making model validation stricter

biosimulators · Apr 13, 2021 · 502cad4 · 502cad4
1 parent 7175c95
commit 502cad4
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/biosimulators_boolnet/core.py b/biosimulators_boolnet/core.py
@@ -88,6 +88,10 @@ def exec_sed_task(task, variables, log=None):
     validation.validate_data_generator_variables(variables)
     target_x_paths_keys = get_variable_target_x_path_keys(variables, task.model.source)
 
+    # validate model
+    validation.validate_model(task.model.source, ModelLanguage.SBML,
+                              name='`{}` for task `{}`'.format(task.model.id, task.id))
+
     # get BoolNet
     boolnet = get_boolnet()
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.51
+biosimulators_utils[logging,sbml] >= 0.1.51
 lxml
 numpy
 rpy2
diff --git a/tests/fixtures/example-model.xml b/tests/fixtures/example-model.xml
@@ -3,21 +3,21 @@
   <model id="model_id">
 
     <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout>
+      <layout:layout layout:id="layout">
         <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:species="G0">
+          <layout:speciesGlyph layout:species="G0" layout:id="glyph_G0">
             <layout:boundingBox>
               <layout:position layout:x="297" layout:y="138"/>
               <layout:dimensions layout:height="25" layout:width="45"/>
             </layout:boundingBox>
           </layout:speciesGlyph>
-          <layout:speciesGlyph layout:species="G1">
+          <layout:speciesGlyph layout:species="G1" layout:id="glyph_G1">
             <layout:boundingBox>
               <layout:position layout:x="250" layout:y="270"/>
               <layout:dimensions layout:height="25" layout:width="45"/>
             </layout:boundingBox>
           </layout:speciesGlyph>
-          <layout:speciesGlyph layout:species="G2">
+          <layout:speciesGlyph layout:species="G2" layout:id="glyph_G2">
             <layout:boundingBox>
               <layout:position layout:x="439" layout:y="271"/>
               <layout:dimensions layout:height="25" layout:width="45"/>
@@ -29,8 +29,8 @@
 
     <qual:listOfQualitativeSpecies xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">
       <qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:constant="true" qual:id="G0"/>
-      <qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:id="G1"/>
-      <qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:id="G2"/>
+      <qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:constant="false" qual:id="G1"/>
+      <qual:qualitativeSpecies qual:maxLevel="1" qual:compartment="comp1" qual:constant="false" qual:id="G2"/>
     </qual:listOfQualitativeSpecies>
 
     <qual:listOfTransitions xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">