Adopting click as command line interfaces (#30)

* initial

* fixing the toml

* final touches on adopting click

* deleting test elements

* help for include_empty_properties

* typo

* default for convert

* adopting the tests for click

* creating convert_click

* cleaning the converter file

* adding new tests for click

* final modifications in click

Author: Peyman-N

.gitignore

@@ -6,6 +6,9 @@ __pycache__/
 # C extensions
 *.so
 
+#vscode
+.vscode
+
 # Distribution / packaging
 .Python
 build/

bids2openminds/converter.py

@@ -1,23 +1,20 @@
 from warnings import warn
 from bids import BIDSLayout, BIDSValidator
 import os
+import click
 from . import main
 from . import utility
 from . import globals
 
-
-
-def convert(bids_dir, output_filename=None):
-
-    if not (os.path.isdir(bids_dir)):
+def convert(input_path, output_path=None, multiple_files=False, include_empty_properties=False):  
+    if not (os.path.isdir(input_path)):
         raise NotADirectoryError(
-            f"The input directory is not valid, you have specified {bids_dir} which is not a directory."
+            f"The input directory is not valid, you have specified {input_path} which is not a directory."
         )
+    # if not(BIDSValidator().is_bids(input_path)):
+    #  raise NotADirectoryError(f"The input directory is not valid, you have specified {input_path} which is not a BIDS directory.")
 
-    # if not(BIDSValidator().is_bids(bids_dir)):
-    #  raise NotADirectoryError(f"The input directory is not valid, you have specified {bids_dir} which is not a BIDS directory.")
-
-    bids_layout = BIDSLayout(bids_dir)
+    bids_layout = BIDSLayout(input_path)
 
     layout_df = bids_layout.to_df()
 
@@ -32,22 +29,40 @@ def convert(bids_dir, output_filename=None):
 
     [subjects_dict, subject_state_dict, subjects_list] = main.create_subjects(subjects_id, layout_df, bids_layout)
 
-    [files_list, file_repository] = main.create_file(layout_df, bids_dir)
+    [files_list, file_repository] = main.create_file(layout_df, input_path)
 
     dataset_version = main.create_dataset_version(
         bids_layout, dataset_description, layout_df, subjects_list, file_repository
     )
 
     dataset = main.create_dataset(dataset_description, dataset_version)
-
+    
     failures = globals.collection.validate(ignore=["required", "value"])
     assert len(failures) == 0
 
-    if output_filename is None:
-        output_filename = os.path.join(bids_dir, "openminds.jsonld")
-    globals.collection.save(output_filename)
+    if output_path is None:
+        if multiple_files:
+            output_path=os.path.join(input_path, "openminds")
+        else:
+            output_path = os.path.join(input_path, "openminds.jsonld")
+
+    globals.collection.save(output_path,individual_files=multiple_files,include_empty_properties=include_empty_properties)
+
+    print(f"Conversion was successful, the openMINDS file is in {output_path}")
+
+
+
+@click.command()
+@click.argument("input-path", type=click.Path(file_okay=False,exists=True))
+@click.option("-o","--output-path",default=None,type=click.Path(file_okay=True,writable=True),help="The output path or filename for OpenMINDS file/files.")
+@click.option("--single-file","multiple_files",flag_value=False,default=False,help="Save the entire collection into a single file (default).")
+@click.option("--multiple-files","multiple_files",flag_value=True,help="Each node is saved into a separate file within the specified directory. 'output-path' if specified, must be a directory.")
+@click.option("-e","--include-empty-properties",is_flag=True,default=False,help="Whether to include empty properties in the final file.")
+def convert_click(input_path, output_path, multiple_files, include_empty_properties):
+    convert(input_path, output_path, multiple_files, include_empty_properties)
+
 
 
 if __name__ == "__main__":
-    bids_dir = input("Enter the BIDS directory path: ")
-    convert(bids_dir)
+    input_path = input("Enter the BIDS directory path: ")
+    convert(input_path)

pyproject.toml

@@ -4,6 +4,7 @@ version = "0.0.0"
 dependencies = [
   "bids",
   "openminds >= 0.2.2",
+  "click>=8.1",
   "pandas",
 ]
 requires-python = ">=3.9"
@@ -19,6 +20,9 @@ classifiers = [
   "Programming Language :: Python"
 ]
 
+[project.scripts]
+bids2openminds="bids2openminds.converter:convert_click"
+
 [build-system]
 requires = ["setuptools >= 61.0"]
 build-backend = "setuptools.build_meta"

test/test_example_datasets_click.py

@@ -0,0 +1,32 @@
+import os
+from openminds import Collection
+from bids2openminds.converter import convert_click
+from click.testing import CliRunner
+
+(test_data_set,number_of_openminds_files)= ("ds003",98)
+
+def test_example_datasets_click():
+    test_dir = os.path.join("bids-examples",test_data_set)
+    runner = CliRunner()
+    result = runner.invoke(convert_click, [test_dir])
+    assert result.exit_code == 0
+    c = Collection()
+    c.load(os.path.join(test_dir, "openminds.jsonld"))
+
+#todo This section has a problem which have been solved in pull request number 32
+""" def test_example_datasets_click_seperate_files():
+    test_dir = os.path.join("bids-examples", test_data_set)
+    runner = CliRunner()
+    result = runner.invoke(convert_click, ["--multiple-file",test_dir])
+    assert result.exit_code == 0
+    path_openminds=os.path.join(test_dir, "openminds")
+    numer_of_files=len(os.listdir(path_openminds))
+    assert numer_of_files==number_of_openminds_files """
+
+def test_example_datasets_click_output_location():
+    test_dir = os.path.join("bids-examples", test_data_set)
+    runner = CliRunner()
+    result = runner.invoke(convert_click, ["-o","test_openminds.jsonld",test_dir])
+    assert result.exit_code == 0
+    c = Collection()
+    c.load("test_openminds.jsonld")