Create `ChromatographyConfiguration` instances and upload to Mongo

brynnz22 commented 4 months ago

After conducting the first round of mapping, the initial draft spreadsheet for ChromatographyConfiguration instances have been created. What is left:

[x] @SamuelPurvine maps the DMS slots as best as possible
[x] @kheal draft ChromatographyConfigurations in yaml form ~~- [ ] #773~~ ~~- [ ] Add ChemicalEntity ids to ChromatographyConfigurations yamls @kheal ~~
[x] Mint ChromatographyConfiguration ids and add to ChromatographyConfigurations yamls @brynnz22
[x] Convert to json and ingest into Berkeley Mongo. @brynnz22

LATER

Expand modeling of ChromatographyConfiguration to be able to describe gradients and capture more detailed column information. captured this on the [Berkeley-Schema Refactor Roll Out board](https://github.com/orgs/microbiomedata/projects/129)
Expand these using a queries:run update to add in ordered_mobile_phases information once #773 is complete

Follow up notes After discussion - ordered_mobile_phases.substances_used.known_as slot that uses the ChemicalEntity class - is this inlined or by id? [ANSWER: by ID, see new issue in above task list]. If id, then we need to create a new issue to create these ChemicalEntity instances and mint ids. And then map ids back to this slot for the ChromatographyConfiguraiton instances.

kheal commented 3 months ago

Draft of ChromatographyConfiguration yamls is found in this draft PR https://github.com/microbiomedata/berkeley-schema-fy24/pull/230

brynnz22 commented 3 months ago

Blocked for now until Berkeley become production since Berkeley Mongo is not replacing production Mongo.

brynnz22 commented 1 month ago

@kheal Here is the last draft we landed on for the chrom configs. Not sure if you need to adjust these for the Chemical Entity modeling you and @sierra-moxon have been working on: /Users/zalm693/development/sandbox/mass_spec_ingest/mass_spec_mapping/final_jsons/chrom_config/chrom_config_in_progress.json

kheal commented 1 month ago

Thanks @brynnz22. No need to adjust yet, but it's great to have them here for reference.

brynnz22 commented 4 days ago

closing this. It doesn't include expanding those configurations for the chemical entity stuff - not sure if you need to create another issue for that or if you have created one @kheal

microbiomedata / issues

Create `ChromatographyConfiguration` instances and upload to Mongo #749