fixed: corrected documentation of supported observables

biosimulators · Aug 21, 2021 · bf63a42 · bf63a42
1 parent a414706
commit bf63a42
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Showing 5 changed files with 59 additions and 13 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.13"
+ARG VERSION="0.1.14"
 ARG SIMULATOR_VERSION="2.2.0"
 
 # metadata

diff --git a/biosimulators.json b/biosimulators.json
@@ -347,14 +347,21 @@
         "namespace": "SIO",
         "id": "SIO_000418"
       }],
-      "dependentVariableTargetPatterns": [
-        {
+      "dependentVariableTargetPatterns": [{
           "variables": "species concentrations",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
         },
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
         }
       ],
       "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
@@ -408,14 +415,21 @@
         "namespace": "SIO",
         "id": "SIO_000418"
       }],
-      "dependentVariableTargetPatterns": [
-        {
+      "dependentVariableTargetPatterns": [{
           "variables": "species concentrations",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
         },
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
         }
       ],
       "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
@@ -495,14 +509,21 @@
         "namespace": "SIO",
         "id": "SIO_000418"
       }],
-      "dependentVariableTargetPatterns": [
-        {
+      "dependentVariableTargetPatterns": [{
           "variables": "species concentrations",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
         },
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
         }
       ],
       "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
@@ -618,14 +639,21 @@
         "namespace": "SIO",
         "id": "SIO_000418"
       }],
-      "dependentVariableTargetPatterns": [
-        {
+      "dependentVariableTargetPatterns": [{
           "variables": "species counts",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
         },
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
         }
       ],
       "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
@@ -725,14 +753,21 @@
         }
       ],
       "dependentDimensions": [],
-      "dependentVariableTargetPatterns": [
-        {
+      "dependentVariableTargetPatterns": [{
           "variables": "species concentrations",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
         },
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
         }
       ],
       "availableSoftwareInterfaceTypes": ["library", "command-line application", "desktop application", "BioSimulators Docker image"],
@@ -787,4 +822,4 @@
     "validated": false,
     "validationTests": null
   }
-}
+}
diff --git a/biosimulators_tellurium/_version.py b/biosimulators_tellurium/_version.py
@@ -1 +1 @@
-__version__ = '0.1.13'
+__version__ = '0.1.14'
diff --git a/tests/fixtures/BIOMD0000000297-with-reports.omex b/tests/fixtures/BIOMD0000000297-with-reports.omex
diff --git a/tests/test_core_main.py b/tests/test_core_main.py
@@ -124,11 +124,22 @@ def _assert_combine_archive_outputs(self, dirname, reports=True, plots=True):
                 ],
             )
 
+            if reports and not plots:
+                report.data_sets.append(DataSet(id='data_set_kswe', label='kwse'))
+                report.data_sets.append(DataSet(id='data_set_kswe_prime', label="kwse'"))
+                report.data_sets.append(DataSet(id='data_set_R1', label="Clb-Sic dissociation"))
+                report.data_sets.append(DataSet(id='data_set_compartment', label="compartment"))
+
             report_results = ReportReader().run(report, dirname, 'ex1/BIOMD0000000297.sedml/report_1_task1')
             for data_set_result in report_results.values():
                 self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
             numpy.testing.assert_allclose(report_results[report.data_sets[0].id], numpy.linspace(0., 140., 140 + 1))
 
+            if reports and not plots:
+                print(report_results.keys())
+                numpy.testing.assert_allclose(report_results['data_set_kswe_prime'], numpy.full((140 + 1,), 2.))
+                numpy.testing.assert_allclose(report_results['data_set_compartment'], numpy.full((140 + 1,), 1.))
+
         # check that expected plots where created at the expected locations
         if plots:
             if not reports: