fix: report report generation report in the cli rather than in generate_reports

Author: celprov

fmriprep/cli/run.py

@@ -225,10 +225,11 @@ def main():
 
         if sentry_sdk is not None and failed_reports:
             sentry_sdk.capture_message(
-                "Report generation failed for %d subjects" % failed_reports,
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
                 level="error",
             )
-        sys.exit(int((errno + failed_reports) > 0))
+        sys.exit(int((errno + len(failed_reports)) > 0))
 
 
 if __name__ == "__main__":

fmriprep/cli/workflow.py

@@ -86,12 +86,19 @@ def build_workflow(config_file, retval):
     # Called with reports only
     if config.execution.reports_only:
         build_log.log(25, "Running --reports-only on participants %s", ", ".join(subject_list))
-        retval["return_code"] = generate_reports(
+        failed_reports = generate_reports(
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
             config=data.load("reports-spec.yml"),
         )
+        if failed_reports:
+            config.loggers.cli.error(
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
+            )
+
+        retval["return_code"] = len(failed_reports)
         return retval
 
     # Build main workflow

fmriprep/reports/core.py

@@ -24,8 +24,6 @@
 
 from nireports.assembler.report import Report
 
-from .. import config
-
 
 def generate_reports(subject_list, output_dir, run_uuid, config=None, work_dir=None):
     """Generate reports for a list of subjects."""
@@ -62,9 +60,4 @@ def generate_reports(subject_list, output_dir, run_uuid, config=None, work_dir=N
                 file=str(Path(output_dir) / "logs" / f"report-{run_uuid}-{subject_label}.err"),
             )
 
-    if errors:
-        logger.debug(
-            "Report generation was not successful for the following participants : %s.",
-            ", ".join(errors),
-        )
-    return len(errors)
+    return errors