Unify modelapi export and XML error handling

Author: wshlavacek

bionetgen/modelapi/bngfile.py

@@ -2,9 +2,11 @@
 import os, re
 import shutil
 import tempfile
+from typing import NoReturn
 
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGFileError
+from bionetgen.core.utils.logging import BNGLogger
 from bionetgen.core.utils.utils import find_BNG_path, run_command, ActionList
 
 # This allows access to the CLIs config setup
@@ -46,6 +48,7 @@ def __init__(
         self, path, BNGPATH=def_bng_path, generate_network=False, suppress=True
     ) -> None:
         self.path = path
+        self.logger = BNGLogger()
         self.generate_network = generate_network
         self.suppress = suppress
         AList = ActionList()
@@ -60,6 +63,11 @@ def __init__(
         # the top-level ActionBlock.
         self.parsed_protocol_actions = []
 
+    def _raise_file_error(self, message, path=None, loc=None) -> NoReturn:
+        error_path = self.path if path is None else path
+        self.logger.error(message, loc=loc)
+        raise BNGFileError(error_path, message=message)
+
     def generate_xml(self, xml_file, model_file=None) -> bool:
         """
         generates an BNG-XML file from a given model file. Defaults
@@ -85,7 +93,12 @@ def generate_xml(self, xml_file, model_file=None) -> bool:
                 ["perl", self.bngexec, "--xml", stripped_bngl], suppress=self.suppress
             )
             if rc != 0:
-                return False
+                msg = f"BNG-XML generation failed for {model_file}"
+                self._raise_file_error(
+                    msg,
+                    path=model_file,
+                    loc=f"{__file__} : BNGFile.generate_xml()",
+                )
 
             # we should now have the XML file
             path, model_name = os.path.split(stripped_bngl)
@@ -102,7 +115,12 @@ def generate_xml(self, xml_file, model_file=None) -> bool:
                     ]
                     xml_path = preferred[0] if preferred else candidates[0]
             if not os.path.exists(xml_path):
-                return False
+                msg = f"BNG-XML generation did not produce an XML file for {model_file}"
+                self._raise_file_error(
+                    msg,
+                    path=model_file,
+                    loc=f"{__file__} : BNGFile.generate_xml()",
+                )
             with open(xml_path, "r", encoding="UTF-8") as f:
                 content = f.read()
                 xml_file.write(content)
@@ -268,14 +286,22 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
             # run with --xml
             # TODO: Make output supression an option somewhere
             if xml_type == "bngxml":
+                if self.bngexec is None:
+                    msg = "BNG-XML generation requires BNG2.pl (BioNetGen) to be installed."
+                    self._raise_file_error(msg, loc=f"{__file__} : BNGFile.write_xml()")
                 rc, _ = run_command(
                     ["perl", self.bngexec, "--xml", "temp.bngl"], suppress=self.suppress
                 )
                 if rc != 0:
-                    print("XML generation failed")
-                    return False
+                    msg = f"BNG-XML generation failed for {self.path}"
+                    self._raise_file_error(msg, loc=f"{__file__} : BNGFile.write_xml()")
                 else:
                     # we should now have the XML file
+                    if not os.path.exists("temp.xml"):
+                        msg = "BNG-XML generation did not produce temp.xml"
+                        self._raise_file_error(
+                            msg, loc=f"{__file__} : BNGFile.write_xml()"
+                        )
                     with open("temp.xml", "r", encoding="UTF-8") as f:
                         content = f.read()
                         open_file.write(content)
@@ -284,25 +310,30 @@ def write_xml(self, open_file, xml_type="bngxml", bngl_str=None) -> bool:
                     return True
             elif xml_type == "sbml":
                 if self.bngexec is None:
-                    print(
+                    msg = (
                         "SBML generation requires BNG2.pl (BioNetGen) to be installed."
                     )
-                    return False
+                    self._raise_file_error(msg, loc=f"{__file__} : BNGFile.write_xml()")
                 command = ["perl", self.bngexec, "temp.bngl"]
                 rc, _ = run_command(command, suppress=self.suppress)
                 if rc != 0:
-                    print("SBML generation failed")
-                    return False
+                    msg = f"SBML generation failed for {self.path}"
+                    self._raise_file_error(msg, loc=f"{__file__} : BNGFile.write_xml()")
                 else:
                     # we should now have the SBML file
+                    if not os.path.exists("temp_sbml.xml"):
+                        msg = "SBML generation did not produce temp_sbml.xml"
+                        self._raise_file_error(
+                            msg, loc=f"{__file__} : BNGFile.write_xml()"
+                        )
                     with open("temp_sbml.xml", "r", encoding="UTF-8") as f:
                         content = f.read()
                         open_file.write(content)
                     open_file.seek(0)
                     return True
             else:
-                print("XML type {} not recognized".format(xml_type))
-                return False
+                msg = f"XML type {xml_type} not recognized"
+                self._raise_file_error(msg, loc=f"{__file__} : BNGFile.write_xml()")
         finally:
             os.chdir(cur_dir)
             try:

bionetgen/modelapi/bngparser.py

@@ -1,7 +1,7 @@
 import xmltodict
 
 from bionetgen.main import BioNetGen
-from bionetgen.core.exc import BNGParseError, BNGModelError
+from bionetgen.core.exc import BNGFileError, BNGParseError, BNGModelError
 from tempfile import TemporaryFile
 
 from .bngfile import BNGFile
@@ -147,17 +147,19 @@ def _parse_model_bngpl(self, model_obj) -> None:
             # TODO: Add verbosity option to the library
             # print("Attempting to generate XML")
             with TemporaryFile("w+") as xml_file:
-                if self.bngfile.generate_xml(xml_file):
-                    # TODO: Add verbosity option to the library
-                    xmlstr = xml_file.read()
-                    # < is not a valid XML character, we need to replace it
-                    xmlstr = xmlstr.replace('relation="<', 'relation="&lt;')
-                    self.parse_xml(xmlstr, model_obj)
-                    model_obj.reset_compilation_tags()
-                else:
+                try:
+                    self.bngfile.generate_xml(xml_file)
+                except BNGFileError as exc:
                     raise BNGModelError(
-                        self.bngfile.path, message="XML file couldn't be generated"
-                    )
+                        self.bngfile.path,
+                        message=f"XML file couldn't be generated: {exc.message}",
+                    ) from exc
+                # TODO: Add verbosity option to the library
+                xmlstr = xml_file.read()
+                # < is not a valid XML character, we need to replace it
+                xmlstr = xmlstr.replace('relation="<', 'relation="&lt;')
+                self.parse_xml(xmlstr, model_obj)
+                model_obj.reset_compilation_tags()
         elif model_file.endswith(".xml"):
             with open(model_file, "r") as f:
                 xml_str = f.read()

bionetgen/modelapi/model.py

@@ -1,7 +1,7 @@
 import copy, tempfile, shutil
 
 from bionetgen.main import BioNetGen
-from bionetgen.core.exc import BNGModelError
+from bionetgen.core.exc import BNGFileError, BNGModelError
 
 from .bngparser import BNGParser
 from .blocks import (
@@ -393,20 +393,24 @@ def setup_simulator(self, sim_type="libRR"):
             self.add_action("writeSBML", {})
             # temporary folder instead to make it work
             # with windows
+            tmp_folder = None
             try:
                 tmp_folder = tempfile.mkdtemp()
                 sbml_name = f"{self.model_name}_sbml.xml"
                 # write the sbml
                 with open(sbml_name, "w+") as f:
-                    if not (
+                    try:
                         self.bngparser.bngfile.write_xml(
                             f, xml_type="sbml", bngl_str=str(self)
                         )
-                    ):
+                    except BNGFileError as exc:
                         raise BNGModelError(
                             self.model_path,
-                            message="SBML couldn't be generated for libRR simulator",
-                        )
+                            message=(
+                                "SBML couldn't be generated for libRR simulator: "
+                                f"{exc.message}"
+                            ),
+                        ) from exc
                 self.actions.clear_actions()
                 # get the simulator
                 import bionetgen as bng
@@ -416,8 +420,9 @@ def setup_simulator(self, sim_type="libRR"):
                 selections = ["time"] + [obs for obs in self.observables]
                 self.simulator.simulator.timeCourseSelections = selections
             finally:
-                shutil.rmtree(tmp_folder)
-            self.actions = curr_actions
+                if tmp_folder is not None:
+                    shutil.rmtree(tmp_folder)
+                self.actions = curr_actions
         elif sim_type == "cpy":
             # get the simulator
             import bionetgen as bng