Simple command line tool to perform graphGL queries for NCI Genomics Data Commons. Given a "bare GraphQL" query (as described here), this script constructs and passes a JSON query, and writes out the response.
- Obtain GDC authentication token. Save this to
token.txt. - Construct GraphQL query, such as,
{
case (project_id: "TCGA-ALCH", first: 0) {
id
submitter_id
}
_case_count (project_id: "TCGA-ALCH")
}
Save this to query.json.
- Perform query with,
queryGDC -t token.txt query.json
Execute given GraphQL file as a query to GDC
Usage: queryGDC [options] query.json
-t token.txt: define token on command line. Mandatory
-v: print diagnostic information to stderr
-r: repeat query in case of errors until succeeds. Meant to deal with timeout errors.
-d: dry run. Print query but do not execute
token.txt contains GDC authentication token (see https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Authentication/ )
query.json contains "bare queryGL" script (see https://docs.gdc.cancer.gov/API/Users_Guide/Submission/#querying-submitted-data-using-graphql )
queryGDC token.txt -
will read query from STDIN
On occasion, we see the following error:
result="<html><head><title>Hold up there!</title></head><body><center><h1>Hold up there!</h1><p>You are posting too quickly. Wait for few moments and try again.</p></body></html>"
A test for this response was implemented in queryGDC, and results in waiting 5 seconds before trying again
- Definition of GraphQL language
- Tutorial about GraphQL queries
- graphQL documentation at GDC
- GDC Data Model
- GraphiQL A graphical interface for the GDC GraphQL