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FAIRmat-NFDI / pynxtools

https://fairmat-nfdi.github.io/pynxtools/
Apache License 2.0
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Allow report of missing fields #167

Open domna opened 8 months ago

domna commented 8 months ago

When the reader runs and does not find required fields it should not stop, but rather set the @partial attribute and report which fields are missing. There could also be a feature which just reports which fields are missing without writing a file. See #133

RubelMozumder commented 8 months ago

PR: https://github.com/FAIRmat-NFDI/pynxtools/pull/175

domna commented 8 months ago

PR: #175

Its better to write Fixes #167 in the PR, because then github automatically links the PR and closes the issue automatically as soon as the branch is merged to the default branch. I added this there so you should see the PR linked below.

sherjeelshabih commented 4 months ago

Can this be closed? @RubelMozumder @domna

RubelMozumder commented 4 months ago

@sherjeelshabih, Yeah, we can close it, I found the logger is working perfectly both in Nomad and pynxtools when running converter from jupyter lab or the command line. REader user and developer will be aware of any missing fields, groups or attributes.

domna commented 4 months ago

@sherjeelshabih I'm not sure whether we should keep it open as we don't error out with the reader anymore but we don't implemented the part of writing the @partial attribute. I think it would be useful to denote in the produced file that this is not a valid NeXus file at least.

RubelMozumder commented 4 months ago

@sherjeelshabih I'm not sure whether we should keep it open as we don't error out with the reader anymore but we don't implemented the part of writing the @partial attribute. I think it would be useful to denote in the produced file that this is not a valid NeXus file at least.

Sorry, I did not notice it. Just a short comment on the partial attributes. Alongside with the @partial, you might also think to have the list of the missing fields on the parent data object let say under @missing_concepts. So later on without the log info, viewer or user might also get deeper info for @partial from the nexus file in any platform.

sherjeelshabih commented 4 months ago

Feel free to reopen this issue as you see fit. I guess we have added functionality to pick up files with the @partial list and merge them. But this as you say is about writing out the @partial list automatically.