Generate PEtab yaml files for PEtab-dev/PEtab#183

hackathon_contributions_new_data_format/Alkan_SciSignal2018/Alkan_SciSignal2018.yaml

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+parameter_file: parameters_Alkan_SciSignal2018.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Alkan_SciSignal2018.tsv
+  measurement_files:
+  - measurementData_Alkan_SciSignal2018.tsv
+  sbml_file: model_Alkan_SciSignal2018.xml

hackathon_contributions_new_data_format/Bachmann_MSB2011/Bachmann_MSB2011.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Bachmann_MSB2011.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Bachmann_MSB2011.tsv
+  measurement_files:
+  - measurementData_Bachmann_MSB2011.tsv
+  sbml_file: model_Bachmann_MSB2011.xml

hackathon_contributions_new_data_format/Becker_Science2010/Becker_Science2010.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Becker_Science2010.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Becker_Science2010.tsv
+  measurement_files:
+  - measurementData_Becker_Science2010.tsv
+  sbml_file: model_Becker_Science2010.xml

hackathon_contributions_new_data_format/Beer_MolBioSystems2014/Beer_MolBioSystems2014.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Beer_MolBioSystems2014.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Beer_MolBioSystems2014.tsv
+  measurement_files:
+  - measurementData_Beer_MolBioSystems2014.tsv
+  sbml_file: model_Beer_MolBioSystems2014.xml

hackathon_contributions_new_data_format/Blasi_CellSystems2016/Blasi_CellSystems2016.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Blasi_CellSystems2016.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Blasi_CellSystems2016.tsv
+  measurement_files:
+  - measurementData_Blasi_CellSystems2016.tsv
+  sbml_file: model_Blasi_CellSystems2016.xml

hackathon_contributions_new_data_format/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Boehm_JProteomeRes2014.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Boehm_JProteomeRes2014.tsv
+  measurement_files:
+  - measurementData_Boehm_JProteomeRes2014.tsv
+  sbml_file: model_Boehm_JProteomeRes2014.xml

hackathon_contributions_new_data_format/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Borghans_BiophysChem1997.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Borghans_BiophysChem1997.tsv
+  measurement_files:
+  - measurementData_Borghans_BiophysChem1997.tsv
+  sbml_file: model_Borghans_BiophysChem1997.xml

hackathon_contributions_new_data_format/Brannmark_JBC2010/Brannmark_JBC2010.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Brannmark_JBC2010.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Brannmark_JBC2010.tsv
+  measurement_files:
+  - measurementData_Brannmark_JBC2010.tsv
+  sbml_file: model_Brannmark_JBC2010.xml

hackathon_contributions_new_data_format/Bruno_JExpBio2016/Bruno_JExpBio2016.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Bruno_JExpBio2016.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Bruno_JExpBio2016.tsv
+  measurement_files:
+  - measurementData_Bruno_JExpBio2016.tsv
+  sbml_file: model_Bruno_JExpBio2016.xml

hackathon_contributions_new_data_format/Casaletto_PNAS2019/Casaletto_PNAS2019.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Casaletto_PNAS2019.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Casaletto_PNAS2019.tsv
+  measurement_files:
+  - measurementData_Casaletto_PNAS2019.tsv
+  sbml_file: model_Casaletto_PNAS2019.xml

hackathon_contributions_new_data_format/Chen_MSB2009/Chen_MSB2009.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Chen_MSB2009.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Chen_MSB2009.tsv
+  measurement_files:
+  - measurementData_Chen_MSB2009.tsv
+  sbml_file: model_Chen_MSB2009.xml

hackathon_contributions_new_data_format/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Crauste_CellSystems2017.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Crauste_CellSystems2017.tsv
+  measurement_files:
+  - measurementData_Crauste_CellSystems2017.tsv
+  sbml_file: model_Crauste_CellSystems2017.xml

hackathon_contributions_new_data_format/Elowitz_Nature2000/Elowitz_Nature2000.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Elowitz_Nature2000.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Elowitz_Nature2000.tsv
+  measurement_files:
+  - measurementData_Elowitz_Nature2000.tsv
+  sbml_file: model_Elowitz_Nature2000.xml

hackathon_contributions_new_data_format/Fiedler_BMC2016/Fiedler_BMC2016.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Fiedler_BMC2016.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Fiedler_BMC2016.tsv
+  measurement_files:
+  - measurementData_Fiedler_BMC2016.tsv
+  sbml_file: model_Fiedler_BMC2016.xml

hackathon_contributions_new_data_format/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Fujita_SciSignal2010.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Fujita_SciSignal2010.tsv
+  measurement_files:
+  - measurementData_Fujita_SciSignal2010.tsv
+  sbml_file: model_Fujita_SciSignal2010.xml

hackathon_contributions_new_data_format/Hass_PONE2017/Hass_PONE2017.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Hass_PONE2017.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Hass_PONE2017.tsv
+  measurement_files:
+  - measurementData_Hass_PONE2017.tsv
+  sbml_file: model_Hass_PONE2017.xml

hackathon_contributions_new_data_format/Isensee_JCB2018/Isensee_JCB2018.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Isensee_JCB2018.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Isensee_JCB2018.tsv
+  measurement_files:
+  - measurementData_Isensee_JCB2018.tsv
+  sbml_file: model_Isensee_JCB2018.xml

hackathon_contributions_new_data_format/Korkut_eLIFE2015/Korkut_eLIFE2015.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Korkut_eLIFE2015.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Korkut_eLIFE2015.tsv
+  measurement_files:
+  - measurementData_Korkut_eLIFE2015.tsv
+  sbml_file: model_Korkut_eLIFE2015.xml

hackathon_contributions_new_data_format/Lucarelli_CellSystems2018/Lucarelli_CellSystems2018.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Lucarelli_CellSystems2018.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Lucarelli_CellSystems2018.tsv
+  measurement_files:
+  - measurementData_Lucarelli_CellSystems2018.tsv
+  sbml_file: model_Lucarelli_CellSystems2018.xml

hackathon_contributions_new_data_format/Merkle_PCB2016/Merkle_PCB2016.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Merkle_PCB2016.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Merkle_PCB2016.tsv
+  measurement_files:
+  - measurementData_Merkle_PCB2016.tsv
+  sbml_file: model_Merkle_PCB2016.xml

hackathon_contributions_new_data_format/Parmar_PCB2019/Parmar_PCB2019.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Parmar_PCB2019.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Parmar_PCB2019.tsv
+  measurement_files:
+  - measurementData_Parmar_PCB2019.tsv
+  sbml_file: model_Parmar_PCB2019.xml

hackathon_contributions_new_data_format/Perelson_Science1996/Perelson_Science1996.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Perelson_Science1996.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Perelson_Science1996.tsv
+  measurement_files:
+  - measurementData_Perelson_Science1996.tsv
+  sbml_file: model_Perelson_Science1996.xml

hackathon_contributions_new_data_format/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Raia_CancerResearch2011.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Raia_CancerResearch2011.tsv
+  measurement_files:
+  - measurementData_Raia_CancerResearch2011.tsv
+  sbml_file: model_Raia_CancerResearch2011.xml

hackathon_contributions_new_data_format/Schwen_PONE2014/Schwen_PONE2014.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Schwen_PONE2014.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Schwen_PONE2014.tsv
+  measurement_files:
+  - measurementData_Schwen_PONE2014.tsv
+  sbml_file: model_Schwen_PONE2014.xml

hackathon_contributions_new_data_format/Sneyd_PNAS2002/Sneyd_PNAS2002.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Sneyd_PNAS2002.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Sneyd_PNAS2002.tsv
+  measurement_files:
+  - measurementData_Sneyd_PNAS2002.tsv
+  sbml_file: model_Sneyd_PNAS2002.xml

hackathon_contributions_new_data_format/Sobotta_Frontiers2017/Sobotta_Frontiers2017.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Sobotta_Frontiers2017.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Sobotta_Frontiers2017.tsv
+  measurement_files:
+  - measurementData_Sobotta_Frontiers2017.tsv
+  sbml_file: model_Sobotta_Frontiers2017.xml

hackathon_contributions_new_data_format/Swameye_PNAS2003/Swameye_PNAS2003.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Swameye_PNAS2003.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Swameye_PNAS2003.tsv
+  measurement_files:
+  - measurementData_Swameye_PNAS2003.tsv
+  sbml_file: model_Swameye_PNAS2003.xml

hackathon_contributions_new_data_format/Weber_BMC2015/Weber_BMC2015.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Weber_BMC2015.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Weber_BMC2015.tsv
+  measurement_files:
+  - measurementData_Weber_BMC2015.tsv
+  sbml_file: model_Weber_BMC2015.xml

hackathon_contributions_new_data_format/Zheng_PNAS2012/Zheng_PNAS2012.yaml

@@ -0,0 +1,7 @@
+parameter_file: parameters_Zheng_PNAS2012.tsv
+petab_version: 0.0.0a17
+problems:
+- condition_file: experimentalCondition_Zheng_PNAS2012.tsv
+  measurement_files:
+  - measurementData_Zheng_PNAS2012.tsv
+  sbml_file: model_Zheng_PNAS2012.xml

hackathon_contributions_new_data_format/create_petab_yaml.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+
+import os
+import pandas as pd
+import yaml
+import petab
+
+
+def create_petab_yaml(model_dir):
+    data = {
+        'petab_version': petab.__version__,
+        'parameter_file': petab.get_default_parameter_file_name(model_dir),
+        'problems': [
+            {
+                'sbml_file':
+                    petab.get_default_sbml_file_name(model_dir),
+                'condition_file':
+                    petab.get_default_condition_file_name(model_dir),
+                'measurement_files':
+                [
+                    petab.get_default_measurement_file_name(model_dir),
+                ],
+            },
+        ]
+    }
+
+    petab.validate(data)
+
+    out_file = os.path.join(model_dir, f'{model_dir}.yaml')
+    print('git add ' + out_file)
+    with open(out_file, 'w') as outfile:
+        yaml.dump(data, outfile, default_flow_style=False)
+
+
+def main():
+    model_list = os.scandir()
+    model_list = sorted(f.name for f in model_list if f.is_dir())
+
+    for benchmark_model in model_list:
+        print('# ', benchmark_model)
+        try:
+            create_petab_yaml(benchmark_model)
+        except ValueError as e:
+            print(e)
+
+        # print('='*100)
+        # break
+
+
+if __name__ == '__main__':
+    main()