From 63c9fd8d5e19b4538a4f5f0edf0794e0a929deee Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 19 Sep 2024 18:22:12 +0300 Subject: Update docs to highlight sparql conf params in SECRETS file. Signed-off-by: Munyoki Kilyungi --- README.md | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f7fe2c8..8a9b46f 100644 --- a/README.md +++ b/README.md @@ -126,11 +126,24 @@ These configurations should be set in an external config file, pointed to with t - TMPDIR - SPARQL_USER - SPARQL_ENDPOINT (ex: "http://localhost:9082/sparql-auth/") -- SPARQL_PASSWORD -- SPARQL_AUTH_URI +- GN3_SECRETS TMPDIR also needs to be set correctly for the R script(s) because they pass results on as files on the local system (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp). Note that the Guix build system should take care of the paths. +### Secrets + +All of GN3's secret parameters are found inside the "GN3_SECRETS". This file should contain the following: + +``` +SPARQL_USER = "XXX" +SPARQL_PASSWORD = "XXXXXXXXXX" +SPARQL_AUTH_URI="http://localhost:9082/sparql-auth/" +SPARQL_CRUD_AUTH_URI="http://localhost:9082/sparql-graph-crud-auth" +FAHAMU_AUTH_TOKEN="XXXXXX" +``` + +Note: The sparql configurations are important for running tests I.e. `pytest -k rdf`. + ## Command-Line Utility Scripts This project has a number of utility scripts that are needed in specific cirscumstances, and whose purpose is to support the operation of this application in one way or another. Have a look at the [Scripts.md file](./docs/Scripts.md] to see the details for each of the scripts that are available. -- cgit v1.2.3