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Unify modelapi export and XML error handling #94

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51 changes: 41 additions & 10 deletions bionetgen/modelapi/bngfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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()
Expand All @@ -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
Expand All @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand All @@ -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:
Expand Down
24 changes: 13 additions & 11 deletions bionetgen/modelapi/bngparser.py
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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()
Expand Down
19 changes: 12 additions & 7 deletions bionetgen/modelapi/model.py
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Original file line number Diff line number Diff line change
@@ -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 (
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down
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