Merge pull request #1647 from FCP-INDI/fix/anat-only

🐛 Allow anatomical-data only runs

Author: sgiavasis

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1638) in which working connectivity matrix filepaths were generated incorrectly, preventing generating matrices depending on container bindings
 - Fixed broken links in README
+- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1575) in which anatomical-only configurations required functional data directories
 
 ## [1.8.2] - 2021-12-02
 

CPAC/pipeline/cpac_pipeline.py

@@ -1340,7 +1340,21 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None,
         pipeline_blocks += qc_stack
 
     # Connect the entire pipeline!
-    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
+    try:
+        wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
+    except LookupError as lookup_error:
+        errorstrings = lookup_error.args[0].split('\n')
+        missing_key = errorstrings[
+            errorstrings.index('[!] C-PAC says: The listed resource is not '
+                               'in the resource pool:') + 1]
+        if missing_key.endswith('_bold') and 'func' not in sub_dict:
+            raise FileNotFoundError(
+                'The provided pipeline configuration requires functional '
+                'data but no functional data were found for ' +
+                '/'.join([sub_dict[key] for key in ['site', 'subject_id',
+                         'unique_id'] if key in sub_dict]) + '. Please check '
+                'your data and pipeline configurations.') from lookup_error
+        raise lookup_error
 
     # Write out the data
     # TODO enforce value with schema validation

CPAC/pipeline/engine.py

@@ -1894,10 +1894,10 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
     if data_paths:
         rpool = ingress_raw_anat_data(wf, rpool, cfg, data_paths, unique_id,
                                       part_id, ses_id)
-
-        wf, rpool, diff, blip, fmap_rp_list = \
-            ingress_raw_func_data(wf, rpool, cfg, data_paths, unique_id,
-                                  part_id, ses_id)
+        if 'func' in data_paths:
+            wf, rpool, diff, blip, fmap_rp_list = \
+                ingress_raw_func_data(wf, rpool, cfg, data_paths, unique_id,
+                                      part_id, ses_id)
 
     # grab already-processed data from the output directory
     rpool = ingress_output_dir(cfg, rpool, unique_id, creds_path)

CPAC/pipeline/test/test_engine.py

@@ -28,10 +28,10 @@ def test_ingress_func_raw_data(pipe_config, bids_dir, test_dir):
 
     rpool = ResourcePool(name=unique_id, cfg=cfg)
 
-    wf, rpool, diff, blip, fmap_rp_list = ingress_raw_func_data(wf, rpool, cfg,
-                                                                sub_data_dct,
-                                                                unique_id,
-                                                                part_id, ses_id)
+    if 'func' in sub_data_dct:
+        wf, rpool, diff, blip, fmap_rp_list = \
+            ingress_raw_func_data(wf, rpool, cfg, sub_data_dct, unique_id,
+                                  part_id, ses_id)
 
     rpool.gather_pipes(wf, cfg, all=True)