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Merge pull request #102 from biosimulators/check-datagens
feat: check all SED-ML XPath targets and warn appropriately
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| __version__ = '0.1.169' | ||
| __version__ = '0.1.170' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim_noexist']/@initialConcentration" newValue="0.084410675"/> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| </sedML> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfPoints="140"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task1" modelReference="model" simulationReference="sim1"/> | ||
| </listOfTasks> | ||
| <listOfDataGenerators> | ||
| <dataGenerator id="time_task1" name="Time"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> var_time_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="var_time_task1" symbol="urn:sedml:symbol:time" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="BE_1_task1" name="[BE]"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> p1_BE_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="p1_BE_task1" name="BE" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| </listOfDataGenerators> | ||
| <listOfOutputs> | ||
| <report id="autogen_report_for_task1" name="Auto-generated report for task1, including all symbols in SBML with mathematical meaning, both constant and variable."> | ||
| <listOfDataSets> | ||
| <dataSet id="autogen_task1_time" label="Time" dataReference="time_task1"/> | ||
| <dataSet id="autogen_task1_BE" label="BE" dataReference="BE_1_task1"/> | ||
| </listOfDataSets> | ||
| </report> | ||
| </listOfOutputs> | ||
| </sedML> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfPoints="140"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task1" modelReference="model" simulationReference="sim1"/> | ||
| </listOfTasks> | ||
| <listOfDataGenerators> | ||
| <dataGenerator id="time_task1" name="Time"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> var_time_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="var_time_task1" symbol="urn:sedml:symbol:time" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="BE_1_task1" name="[BE]"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> p1_BE_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="p1_BE_task1" name="BE" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE']" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| </listOfDataGenerators> | ||
| <listOfOutputs> | ||
| <report id="autogen_report_for_task1" name="Auto-generated report for task1, including all symbols in SBML with mathematical meaning, both constant and variable."> | ||
| <listOfDataSets> | ||
| <dataSet id="autogen_task1_time" label="Time" dataReference="time_task1"/> | ||
| <dataSet id="autogen_task1_BE" label="BE" dataReference="BE_1_task1"/> | ||
| </listOfDataSets> | ||
| </report> | ||
| </listOfOutputs> | ||
| </sedML> |
15 changes: 15 additions & 0 deletions
15
tests/fixtures/BIOMD0000000297_compchange_and_attchange_bad_xpath_.sedml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| <computeChange target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn type="integer"> 5 </cn> | ||
| </math> | ||
| </computeChange> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| </sedML> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <computeChange target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <cn type="integer"> 5 </cn> | ||
| </math> | ||
| </computeChange> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| </sedML> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfPoints="140"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task1" modelReference="model" simulationReference="sim1"/> | ||
| </listOfTasks> | ||
| <listOfDataGenerators> | ||
| <dataGenerator id="time_task1" name="Time"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> var_time_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="var_time_task1" symbol="urn:sedml:symbol:time" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="BE_1_task1" name="[BE]"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> p1_BE_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="p1_BE_task1" name="BE" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| </listOfDataGenerators> | ||
| <listOfOutputs> | ||
| <report id="autogen_report_for_task1" name="Auto-generated report for task1, including all symbols in SBML with mathematical meaning, both constant and variable."> | ||
| <listOfDataSets> | ||
| <dataSet id="autogen_task1_time" label="Time" dataReference="time_task1"/> | ||
| <dataSet id="autogen_task1_BE" label="BE" dataReference="BE_1_task1"/> | ||
| </listOfDataSets> | ||
| </report> | ||
| </listOfOutputs> | ||
| </sedML> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfPoints="140"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task1" modelReference="model" simulationReference="sim1"/> | ||
| </listOfTasks> | ||
| <listOfDataGenerators> | ||
| <dataGenerator id="time_task1" name="Time"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> var_time_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="var_time_task1" symbol="urn:sedml:symbol:time" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| <dataGenerator id="BE_1_task1" name="[BE]"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> p1_BE_task1 </ci> | ||
| </math> | ||
| <listOfVariables> | ||
| <variable id="p1_BE_task1" name="BE" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE']" taskReference="task1"/> | ||
| </listOfVariables> | ||
| </dataGenerator> | ||
| </listOfDataGenerators> | ||
| <listOfOutputs> | ||
| <report id="autogen_report_for_task1" name="Auto-generated report for task1, including all symbols in SBML with mathematical meaning, both constant and variable."> | ||
| <listOfDataSets> | ||
| <dataSet id="autogen_task1_time" label="Time" dataReference="time_task1"/> | ||
| <dataSet id="autogen_task1_BE" label="BE" dataReference="BE_1_task1"/> | ||
| </listOfDataSets> | ||
| </report> | ||
| </listOfOutputs> | ||
| </sedML> |
33 changes: 33 additions & 0 deletions
33
tests/fixtures/BIOMD0000000297_repeat_bad_xpath_change.sedml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="4"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim0" initialTime="0" outputStartTime="0" outputEndTime="100" numberOfPoints="100"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task0" modelReference="model" simulationReference="sim0"/> | ||
| <repeatedTask id="task1" range="uniform_linear_for_S1" resetModel="true"> | ||
| <listOfRanges> | ||
| <uniformRange id="uniform_linear_for_S1" start="1" end="15" numberOfPoints="25" type="linear"/> | ||
| </listOfRanges> | ||
| <listOfChanges> | ||
| <setValue modelReference="model" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']" range="uniform_linear_for_S1"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> uniform_linear_for_S1 </ci> | ||
| </math> | ||
| </setValue> | ||
| </listOfChanges> | ||
| <listOfSubTasks> | ||
| <subTask order="0" task="task0"/> | ||
| </listOfSubTasks> | ||
| </repeatedTask> | ||
| </listOfTasks> | ||
| </sedML> |
30 changes: 30 additions & 0 deletions
30
tests/fixtures/BIOMD0000000297_repeat_bad_xpath_nochange.sedml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="4"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim0" initialTime="0" outputStartTime="0" outputEndTime="100" numberOfPoints="100"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task0" modelReference="model" simulationReference="sim0"/> | ||
| <repeatedTask id="task1" range="uniform_linear_for_S1" resetModel="true"> | ||
| <listOfRanges> | ||
| <uniformRange id="uniform_linear_for_S1" start="1" end="15" numberOfPoints="25" type="linear"/> | ||
| </listOfRanges> | ||
| <listOfChanges> | ||
| <setValue modelReference="model" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE_noexist']" range="uniform_linear_for_S1"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> uniform_linear_for_S1 </ci> | ||
| </math> | ||
| </setValue> | ||
| </listOfChanges> | ||
| <listOfSubTasks> | ||
| <subTask order="0" task="task0"/> | ||
| </listOfSubTasks> | ||
| </repeatedTask> | ||
| </listOfTasks> | ||
| </sedML> |
33 changes: 33 additions & 0 deletions
33
tests/fixtures/BIOMD0000000297_repeat_good_xpath_change.sedml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="4"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| <listOfChanges> | ||
| <changeAttribute target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Trim']/@initialConcentration" newValue="0.084410675"/> | ||
| </listOfChanges> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim0" initialTime="0" outputStartTime="0" outputEndTime="100" numberOfPoints="100"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task0" modelReference="model" simulationReference="sim0"/> | ||
| <repeatedTask id="task1" range="uniform_linear_for_S1" resetModel="true"> | ||
| <listOfRanges> | ||
| <uniformRange id="uniform_linear_for_S1" start="1" end="15" numberOfPoints="25" type="linear"/> | ||
| </listOfRanges> | ||
| <listOfChanges> | ||
| <setValue modelReference="model" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE']" range="uniform_linear_for_S1"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> uniform_linear_for_S1 </ci> | ||
| </math> | ||
| </setValue> | ||
| </listOfChanges> | ||
| <listOfSubTasks> | ||
| <subTask order="0" task="task0"/> | ||
| </listOfSubTasks> | ||
| </repeatedTask> | ||
| </listOfTasks> | ||
| </sedML> |
30 changes: 30 additions & 0 deletions
30
tests/fixtures/BIOMD0000000297_repeat_good_xpath_nochange.sedml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="2"> | ||
| <listOfModels> | ||
| <model id="model" language="urn:sedml:language:sbml" source="BIOMD0000000297.xml"> | ||
| </model> | ||
| </listOfModels> | ||
| <listOfSimulations> | ||
| <uniformTimeCourse id="sim0" initialTime="0" outputStartTime="0" outputEndTime="100" numberOfPoints="100"> | ||
| <algorithm kisaoID="KISAO:0000019"/> | ||
| </uniformTimeCourse> | ||
| </listOfSimulations> | ||
| <listOfTasks> | ||
| <task id="task0" modelReference="model" simulationReference="sim0"/> | ||
| <repeatedTask id="task1" range="uniform_linear_for_S1" resetModel="true"> | ||
| <listOfRanges> | ||
| <uniformRange id="uniform_linear_for_S1" start="1" end="15" numberOfPoints="25" type="linear"/> | ||
| </listOfRanges> | ||
| <listOfChanges> | ||
| <setValue modelReference="model" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='BE']" range="uniform_linear_for_S1"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <ci> uniform_linear_for_S1 </ci> | ||
| </math> | ||
| </setValue> | ||
| </listOfChanges> | ||
| <listOfSubTasks> | ||
| <subTask order="0" task="task0"/> | ||
| </listOfSubTasks> | ||
| </repeatedTask> | ||
| </listOfTasks> | ||
| </sedML> |
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