All stages executed by MCAR curation luigi pipeline are now mentioned in the configuration file mcar-luigi.cfg.
This configuration file specifies the value of the skip parameter for any given stage iff (if and only if) the stage supports it, i.e. iff the stage inherits from SkippableMixin.
These stages inherit from SkippableMixin, so one can skip:
class Align(SkippableMixin(True), ElementValidationTask):
class DetectErrors(SkippableMixin(), ElementValidationTask):
class EnsureNeuritesOutsideSoma(SkippableMixin(True), ElementValidationTask):
class ErrorsReport(SkippableMixin(), SetValidationTask):
class ExtractMarkers(SkippableMixin(), ElementValidationTask):
class PlotErrors(SkippableMixin(), ElementValidationTask):
class PlotMarkers(SkippableMixin(), ElementValidationTask):
class PlotMorphologies(SkippableMixin(), ElementValidationTask):
class Recenter(SkippableMixin(), ElementValidationTask):
class Resample(SkippableMixin(), ElementValidationTask):
These stages don't inherit from SkippableMixin, so one cannot skip:
class CheckNeurites(ElementValidationTask):
class Collect(ElementValidationTask):
class Curate(ValidationWorkflow):
class Orient(ElementValidationTask):
class Sanitize(ElementValidationTask):
Note
After this PR the output of the workflow should not change, this PR just cleans up the configurations to make sure that they correspond to what is actually being run.
Checklist
[x] This PR refers to an issue from the issue tracker.
(if it is not the case, please create an issue first).
Fixes #71
Description
luigipipeline are now mentioned in the configuration filemcar-luigi.cfg.This configuration file specifies the value of the
skipparameter for any given stage iff (if and only if) the stage supports it, i.e. iff the stage inherits fromSkippableMixin.These stages inherit from SkippableMixin, so one can
skip:class Align(SkippableMixin(True), ElementValidationTask):class DetectErrors(SkippableMixin(), ElementValidationTask):class EnsureNeuritesOutsideSoma(SkippableMixin(True), ElementValidationTask):class ErrorsReport(SkippableMixin(), SetValidationTask):class ExtractMarkers(SkippableMixin(), ElementValidationTask):class PlotErrors(SkippableMixin(), ElementValidationTask):class PlotMarkers(SkippableMixin(), ElementValidationTask):class PlotMorphologies(SkippableMixin(), ElementValidationTask):class Recenter(SkippableMixin(), ElementValidationTask):class Resample(SkippableMixin(), ElementValidationTask):These stages don't inherit from SkippableMixin, so one cannot
skip:class CheckNeurites(ElementValidationTask):class Collect(ElementValidationTask):class Curate(ValidationWorkflow):class Orient(ElementValidationTask):class Sanitize(ElementValidationTask):Note
After this PR the output of the workflow should not change, this PR just cleans up the configurations to make sure that they correspond to what is actually being run.
Checklist