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commit 1ac926fef7305e28fa7827ea842be0260a50336a Author: Afif Elghraoui <[email protected]> Date: Mon Nov 7 20:34:34 2016 -0800 Imported Upstream version 0.5.4 --- cobra/VERSION | 2 +- cobra/io/sbml3.py | 66 ++++++++++++++++++++++++++++++++++++++------------ cobra/test/io_tests.py | 10 ++++++-- 3 files changed, 60 insertions(+), 18 deletions(-) diff --git a/cobra/VERSION b/cobra/VERSION index cb0c939..7d85683 100644 --- a/cobra/VERSION +++ b/cobra/VERSION @@ -1 +1 @@ -0.5.2 +0.5.4 diff --git a/cobra/io/sbml3.py b/cobra/io/sbml3.py index a9faea7..23ffe22 100644 --- a/cobra/io/sbml3.py +++ b/cobra/io/sbml3.py @@ -1,10 +1,11 @@ from collections import defaultdict from warnings import warn, catch_warnings, simplefilter from decimal import Decimal -from ast import parse as ast_parse, Name, Or, And, BoolOp +from ast import Name, Or, And, BoolOp from gzip import GzipFile from bz2 import BZ2File from tempfile import NamedTemporaryFile +from sys import exc_info import re from six import iteritems, string_types @@ -113,7 +114,9 @@ def get_attrib(tag, attribute, type=lambda x: x, require=False): msg = "required attribute '%s' not found in tag '%s'" % \ (attribute, tag.tag) if tag.get("id") is not None: - msg += "with id '%s'" % tag.get("id") + msg += " with id '%s'" % tag.get("id") + elif tag.get("name") is not None: + msg += " with name '%s'" % tag.get("name") raise CobraSBMLError(msg) return type(value) if value is not None else None @@ -253,7 +256,8 @@ def parse_xml_into_model(xml, number=float): xml_model.findall(COMPARTMENT_XPATH)} # add metabolites for species in xml_model.findall(SPECIES_XPATH % 'false'): - met = Metabolite(clip(species.get("id"), "M_")) + met = get_attrib(species, "id", require=True) + met = Metabolite(clip(met, "M_")) met.name = species.get("name") annotate_cobra_from_sbml(met, species) met.compartment = species.get("compartment") @@ -293,7 +297,8 @@ def parse_xml_into_model(xml, number=float): reactions = [] for sbml_reaction in xml_model.iterfind( ns("sbml:listOfReactions/sbml:reaction")): - reaction = Reaction(clip(sbml_reaction.get("id"), "R_")) + reaction = get_attrib(sbml_reaction, "id", require=True) + reaction = Reaction(clip(reaction, "R_")) reaction.name = sbml_reaction.get("name") annotate_cobra_from_sbml(reaction, sbml_reaction) lb_id = get_attrib(sbml_reaction, "fbc:lowerFluxBound", require=True) @@ -547,7 +552,13 @@ def read_sbml_model(filename, number=float, **kwargs): xmlfile.write(outfile, encoding="UTF-8") filename = outfile.name return read_sbml2(filename, **kwargs) - return parse_xml_into_model(xml, number=number, **kwargs) + try: + return parse_xml_into_model(xml, number=number, **kwargs) + except Exception: + raise CobraSBMLError( + "Something went wrong reading the model. You can get a detailed " + "report using the `cobra.io.sbml3.validate_sbml_model` function " + "or using the online validator at http://sbml.org/validator";) id_required = {ns(i) for i in ("sbml:model", "sbml:reaction:", "sbml:species", @@ -558,7 +569,29 @@ invalid_id_detector = re.compile("|".join(re.escape(i[0]) for i in _renames)) def validate_sbml_model(filename, check_model=True): - """returns the model along with a list of errors""" + """Returns the model along with a list of errors. + + Parameters + ---------- + filename : str + The filename of the SBML model to be validated. + check_model: bool, optional + Whether to also check some basic model properties such as reaction + boundaries and compartment formulas. + + Returns + ------- + model : :class:`~cobra.core.Model.Model` object + The cobra model if the file could be read succesfully or None + otherwise. + errors : dict + Warnings and errors grouped by their respective types. + + Raises + ------ + CobraSBMLError + If the file is not a valid SBML Level 3 file with FBC. + """ xmlfile = parse_stream(filename) xml = xmlfile.getroot() # use libsbml if not l3v1 with fbc v2 @@ -566,10 +599,10 @@ def validate_sbml_model(filename, check_model=True): get_attrib(xml, "fbc:required") is None: raise CobraSBMLError("XML is not SBML level 3 v1 with fbc v2") - sbml_errors = [] + errors = {k: [] for k in ("validator", "warnings", "SBML errors", "other")} - def err(err_msg): - sbml_errors.append(err_msg) + def err(err_msg, group="validator"): + errors[group].append(err_msg) # make sure there is exactly one model xml_models = xml.findall(ns("sbml:model")) @@ -624,9 +657,12 @@ def validate_sbml_model(filename, check_model=True): try: model = parse_xml_into_model(xml) except CobraSBMLError as e: - err(str(e)) - return (None, sbml_errors) - sbml_errors.extend(str(i.message) for i in warning_list) + err(str(e), "SBML errors") + return (None, errors) + except Exception as e: + err(str(e), "other") + return (None, errors) + errors["warnings"].extend(str(i.message) for i in warning_list) # check genes xml_genes = { @@ -637,10 +673,10 @@ def validate_sbml_model(filename, check_model=True): err("No gene specfied with id 'G_%s'" % gene.id) if check_model: - sbml_errors.extend(check_reaction_bounds(model)) - sbml_errors.extend(check_metabolite_compartment_formula(model)) + errors["validator"].extend(check_reaction_bounds(model)) + errors["validator"].extend(check_metabolite_compartment_formula(model)) - return model, sbml_errors + return model, errors def write_sbml_model(cobra_model, filename, use_fbc_package=True, **kwargs): diff --git a/cobra/test/io_tests.py b/cobra/test/io_tests.py index 7125d47..4d7b0b5 100644 --- a/cobra/test/io_tests.py +++ b/cobra/test/io_tests.py @@ -6,6 +6,7 @@ from unittest import TestCase, TestLoader, TextTestRunner, skipIf, \ expectedFailure from functools import partial from pickle import load, dump +from six import iteritems import sys if __name__ == "__main__": @@ -146,11 +147,16 @@ class TestCobraIOSBMLfbc2Bz2(TestCobraIOSBMLfbc2): class TestCobraSBMLValidation(TestCase): - def test_bad_valiation(self): + def test_sbml_error(self): + filename = join(data_directory, "invalid0.xml") + with self.assertRaises(io.sbml3.CobraSBMLError): + io.read_sbml_model(filename) + + def test_bad_validation(self): for i in range(3): filename = join(data_directory, "invalid%d.xml" % i) m, errors = io.sbml3.validate_sbml_model(filename) - self.assertTrue(len(errors) >= 1) + self.assertTrue(any(len(v) >= 1 for v in iteritems(errors))) @skipIf(not libsbml, "libsbml required") -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
