i1713: Fix path to password

[richfitz]

Once this is merged, you will be able to do

jenner:datbase_connection("science")

and get a connection.

@xiangli313 - how should we update this so that it works most neatly from within an import script? Can you think of a good way of doing it detecting where we are so that the import.sh files can get a bit smaller again?

[xiangli313]

I got an error message

con <- jenner::database_connection("science")
 Show Traceback
 
 Rerun with Debug
 Error in vault_addr(addr) : vault address not found 

I don't quite understand what you mean by saying "detecting where we are". Do you mean the hostname thing in the bash script?

[richfitz]

Can you try again now please @xiangli313?

[xiangli313]

In a meeting, will do in 30mins. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Rich FitzJohn <notifications@github.com> Sent: Friday, April 27, 2018 10:00:14 AM To: vimc/jenner Cc: Li, Xiang; Mention Subject: Re: [vimc/jenner] i1713: Fix path to password (#16) Can you try again now please @xiangli313<https://github.com/xiangli313>? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#16 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AZuB9OFSy7djj1HddeA1asqnWYJGLKszks5tst4egaJpZM4Tjimo>.

[richfitz]

OK, now in import.sh scripts we'd do:

#!/usr/bin/env bash
set -ex

MONTAGU_NETWORK=montagu_default
MONTAGU_DOCKER=docker.montagu.dide.ic.ac.uk:5000
MONTAGU_DB_HOST=$(hostname)
MONTAGU_IMPORT_IMAGE=$MONTAGU_DOCKER/montagu-db-import:master
WORKDIR=/montagu-import

echo "*** Importing new 201801rft modelling group"
docker pull $MONTAGU_IMPORT_IMAGE
docker run --rm -it \
       --network $MONTAGU_NETWORK \
       -e MONTAGU_DB_HOST=$MONTAGU_DB_HOST \
       -u `id -u $USER` \
       -v ${PWD}:${WORKDIR} \
       -w ${WORKDIR} \
       ${MONTAGU_IMPORT_IMAGE} \
       Rscript --no-environ import.R

and within the import.R file we'd do

con <- jenner::database_connection(NULL, "import")

and that should wire everything up correctly.

For local testing you will need an .Renviron file containing MONTAGU_DB_HOST=science only

[xiangli313]

I am setting the .Renviron as

MONTAGU_DB_HOST=science

then I got error message regarding authentication

con <- jenner::database_connection(NULL, "import")
Authenticating using github...
 Show Traceback
 
 Rerun with Debug
 Error: GET https://api.github.com/user: 401 Requires authentication []