CM02 filesPattern changed
cmproc7:20241125/RAW_DATA/20241125_PJ_mx2597_MdR_f-ACG2-ACTB_g4 % cm_process_start --directory /data/visitor/mx2598/cm02/20241206/RAW_DATA/20241206_PJ_mx2598_JC_HA-ab-37_grid1_good-squares --protein HA-ab --sample HA-ab-37_grid1 --magnification 165000 --dosePerFrame 0.76 --imagesCount 40 --samplingRate 0.73 --partSize 360 --gainFilePath /data/visitor/mx2598/cm02/20241206/RAW_DATA/20241206_PJ_mx2598_JC_HA-ab-37_grid1_good-squares/20241206_113245_EER_GainReference.gain --celery_worker cmproc7
Scipion v3.4.0 - Eugenius
ERROR! No movies available in directory /data/visitor/mx2598/cm02/20241206/RAW_DATA/20241206_PJ_mx2598_JC_HA-ab-37_grid1_good-squares with the filesPattern Images-Disc*/GridSquare_*/Data/FoilHole_*_fractions.tiff.
The file pattern is Images-Disc*/GridSquare_*/Data/FoilHole_*_Fractions.tiff
.
When doing cm_process_start --filesPattern 'Images-Disc*/GridSquare_*/Data/FoilHole_*_Fractions.tiff'
it solves the issue above but a second issues arises:
> Traceback (most recent call last):
> File "/opt/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 203, in run
> self._run()
> File "/opt/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 254, in _run
> resultFiles = self._runFunc()
> File "/opt/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 250, in _runFunc
> return self._func(*self._args)
> File "/mnt/multipath-shares/sware/exp/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/scipion-em-esrf/src/esrf/protocols/protocol_monitor_ispyb.py", line 244, in monitorStep
> monitor.loop()
> File "/opt/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/miniconda3/envs/scipion3/lib/python3.8/site-packages/emfacilities/protocols/protocol_monitor.py", line 177, in loop
> finished = self.step()
> File "/mnt/multipath-shares/sware/exp/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/scipion-em-esrf/src/esrf/protocols/protocol_monitor_ispyb.py", line 334, in step
> self.uploadImportMovies(prot)
> File "/mnt/multipath-shares/sware/exp/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/scipion-em-esrf/src/esrf/protocols/protocol_monitor_ispyb.py", line 985, in uploadImportMovies
> self.uploadMoviesEPUTiff(prot, movieFullPath)
> File "/mnt/multipath-shares/sware/exp/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/scipion-em-esrf/src/esrf/protocols/protocol_monitor_ispyb.py", line 600, in uploadMoviesEPUTiff
> dictFileNameParameters = UtilsPath.getEpuMovieFileNameParameters(
> File "/mnt/multipath-shares/sware/exp/pxsoft/scipion/v3_20240517_cuda11.4.4/ubuntu20.04/scipion-em-esrf/src/esrf/utils/esrf_utils_path.py", line 535, in getEpuMovieFileNameParameters
> if not dictResult["hour"].isdigit():
> KeyError: 'hour'
I patched these lines and the ispyb upload works again
https://gitlab.esrf.fr/sb/scipion-em-esrf/-/blob/devel/src/esrf/utils/esrf_utils_path.py#L516
https://gitlab.esrf.fr/sb/scipion-em-esrf/-/blob/devel/src/esrf/utils/esrf_utils_path.py#L609
https://gitlab.esrf.fr/sb/scipion-em-esrf/-/blob/devel/src/esrf/utils/esrf_utils_path.py#L791
But --filesPattern
is free then you cannot rely on parsing the file name.