Merge pull request #436 from NeuroML/fix-file-compatibility-check

Fix file compatibility check

Author: sanjayankur31

pyneuroml/io.py

@@ -18,6 +18,7 @@
 import lems.model.model as lems_model
 import neuroml.loaders as loaders
 import neuroml.writers as writers
+from lxml import etree
 from neuroml import NeuroMLDocument
 
 from pyneuroml.errors import ARGUMENT_ERR, FILE_NOT_FOUND_ERR, NMLFileTypeError
@@ -27,15 +28,6 @@
 logger.setLevel(logging.INFO)
 
 
-# extension: standard
-pynml_file_type_dict = {
-    "xml": "LEMS",
-    "nml": "NeuroML",
-    "sedml": "SED-ML",
-    "sbml": "SBML",
-}
-
-
 def read_neuroml2_file(
     nml2_file_name: str,
     include_includes: bool = False,
@@ -256,7 +248,7 @@ def confirm_neuroml_file(filename: str, sys_error: bool = False) -> None:
     )
 
     try:
-        confirm_file_type(filename, ["nml"])
+        confirm_file_type(filename, ["nml"], "neuroml")
     except NMLFileTypeError as e:
         if filename.startswith("LEMS_"):
             logger.warning(error_string)
@@ -276,9 +268,6 @@ def confirm_lems_file(filename: str, sys_error: bool = False) -> None:
     :param sys_error: toggle whether function should exit or raise exception
     :type sys_error: bool
     """
-    # print('Checking file: %s'%filename)
-    # Some conditions to check if a LEMS file was entered
-    # TODO: Ideally we'd like to check the root node: checking file extensions is brittle
     error_string = textwrap.dedent(
         """
     *************************************************************************************
@@ -288,7 +277,7 @@ def confirm_lems_file(filename: str, sys_error: bool = False) -> None:
     """
     )
     try:
-        confirm_file_type(filename, ["xml"])
+        confirm_file_type(filename, ["xml"], "lems")
     except NMLFileTypeError as e:
         if filename.endswith("nml"):
             logger.warning(error_string)
@@ -302,15 +291,22 @@ def confirm_lems_file(filename: str, sys_error: bool = False) -> None:
 def confirm_file_type(
     filename: str,
     file_exts: typing.List[str],
+    root_tag: typing.Optional[str] = None,
     error_str: typing.Optional[str] = None,
     sys_error: bool = False,
 ) -> None:
-    """Confirm that a file exists and has the necessary extension
+    """Confirm that a file exists and is of the provided type.
+
+    First we rely on file extensions to test for type, since this is the
+    simplest way. If this test fails, we read the full file and test the root
+    tag if one has been provided.
 
     :param filename: filename to confirm
     :type filename: str
     :param file_exts: list of valid file extensions, without the leading dot
     :type file_exts: list of strings
+    :param root_tag: root tag for file, used if extensions do not match
+    :type root_tag: str
     :param error_str: an optional error string to print along with the thrown
         exception
     :type error_str: string (optional)
@@ -320,11 +316,32 @@ def confirm_file_type(
     """
     confirm_file_exists(filename)
     filename_ext = filename.split(".")[-1]
-    file_types = [f"{x} ({pynml_file_type_dict[x]})" for x in file_exts]
-    if filename_ext not in file_exts:
-        error_string = (
-            f"Expected file extension(s): {', '.join(file_types)}; got {filename_ext}"
-        )
+
+    matched = False
+
+    if filename_ext in file_exts:
+        matched = True
+
+    got_root_tag = None
+
+    if matched is False:
+        if root_tag is not None:
+            with open(filename) as i_file:
+                xml_tree = etree.parse(i_file)
+                tree_root = xml_tree.getroot()
+                got_root_tag = tree_root.tag
+
+                if got_root_tag.lower() == root_tag.lower():
+                    matched = True
+
+    if matched is False:
+        error_string = f"Expected file extension does not match: {', '.join(file_exts)}; got {filename_ext}."
+
+        if root_tag is not None:
+            error_string += (
+                f" Expected root tag does not match: {root_tag}; got {got_root_tag}"
+            )
+
         if error_str is not None:
             error_string += "\n" + error_str
         if sys_error is True:

tests/test_io.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+"""
+Tests for io methods
+
+File: tests/test_io.py
+
+Copyright 2024 NeuroML contributors
+"""
+
+import logging
+import os
+
+from pyneuroml.errors import NMLFileTypeError
+from pyneuroml.io import confirm_file_type
+
+from . import BaseTestCase
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+
+
+class TestIo(BaseTestCase):
+    """Test io module"""
+
+    def test_confirm_file_type(self):
+        """Test confirm_file_type method."""
+
+        # LEMS file with xml extension
+        test_lems_file = "a_test_lems_file.xml"
+        with open(test_lems_file, "w") as f:
+            print("<LEMS> </LEMS>", file=f)
+        confirm_file_type(test_lems_file, ["xml"])
+
+        # lems file with non xml extension but provided tag
+        test_lems_file2 = "a_test_lems_file.lems"
+        with open(test_lems_file2, "w") as f:
+            print("<LEMS> </LEMS>", file=f)
+
+        confirm_file_type(test_lems_file2, ["xml"], "lems")
+
+        # lems file with non xml and bad tag: should fail
+        with self.assertRaises(NMLFileTypeError):
+            test_lems_file3 = "a_bad_test_lems_file.lems"
+            with open(test_lems_file3, "w") as f:
+                print("<LAMS> </LAMS>", file=f)
+
+            confirm_file_type(test_lems_file3, ["xml"], "lems")
+
+        os.unlink(test_lems_file)
+        os.unlink(test_lems_file2)
+        os.unlink(test_lems_file3)