Fixes for the automatic ORM update workflow (#216)

* Add outputs name to orm update checks

* Change database dist location

* Missed translation of items into orm update

* Incorrect working dir

* Allow ORM update on other branches

* Pass env to script

* Grant permissions in orm workflow

* Nested job permissions needed

* Move from hub to gh commands

* Edit flags on gh pr commands

* New flags for finding existing PRs

* Previous commit always returns true

* Update ISPyB ORM schema to database schema v4.2.1 (#217)

Generated with
sqlacodegen            2.3.0.post1
SQLAlchemy             1.4.53

Co-authored-by: Stephen Riggs <122790971+stephen-riggs@users.noreply.github.com>
Co-authored-by: ISPyB-API Azure build <DiamondLightSource-build-server@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: ISPyB-API Azure build <DiamondLightSource-build-server@users.noreply.github.com>

.github/workflows/scripts/create-orm-update-pull-request

@@ -7,16 +7,8 @@ git config credential.helper "store --file=.git/credentials"
 echo "https://${GITHUB_TOKEN}:@github.com" > .git/credentials
 echo
 
-echo "##[section]Installing github cli"
-pushd .. >/dev/null
-wget -nv https://github.com/github/hub/releases/download/v2.6.0/hub-linux-amd64-2.6.0.tgz -O - | tar xz
-export PATH=$(pwd)/hub-linux-amd64-2.6.0/bin/:${PATH}
-popd >/dev/null
-hub --version
-echo
-
 echo "##[section]Check for existing pull request"
-hub pr list -b main -f '%H%n' | grep "^orm-update$" && {
+echo $( gh pr list -B ${BRANCH} -H orm-update ) | grep orm-update && {
  echo Pull request already exists. Stopping here.
  exit
 } || {
@@ -39,8 +31,7 @@ echo
 
 echo "##[section]Creating pull request"
 git push -f --set-upstream origin orm-update
-HUB_VERBOSE=1 hub pull-request -b main -f -m "ISPyB ORM schema update v${DATABASE_SCHEMA}
-
+gh pr create -B ${BRANCH} -H orm-update -t "ISPyB ORM schema update v${DATABASE_SCHEMA}" -b "
 This is an automated pull request to update the ISPyB ORM schema.
 
 Before merging this pull request you may want to

.github/workflows/test-and-publish.yml

@@ -76,6 +76,9 @@ jobs:
 
  update_ORM:
  name: Call orm update workflow
+ permissions:
+ contents: write
+ pull-requests: write
  needs:
  - build
  - get-env-vars

.github/workflows/update-orm.yml

@@ -11,17 +11,21 @@ jobs:
  orm-update:
  name: Update ORM
  runs-on: ubuntu-latest
- container: mariadb
+ permissions:
+ contents: write
+ pull-requests: write
+
  services:
  mariadb:
  image: mariadb:10.6
  env:
- MYSQL_DATABASE: ispybtest
- MYSQL_ROOT_PASSWORD: mysql_root_pwd
+ MARIADB_DATABASE: ispybtest
+ MARIADB_ROOT_PASSWORD: mariadb_root_pwd
  ports:
  - 3306:3306
+ options: --health-cmd="healthcheck.sh --connect --innodb_initialized" --health-interval=10s --health-timeout=5s --health-retries=3
  outputs:
- output1: ${{ steps.checkUpdate.needsUpdate }}
+ needsUpdate: ${{ steps.checkUpdate.outputs.needsUpdate }}
 
  steps:
  - uses: actions/checkout@v4
@@ -45,57 +49,57 @@ jobs:
  working-directory: ./src/ispyb/sqlalchemy
 
  - name: Install sqlacodegen
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  run: |
  set -eux
  pip install -r requirements_orm.txt
  pip install pre-commit
 
  - name: Get database schema
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  uses: actions/download-artifact@v4
  with:
- name: ispyb-database.tar.gz
+ name: package-distributions
  path: dist/
 
+ - uses: shogo82148/actions-setup-mysql@v1
+ with:
+ distribution: 'mariadb'
+ mysql-version: '10.6'
+ auto-start: false
+
  - name: Set up reference database schema
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  run: |
  set -eu
- cat >~/.my.cnf <<EOF
+ cat > .my.cnf <<EOF
  [client]
- user=root
- host=127.0.0.1
- password=mysql_root_pwd
- database=ispybtest
+ user = root
+ password = mariadb_root_pwd
+ host = 127.0.0.1
+ port = 3306
+ database = ispybtest
  EOF
- 
- echo "Installing mariadb-client"
- sudo apt-get install mariadb-client
-
- mkdir schema
- cd schema
- tar xfz "$(System.ArtifactsDirectory)/package/ispyb-database.tar.gz"
- patch -p1 < "$(Build.SourcesDirectory)/src/ispyb/sqlalchemy/sqlacodegen.patch"
- ln ~/.my.cnf .my.cnf -s
+
+ tar xfz "dist/ispyb-database.tar.gz"
+ patch -p1 < "src/ispyb/sqlalchemy/sqlacodegen.patch"
  
  printf 'Waiting for MySQL database to accept connections'
- until mysql -e "SHOW DATABASES" >/dev/null; do printf '.'; sleep 0.5; done
+ until mariadb --defaults-file=.my.cnf -e "SHOW DATABASES" >/dev/null; do printf '.'; sleep 0.5; done
  printf '\n'
 
  echo "Installing reference database"
  ./build.sh
 
  echo
  echo "Installed tables:"
- mysql -D ispyb_build -e "SHOW TABLES"
- working-directory: dist
+ mariadb --defaults-file=.my.cnf -D ispyb_build -e "SHOW TABLES"
 
  - name: Generate ORM
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  run: |
  set -eux
- sqlacodegen mysql+mysqlconnector://root:mysql_root_pwd@127.0.0.1/ispyb_build --noinflect --nojoined --outfile _auto_db_schema.py.in
+ sqlacodegen mysql+mysqlconnector://root:mariadb_root_pwd@127.0.0.1/ispyb_build --noinflect --nojoined --outfile _auto_db_schema.py.in
  # This code produces false positives due to non-deterministic ordering.
  # Add an identifier to the file, and only update/PR the changes when the
  # identifier indicates the file is out of date.
@@ -105,18 +109,20 @@ jobs:
  working-directory: ./src/ispyb/sqlalchemy
 
  - name: Show differences
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  run: git diff
 
  - name: Store artifact
- if: ${{ steps.checkUpdate.needsUpdate == 'true' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  uses: actions/upload-artifact@v4
  with:
  name: ORM
  path: ./src/ispyb/sqlalchemy/_auto_db_schema.py
 
  - name: Create ORM pull request
- if: ${{ steps.checkUpdate.needsUpdate == 'true' && github.ref_name == 'main' }}
+ if: ${{ steps.checkUpdate.outputs.needsUpdate == 'true' }}
  run: .github/workflows/scripts/create-orm-update-pull-request
  env:
  GITHUB_TOKEN: ${{ github.token }}
+ DATABASE_SCHEMA: ${{ inputs.DATABASE_SCHEMA }}
+ BRANCH: ${{ github.ref_name }}

src/ispyb/sqlalchemy/_auto_db_schema.py

@@ -1,4 +1,4 @@
-__schema_version__ = "4.2.0"
+__schema_version__ = "4.2.1"
 # coding: utf-8
 from sqlalchemy import (
  BINARY,
@@ -1697,8 +1697,8 @@ class DiffractionPlan(Base):
 class LabContact(Base):
  __tablename__ = "LabContact"
  __table_args__ = (
- Index("personAndProposal", "personId", "proposalId", unique=True),
  Index("cardNameAndProposal", "cardName", "proposalId", unique=True),
+ Index("personAndProposal", "personId", "proposalId", unique=True),
  )
 
  labContactId = Column(INTEGER(10), primary_key=True)