Add specific datatypes for Cytoscape and Kepler.gl #20117
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bgruening
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May 2, 2025
lib/galaxy/datatypes/tabular.py
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| class GeoCSV(CSV): | ||
| """ | ||
| CSV format compatible with Kepler.gl, expected to contain latitude and longitude fields. | ||
| https://docs.kepler.gl/docs/keplergl-schema |
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This link does not work for me.
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I replaced the link.
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Is there a real spec somewhere? I'm not sure we need a sniffer here. I guess at least for the start we can just add a subclass of csv that is called geocsv?
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I updated the link, but if you prefer I can remove the sniffer and just introduce it as sub class without sniffer instead.
| class CytoscapeJson(Json): | ||
| """ | ||
| Cytoscape JSON format for network visualization, typically containing 'nodes' and 'edges' in a JSON object. | ||
| https://js.cytoscape.org/#notation/elements-json |
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You can add this link also to the datatypes_conf file as description and description_url
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bgruening
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May 3, 2025
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This PR adds two new datatype definitions: cytoscapejson and keplercsv, which are subtypes of json and csv, respectively. These formats are consumed by Cytoscape and Kepler.gl. Introducing specific datatypes improves user guidance and prevents the list of selectable datatypes from being cluttered with incompatible formats.
While only tangentially related to this PR, I believe there is a broader need for a systematic, large-scale evaluation of all datatypes and sniffers in an all-against-all fashion. Such an analysis would improve the robustness and accuracy of datatype detection across the platform.
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