Adds populate_intended_for to process_extra_commands

It also adds the corresponding test

Author: pvelasco

heudiconv/main.py

@@ -3,7 +3,7 @@
 import sys
 
 from . import __version__, __packagename__
-from .bids import populate_bids_templates, tuneup_bids_json_files
+from .bids import populate_bids_templates, tuneup_bids_json_files, populate_intended_for
 from .convert import prep_conversion
 from .due import due, Doi
 from .parser import get_study_sessions
@@ -47,13 +47,13 @@ def process_extra_commands(outdir, command, files, dicom_dir_template,
                            heuristic, session, subjs, grouping):
     """
     Perform custom command instead of regular operations. Supported commands:
-    ['treat-json', 'ls', 'populate-templates']
+    ['treat-json', 'ls', 'populate-templates', 'populate_intended_for']
 
     Parameters
     ----------
     outdir : str
         Output directory
-    command : {'treat-json', 'ls', 'populate-templates'}
+    command : {'treat-json', 'ls', 'populate-templates', 'populate_intended_for'}
         Heudiconv command to run
     files : list of str
         List of files
@@ -108,6 +108,12 @@ def process_extra_commands(outdir, command, files, dicom_dir_template,
         ensure_heuristic_arg(heuristic)
         from .utils import get_heuristic_description
         print(get_heuristic_description(heuristic, full=True))
+    elif command == 'populate_intended_for':
+        for subj in subjs:
+            session_path = op.join(outdir, 'sub-' + subj)
+            if session:
+                session_path = op.join(session_path, 'ses-' + session)
+            populate_intended_for(session_path)
     else:
         raise ValueError("Unknown command %s" % command)
     return

heudiconv/tests/test_main.py

@@ -1,7 +1,8 @@
 # TODO: break this up by modules
 
 from heudiconv.cli.run import main as runner
-from heudiconv.main import workflow
+from heudiconv.main import (workflow,
+                            process_extra_commands)
 from heudiconv import __version__
 from heudiconv.utils import (create_file_if_missing,
                              set_readonly,
@@ -290,3 +291,33 @@ def test_no_etelemetry():
     with patch.dict('sys.modules', {'etelemetry': None}):
         workflow(outdir='/dev/null', command='ls',
                  heuristic='reproin', files=[])
+
+
+# Test two scenarios:
+# -study without sessions
+# -study with sessions
+# The "expected_folder" is the session folder without the tmpdir
+@pytest.mark.parametrize(
+    "session, expected_folder", [
+        ('', '/foo/sub-{sID}'),
+        ('pre', '/foo/sub-{sID}/ses-pre')
+    ]
+)
+def test_populate_intended_for(session, expected_folder, capfd):
+    """
+    Tests for "process_extra_commands" when the command is
+    'populate_intended_for'
+    """
+    # Because the function .utils.populate_intended_for already has its own
+    # tests, here we just test that "process_extra_commands", when 'command'
+    # is 'populate_intended_for' does what we expect (loop through the list of
+    # subjects and calls 'populate_intended_for'). We call it using folders
+    # that don't exist, and check that the output is the expected.
+    bids_folder = expected_folder.split('sub-')[0]
+    subjects = ['1', '2']
+    process_extra_commands(bids_folder, 'populate_intended_for', [], '',
+                           '', session, subjects, None)
+    captured_output = capfd.readouterr().err
+    for s in subjects:
+        expected_info = 'Adding "IntendedFor" to the fieldmaps in ' + expected_folder.format(sID=s)
+        assert expected_info in captured_output