config import fix_spacy_model_name
 from medcat.utils.legacy.convert_vocab import get_vocab_from_old
 from medcat.utils.legacy.helpers import fix_subnames
 
@@ -67,7 +69,8 @@ def convert(self) -> CAT:
             CAT: The model pack.
         """
         cdb = get_cdb_from_old(
-            os.path.join(self.old_model_folder, self.cdb_name))
+            os.path.join(self.old_model_folder, self.cdb_name),
+            fix_spacy_model_name=False)
         vocab_path = os.path.join(self.old_model_folder, self.vocab_name)
         if os.path.exists(vocab_path):
             vocab = get_vocab_from_old(vocab_path)
@@ -79,7 +82,14 @@ def convert(self) -> CAT:
             config = get_config_from_old(cnf_path)
         else:
             config = cdb.config
-        cat = CAT(cdb, vocab, config)
+        with temp_changed_config(
+            config.general.nlp, "modelname",
+            os.path.join(self.old_model_folder,
+                         config.general.nlp.modelname)):
+            cat = CAT(cdb, vocab, config)
+        # NOTE: its probably easier if we change the spacy model name
+        #       afterwards
+        fix_spacy_model_name(config, cat.pipe.tokenizer)
         fix_subnames(cat)
         # MetaCATs
         meta_cat_folders = [

medcat-v2/medcat/utils/legacy/convert_cdb.py

@@ -5,6 +5,8 @@
 from medcat.config import Config
 from medcat.cdb.concepts import get_new_cui_info, get_new_name_info, TypeInfo
 from medcat.utils.legacy.convert_config import get_config_from_nested_dict
+from medcat.utils.legacy.convert_config import (
+    fix_spacy_model_name as apply_spacy_model_fix)
 
 
 logger = logging.getLogger(__name__)
@@ -209,11 +211,14 @@ def update_names(cdb: CDB, data: dict):
         setattr(cdb, name_to, data[name_from])
 
 
-def convert_data(all_data: dict) -> CDB:
+def convert_data(all_data: dict, fix_spacy_model_name: bool = True) -> CDB:
     """Convert the raw v1 data into a CDB.
 
     Args:
         all_data (dict): The raw v1 data off disk.
+        fix_spacy_model_name (bool): Whether to fix the spacy model name.
+            Older models may have unsuported spacy model names. So these
+            may sometimes need to be fixed. Defaults to True.
 
     Returns:
         CDB: The v2 CDB.
@@ -226,17 +231,23 @@ def convert_data(all_data: dict) -> CDB:
     if 'config' in all_data:
         logger.info("Loading old style CDB with config included.")
         cdb.config = get_config_from_nested_dict(all_data['config'])
+        if fix_spacy_model_name:
+            apply_spacy_model_fix(cdb.config)
     return cdb
 
 
-def get_cdb_from_old(old_path: str) -> CDB:
+def get_cdb_from_old(old_path: str,
+                     fix_spacy_model_name: bool = True) -> CDB:
     """Get the v2 CDB from a v1 CDB path.
 
     Args:
         old_path (str): The v1 CDB path.
+        fix_spacy_model_name (bool): Whether to fix the spacy model name.
+            Older models may have unsuported spacy model names. So these
+            may sometimes need to be fixed. Defaults to True.
 
     Returns:
         CDB: The v2 CDB.
     """
     data = load_old_raw_data(old_path)
-    return convert_data(data)
+    return convert_data(data, fix_spacy_model_name)

medcat-v2/medcat/utils/legacy/convert_config.py

@@ -8,6 +8,7 @@
 
 from medcat.utils.legacy.helpers import fix_old_style_cnf
 from medcat.config.config import SerialisableBaseModel
+from medcat.tokenizing.tokenizers import BaseTokenizer
 
 
 logger = logging.getLogger(__name__)
@@ -126,8 +127,8 @@ def _relocate(cnf: Config, old_data: dict) -> Config:
         orig_val = cast(Any, orig_val)
         target_model = cast(BaseModel, target_model)
         fname = new_path.split(".")[-1]
-        logger.info("Relocating from %s to %s (%s)", orig_path, new_path,
-                    type(orig_val).__name__)
+        logger.info("Relocating from %s to %s (%s) [%s]", orig_path, new_path,
+                    type(orig_val).__name__, orig_val)
         _safe_setattr(target_model, fname, orig_val)
     return cnf
 
@@ -167,13 +168,25 @@ def get_config_from_nested_dict(old_data: dict) -> Config:
     # but we now default to regex
     cnf.general.nlp.provider = 'spacy'
     cnf = _make_changes(cnf, old_data)
+    return cnf
+
+
+def fix_spacy_model_name(
+        cnf: Config,
+        tokenizer: BaseTokenizer | None = None) -> None:
     if cnf.general.nlp.modelname in ('spacy_model', 'en_core_sci_md',
                                      'en_core_sci_lg'):
         logger.info("Fixing spacy model. "
                     "Moving from '%s' to 'en_core_web_md'!",
                     cnf.general.nlp.modelname)
         cnf.general.nlp.modelname = 'en_core_web_md'
-    return cnf
+        # NOTE: the tokenizer uses an internally cached name that we need to
+        #       fix here as well so that the name of the subsequently saved
+        #       files is more descriptive than just 'spacy_model'
+        if tokenizer:
+            from medcat.tokenizing.spacy_impl.tokenizers import SpacyTokenizer
+            cast(SpacyTokenizer,
+                 tokenizer)._spacy_model_name = cnf.general.nlp.modelname
 
 
 def get_config_from_old(path: str) -> Config: