using all as a default option for interface_name in cli; checking name of modules and available interfaces

Author: djarecka

specs/fsl_conv_param.yml renamed to specs/fsl_preprocess_param.yml

@@ -8,8 +8,7 @@
 import typing as ty
 import inspect
 import click
-import pytest
-
+import warnings
 
 
 class FSLConverter:
@@ -32,8 +31,7 @@ class FSLConverter:
                     ]
 
 
-    def __init__(self, interface_name,
-                 interface_spec_file=Path(os.path.dirname(__file__)) / "../specs/fsl_conv_param.yml"):
+    def __init__(self, interface_name, interface_spec_file):
         self.interface_name = interface_name
         with interface_spec_file.open() as f:
             self.interface_spec = yaml.safe_load(f)[self.interface_name]
@@ -414,16 +412,53 @@ def string_formats(self, argstr, name):
         return argstr_new
 
 
+FSL_MODULES = ['aroma', 'dti', 'epi', 'fix', 'maths', 'model', 'possum', 'preprocess', 'utils']
 
 @click.command()
-@click.option("-i", "--interface_name", required=True,
-              help="name of the interface (name used in Nipype, e.g. BET)")
-@click.option("-m", "--module_name", required=True, help="name of the module (e.g. preprocess)")
+@click.option("-i", "--interface_name", required=True, default="all",
+              help="name of the interface (name used in Nipype, e.g. BET) or all (default)"
+                   "if all is used all interfaces from the spec file will be created")
+@click.option("-m", "--module_name", required=True, help=f"name of the module from the list {FSL_MODULES}")
 def create_pydra_spec(interface_name, module_name):
-    converter = FSLConverter(interface_name=interface_name)
+    if module_name not in FSL_MODULES:
+        raise Exception(f"module name {module_name} not available;"
+                        f"should be from the list {FSL_MODULES}")
+
+    spec_file = Path(os.path.dirname(__file__)) / f"../specs/fsl_{module_name}_param.yml"
+    if not spec_file.exists():
+        raise Exception(f"the specification file doesn't exist for the module {module_name},"
+                        f"create the specification file in {spec_file.parent}")
+
+    def all_interfaces(module):
+        nipype_module = getattr(fsl, module)
+        all_specs = [el for el in dir(nipype_module) if "InputSpec" in el]
+        all_interf = [el.replace("InputSpec", "") for el in all_specs]
+
+        # interfaces in the spec file
+        with open(spec_file) as f:
+            spec_interf = yaml.safe_load(f).keys()
+
+        if set(all_interf) - set(spec_interf):
+            warnings.warn(f"some interfaces are not in the spec file: "
+                          f"{set(all_interf) - set(spec_interf)}, "
+                          f"and pydra interfaces will not be created for them")
+        return spec_interf
+
+    if interface_name == "all":
+        interface_list = all_interfaces(module_name)
+    elif interface_name in all_interfaces(module_name):
+        interface_list = [interface_name]
+    else:
+        raise Exception(f"interface_name has to be 'all' "
+                        f"or a name from the list {all_interfaces(module_name)}")
+
     dirname_interf = Path(__file__).parent.parent / f"pydra/tasks/fsl/{module_name}"
     dirname_interf.mkdir(exist_ok=True)
-    converter.pydra_specs(write=True, dirname=dirname_interf)
+
+    for interface_el in interface_list:
+        converter = FSLConverter(interface_name=interface_el,
+        interface_spec_file=Path(os.path.dirname(__file__)) / "../specs/fsl_preprocess_param.yml")
+        converter.pydra_specs(write=True, dirname=dirname_interf)
 
 if __name__ == '__main__':
     create_pydra_spec()