Add read permission to opensafely/server-instructions

[Jongmassey]

This gives the auto-generated PAT used for git operations within this codespace read permissions to the server-instructions repo which contains the stata license file needed to run stata actions.

Fixes https://github.com/opensafely-core/research-template-docker/issues/27

[Jongmassey]

NB this adds an authorisation dialog on codespace startup

we should add this to the docs

[Jongmassey]

To test this I did the following (which I won't commit to this branch as we don't want it in the main research template).

With a project.yaml of:

version: '3.0'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 1000

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset.csv
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv
  stata_action:
    run: stata-mp:latest analysis/stata.do
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        dataset: null.csv

And a stata.do file of:

capture noisily import delimited ./output/output/dataset.csv, clear

Gives the following output:

rstudio@codespaces-1a7114:/workspaces/research-template$ opensafely run run_all -f
Fetching missing docker image: docker pull ghcr.io/opensafely-core/stata-mp:latest
latest: Pulling from opensafely-core/stata-mp
31bd5f451a84: Pull complete 
1a6ee09d066f: Pull complete 
55f7cdae42fa: Pull complete 
a42e12a75987: Pull complete 
e86a092ef517: Pull complete 
ca811edb1d98: Pull complete 
3734afaf51d6: Pull complete 
038ea78eb362: Pull complete 
586414386b09: Pull complete 
1c8b1ff1d550: Pull complete 
4f4fb700ef54: Pull complete 
66c39923669a: Pull complete 
f943eb11a513: Pull complete 
e6b308b3e3b4: Pull complete 
a5018df23185: Pull complete 
5ef36c74616d: Pull complete 
33f3283b6e62: Pull complete 
Digest: sha256:e98addabe212a12ed2baf0854e5568c361c280863c38047cb8d472216ba1cf21
Status: Downloaded newer image for ghcr.io/opensafely-core/stata-mp:latest
ghcr.io/opensafely-core/stata-mp:latest
Fetching missing docker image: docker pull ghcr.io/opensafely-core/ehrql:v1
v1: Pulling from opensafely-core/ehrql
3c67549075b6: Pull complete 
49bd3e0ffcce: Pull complete 
903589a32593: Pull complete 
c3f0f10ca1d7: Pull complete 
f4bd2e5548ba: Pull complete 
fbbbb4d109e4: Pull complete 
4f4fb700ef54: Pull complete 
aeb773ef00f3: Pull complete 
fbef4effabd9: Pull complete 
e4f364c7a1bc: Pull complete 
d26146715345: Pull complete 
0fbd16982438: Pull complete 
1a293b34cc2f: Pull complete 
b2a6e8a1b7e8: Pull complete 
Digest: sha256:97baa6d30e2fb18535979b950cd387c9d653fa8de184a9afa0d219f49c0e0d7a
Status: Downloaded newer image for ghcr.io/opensafely-core/ehrql:v1
ghcr.io/opensafely-core/ehrql:v1
Fetching missing docker image: docker pull ghcr.io/opensafely-core/busybox
Using default tag: latest
latest: Pulling from opensafely-core/busybox
22b70bddd3ac: Pull complete 
Digest: sha256:dacd1aa51e0b27c0e36c4981a7a8d9d8ec2c4a74bf125c0a44d0709497a522e9
Status: Downloaded newer image for ghcr.io/opensafely-core/busybox:latest
ghcr.io/opensafely-core/busybox:latest

Running actions: generate_dataset, stata_action

jobrunner.run loop started
generate_dataset: Preparing your code and workspace files
generate_dataset: Copying in code from /workspaces/research-template
generate_dataset: Prepared and ready to run
generate_dataset: Executing job on the backend
generate_dataset: Job has finished executing and is waiting to be finalized
generate_dataset: Recording job results
generate_dataset: Extracting output file: output/dataset.csv
generate_dataset: Logs written to: /workspaces/research-template/metadata/generate_dataset.log
generate_dataset: Finished recording results
generate_dataset: Completed successfully
generate_dataset: Cleaning up container and volume
stata_action: Preparing your code and workspace files
stata_action: Copying in code from /workspaces/research-template
stata_action: Copying input file: output/dataset.csv
stata_action: Prepared and ready to run
stata_action: Executing job on the backend
stata_action: Job has finished executing and is waiting to be finalized
stata_action: Recording job results
stata_action: Logs written to: /workspaces/research-template/metadata/stata_action.log
stata_action: Finished recording results
stata_action: No outputs found matching patterns:
 - null.csv
stata_action: Cleaning up container and volume

=> generate_dataset
   Completed successfully

   log file: metadata/generate_dataset.log
   outputs:
     output/dataset.csv  - highly_sensitive

=> stata_action
   No outputs found matching patterns:
    - null.csv

   Did you mean to match one of these files instead?
    - stata.log

   log file: metadata/stata_action.log
   outputs:
     (no outputs)