Update test documentation (#175)

* Format `test/README.md`

* Rename `.env.test` -> `.env.test.sample` and add `INFORMDB_PAT`

* Add `INFORMDB_PAT` requirement to `test/` docs

test/.env.test → test/.env.test.sample

@@ -3,6 +3,8 @@ DEBUG=True
 PIXL_DICOM_TRANSFER_TIMEOUT=120
 PIXL_QUERY_TIMEOUT=120
 
+INFORMDB_PAT=
+
 # PIXL PostgreSQL instance
 PIXL_DB_HOST=postgres
 PIXL_DB_PORT=5432
@@ -45,12 +47,12 @@ ENABLE_DICOM_WEB=true
 ORTHANC_AUTOROUTE_ANON_TO_AZURE=false
 PIXL_DICOM_TRANSFER_TIMEOUT=240
 
-# UCVNA DICOM node information  
+# UCVNA DICOM node information
 VNA_AE_TITLE=VNA
 VNA_DICOM_PORT=4242
 VNA_IP_ADDR=vna
 
-# UCVNAQR DICOM node information  
+# UCVNAQR DICOM node information
 VNAQR_AE_TITLE=VNAQR
 VNAQR_DICOM_PORT=4242
 VNAQR_IP_ADDR=vna-qr

test/.gitignore

@@ -0,0 +1 @@
+.env.test

test/README.md

@@ -1,17 +1,27 @@
 # PIXL System Tests
 
-This directory contains a system/integration test that runs locally and aims to 
-test the essential functionality of the full PIXL system. 
- 
-**Given** a DICOM image in an Orthanc instance (mocked vendor 
-neutral archive, VNA) and a single patient with the same identifier in a  
+This directory contains a system/integration test that runs locally and aims to
+test the essential functionality of the full PIXL system.
+
+**Given** a DICOM image in an Orthanc instance (mocked vendor
+neutral archive, VNA) and a single patient with the same identifier in a
 postgres instance (mocked EMAP database, star schema).
-**When** a message containing the patient and study identifier is added to the 
+**When** a message containing the patient and study identifier is added to the
 queue and the consumers started.
 **Then** a row in the "anon" EMAP data instance of the PIXL postgres instance exists
 and the DICOM study exists in the "anon" PIXL Orthanc instance.
 
-Run with
+Spinning up the Docker containers requires the `$INFORMDB_PAT` environment variable to be set to a
+valid [GitHub Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token)
+with read access to the [UCLH-Foundry/Inform-DB](https://github.com/UCLH-Foundry/Inform-DB) repo.
+
+1. Create a [fine-grained Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-fine-grained-personal-access-token)
+   with **read** access to the *UCLH-Foundry/Inform-DB* repo
+2. Create `.env.test` with `cp .env.test.sample .env.test`
+3. Add your `githb_pat***` token to `.env.test` as `INFORMDB_PAT=***`
+
+Then, run the system test with:
+
 ```bash
 ./run-system-test.sh
 ```