Libpitt/67 assay docs

[libpitt]

Change log:

1. Port over assay related docs

[maxsibilla]

http://localhost:4000/param-search/

• SmartAPI for SenNet's Search API (https://smart-api.info/ui/10ed9b5eb8ff960d4431befc591ed842)
• Modify param-search query to be param-search/datasets?ingest_metadata.metadata.is_targeted=No
• Under Examples:
  1. GET https://search.api.sennetconsortium.org/param-search/datasets?dataset_type=RNAseq&ingest_metadata.metadata.is_targeted=No
  2. Change the second example to use Histology datasets: GET https://search.api.sennetconsortium.org/param-search/datasets?origin_sample.organ=LL&dataset_type=Histology
  3. GET https://search.api.sennetconsortium.org/param-search/datasets?origin_sample.organ=LL&dataset_type=Histology&produce-clt-manifest=true
  4. Copy the above link into the command line example
• I would remove the entire Common document elements section as this is more relevant for HM

http://localhost:4000/param-search/schema-dataset.html

• SmartAPI for SenNet's Search API (https://smart-api.info/ui/10ed9b5eb8ff960d4431befc591ed842)
• Dataset schema example: GET https://search.api.sennetconsortium.org/param-search/datasets?dataset_type=RNAseq&ingest_metadata.metadata.is_targeted=No
• Under Dataset Attributes change hubmap_id to sennet_id` (also change HBM to SNT)
  • Remove dbgap_ attribute rows
  • Change metadata.metadata to ingest_metadata.metadata (this will probably change in the future so maybe add a "TODO" to change it back)
  • Also the link assay type schema doesn't go anywhere (might be an issue on the HM doc site too)
  • Change donor to sources
  • Change origin_samples to origin_sample

[maxsibilla]

http://localhost:4000/param-search/schema-source.html

• SmartAPI for SenNet's Search API (https://smart-api.info/ui/10ed9b5eb8ff960d4431befc591ed842)
• Change Donor everywhere to be Source
• Change example to GET https://search.api.sennetconsortium.org/param-search/sources?group_name=TMC%20-%20Johns%20Hopkins%20University
• Second example GET https://search.api.sennetconsortium.org/param-search/sources?metadata.living_donor_data.preferred_term=Male
• Under Dataset Attributes:
  • Change hubmap_id to sennet_id (also change HBM to SNT)
• Under Metadata Schema change link to SmartAPI for Entity API to https://smart-api.info/ui/7d838c9dee0caa2f8fe57173282c5812 (I need to update the spec to have a SourceMetadata section)
• DonorSchema should be Source Schema

[maxsibilla]

http://localhost:4000/param-search/schema-sample.html

• Update SmartAPI link
• Modify first example: GET https://search.api.sennetconsortium.org/param-search/samples?sample_category=Block
• Change hubmap_id to sennet_id (also change HBM to SNT)
• I am checking if we need Sample Metadata Schema section

[maxsibilla]

http://localhost:4000/param-search/data-query-download-example.html

• Link to the Command Line Transfer Tool documentation: http://localhost:4000/libraries/clt/ (use this throughout the page)
• SmartAPI for SenNet's Search API (https://smart-api.info/ui/10ed9b5eb8ff960d4431befc591ed842)
• Example Query and Download:
  • change metadata.metadata.acquisition_instrument_model to ingest_metadata.metadata
  • change origin_samples.organ to origin_sample.organ
  • Update query: GET https://search.api.sennetconsortium.org/param-search/datasets?dataset_type=Histology&ingest_metadata.metadata.acquisition_instrument_model=BZ-X800&origin_sample.organ=HT
  • Update command line: curl "https://search.api.sennetconsortium.org/param-search/datasets?dataset_type=Histology&ingest_metadata.metadata.acquisition_instrument_model=BZ-X800&origin_sample.organ=HT&produce-clt-manifest=true" > dataset-manifest-for-download.out
  • Results:

    SNT948.QRZW.946 /
    SNT976.WLTL.469 /
    ...