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Adds documentation to pynxtools 8000 #205
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@sherjeelshabih I will build ci/cd parts here and then we can merge and do the additional doc changes in a new PR. Good? |
Pull Request Test Coverage Report for Build 7531147355
💛 - Coveralls |
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We use a Python tool to make converting our research data easier. This has a number of [readers](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers) that support multiple file formats. You can browse the separate folders to find the reader that might work for you. A generic reader is the [JSON Map Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/json_map). | ||
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We will use the [XPS Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/xps) with Vamas (.vms) files as an example. |
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Most probably this will change to
"We will use the XPS Reader with a file from SpecsLabProdigy file (.sle) as an example."
Need to update pynxtools and the example file first.
- file1.vms | ||
- otherfile.vms |
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- file1.vms | |
- otherfile.vms | |
- main_data_file.sle | |
- metadata_file.slh | |
- eln_data_sle.yaml |
Again, this cannot be changed now, it is just to get keep track of what needs to be changed later.
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Next, you will run the conversion routine: | ||
```console | ||
dataconverter --reader xps |
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dataconverter --reader xps | |
dataconverter --reader xps --nxdl NXmpes --input-file "main_data_file.sle" --input-file "metadata_file.slh" --input-file "eln_data_sle.yaml" --output "output.nxs" |
<img src="media/create-new-upload.gif" /> | ||
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## Upload your NeXus file |
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Shall we add other process where you upload your original file and choose the NeXusDataConverter?
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Nomad also interprets and ```normalizes``` this data to make it interoperable with other corners of Material's research. To browse this ```normalized``` data you can browse the ```DATA``` tab. Here you see all the information Nomad has picked up and made available for search and comparison with synthesis, experimental, and computational materials data. | ||
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<img src="media/data-tab.gif" /> |
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Add GIF for browsing of instrument metadata once the example file is updated.
pynxtools shall be the place to host the pynxtools & nexus definitions combined documentation.
It should also be integrated in nomad at some point, maybe with the mkdocs-monorepo-plugin
This replaces FAIRmat-NFDI/nexus_definitions#75 and FAIRmat-NFDI/nexus_definitions#121
Todo: