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| author | Munyoki Kilyungi | 2024-09-19 18:22:12 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2024-09-23 12:32:51 +0300 |
| commit | 63c9fd8d5e19b4538a4f5f0edf0794e0a929deee (patch) | |
| tree | 20df57b5a2ace00c80e025031e65ef3b6955d3b7 | |
| parent | 0fd98748b325860f1e91fabf4b1e8c924508946e (diff) | |
| download | genenetwork3-63c9fd8d5e19b4538a4f5f0edf0794e0a929deee.tar.gz | |
Update docs to highlight sparql conf params in SECRETS file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rw-r--r-- | README.md | 17 |
1 files changed, 15 insertions, 2 deletions
@@ -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. |