enh: adapt the call to Report to its nireports implementation

Author: celprov

fmriprep/reports/core.py

@@ -22,7 +22,7 @@
 #
 from pathlib import Path
 
-from nireports.reports.core import Report as _Report
+from nireports.assembler.report import Report as _Report
 
 # This patch is intended to permit fMRIPrep 20.2.0 LTS to use the YODA-style
 # derivatives directory. Ideally, we will remove this in 20.3.x and use an
@@ -52,22 +52,17 @@ def _load_config(self, config):
 # The following are the interface used directly by fMRIPrep
 #
 
-def generate_reports(
-    subject_list, output_dir, run_uuid, config=None, work_dir=None, packagename=None
-):
+
+def generate_reports(subject_list, output_dir, run_uuid, config=None, work_dir=None):
     """Generate reports for a list of subjects."""
     reportlets_dir = None
     if work_dir is not None:
         reportlets_dir = Path(work_dir) / "reportlets"
 
     report_errors = []
     for subject_label in subject_list:
-
-        # Problem subject_label is not a path to a file, I think
-        entities = config.execution.layout.get_file(subject_label).get_entities()
-        entities.pop("extension", None)
-        entities.pop("echo", None)
-        entities.pop("part", None)
+        entities = {}
+        entities["sub"] = subject_label
 
         robj = Report(
             output_dir,
@@ -77,14 +72,16 @@ def generate_reports(
             plugins=None,
             plugin_meta=None,
             metadata=None,
-            **entities
+            **entities,
         )
 
-        # Problem: this does not make sense anymore because generate_report in nireports always returns 0
-        report_errors.append(robj.generate_report()) 
-    
+        # Count nbr of subject for which report generation failed
+        errno = 0
+        try:
+            robj.generate_report()
+        except:
+            errno += 1
 
-    errno = sum(report_errors)
     if errno:
         import logging