[SYNPY-1786] Added examples for getting data into a grid#1335
[SYNPY-1786] Added examples for getting data into a grid#1335andrewelamb wants to merge 12 commits intodevelopfrom
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andrewelamb
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| # 5. Store the record set with the path to the CSV file as an annotation. | ||
| # TODO: Add functionality to store data in a RecordSet programmatically | ||
| # This doesn't store the data in the RecordSet |
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I clarified it, but essentially it's a placeholder for SYNPY-1781
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Got it. Technically you can already do this but we would have to merge the CSV client side and upload a new complete copy of the data.
We should wait though to use the import featurem
BryanFauble
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BryanFauble
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Thanks for adding these examples, they'll be really helpful for folks getting started with Grid curation. There are a few small things to clean up before we merge.
Note: This comment was drafted with AI assistance and reviewed by me for accuracy.
linglp
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linglp
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@andrewelamb Thanks for putting together the documentation. In your example, you are reading the data model CSV and trying to use its rows as annotation data, and even when I tested with our own example CSVs, headers like "Valid Values" (it should be ValidValues) will trigger an error.
Also, based on my understanding, Bulk RNA-seq Assay or Biospecimen would be better examples for file-based tasks since they describe actual data files. Patient records is tabular data records rather than file-based in my opinions.
After you finish all the changes, could you run both scripts on your end to make sure that everything is working smoothly? I had some issues when I tested it out on my end.
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@BryanFauble It looks like you requested a change, could you re-review? |
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| # 3. Get annotations from CSV file | ||
| annotations = pd.read_csv(CSV_PATH).to_dict(orient="records") |
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This currently bypasses the grid altogether by pushing data in as annotations. Can we add a TODO comment here?
Nit: Could we leverage the entity view API to push the CSV directly into the entity view?
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Problem:
Curator Extension users asked for simple example scripts for adding data into a grid for both file-based and record-based curation.
Solution:
Two simple examples were added.