From 9abb2f19df0f9459899781dd3628e7dcc32397ae Mon Sep 17 00:00:00 2001
From: anmol thapar <mr.anmolthapar@gmail.com>
Date: Tue, 8 Oct 2024 10:28:01 +0100
Subject: [PATCH 1/4] Add data migration script to set default species field
 for all projects

---
 README.md                              | 11 +++++++++++
 migrations/20241008_default_species.sh | 13 +++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100755 migrations/20241008_default_species.sh

diff --git a/README.md b/README.md
index 4aa0e94..6074688 100644
--- a/README.md
+++ b/README.md
@@ -34,3 +34,14 @@ We have one copy of `beebop` deployed:
 * server: `beebop.dide.ic.ac.uk`
 * config: `prod.yml`
 * command to run: `./beebop start prod`
+
+### Running data migrations
+
+All data migrations are stored in the migration folder in the server. The naming convention is `YYYYMMDDHHMMSS_<migration_name>.sh`.
+
+To run them, you can use the following command from the **root**, and replace the migration file with the one you want to run:
+
+```bash
+docker exec beebop-redis bash -c "$(cat ./migrations/<migration_file>)"
+
+```
diff --git a/migrations/20241008_default_species.sh b/migrations/20241008_default_species.sh
new file mode 100755
index 0000000..4ef9e10
--- /dev/null
+++ b/migrations/20241008_default_species.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+set -eu
+
+# This script will set the species field to "Streptococcus pneumoniae" for all projects in the database
+
+projectKeys=$(redis-cli --scan | grep -E ^beebop:project:[a-zA-Z0-9]+$)
+
+
+echo "Number of found projects: $(echo "$projectKeys" | wc -w)"
+
+for key in $projectKeys; do
+    redis-cli HSET "$key" species "Streptococcus pneumoniae"
+done
\ No newline at end of file

From e7b77d8e5f3d1f34692eaca4816a7759c4da5523 Mon Sep 17 00:00:00 2001
From: anmol thapar <mr.anmolthapar@gmail.com>
Date: Wed, 9 Oct 2024 09:21:11 +0100
Subject: [PATCH 2/4] Set default species field for all projects if it is empty

---
 migrations/20241008_default_species.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/migrations/20241008_default_species.sh b/migrations/20241008_default_species.sh
index 4ef9e10..f3da5bf 100755
--- a/migrations/20241008_default_species.sh
+++ b/migrations/20241008_default_species.sh
@@ -9,5 +9,8 @@ projectKeys=$(redis-cli --scan | grep -E ^beebop:project:[a-zA-Z0-9]+$)
 echo "Number of found projects: $(echo "$projectKeys" | wc -w)"
 
 for key in $projectKeys; do
-    redis-cli HSET "$key" species "Streptococcus pneumoniae"
+    currentSpecies=$(redis-cli HGET "$key" species)
+    if [ -z "$currentSpecies" ]; then
+        redis-cli HSET "$key" species "Streptococcus pneumoniae"
+    fi
 done
\ No newline at end of file

From abc3c238e4e3bc6a3f64e77b0ebfcdb336a5ffc6 Mon Sep 17 00:00:00 2001
From: absternator <mr.anmolthapar@gmail.com>
Date: Wed, 9 Oct 2024 08:27:01 +0000
Subject: [PATCH 3/4] fix: test 1

---
 src/beebop_deploy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/beebop_deploy.py b/src/beebop_deploy.py
index 1667d48..1f5738c 100644
--- a/src/beebop_deploy.py
+++ b/src/beebop_deploy.py
@@ -173,7 +173,7 @@ def api_configure(container, cfg):
         print("[api] Storage db already exists, doing nothing")
     else:
         print("[api] Downloading storage database")
-        args = ["./scripts/download_db"]
+        args = ["./scripts/download_databases"]
         mounts = [docker.types.Mount("/beebop/storage",
                   cfg.volumes["storage"])]
         container.client.containers.run(str(cfg.api_ref), args, mounts=mounts,

From 5fb934f3ddf60fb8340c3eebe33c5cc0fb707af7 Mon Sep 17 00:00:00 2001
From: absternator <mr.anmolthapar@gmail.com>
Date: Wed, 9 Oct 2024 09:01:40 +0000
Subject: [PATCH 4/4] chore: remove push tests not on main

---
 .github/workflows/Pytest.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/Pytest.yml b/.github/workflows/Pytest.yml
index b36cd69..1a2d9f1 100644
--- a/.github/workflows/Pytest.yml
+++ b/.github/workflows/Pytest.yml
@@ -2,8 +2,6 @@ on:
   push:
     branches:
       - main
-      - master
-      - "bacpop-*"
   pull_request:
     branches:
       - main