diff --git a/kadmos/cmdows/cmdows.py b/kadmos/cmdows/cmdows.py index e103ebbf99cc07d53c7ed13e25c3139312331e84..d1ef5e03c8fff63f9ae630a3a173fb6f606ca39d 100644 --- a/kadmos/cmdows/cmdows.py +++ b/kadmos/cmdows/cmdows.py @@ -301,7 +301,7 @@ class CMDOWS(object): # Add elements el.add("creator", creator) el.add("description", description) - el.add("timestamp", str(datetime.now()) if timestamp is None else timestamp) + el.add("timestamp", str(datetime.now()).replace(' ', 'T') if timestamp is None else timestamp) el.add("fileVersion", fileVersion) el.add("cmdowsVersion", cmdowsVersion) return diff --git a/kadmos/graph/graph_kadmos.py b/kadmos/graph/graph_kadmos.py index 62eef74d9f6c2fd81256ca7d68b61511a881f306..8c76ddced27370cc50898dc8de9ed3f5ee6dab58 100644 --- a/kadmos/graph/graph_kadmos.py +++ b/kadmos/graph/graph_kadmos.py @@ -1166,7 +1166,7 @@ class KadmosGraph(nx.DiGraph, EquationMixin, VistomsMixin): projectSpecific=function.finddict('projectSpecific')) for inp in function.findall('inputs/input'): - self.add_edge(inp.findtext('parameterUID'), function.get('uID'), + self.add_edge(inp.findtext('parameterUID').replace("'", '"'), function.get('uID'), valid_ranges=inp.finddict('validRanges', ordered=False, camel_case_conversion=True)) if not function.findall('inputs/input'): @@ -1181,7 +1181,7 @@ class KadmosGraph(nx.DiGraph, EquationMixin, VistomsMixin): # # # for output in function.findall('outputs/output'): - self.add_edge(function.get('uID'), output.findtext('parameterUID')) + self.add_edge(function.get('uID'), output.findtext('parameterUID').replace("'", '"')) if not function.findall('outputs/output'): # Determine assumed output file location (same folder as CMDOWS file) @@ -1193,6 +1193,7 @@ class KadmosGraph(nx.DiGraph, EquationMixin, VistomsMixin): else: logger.warning('Could not find outputs for function: ' + function.get('uID')) + # Add inputs and outputs based on XML io_list = inputs_list+outputs_list _perform_check_list(io_list, check_list, keep_running=keep_running) @@ -1223,7 +1224,7 @@ class KadmosGraph(nx.DiGraph, EquationMixin, VistomsMixin): def _load_cmdows_parameters(self, cmdows): for variable in cmdows.findall('parameters/parameter'): - self.add_node(variable.get('uID'), + self.add_node(variable.get('uID').replace("'", '"'), category='variable', shape='o', label=variable.findtext('label'), @@ -1242,8 +1243,10 @@ class KadmosGraph(nx.DiGraph, EquationMixin, VistomsMixin): cmdows_edges = cmdows_data_graph.find('edges') if cmdows_edges is not None: for edge in list(cmdows_edges): - from_id = edge.findtext('fromExecutableBlockUID', default=edge.findtext('fromParameterUID')) - to_id = edge.findtext('toExecutableBlockUID', default=edge.findtext('toParameterUID')) + from_id = edge.findtext('fromExecutableBlockUID', default=edge.findtext('fromParameterUID')).replace("'", '"') + to_id = edge.findtext('toExecutableBlockUID', default=edge.findtext('toParameterUID')).replace("'", '"') + self.assert_node_exists(from_id) + self.assert_node_exists(to_id) self.add_edge(from_id, to_id) else: logger.warning('No dataGraph element found in the CMDOWS file. Ignoring missing information.') diff --git a/kadmos/graph/mixin_equation.py b/kadmos/graph/mixin_equation.py index b3c20ffc8831a98f42a7151a74d787f0287c9908..ff9f4d61f86d8d7a5a4456c8e3b455546bf95cc8 100644 --- a/kadmos/graph/mixin_equation.py +++ b/kadmos/graph/mixin_equation.py @@ -269,7 +269,7 @@ class EquationMixin(object): label=function.findtext('label'), function_type=function.findtext('functionType')) for inp in function.findall('inputs/input'): - self.add_edge(inp.findtext('parameterUID'), function.get('uID'), + self.add_edge(inp.findtext('parameterUID').replace("'", '"'), function.get('uID'), equation_label=inp.findtext('equationLabel'), valid_ranges=inp.finddict('validRanges', ordered=False, camel_case_conversion=True)) for outp in function.findall('outputs/output'): @@ -277,5 +277,5 @@ class EquationMixin(object): equations = cmdows.xpath('.//*[@uID="' + outp.find('equationsUID').text + '"]')[0] else: equations = outp.findall('equations/equation') - self.add_edge(function.get('uID'), outp.findtext('parameterUID'), + self.add_edge(function.get('uID'), outp.findtext('parameterUID').replace("'", '"'), equations={eq.get('language'): eq.text for eq in equations})