diff --git a/Dockerfile b/Dockerfile index 772bfa5..77de0fc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # Base OS FROM python:3.9-slim-buster -ARG VERSION="0.0.7" +ARG VERSION="0.0.8" ARG SIMULATOR_VERSION=3.0.0b # metadata diff --git a/biosimulators_ginsim/_version.py b/biosimulators_ginsim/_version.py index 2792152..9123cf0 100644 --- a/biosimulators_ginsim/_version.py +++ b/biosimulators_ginsim/_version.py @@ -1 +1 @@ -__version__ = '0.0.7' +__version__ = '0.0.8' diff --git a/biosimulators_ginsim/utils.py b/biosimulators_ginsim/utils.py index aa003db..1581529 100644 --- a/biosimulators_ginsim/utils.py +++ b/biosimulators_ginsim/utils.py @@ -18,6 +18,7 @@ from kisao.utils import get_preferred_substitute_algorithm_by_ids from ginsim.gateway import japi as ginsim_japi import biolqm # noqa: F401 +import biosimulators_utils.model_lang.sbml.utils import biosimulators_utils.sedml.validation import biosimulators_utils.xml.utils import lxml.etree # noqa: F401 @@ -111,14 +112,14 @@ def get_variable_target_xpath_ids(variables, model_etree): corresponding qualitative species """ namespaces = biosimulators_utils.xml.utils.get_namespaces_for_xml_doc(model_etree) - + sbml_qual_prefix, sbml_qual_uri = biosimulators_utils.model_lang.sbml.utils.get_package_namespace('qual', namespaces) return biosimulators_utils.sedml.validation.validate_target_xpaths( variables, model_etree, attr={ 'namespace': { - 'prefix': 'qual', - 'uri': namespaces['qual'], + 'prefix': sbml_qual_prefix, + 'uri': sbml_qual_uri, }, 'name': 'id', } diff --git a/requirements.txt b/requirements.txt index f2bb947..5f06587 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -biosimulators_utils[logging,sbml] >= 0.1.120 +biosimulators_utils[logging,sbml] >= 0.1.122 ginsim >= 0.4.4 kisao >= 2.28 lxml diff --git a/tests/test_utils.py b/tests/test_utils.py index 56e3e05..415ee01 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -47,8 +47,9 @@ def test_validate_simulation(self): def test_get_variable_target_xpath_ids(self): with mock.patch('lxml.etree.parse', return_value=None): with mock.patch('biosimulators_utils.xml.utils.get_namespaces_for_xml_doc', return_value={'qual': None}): - with mock.patch('biosimulators_utils.sedml.validation.validate_target_xpaths', return_value={'x': 'X'}): - self.assertEqual(get_variable_target_xpath_ids([Variable(target='x')], None), {'x': 'X'}) + with mock.patch('biosimulators_utils.model_lang.sbml.utils.get_package_namespace', return_value=('qual', None)): + with mock.patch('biosimulators_utils.sedml.validation.validate_target_xpaths', return_value={'x': 'X'}): + self.assertEqual(get_variable_target_xpath_ids([Variable(target='x')], None), {'x': 'X'}) def test_read_model(self): filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'SuppMat_Model_Master_Model.zginml')