Generate dataset_description.json and README.md when they do not exist and update the json file when the subject is missing

phys2bids/bids.py

@@ -242,3 +242,44 @@ def participants_file(outdir, yml, sub):
             participants_data = ['n/a'] * header_length
             participants_data[p_id_idx] = f'sub-{sub}'
             utils.append_list_as_row(file_path, participants_data)
+
+
+def dataset_description_file(outdir):
+    """
+    Create dataset_description.json file if it does not exist.
+    If it exists, do nothing.
+
+    Parameters
+    ----------
+    outdir: path
+        Full path to the output directory.
+
+    """
+    # dictionary that will be written for the basic dataset description version
+    data_dict = {"Name": os.path.splitext(os.path.basename(outdir))[0],
+                 "BIDSVersion": "1.4.0", "DatasetType": "raw"}
+    file_path = os.path.join(outdir, 'dataset_description.json')
+    # check if dataset_description.json exists, if it doesn't create it
+    if not os.path.exists(file_path):
+        LGR.warning('phys2bids could not find dataset_description.json,'
+                    'generating it with provided info')
+        utils.writejson(file_path, data_dict)
+
+
+def readme_file(outdir):
+    """
+    Create README file if it does not exist.
+    If it exists, do nothing.
+
+    Parameters
+    ----------
+    outdir: path
+        Full path to the output directory.
+
+    """
+    file_path = os.path.join(outdir, 'README.md')
+    if not os.path.exists(file_path):
+        text = 'Empty README, please fill in describing the dataset in more detail.'
+        LGR.warning('phys2bids could not find README,'
+                    'generating it EMPTY, please fill in the necessary info')
+        utils.writefile(file_path, '', text)

phys2bids/phys2bids.py

@@ -33,8 +33,7 @@
 
 from numpy import savetxt
 
-from phys2bids import utils, viz, _version
-from phys2bids.bids import bidsify_units, use_heuristic, participants_file
+from phys2bids import utils, viz, _version, bids
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
 
@@ -190,7 +189,7 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
     LGR.info(f'Reading the file {infile}')
     phys_in = populate_phys_input(infile, chtrig)
     for index, unit in enumerate(phys_in.units):
-        phys_in.units[index] = bidsify_units(unit)
+        phys_in.units[index] = bids.bidsify_units(unit)
     LGR.info('Reading infos')
     phys_in.print_info(filename)
     # #!# Here the function viz.plot_channel should be called
@@ -268,7 +267,11 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
         # Generate participants.tsv file if it doesn't exist already.
         # Update the file if the subject is not in the file.
         # Do not update if the subject is already in the file.
-        participants_file(outdir, yml, sub)
+        bids.participants_file(outdir, yml, sub)
+        # Generate dataset_description.json file if it doesn't exist already.
+        bids.dataset_description_file(outdir)
+        # Generate README file if it doesn't exist already.
+        bids.readme_file(outdir)
     elif heur_file and not sub:
         LGR.warning('While "-heur" was specified, option "-sub" was not.\n'
                     'Skipping BIDS formatting.')
@@ -279,10 +282,10 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
         if heur_file and sub:
             if output_amount > 1:
                 # Add "recording-freq" to filename if more than one freq
-                outfile = use_heuristic(heur_file, sub, ses, filename,
-                                        outdir, uniq_freq)
+                outfile = bids.use_heuristic(heur_file, sub, ses, filename,
+                                             outdir, uniq_freq)
             else:
-                outfile = use_heuristic(heur_file, sub, ses, filename, outdir)
+                outfile = bids.use_heuristic(heur_file, sub, ses, filename, outdir)
 
         else:
             outfile = os.path.join(outdir,

phys2bids/tests/test_bids.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from phys2bids.bids import bidsify_units, use_heuristic
+from phys2bids.bids import bidsify_units, use_heuristic, readme_file, dataset_description_file
 from phys2bids.bids import UNIT_ALIASES
 
 
@@ -58,3 +58,17 @@ def test_use_heuristic(tmpdir, test_sub, test_ses):
                    f'_task-test_rec-biopac_run-01_recording-test_physio')
 
     assert os.path.normpath(test_result) == os.path.normpath(str(heur_path))
+
+
+@pytest.mark.parametrize('outdir', '.')
+def test_README_file(outdir):
+    readme_file(outdir)
+    assert os.path.join(outdir, "README.md")
+    os.remove(os.path.join(outdir, "README.md"))
+
+
+@pytest.mark.parametrize('outdir', '.')
+def test_dataset_description_file(outdir):
+    dataset_description_file(outdir)
+    assert os.path.join(outdir, "dataset_description.json")
+    os.remove(os.path.join(outdir, "dataset_description.json"))