diff --git a/petabtests/cases/v2.0.0/pysb/0006/0006.py b/petabtests/cases/v2.0.0/pysb/0006/0006.py index fc638c6..d2a58d8 100644 --- a/petabtests/cases/v2.0.0/pysb/0006/0006.py +++ b/petabtests/cases/v2.0.0/pysb/0006/0006.py @@ -29,10 +29,10 @@ ) problem.add_measurement( - "obs_a", "c0", time=0, measurement=0.7, observable_parameters=(10,) + "obs_a", "", time=0, measurement=0.7, observable_parameters=(10,) ) problem.add_measurement( - "obs_a", "c0", time=10, measurement=0.1, observable_parameters=(15,) + "obs_a", "", time=10, measurement=0.1, observable_parameters=(15,) ) problem.add_parameter( diff --git a/petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv b/petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv index 16cb6a1..bcf38d9 100644 --- a/petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv +++ b/petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv @@ -1,3 +1,3 @@ observableId experimentId time measurement observableParameters -obs_a c0 0 0.7 10 -obs_a c0 10 0.1 15 +obs_a 0 0.7 10 +obs_a 10 0.1 15 diff --git a/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv b/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv index d9f49d5..27253c5 100644 --- a/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv +++ b/petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv @@ -1,3 +1,3 @@ observableId experimentId time simulation observableParameters -obs_a c0 0 10.0 10 -obs_a c0 10 6.42857855596045 15 +obs_a 0 10.0 10 +obs_a 10 6.42857855596045 15 diff --git a/petabtests/cases/v2.0.0/pysb/0009/0009.py b/petabtests/cases/v2.0.0/pysb/0009/0009.py index ff15463..8c30e6f 100644 --- a/petabtests/cases/v2.0.0/pysb/0009/0009.py +++ b/petabtests/cases/v2.0.0/pysb/0009/0009.py @@ -72,4 +72,5 @@ measurement_dfs=[problem.measurement_df], simulation_dfs=[simulation_df], parameter_df=problem.parameter_df, + experiment_dfs=[problem.experiment_df], ) diff --git a/petabtests/cases/v2.0.0/pysb/0009/_0009.yaml b/petabtests/cases/v2.0.0/pysb/0009/_0009.yaml index df06036..4e0d35b 100644 --- a/petabtests/cases/v2.0.0/pysb/0009/_0009.yaml +++ b/petabtests/cases/v2.0.0/pysb/0009/_0009.yaml @@ -3,7 +3,8 @@ parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv - experiment_files: [] + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv model_files: diff --git a/petabtests/cases/v2.0.0/pysb/0009/_experiments.tsv b/petabtests/cases/v2.0.0/pysb/0009/_experiments.tsv new file mode 100644 index 0000000..430d0ee --- /dev/null +++ b/petabtests/cases/v2.0.0/pysb/0009/_experiments.tsv @@ -0,0 +1,3 @@ +experimentId time conditionId +e0 -inf preeq_c0 +e0 0.0 c0 diff --git a/petabtests/cases/v2.0.0/sbml/0001/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0001/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0001/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml b/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml +++ b/petabtests/cases/v2.0.0/sbml/0002/_0002.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv index aba08a4..61ad42d 100644 --- a/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv +++ b/petabtests/cases/v2.0.0/sbml/0002/_conditions.tsv @@ -1,5 +1,3 @@ conditionId targetId targetValue valueType c0 a0 0.8 constant c1 a0 0.9 constant -c0 b0 constant -c1 b0 constant diff --git a/petabtests/cases/v2.0.0/sbml/0003/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0003/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0003/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0004/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0004/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0004/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml b/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml +++ b/petabtests/cases/v2.0.0/sbml/0005/_0005.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0006/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0006/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0006/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0007/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0007/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0007/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0008/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0008/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0008/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml b/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml +++ b/petabtests/cases/v2.0.0/sbml/0009/_0009.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml b/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml +++ b/petabtests/cases/v2.0.0/sbml/0010/_0010.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml b/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml +++ b/petabtests/cases/v2.0.0/sbml/0011/_0011.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml b/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml +++ b/petabtests/cases/v2.0.0/sbml/0012/_0012.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml b/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml +++ b/petabtests/cases/v2.0.0/sbml/0013/_0013.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0014/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0014/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0014/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0015/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0015/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0015/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0016/_experiments.tsv b/petabtests/cases/v2.0.0/sbml/0016/_experiments.tsv deleted file mode 100644 index 9ae6a66..0000000 --- a/petabtests/cases/v2.0.0/sbml/0016/_experiments.tsv +++ /dev/null @@ -1,2 +0,0 @@ -experimentId conditionId time -experiment____c0 c0 0 diff --git a/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml b/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml +++ b/petabtests/cases/v2.0.0/sbml/0017/_0017.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv index 287e74a..b8d6da1 100644 --- a/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv +++ b/petabtests/cases/v2.0.0/sbml/0017/_conditions.tsv @@ -2,6 +2,5 @@ conditionId targetId targetValue valueType preeq_c0 k1 0.3 constant c0 k1 0.8 constant preeq_c0 B 2.0 initial -c0 B initial preeq_c0 A 0.0 initial c0 A 1.0 initial diff --git a/petabtests/cases/v2.0.0/sbml/0018/_0018.yaml b/petabtests/cases/v2.0.0/sbml/0018/_0018.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0018/_0018.yaml +++ b/petabtests/cases/v2.0.0/sbml/0018/_0018.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/cases/v2.0.0/sbml/0018/_conditions.tsv b/petabtests/cases/v2.0.0/sbml/0018/_conditions.tsv index 287e74a..b8d6da1 100644 --- a/petabtests/cases/v2.0.0/sbml/0018/_conditions.tsv +++ b/petabtests/cases/v2.0.0/sbml/0018/_conditions.tsv @@ -2,6 +2,5 @@ conditionId targetId targetValue valueType preeq_c0 k1 0.3 constant c0 k1 0.8 constant preeq_c0 B 2.0 initial -c0 B initial preeq_c0 A 0.0 initial c0 A 1.0 initial diff --git a/petabtests/cases/v2.0.0/sbml/0019/0019.py b/petabtests/cases/v2.0.0/sbml/0019/0019.py index d2441db..ddcaac1 100644 --- a/petabtests/cases/v2.0.0/sbml/0019/0019.py +++ b/petabtests/cases/v2.0.0/sbml/0019/0019.py @@ -18,9 +18,8 @@ # problem -------------------------------------------------------------------- problem = Problem() # TODO use mapping here -problem.add_condition("c0") -problem.add_measurement("obs_a", "c0", 0, 0.7) -problem.add_measurement("obs_a", "c0", 10, 0.1) +problem.add_measurement("obs_a", "", 0, 0.7) +problem.add_measurement("obs_a", "", 10, 0.1) problem.add_observable("obs_a", "maps_to_A", 0.5) problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN) problem.add_parameter("maps_to_b0", lb=0, ub=10, nominal_value=0, scale=LIN) diff --git a/petabtests/cases/v2.0.0/sbml/0019/_measurements.tsv b/petabtests/cases/v2.0.0/sbml/0019/_measurements.tsv index 25969da..59bd3e4 100644 --- a/petabtests/cases/v2.0.0/sbml/0019/_measurements.tsv +++ b/petabtests/cases/v2.0.0/sbml/0019/_measurements.tsv @@ -1,3 +1,3 @@ observableId experimentId time measurement -obs_a c0 0 0.7 -obs_a c0 10 0.1 +obs_a 0 0.7 +obs_a 10 0.1 diff --git a/petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv b/petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv index 3b04603..8322fe9 100644 --- a/petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv +++ b/petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv @@ -1,3 +1,3 @@ observableId experimentId time simulation -obs_a c0 0 1.0 -obs_a c0 10 0.42857190373069665 +obs_a 0 1.0 +obs_a 10 0.42857190373069665 diff --git a/petabtests/cases/v2.0.0/sbml/0020/_0020.yaml b/petabtests/cases/v2.0.0/sbml/0020/_0020.yaml index c3170c2..8b85ee0 100644 --- a/petabtests/cases/v2.0.0/sbml/0020/_0020.yaml +++ b/petabtests/cases/v2.0.0/sbml/0020/_0020.yaml @@ -1,14 +1,16 @@ +extensions: [] format_version: 2.0.0 parameter_file: _parameters.tsv problems: - condition_files: - _conditions.tsv + experiment_files: + - _experiments.tsv measurement_files: - _measurements.tsv - observable_files: - - _observables.tsv model_files: _model: language: sbml location: _model.xml -extensions: [] + observable_files: + - _observables.tsv diff --git a/petabtests/file.py b/petabtests/file.py index 4219be2..188507b 100644 --- a/petabtests/file.py +++ b/petabtests/file.py @@ -258,6 +258,12 @@ def write_problem( tmp_exp_file = Path(dir_, "experiments.tsv") if tmp_exp_file.exists(): tmp_exp_file.rename(exp_file) + # update in yaml + with open(yaml_path) as f: + config = yaml.safe_load(f) + config[PROBLEMS][0][EXPERIMENT_FILES] = ["_experiments.tsv"] + with open(yaml_path, "w") as f: + yaml.dump(config, f, default_flow_style=False) format_version = 2 # FIXME Until a first libpetab with petab.v1 subpackage is released diff --git a/test/test_generate.py b/test/test_generate.py index ba5482f..790a157 100644 --- a/test/test_generate.py +++ b/test/test_generate.py @@ -22,7 +22,7 @@ def test_create_case(): Mostly for debugging purposes. """ - format_ = "pysb" + format_ = "sbml" version = "v2.0.0" - id_ = "0002" + id_ = "0019" create_case(format_=format_, version=version, id_=id_)