README

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ghql

GitHub Authentication

Note: To be clear, this R package isn’t just for the GitHub GraphQL API, but it is the most public GraphQL API we can think of, so is used in examples throughout here.

See https://developer.github.com/v4/guides/intro-to-graphql/ for getting an OAuth token.

Install

install.packages("ghql")

remotes::install_github("ropensci/ghql")

library("ghql")
library("jsonlite")

initialize client

token <- Sys.getenv("GITHUB_GRAPHQL_TOKEN")
con <- GraphqlClient$new(
  url = "https://api.github.com/graphql",
  headers = list(Authorization = paste0("Bearer ", token))
)

load schema

Since not every GraphQL server has a schema at the base URL, have to manually load the schema in this case

Queries

qry <- Query$new()

When you construct queries we check that they are properly formatted using the graphql that leverages the libgraphqlparser C++ parser. If the query is malformed, we return a message as to why the query is malformed.

qry$query('mydata', '{
  repositoryOwner(login:"sckott") {
    repositories(first: 5, orderBy: {field:PUSHED_AT,direction:DESC}, isFork:false) {
      edges {
        node {
          name
          stargazers {
            totalCount
          }
        }
      }
    }
  }
}')
qry
#> <ghql: query>
#>   queries:
#>     mydata
qry$queries$mydata
#>  
#>  {
#>   repositoryOwner(login:"sckott") {
#>     repositories(first: 5, orderBy: {field:PUSHED_AT,direction:DESC}, isFork:false) {
#>       edges {
#>         node {
#>           name
#>           stargazers {
#>             totalCount
#>           }
#>         }
#>       }
#>     }
#>   }
#> }

# returns json
(x <- con$exec(qry$queries$mydata))
#> [1] "{\"data\":{\"repositoryOwner\":{\"repositories\":{\"edges\":[{\"node\":{\"name\":\"Headstart\",\"stargazers\":{\"totalCount\":124}}},{\"node\":{\"name\":\"extcite\",\"stargazers\":{\"totalCount\":5}}},{\"node\":{\"name\":\"serrano\",\"stargazers\":{\"totalCount\":19}}},{\"node\":{\"name\":\"soylocs\",\"stargazers\":{\"totalCount\":2}}},{\"node\":{\"name\":\"makeregistry\",\"stargazers\":{\"totalCount\":3}}}]}}}}\n"
# parse to an R list
jsonlite::fromJSON(x)
#> $data
#> $data$repositoryOwner
#> $data$repositoryOwner$repositories
#> $data$repositoryOwner$repositories$edges
#>      node.name node.totalCount
#> 1    Headstart             124
#> 2      extcite               5
#> 3      serrano              19
#> 4      soylocs               2
#> 5 makeregistry               3

Parameterize a query by a variable

qry <- Query$new()
qry$query('getgeninfo', 'query getGeneInfo($genId: String!){
  geneInfo(geneId: $genId) {
    id
    symbol
    chromosome
    start
    end
    bioType
    __typename
  }
}')

variables <- list(genId = 'ENSG00000137033')

con <- GraphqlClient$new('https://genetics-api.opentargets.io/graphql')
res <- con$exec(qry$queries$getgeninfo, variables)
jsonlite::fromJSON(res)
#> $data
#> $data$geneInfo
#> $data$geneInfo$id
#> [1] "ENSG00000137033"
#> 
#> $data$geneInfo$symbol
#> [1] "IL33"
#> 
#> $data$geneInfo$chromosome
#> [1] "9"
#> 
#> $data$geneInfo$start
#> [1] 6215786
#> 
#> $data$geneInfo$end
#> [1] 6257983
#> 
#> $data$geneInfo$bioType
#> [1] "protein_coding"
#> 
#> $data$geneInfo$`__typename`
#> [1] "Gene"

Example: Datacite

con <- GraphqlClient$new("https://api.datacite.org/graphql")
qry <- Query$new()
qry$query('dc', '{
  publications(query: "climate") {
    totalCount

    nodes {
      id
      titles {
        title
      }
      descriptions {
        description
      }
      creators {
        name
        familyName
      }
      fundingReferences {
        funderIdentifier
        funderName
        awardTitle
        awardNumber
      }
    }
  }
}')
res <- con$exec(qry$queries$dc)
head(jsonlite::fromJSON(res)$data$publications$nodes)
#>                                  id
#> 1 https://doi.org/10.7915/cig1zc7s1
#> 2 https://doi.org/10.7915/cig3804z3
#> 3 https://doi.org/10.7915/cig56d5q6
#> 4 https://doi.org/10.7915/cig4jm245
#> 5 https://doi.org/10.7915/cig0ns0kz
#> 6 https://doi.org/10.7915/cig0xp6v4
#>                                                                                                           titles
#> 1                                                                               Forest Growth and Climate Change
#> 2                                                                                        Forest Fire and Climate
#> 3                                                           Climate and Water Policy Workshop: Executive Summary
#> 4                                                                                                  Forest Change
#> 5                                                             Impacts of Climate Change on PNW Timber Production
#> 6 HB 1303 Interim Report: A Comprehensive Assessment of the Impacts of Climate Change on the State of Washington
#>   descriptions                  creators fundingReferences
#> 1         NULL Climate Impacts Group, NA              NULL
#> 2         NULL Climate Impacts Group, NA              NULL
#> 3         NULL Climate Impacts Group, NA              NULL
#> 4         NULL Climate Impacts Group, NA              NULL
#> 5         NULL Climate Impacts Group, NA              NULL
#> 6         NULL Climate Impacts Group, NA              NULL

run a local GraphQL server

(con <- GraphqlClient$new("http://localhost:4000/graphql"))
#> <ghql client>
#>   url: http://localhost:4000/graphql

xxx <- Query$new()
xxx$query('query', '{
  __schema {
    queryType {
      name, 
      fields {
        name,
        description
      }
    }
  }
}')

con$exec(xxx$queries$query)
#> $data
#> $data$`__schema`
#> $data$`__schema`$queryType
#> $data$`__schema`$queryType$name
#> [1] "Query"
#> 
#> $data$`__schema`$queryType$fields
#>    name description
#> 1 hello            
#> 2  name