thriver

The aim of thriver is to make interacting with the Thrive API easy for R users

Installation

devtools::install_github("insilica/thriver")

Usage

You will need to request an API key to access the Thrive API. On your first request, you will be prompted for your API key.

If you accidentally set it to the wrong value, you can always

set_thrive_api_key()

Note: On macOS you may need to set permissions on your thrive_api_key in Keychain Access

File Handling

You will need the patient id and be a provider in their practice. Get a list of files associated with the patient

> get_patient_file_list(893)
<graphql_query>
List of 1
 $ data:List of 1
  ..$ Patient:List of 1
  .. ..$ files:List of 1
  .. .. ..$ :List of 3
  .. .. .. ..$ filename: chr "TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf"
  .. .. .. ..$ url     : chr "https://thriveapp.health/files/patient/893/12f7193b-e81e-4eef-8fdb-c683d21de3ce/TCGA.PRAD.mutect.deca36be-bf05-"| __truncated__
  .. .. .. ..$ uuid    : chr "12f7193b-e81e-4eef-8fdb-c683d21de3ce"

Get the maf file to generate a PDF report

> thriver::get_file("https://thriveapp.health/files/patient/893/12f7193b-e81e-4eef-8fdb-c683d21de3ce/TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf","TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf")
[1] "/Users/james/Insilica/test-thriver/TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf"

Upload the PDF report

> thriver::post_file(893,"~/Insilica/test-thriver/Gene_Report.pdf")
$success
[1] TRUE

Report is present in the patient's file list

> thriver::get_patient_file_list(893)
<graphql_query>
List of 1
 $ data:List of 1
  ..$ Patient:List of 1
  .. ..$ files:List of 2
  .. .. ..$ :List of 3
  .. .. .. ..$ filename: chr "TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf"
  .. .. .. ..$ url     : chr "https://thriveapp.health/files/patient/893/12f7193b-e81e-4eef-8fdb-c683d21de3ce/TCGA.PRAD.mutect.deca36be-bf05-"| __truncated__
  .. .. .. ..$ uuid    : chr "12f7193b-e81e-4eef-8fdb-c683d21de3ce"
  .. .. ..$ :List of 3
  .. .. .. ..$ filename: chr "Gene_Report.pdf"
  .. .. .. ..$ url     : chr "https://thriveapp.health/files/patient/893/9fb27254-9ad8-4b67-bc99-4c43cd3a990e/Gene_Report.pdf"
  .. .. .. ..$ uuid    : chr "9fb27254-9ad8-4b67-bc99-4c43cd3a990e"

That report was incorrect, delete it!

> thriver::delete_file(893,"9fb27254-9ad8-4b67-bc99-4c43cd3a990e")
$success
[1] TRUE

Chaos averted, order restored

> thriver::get_patient_file_list(893)
<graphql_query>
List of 1
 $ data:List of 1
  ..$ Patient:List of 1
  .. ..$ files:List of 1
  .. .. ..$ :List of 3
  .. .. .. ..$ filename: chr "TCGA.PRAD.mutect.deca36be-bf05-441a-b2e4-394228f23fbe.DR-10.0.somatic.case_id.75a7afb5-66d5-47e3-8a8a-3e3a1e749a96.maf"
  .. .. .. ..$ url     : chr "https://thriveapp.health/files/patient/893/12f7193b-e81e-4eef-8fdb-c683d21de3ce/TCGA.PRAD.mutect.deca36be-bf05-"| __truncated__
  .. .. .. ..$ uuid    : chr "12f7193b-e81e-4eef-8fdb-c683d21de3ce"

graphql_query

Outside of file handling, the Thrive API is accessed through graphql endpoints. You can view the API documentation in your favorite GraphQL IDE using the header format:

Header Name:  "Authorization"
Header Value: "Bearer <thrive_api_key>"

There are a few basic functions included in this package, but if you need to do something more complicated you can always make a custom query call:

thriver::graphql_query("{Profile {providerId verifiedEmails}}")
#> <graphql_query>
#> List of 1
#> $ data:List of 1
#> ..$ Profile:List of 2
#> .. ..$ providerId    : int 18
#> .. ..$ verifiedEmails:List of 1
#> .. .. ..$ : chr "james@insilica.co"

thriver::graphql_query() returns an S3 graphql_query object

structure(
    list(
      content = parsed, # Parsed reponse body JSON as a list
      response = resp, # Raw response
    ),
    class = "graphql_query"
  )

Developer Notes

generate documentation

devtools::document()

load for testing locally

remotes::install_local("/Users/james/Insilica/thriver", build_vignettes = TRUE)
library("thriver", lib.loc="~/Insilica/thriver")