Function to create problem yaml file (#398)

* resolves 386

* resolves #397

* include create_default_yaml() as part of problem.to_file()

* allow for list of files in creation of yaml file

petab/petab_schema.yaml

@@ -59,6 +59,10 @@ properties:
           type: array
           description: List of PEtab observable files.
 
+          items:
+            type: string
+            description: PEtab observable file name or URL.
+
         visualization_files:
           type: array
           description: List of PEtab visualization files.

petab/problem.py

@@ -265,7 +265,8 @@ def to_files(self,
                  measurement_file: Optional[str] = None,
                  parameter_file: Optional[str] = None,
                  visualization_file: Optional[str] = None,
-                 observable_file: Optional[str] = None) -> None:
+                 observable_file: Optional[str] = None,
+                 yaml_file: Optional[str] = None) -> None:
         """
         Write PEtab tables to files for this problem
 
@@ -282,6 +283,7 @@ def to_files(self,
             parameter_file: Parameter table destination
             visualization_file: Visualization table destination
             observable_file: Observables table destination
+            yaml_file: YAML file destination
 
         Raises:
             ValueError: If a destination was provided for a non-existing
@@ -333,6 +335,12 @@ def error(name: str) -> ValueError:
             else:
                 raise error("visualization")
 
+        if yaml_file:
+            yaml.create_problem_yaml(sbml_file, condition_file,
+                                     measurement_file, parameter_file,
+                                     observable_file, yaml_file,
+                                     visualization_file)
+
     def get_optimization_parameters(self):
         """
         Return list of optimization parameter IDs.

petab/yaml.py

@@ -2,13 +2,12 @@
 
 import os
 
-from typing import Any, Dict, Union, Optional
+from typing import Any, Dict, Union, Optional, List
 
 import jsonschema
 import yaml
 from .C import *  # noqa: F403
 
-
 SCHEMA = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                       "petab_schema.yaml")
 
@@ -159,4 +158,49 @@ def write_yaml(yaml_config: Dict[str, Any], filename: str) -> None:
     """
 
     with open(filename, 'w') as outfile:
-        yaml.dump(yaml_config, outfile, default_flow_style=False)
+        yaml.dump(yaml_config, outfile, default_flow_style=False,
+                  sort_keys=False)
+
+
+def create_problem_yaml(sbml_files: Union[str, List[str]],
+                        condition_files: Union[str, List[str]],
+                        measurement_files: Union[str, List[str]],
+                        parameter_file: str,
+                        observable_files: Union[str, List[str]],
+                        yaml_file: str,
+                        visualization_files: Optional[Union[str, List[str]]]
+                        = None) -> None:
+    """
+    Create and write default YAML file for a single PEtab problem
+
+    Arguments:
+        sbml_files: Path of SBML model file or list of such
+        condition_files: Path of condition file or list of such
+        measurement_files: Path of measurement file or list of such
+        parameter_file: Path of parameter file
+        observable_files: Path of observable file or lsit of such
+        yaml_file: Path to which YAML file should be written
+        visualization_files: Optional Path to visualization file or list of
+        such
+    """
+    if isinstance(sbml_files, str):
+        sbml_files = [sbml_files]
+    if isinstance(condition_files, str):
+        condition_files = [condition_files]
+    if isinstance(measurement_files, str):
+        measurement_files = [measurement_files]
+    if isinstance(observable_files, str):
+        observable_files = [observable_files]
+    if isinstance(visualization_files, str):
+        visualization_files = [visualization_files]
+
+    problem_dic = {CONDITION_FILES: condition_files,
+                   MEASUREMENT_FILES: measurement_files,
+                   SBML_FILES: sbml_files,
+                   OBSERVABLE_FILES: observable_files}
+    if visualization_files is not None:
+        problem_dic.update({'visualization_files': visualization_files})
+    yaml_dic = {PARAMETER_FILE: parameter_file,
+                FORMAT_VERSION: 1,
+                PROBLEMS: [problem_dic]}
+    write_yaml(yaml_dic, yaml_file)

tests/test_petab.py

@@ -531,7 +531,8 @@ def test_to_files(petab_problem):  # pylint: disable=W0621
             measurement_file=measurement_file,
             parameter_file=parameter_file,
             visualization_file=None,
-            observable_file=observable_file)
+            observable_file=observable_file,
+            yaml_file=None)
 
         # exemplarily load some
         parameter_df = petab.get_parameter_df(parameter_file)

tests/test_yaml.py

@@ -1,7 +1,8 @@
 """Test for petab.yaml"""
+import tempfile
 
 import pytest
-from petab.yaml import validate
+from petab.yaml import validate, create_problem_yaml
 
 from jsonschema.exceptions import ValidationError
 
@@ -18,3 +19,36 @@ def test_validate():
     # should be well-formed
     file_ = "doc/example/example_Fujita/Fujita.yaml"
     validate(file_)
+
+
+def test_create_problem_yaml():
+    with tempfile.TemporaryDirectory() as folder:
+        # test with single problem files
+        # create target files
+        sbml_file = tempfile.mkstemp(dir=folder)[1]
+        condition_file = tempfile.mkstemp(dir=folder)[1]
+        measurement_file = tempfile.mkstemp(dir=folder)[1]
+        parameter_file = tempfile.mkstemp(dir=folder)[1]
+        observable_file = tempfile.mkstemp(dir=folder)[1]
+        yaml_file = tempfile.mkstemp(dir=folder)[1]
+        visualization_file = tempfile.mkstemp(dir=folder)[1]
+        create_problem_yaml(sbml_file, condition_file, measurement_file,
+                            parameter_file, observable_file, yaml_file,
+                            visualization_file)
+        validate(yaml_file)
+
+        # test for list of files
+        # create additional target files
+        sbml_file2 = tempfile.mkstemp(dir=folder)[1]
+        condition_file2 = tempfile.mkstemp(dir=folder)[1]
+        measurement_file2 = tempfile.mkstemp(dir=folder)[1]
+        observable_file2 = tempfile.mkstemp(dir=folder)[1]
+        yaml_file2 = tempfile.mkstemp(dir=folder)[1]
+
+        sbml_files = [sbml_file, sbml_file2]
+        condition_files = [condition_file, condition_file2]
+        measurement_files = [measurement_file, measurement_file2]
+        observable_files = [observable_file, observable_file2]
+        create_problem_yaml(sbml_files, condition_files, measurement_files,
+                            parameter_file, observable_files, yaml_file2)
+        validate(yaml_file2)