RF: Load report assembler from nireports (#3177)

This transition is inspired by how MRIQC defines `generate_reports`
using _nireports_' Report()

mnt: load Report from nireports instead of niworkflows
mnt: adapt function arguments accordingly
mnt: delete run_reports function
mnt: delete Report patch subclass that is no longer necessary

Author: effigies

fmriprep/cli/run.py

@@ -219,17 +219,23 @@ def main():
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
             config=data.load("reports-spec.yml"),
-            packagename="fmriprep",
         )
         write_derivative_description(config.execution.bids_dir, config.execution.fmriprep_dir)
         write_bidsignore(config.execution.fmriprep_dir)
 
+        if failed_reports:
+            config.loggers.cli.error(
+                "Report generation was not successful for the following participants : %s.",
+                ", ".join(failed_reports),
+            )
+
         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

@@ -86,13 +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"),
-            packagename="fmriprep",
         )
+        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

@@ -22,100 +22,42 @@
 #
 from pathlib import Path
 
-from niworkflows.reports.core import Report as _Report
+from nireports.assembler.report import 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
-# updated niworkflows.
 
-
-class Report(_Report):
-    def _load_config(self, config):
-        from yaml import safe_load as load
-
-        settings = load(config.read_text())
-        self.packagename = self.packagename or settings.get("package", None)
-
-        # Removed from here: Appending self.packagename to self.root and self.out_dir
-        # In this version, pass reportlets_dir and out_dir with fmriprep in the path.
-
-        if self.subject_id is not None:
-            self.root = self.root / f"sub-{self.subject_id}"
-
-        if "template_path" in settings:
-            self.template_path = config.parent / settings["template_path"]
-
-        self.index(settings["sections"])
-
-
-#
-# The following are the interface used directly by fMRIPrep
-#
-
-
-def run_reports(
-    out_dir,
-    subject_label,
-    run_uuid,
-    config=None,
-    reportlets_dir=None,
-    packagename=None,
-):
-    """
-    Run the reports.
-
-    .. testsetup::
-
-    >>> copytree_or_skip("data/tests/work", testdir)
-    >>> (testdir / 'fmriprep').mkdir(parents=True, exist_ok=True)
-
-    .. doctest::
-
-    >>> run_reports(testdir / 'out', '01', 'madeoutuuid', packagename='fmriprep',
-    ...             reportlets_dir=testdir / 'work' / 'reportlets' / 'fmriprep')
-    0
-
-    """
-    return Report(
-        out_dir,
-        run_uuid,
-        config=config,
-        subject_id=subject_label,
-        packagename=packagename,
-        reportlets_dir=reportlets_dir,
-    ).generate_report()
-
-
-def generate_reports(
-    subject_list, output_dir, run_uuid, config=None, work_dir=None, packagename=None
-):
-    """Execute run_reports on a list of subjects."""
+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 = [
-        run_reports(
+
+    errors = []
+    for subject_label in subject_list:
+        entities = {}
+        entities["subject"] = subject_label
+
+        robj = Report(
             output_dir,
-            subject_label,
             run_uuid,
-            config=config,
-            packagename=packagename,
+            bootstrap_file=config,
             reportlets_dir=reportlets_dir,
+            plugins=None,
+            plugin_meta=None,
+            metadata=None,
+            **entities,
         )
-        for subject_label in subject_list
-    ]
 
-    errno = sum(report_errors)
-    if errno:
-        import logging
+        # Count nbr of subject for which report generation failed
+        try:
+            robj.generate_report()
+        except:
+            import sys
+            import traceback
 
-        logger = logging.getLogger("cli")
-        error_list = ", ".join(
-            f"{subid} ({err})" for subid, err in zip(subject_list, report_errors) if err
-        )
-        logger.error(
-            "Preprocessing did not finish successfully. Errors occurred while processing "
-            "data from participants: %s. Check the HTML reports for details.",
-            error_list,
-        )
-    return errno
+            errors.append(subject_label)
+            traceback.print_exception(
+                *sys.exc_info(),
+                file=str(Path(output_dir) / "logs" / f"report-{run_uuid}-{subject_label}.err"),
+            )
+
+    return errors