Reset calibration_metadata.yml before saving the initial calibration metadata

There was a reported issue for multiple dark processing that the second dark request for AGIPD fails.

I faced the same issue last days while testing for our next deployment for LPD, DSSC and AGIPD.

Description

When there is a dark request we create a new calibration_metadata.yml file. At the end of DSSC, LPD and AGIPD dark processing a key for modules-mapping is added by Overallmodules_darks_summary notebook.

After reprocessing again the same run using the same out-folder the calibration_metadata.yml file is not created properly.

https://git.xfel.eu/detectors/pycalibration/-/blob/master/src/xfel_calibrate/calibrate.py#L659

I don't really understand why this issue happening even though we are using "w" while create the yml file.

https://git.xfel.eu/detectors/pycalibration/-/blob/master/src/cal_tools/tools.py#L794

This is just a fix to reset the file and save the empty initialized dict before saving the metadata from calibrate.py. Until I understand more why this happens.

How Has This Been Tested?

Relevant Documents (optional)

I have added the malformed yml files. Line 84 is the line with the issue.

calibration_metadata_dssc.yml

calibration_metadata_lpd.yml

Types of changes

Checklist:

• Add a comment pointing to this discussion before merging

Reviewers

@kluyvert @schmidtp

src/cal_tools/tools.py

@@ -789,6 +789,10 @@ class CalibrationMetadata(dict):
             else:
                 print(f"Warning: existing {self._yaml_fn} is malformed, "
                       "will be overwritten")
+        else:
+            # TODO: update after resolving this discussion
+            # https://git.xfel.eu/detectors/pycalibration/-/merge_requests/624
+            self.save()
 
     def save(self):
         with self._yaml_fn.open("w") as fd: