First commit of a script to transform ISA-tab-like metadata to catalog #2
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Instructions for running are located in README.md The script takes a TSV file as input and transforms the provided fields and values into JSON output that should validate successfully against the catalog schema, i.e. ready for 'catalog add'. The current implementation includes dataset metadata transformation and excludes file metadata transformation (todo).
It read from file(s) OR stdin (default), and always writes to stdout. This takes out needless complexity re path handling and leaves that to a caller. Equivalent calls now: ``` % bin/tubby2catalog -t dataset < data/dataset_metadata.tsv % bin/tubby2catalog -t dataset data/dataset_metadata.tsv ```
In any unsupervised execution log-messages are simply not enough.
…operty categories This is done be slightly changing the internal data structure for `additional_display` items during aggregation. Adjust demo data to show feature
This is needed for the catalog tooling/schema-compliance.
To make this flexible, introduce a formating mechanism that can yield
a raw ID string as input for the UUID5 generation. It can be provided
via a new/simple config option. Example:
```
bin/tubby2catalog \
-t dataset \
-c 'dataset_id_fmt={additional_display[sfb1451][project]}{dataset_id}'\
data/dataset_metadata.tsv
```
This configures the UUID5 got be generated from the concatenation of the
'sfb1451'-'project' custom property, plus the 'dataset_id' field.
To make this work, this uses an intermediate metadata representation
that is comprised of mostly dicts, and supports direct addressing of
most properties.
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Instructions for running are located in README.md
The script takes a TSV file as input and transforms the provided fields and values into JSON output that should validate successfully against the catalog schema, i.e. ready for 'catalog add'.
The current implementation includes dataset metadata transformation and excludes file metadata transformation (todo).