.dockerignore

@@ -39,11 +39,12 @@ uploads/*
 CONTRIBUTING.md
 
 # development config files
-.eslintrc.js
 .commitlintrc.js
 .cz-config.js
+.gitlab/
 .gitlab-ci.yml
-.linstagedrc.js
-.prettierrc.js
-.stylelintrc.js
-cypress.json
+.gitlab-ci*
+.husky
+.lintstagedrc.js
+.nvmrc
+.renovaterc

.env.example

-USE_SANDBOXED_ORCID=true
-ORCID_CLIENT_ID=YOUR_ORCID_CLIENT_ID # see https://gitlab.coko.foundation/kotahi/kotahi/-/blob/main/FAQ.md#how-do-i-setup-orcid-for-development
-ORCID_CLIENT_SECRET=YOUR_ORCID_SECRET
-POSTGRES_USER=kotahidev
-POSTGRES_PASSWORD=kotahidev
-POSTGRES_DB=kotahidev
-CLIENT_PORT=4000
-CLIENT_HOST=0.0.0.0
-CLIENT_PROTOCOL=http
-PUBLIC_CLIENT_HOST=0.0.0.0
-SERVER_PROTOCOL=http
-SERVER_HOST=0.0.0.0
-SERVER_PORT=3000
-PUBSWEET_SECRET=kotahidev
-

.eslintignore

+node_modules/
+packages/devdocs/.docusaurus
+packages/devdocs/build
+packages/server/scripts/local

.eslintrc.js

 const { eslint } = require('@coko/lint')
 
+// Added parserOptions to remove the @decorators issues
+eslint.parserOptions = {
+  ecmaVersion: 6,
+  ecmaFeatures: {
+    legacyDecorators: true,
+    experimentalObjectRestSpread: true,
+  },
+}
 eslint.rules['react/jsx-props-no-spreading'] = 0
 
 module.exports = eslint

.fly/kotahi-client-main.toml

+# fly.toml app configuration file generated for kotahi-client-main on 2025-02-11T17:13:36+02:00
+#
+# See https://fly.io/docs/reference/configuration/ for information about how to use this file.
+#
+
+app = 'kotahi-client-main'
+primary_region = 'lhr'
+
+# [build]
+#   image = 'cokoapps/kotahi-client:2025.02.11-0'
+
+[env]
+CLIENT_PORT = '4000'
+SERVER_URL = 'https://kotahi-server-main.fly.dev'
+YJS_WEBSOCKET_SERVER_URL = 'wss://kotahi-server-main.fly.dev:8081'
+
+[http_service]
+internal_port = 4000
+force_https = true
+auto_stop_machines = 'stop'
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[vm]]
+memory = '1gb'
+cpu_kind = 'shared'
+cpus = 1

.fly/kotahi-client-test.toml

+# fly.toml app configuration file generated for kotahi-client-test on 2024-10-17T14:28:34+03:00
+#
+# See https://fly.io/docs/reference/configuration/ for information about how to use this file.
+#
+
+app = 'kotahi-client-test'
+primary_region = 'lhr'
+
+# [build]
+# image = 'cokoapps/kotahi-client:test'
+
+[http_service]
+internal_port = 4000
+force_https = true
+auto_stop_machines = 'stop'
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[vm]]
+memory = '1gb'
+cpu_kind = 'shared'
+cpus = 1
+
+[env]
+SERVER_URL = "https://kotahi-server-test.fly.dev"
+YJS_WEBSOCKET_SERVER_URL = "wss://kotahi-server-test.fly.dev:8081"

.fly/kotahi-dev-docs.toml

+app = 'kotahi-dev-docs'
+primary_region = 'fra'
+
+[http_service]
+internal_port = 80
+force_https = true
+auto_stop_machines = 'stop'
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[vm]]
+memory = '256mb'
+cpu_kind = 'shared'
+cpus = 1

.fly/kotahi-flax-main.toml

+app = 'kotahi-flax-main'
+primary_region = 'lhr'
+
+[build]
+image = 'cokoapps/kotahi-flax:0.5.3'
+
+[http_service]
+internal_port = 80
+force_https = true
+auto_stop_machines = 'off'
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[services]]
+protocol = 'tcp'
+internal_port = 8081
+auto_stop_machines = 'off'
+auto_start_machines = true
+
+[[services.ports]]
+port = 8081
+handlers = ['tls', 'http']
+
+[[vm]]
+memory = '1gb'
+cpu_kind = 'shared'
+cpus = 1
+
+[env]
+FLAX_EXPRESS_PORT = '8081'
+FLAX_CLIENT_API_URL = 'https://kotahi-server-main.fly.dev'

.fly/kotahi-flax-test.toml

+app = 'flax'
+primary_region = 'lhr'
+
+[build]
+image = 'cokoapps/kotahi-flax:0.5.3'
+
+[http_service]
+internal_port = 80
+force_https = true
+auto_stop_machines = "off"
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[services]]
+protocol = "tcp"
+internal_port = 8081
+auto_stop_machines = "off"
+auto_start_machines = true
+
+[[services.ports]]
+port = 8081
+handlers = ["tls", "http"]
+
+[[vm]]
+memory = '1gb'
+cpu_kind = 'shared'
+cpus = 1
+
+[env]
+FLAX_EXPRESS_PORT = "8081"
+FLAX_CLIENT_API_URL = "https://kotahi-server-test.fly.dev"

.fly/kotahi-server-main.toml

+# fly.toml app configuration file generated for kotahi-server-main on 2025-02-11T17:09:51+02:00
+#
+# See https://fly.io/docs/reference/configuration/ for information about how to use this file.
+#
+
+app = 'kotahi-server-main'
+primary_region = 'lhr'
+
+# [build]
+# image = 'cokoapps/kotahi-server:2025.02.11-0'
+
+[env]
+CLIENT_URL = 'https://kotahi-client-main.fly.dev'
+FLAX_CLIENT_API_URL = 'https://kotahi-server-main.fly.dev'
+FLAX_EXPRESS_HOST = 'kotahi-flax-main.fly.dev'
+FLAX_EXPRESS_PORT = 8081
+FLAX_EXPRESS_PROTOCOL = 'https'
+FLAX_SITE_URL = 'http://kotahi-flax-main.fly.dev'
+INSTANCE_GROUPS = 'journal:journal,prc:prc,single_form:preprint1'
+MANUSCRIPTS_TABLE_COLUMNS = 'shortId, submission.$title, created, updated, status, author'
+NODE_ENV = 'production'
+SERVER_PORT = 8080
+SERVER_URL = 'https://kotahi-server-main.fly.dev'
+SERVICE_ANYSTYLE_HOST = 'anystyle-ms.fly.dev'
+SERVICE_ANYSTYLE_PORT = ''
+SERVICE_ANYSTYLE_PROTOCOL = 'https'
+SERVICE_PAGEDJS_HOST = 'pagedjs-ms.fly.dev'
+SERVICE_PAGEDJS_PORT = ''
+SERVICE_PAGEDJS_PROTOCOL = 'https'
+SERVICE_XSWEET_HOST = 'xsweet-ms.fly.dev'
+SERVICE_XSWEET_PORT = ''
+SERVICE_XSWEET_PROTOCOL = 'https'
+USE_SANDBOXED_ORCID = 'true'
+WS_YJS_SERVER_PORT = 8081
+
+[http_service]
+internal_port = 8080
+force_https = true
+auto_stop_machines = 'stop'
+auto_start_machines = true
+min_machines_running = 0
+processes = ['app']
+
+[[services]]
+protocol = 'tcp'
+internal_port = 8080
+
+[[services.ports]]
+port = 80
+handlers = ['http']
+
+[[services.ports]]
+port = 443
+handlers = ['tls', 'http']
+
+[[services]]
+protocol = 'tcp'
+internal_port = 8081
+
+[[services.ports]]
+port = 8081
+handlers = ['tls', 'http']
+
+[[vm]]
+memory = '1gb'
+cpu_kind = 'shared'
+cpus = 1

.fly/kotahi-server-test.toml

+app = "kotahi-server-test"
+primary_region = "lhr"
+
+# [build]
+# image = "cokoapps/kotahi-server:test"
+
+[http_service]
+auto_start_machines = true
+auto_stop_machines = true
+force_https = true
+internal_port = 8_080
+min_machines_running = 0
+processes = ["app"]
+
+# HTTP service configuration (port 8080)
+[[services]]
+internal_port = 8080
+protocol = "tcp"
+
+[[services.ports]]
+handlers = ["http"]
+port = 80           # Map internal HTTP service (8080) to external port 80
+
+[[services.ports]]
+handlers = ["tls", "http"]
+port = 443                 # Map internal HTTP service (8080) to external HTTPS (443)
+
+# WebSocket service configuration (port 8081)
+[[services]]
+internal_port = 8081
+protocol = "tcp"     # Use TCP for WebSocket connections
+
+[[services.ports]]
+handlers = ["tls", "http"] # WebSocket handler
+port = 8081                # External port for WebSocket (same as internal port)
+
+[[vm]]
+cpu_kind = "shared"
+cpus = 1
+memory = "1gb"
+
+[env]
+NODE_ENV = "production"
+CLIENT_URL = "https://kotahi-client-test.fly.dev"
+SERVER_URL = "https://kotahi-server-test.fly.dev"
+WS_YJS_SERVER_PORT = "8081"
+INSTANCE_GROUPS = "journal:journal,prc:prc,single_form:preprint1"
+MANUSCRIPTS_TABLE_COLUMNS = 'shortId, submission.$title, created, updated, status, author'
+USE_SANDBOXED_ORCID = "true"
+SERVICE_PAGEDJS_PROTOCOL = "https"
+SERVICE_PAGEDJS_HOST = "pagedjs-ms.fly.dev"
+SERVICE_PAGEDJS_PORT = ""
+SERVICE_XSWEET_PROTOCOL = "https"
+SERVICE_XSWEET_HOST = "xsweet-ms.fly.dev"
+SERVICE_XSWEET_PORT = ""
+SERVICE_ANYSTYLE_PROTOCOL = "https"
+SERVICE_ANYSTYLE_HOST = "anystyle-ms.fly.dev"
+SERVICE_ANYSTYLE_PORT = ""
+FLAX_EXPRESS_PORT = 8081
+FLAX_EXPRESS_HOST = "flax.fly.dev"
+FLAX_EXPRESS_PROTOCOL = "https"
+FLAX_CLIENT_API_URL = "https://kotahi-server-test.fly.dev"
+FLAX_SITE_URL = "http://flax.fly.dev"
+
+# FLAX_CLIENT_ID=''
+# FLAX_CLIENT_SECRET=''
+
+# REVIEW_SHARED = true
+# REVIEW_HIDE = true
+
+# PUBLISHING_WEBHOOK_URL=https://someserver/webhook-address # see https://gitlab.coko.foundation/kotahi/kotahi/-/blob/main/    FAQ.md#how-do-i-publish-from-kotahi
+# PUBLISHING_WEBHOOK_SECRET=some-secret-string
+# PUBLISHING_WEBHOOK_URL=${PUBLISHING_WEBHOOK_URL:-}
+# PUBLISHING_WEBHOOK_TOKEN=${PUBLISHING_WEBHOOK_TOKEN:-}
+# PUBLISHING_WEBHOOK_REF=${PUBLISHING_WEBHOOK_REF:-}
+
+# TEAM_TIMEZONE=Etc/UTC
+# AUTO_IMPORT_HOUR_UTC=21
+# ARCHIVE_PERIOD_DAYS=60
+# ALLOW_MANUAL_IMPORT=true
+# SEMANTIC_SCHOLAR_IMPORTS_RECENCY_PERIOD_DAYS=42
+
+# NOTIFICATION_EMAIL_AUTOMATED=false
+# NOTIFICATION_EMAIL_CC_ENABLED=false
+
+# USE_APERTURE_EMAIL=${USE_APERTURE_EMAIL:-false}
+# USE_COLAB_EMAIL=false
+# USE_COLAB_BIOPHYSICS_IMPORT=${USE_COLAB_BIOPHYSICS_IMPORT:-false}
+
+# KOTAHI_API_TOKENS=${KOTAHI_API_TOKENS:-}
+# JOURNAL_NAME=${JOURNAL_NAME:-}
+# JOURNAL_ABBREVIATED_NAME=${JOURNAL_ABBREVIATED_NAME:-}
+# JOURNAL_HOMEPAGE=${JOURNAL_HOMEPAGE:-}
+
+# GOOGLE_SPREADSHEET_CLIENT_EMAIL=${GOOGLE_SPREADSHEET_CLIENT_EMAIL:-}
+# GOOGLE_SPREADSHEET_PRIVATE_KEY=${GOOGLE_SPREADSHEET_PRIVATE_KEY:-}
+# GOOGLE_SPREADSHEET_ID=${GOOGLE_SPREADSHEET_ID:-}
+
+# HYPOTHESIS_API_KEY=${HYPOTHESIS_API_KEY:-}
+# HYPOTHESIS_GROUP=${HYPOTHESIS_GROUP:-}
+# HYPOTHESIS_REVERSE_FIELD_ORDER=${HYPOTHESIS_REVERSE_FIELD_ORDER:-}
+# HYPOTHESIS_ALLOW_TAGGING=${HYPOTHESIS_ALLOW_TAGGING:-}
+
+# CROSSREF_LOGIN=${CROSSREF_LOGIN:-}
+# CROSSREF_PASSWORD=${CROSSREF_PASSWORD:-}
+# CROSSREF_REGISTRANT=${CROSSREF_REGISTRANT:-}
+# CROSSREF_DEPOSITOR_NAME=${CROSSREF_DEPOSITOR_NAME:-}
+# CROSSREF_DEPOSITOR_EMAIL=${CROSSREF_DEPOSITOR_EMAIL:-}
+# CROSSREF_PUBLICATION_TYPE=${CROSSREF_PUBLICATION_TYPE:-article}
+# CROSSREF_USE_SANDBOX=${CROSSREF_USE_SANDBOX:-true}
+
+# DOI_PREFIX=${DOI_PREFIX:-}
+
+# PUBLISHED_ARTICLE_LOCATION_PREFIX=${PUBLISHED_ARTICLE_LOCATION_PREFIX:-}
+# PUBLICATION_LICENSE_URL=${PUBLICATION_LICENSE_URL:-}
+
+# GMAIL_NOTIFICATION_EMAIL_AUTH=${GMAIL_NOTIFICATION_EMAIL_AUTH}
+# GMAIL_NOTIFICATION_EMAIL_SENDER_NAME=${GMAIL_NOTIFICATION_EMAIL_SENDER_NAME}
+# GMAIL_NOTIFICATION_PASSWORD=${GMAIL_NOTIFICATION_PASSWORD}
+
+# DISABLE_EVENT_NOTIFICATIONS=${DISABLE_EVENT_NOTIFICATIONS:-}

.gitattributes

+* text eol=lf
+*.ttf binary
+*.jpg binary
+*.png binary
+*.pdf binary
+*.js.mp4 binary

.gitignore

@@ -15,8 +15,32 @@ uploads/
 config/local*.*
 .vscode/launch.json
 .DS_Store
-config/*.env
+packages/server/config/*.env
+packages/server/config/local*
+packages/server/*/config/local*
+packages/server/config/plugins/*
+!packages/server/config/plugins
+!packages/server/config/plugins/example_plugins_manifest.json
+
 minio/data/*
-minio\data\*
-db-data\*
+.minio.sys
 db-data/*
+/.idea
+packages/server/config/journal/docmaps_scheme.json
+.vscode
+.nvmrc
+
+cypress/videos
+cypress/screenshots
+
+# macOS
+.dccache
+
+packages/server/config/translation
+!packages/server/config/translationOverrides.example.js
+
+packages/devdocs/build
+packages/devdocs/.docusaurus
+packages/devdocs/.cache-loader
+
+packages/server/scripts/local

.gitlab-ci.aperture.yml

-variables:
-  IMAGE_ORG: simplej
-  IMAGE_NAME: simplej
-
-stages:
-  - build
-  - test
-  # - review
-  # - staging
-  # - production
-  # - demo
-
-build:
-  image: docker:20.10.5
-  variables:
-    DOCKER_BUILDKIT: 1
-  services:
-    - docker:20.10.5-dind
-  stage: build
-  before_script:
-    - cp app/brand-instances-configs/aperture.json app/brandConfig.json
-  script:
-    - |
-      if [ -z "$DOCKERHUB_USERNAME" ] || [ -z "$DOCKERHUB_PASSWORD" ]; then echo "Not pushing" && exit 0; fi
-      docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD
-      docker build --build-arg instance_name=aperture --file ./Dockerfile-ci --cache-from $IMAGE_ORG/$IMAGE_NAME:latest --tag $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA --tag $IMAGE_ORG/$IMAGE_NAME:latest .   
-      docker push $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-      docker push $IMAGE_ORG/$IMAGE_NAME:latest
-
-lint:
-  allow_failure: true
-  image: $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - cd ${HOME}
-    - npm run lint
-
-test-chrome:
-  image: $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-    # setup data for postgres image
-    POSTGRES_USER: kotahidev
-    POSTGRES_PASSWORD: kotahidev
-    # used by psql
-    PGUSER: kotahidev
-    PGPASSWORD: kotahidev
-    # this is used to ignore self signed certs
-    #START_SERVER_AND_TEST_INSECURE: 1
-  services:
-    - postgres
-  script:
-    - cd ${HOME}
-    - apt-get -y install postgresql-client
-    # this is needed for pgboss initial setup
-    - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-    # use the example env for tests
-    - cp .env.example .env
-    # specify host here else it confuses the linked postgres image
-    - POSTGRES_HOST=postgres yarn test:all:chrome
-
-test-firefox:
-  allow_failure: true # at this point Cypress' support for Firefox is not stable
-  image: $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-    # setup data for postgres image
-    POSTGRES_USER: kotahidev
-    POSTGRES_PASSWORD: kotahidev
-    # used by psql
-    PGUSER: kotahidev
-    PGPASSWORD: kotahidev
-    #START_SERVER_AND_TEST_INSECURE: 1
-  services:
-    - postgres
-  script:
-    - cd ${HOME}
-    - apt-get -y install postgresql-client
-    # this is needed for pgboss initial setup
-    - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-    # use the example env for tests
-    - cp .env.example .env
-    # specify host here else it confuses the linked postgres image
-    - POSTGRES_HOST=postgres yarn test:all:firefox

.gitlab-ci.elife.yml

-variables:
-  IMAGE_ORG: kotahi
-  IMAGE_NAME: kotahi-elife
-
-stages:
-  - build
-  - deploy
-  - test
-
-build:
-  image: docker:20.10.5
-  variables:
-    DOCKER_BUILDKIT: 1
-  services:
-    - docker:20.10.5-dind
-  stage: build
-  before_script:
-    - cp app/brand-instances-configs/elife.json app/brandConfig.json
-  script:
-    - |
-      if [ -z "$DOCKERHUB_USERNAME_ELIFE" ] || [ -z "$DOCKERHUB_PASSWORD_ELIFE" ]; then echo "Not pushing" && exit 0; fi
-      docker login -u $DOCKERHUB_USERNAME_ELIFE -p $DOCKERHUB_PASSWORD_ELIFE
-      docker pull $IMAGE_ORG/$IMAGE_NAME:latest || true
-      docker build \
-      --build-arg instance_name=elife \
-      --build-arg public_client_host=elife.kotahi.cloud \
-      --build-arg public_client_port=443 \
-      --build-arg public_client_protocol=https \
-      --file ./Dockerfile-production \
-      --cache-from $CI_REGISTRY_IMAGE:latest \
-      --tag $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA \
-      --tag $IMAGE_ORG/$IMAGE_NAME:latest .
-      docker build --build-arg instance_name=elife --file ./Dockerfile-ci --cache-from $IMAGE_ORG/$IMAGE_NAME-dev:latest --tag $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA --tag $IMAGE_ORG/$IMAGE_NAME-dev:latest .
-      docker push $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-      docker push $IMAGE_ORG/$IMAGE_NAME:latest
-      docker push $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-      docker push $IMAGE_ORG/$IMAGE_NAME-dev:latest
-
-deploy:
-  stage: deploy
-  image: docker:19.03.13
-  before_script:
-    - export SSH_KEY=$SSH_KEY_ELIFE
-    - export DOCKERHUB_USERNAME=$DOCKERHUB_USERNAME_ELIFE
-    - export DOCKERHUB_PASSWORD=$DOCKERHUB_PASSWORD_ELIFE
-    - export IMAGE_ORG=$IMAGE_ORG
-    - export IMAGE_NAME=$IMAGE_NAME
-    - eval $(ssh-agent -s)
-    - echo "$SSH_KEY" | tr -d '\r' | ssh-add -
-    - mkdir -p ~/.ssh
-    - chmod 700 ~/.ssh
-    - ssh-keyscan $ELIFE_SERVER_IP >> ~/.ssh/known_hosts
-    - chmod 644 ~/.ssh/known_hosts
-  script:
-    - |
-      ssh ubuntu@$ELIFE_SERVER_IP "sudo docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD &&
-      sudo docker pull $IMAGE_ORG/$IMAGE_NAME:latest &&
-      sudo supervisorctl stop kotahi &&
-      cd /home/ubuntu/kotahi &&
-      sudo docker-compose down &&
-      sudo supervisorctl start kotahi"
-
-# lint:
-#   allow_failure: true
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#   script:
-#     - cd ${HOME}
-#     - npm run lint
-
-## TODO: implement this template without error "(node:965) UnhandledPromiseRejectionWarning: TypeError [ERR_INVALID_ARG_TYPE]: The "path" argument must be of type string. Received undefined"
-## Issue: https://gitlab.coko.foundation/kotahi/kotahi/-/issues/183
-# .test_template: &run_test_template
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-
-## TODO: implement this template without error "psql: could not translate host name "postgres" to address: Name or service not known"
-## Issue: https://gitlab.coko.foundation/kotahi/kotahi/-/issues/183
-# .script_template: &run_script_template
-#    - cd ${HOME}
-#    - apt-get -y install postgresql-client
-#    # use the example env for tests
-#    - cp .env.example .env
-#    # this is needed for pgboss initial setup
-#    - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#    # specify host here else it confuses the linked postgres image
-#    - POSTGRES_HOST=postgres yarn test:all:$TEST_ITEM
-    
-# test-chrome:
-#   <<: *run_test_template
-#   variables:
-#     TEST_ITEM: "chrome:elife" 
-#   script:
-#     - *run_script_template
-
-## TODO: when insert this template get an error: "(node:965) UnhandledPromiseRejectionWarning: TypeError [ERR_INVALID_ARG_TYPE]: The "path" argument must be of type string"
-# .vars_template: &vars_insert
-#   variables:
-#     GIT_STRATEGY: none
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-
-test-chrome:
-  image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-    # setup data for postgres image
-    POSTGRES_USER: kotahidev
-    POSTGRES_PASSWORD: kotahidev
-    # used by psql
-    PGUSER: kotahidev
-    PGPASSWORD: kotahidev
-    # this is used to ignore self signed certs
-    #START_SERVER_AND_TEST_INSECURE: 1
-  services:
-    - postgres
-  script:
-    - cd ${HOME}
-    - apt-get -y install postgresql-client
-    # this is needed for pgboss initial setup
-    - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-    # use the example env for tests
-    - cp .env.example .env
-    # specify host here else it confuses the linked postgres image
-    - echo $INSTANCE_NAME
-    - POSTGRES_HOST=postgres yarn test:all:chrome:elife
-
-# test-chrome-samsung:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:elife:samsung
-
-# test-chrome-samsung-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:elife:samsung:tablet
-
-# test-chrome-iPhone:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:elife:iPhone
-
-# test-chrome-iPhone-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:elife:iPhone:tablet
-
-# test-chrome-hd-laptop:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:elife:hd:laptop   
-
-# test-firefox:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife
-
-# test-firefox-samsung:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife:samsung
-
-# test-firefox-samsung-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife:samsung:tablet
-
-# test-firefox-iPhone:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife:iPhone
-
-# test-firefox-iPhone-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife:iPhone:tablet
-
-# test-firefox-hd-laptop:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:elife:hd:laptop
-

.gitlab-ci.ncrc.yml

-variables:
-  IMAGE_ORG: kotahi
-  IMAGE_NAME: kotahi-ncrc
-
-stages:
-  - build
-  - deploy
-  - test
-
-build:
-  image: docker:20.10.5
-  variables:
-    DOCKER_BUILDKIT: 1
-  services:
-    - docker:20.10.5-dind
-  stage: build
-  before_script:
-    - cp app/brand-instances-configs/ncrc.json app/brandConfig.json
-  script:
-    - |
-      if [ -z "$DOCKERHUB_USERNAME_ELIFE" ] || [ -z "$DOCKERHUB_PASSWORD_ELIFE" ]; then echo "Not pushing" && exit 0; fi
-      docker login -u $DOCKERHUB_USERNAME_ELIFE -p $DOCKERHUB_PASSWORD_ELIFE
-      docker pull $IMAGE_ORG/$IMAGE_NAME:latest || true
-      docker build \
-      --build-arg instance_name=ncrc \
-      --build-arg public_client_host=ncrc.kotahi.cloud \
-      --build-arg public_client_port=443 \
-      --build-arg public_client_protocol=https \
-      --file ./Dockerfile-production \
-      --cache-from $CI_REGISTRY_IMAGE:latest \
-      --tag $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA \
-      --tag $IMAGE_ORG/$IMAGE_NAME:latest .
-      docker build --build-arg instance_name=ncrc --file ./Dockerfile-ci --cache-from $IMAGE_ORG/$IMAGE_NAME-dev:latest --tag $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA --tag $IMAGE_ORG/$IMAGE_NAME-dev:latest .
-      docker push $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
-      docker push $IMAGE_ORG/$IMAGE_NAME:latest
-      docker push $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-      docker push $IMAGE_ORG/$IMAGE_NAME-dev:latest
-
-deploy:
-  stage: deploy
-  image: docker:19.03.13
-  before_script:
-    - export SSH_KEY=$SSH_KEY_NCRC
-    - export DOCKERHUB_USERNAME=$DOCKERHUB_USERNAME_ELIFE
-    - export DOCKERHUB_PASSWORD=$DOCKERHUB_PASSWORD_ELIFE
-    - export IMAGE_ORG=$IMAGE_ORG
-    - export IMAGE_NAME=$IMAGE_NAME
-    - eval $(ssh-agent -s)
-    - echo "$SSH_KEY" | tr -d '\r' | ssh-add -
-    - mkdir -p ~/.ssh
-    - chmod 700 ~/.ssh
-    - ssh-keyscan $NCRC_SERVER_IP >> ~/.ssh/known_hosts
-    - chmod 644 ~/.ssh/known_hosts
-  script:
-    - |
-      ssh ubuntu@$NCRC_SERVER_IP "sudo docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD &&
-      sudo docker pull $IMAGE_ORG/$IMAGE_NAME:latest &&
-      sudo supervisorctl stop kotahi &&
-      cd /home/ubuntu/kotahi &&
-      sudo docker-compose down &&
-      sudo supervisorctl start kotahi"
-
-# lint:
-#   allow_failure: true
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#   script:
-#     - cd ${HOME}
-#     - npm run lint
-
-test-chrome:
-  image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-  stage: test
-  variables:
-    GIT_STRATEGY: none
-    # setup data for postgres image
-    POSTGRES_USER: kotahidev
-    POSTGRES_PASSWORD: kotahidev
-    # used by psql
-    PGUSER: kotahidev
-    PGPASSWORD: kotahidev
-    # this is used to ignore self signed certs
-    #START_SERVER_AND_TEST_INSECURE: 1
-  services:
-    - postgres
-  script:
-    - cd ${HOME}
-    - apt-get update
-    - apt-get -y install postgresql-client
-    # this is needed for pgboss initial setup
-    - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-    # use the example env for tests
-    - cp .env.example .env
-    # specify host here else it confuses the linked postgres image
-    - echo $INSTANCE_NAME
-    - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc
-
-# test-chrome-samsung:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc:samsung
-
-# test-chrome-samsung-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc:samsung:tablet
-
-# test-chrome-iPhone:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc:iPhone
-
-# test-chrome-iPhone-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc:iPhone:tablet
-
-# test-chrome-hd-laptop:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:chrome:ncrc:hd:laptop   
-
-# test-firefox:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc
-
-# test-firefox-samsung:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc:samsung
-
-# test-firefox-samsung-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc:samsung:tablet
-
-# test-firefox-iPhone:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc:iPhone
-
-# test-firefox-iPhone-tablet:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc:iPhone:tablet
-
-# test-firefox-hd-laptop:
-#   image: $IMAGE_ORG/$IMAGE_NAME-dev:$CI_COMMIT_SHA
-#   stage: test
-#   variables:
-#     GIT_STRATEGY: none
-#     # setup data for postgres image
-#     POSTGRES_USER: kotahidev
-#     POSTGRES_PASSWORD: kotahidev
-#     # used by psql
-#     PGUSER: kotahidev
-#     PGPASSWORD: kotahidev
-#     # this is used to ignore self signed certs
-#     #START_SERVER_AND_TEST_INSECURE: 1
-#   services:
-#     - postgres
-#   script:
-#     - cd ${HOME}
-#     - apt-get -y install postgresql-client
-#     - psql -h postgres -U kotahidev -d kotahidev -c "create extension pgcrypto;"
-#     - cp .env.example .env
-#     - POSTGRES_HOST=postgres yarn test:all:firefox:ncrc:hd:laptop
-

.gitlab-ci.yml

+# include:
+#   - project: 'cokoapps/ci'
+#     ref: main
+#     file: 'ci-templates.yml'
+
+variables:
+  IMAGE_NAME_DEVELOPMENT: kotahi/kotahi/root-development
+  CLIENT_PREPRODUCTION: $CI_REGISTRY/kotahi/kotahi/client-preproduction:$CI_COMMIT_REF_NAME
+  SERVER_PREPRODUCTION: $CI_REGISTRY/kotahi/kotahi/server-preproduction:$CI_COMMIT_REF_NAME
+  CLIENT_PRODUCTION: cokoapps/kotahi-client
+  SERVER_PRODUCTION: cokoapps/kotahi-server
+  DEV_DOCS: $CI_REGISTRY/kotahi/kotahi/devdocs:$CI_COMMIT_REF_NAME
+  DEPLOY_COMPOSE_FILE: docker-compose.ci.yml
+
 stages:
-  - run-pipeline
-
-elife-pipeline:
-  only:
-    refs:
-      - main
-  stage: run-pipeline
-  trigger:
-    include:
-      - local: .gitlab-ci.elife.yml
-    strategy: depend
-
-ncrc-pipeline:
-  only:
-    refs:
-      - main
-  stage: run-pipeline
-  trigger:
-    include:
-      - local: .gitlab-ci.ncrc.yml
-    strategy: depend
-
-aperture-pipeline:
-  stage: run-pipeline
-  trigger:
-    include:
-      - local: .gitlab-ci.aperture.yml
-    strategy: depend
+  - Build development
+  - Lint & Unit test
+  - Build production
+  - Deploy test
+  - End to end testing
+  - Tear down test
+  - Deploy staging
+  - Release
+  - Publish
+  - Deploy production
+
+build development:
+  stage: Build development
+  interruptible: true
+  image: docker:27-dind
+  services:
+    - docker:27-dind
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login "$CI_REGISTRY" -u "$CI_REGISTRY_USER" --password-stdin
+  script:
+    - docker build
+      --tag $CI_REGISTRY/$IMAGE_NAME_DEVELOPMENT:$CI_COMMIT_REF_NAME.$CI_COMMIT_SHA
+      -f Dockerfile .
+    - docker push $CI_REGISTRY/$IMAGE_NAME_DEVELOPMENT:$CI_COMMIT_REF_NAME.$CI_COMMIT_SHA
+
+lint:
+  stage: Lint & Unit test
+  interruptible: true
+  image: $CI_REGISTRY/$IMAGE_NAME_DEVELOPMENT:$CI_COMMIT_REF_NAME.$CI_COMMIT_SHA
+  script:
+    - cd /home/node/app
+    - yarn coko-lint run
+
+build preproduction client:
+  stage: Build production
+  interruptible: true
+  image: docker:27
+  services:
+    - docker:27-dind
+  only:
+    - staging
+    - main
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login "$CI_REGISTRY" -u "$CI_REGISTRY_USER" --password-stdin
+  script:
+    - cd packages/client
+    - docker build
+      --tag $CLIENT_PREPRODUCTION.$CI_COMMIT_SHA
+      --tag $CLIENT_PREPRODUCTION.latest
+      -f Dockerfile-production .
+    - docker push $CLIENT_PREPRODUCTION.$CI_COMMIT_SHA
+    - docker push $CLIENT_PREPRODUCTION.latest
+
+build preproduction server:
+  stage: Build production
+  interruptible: true
+  image: docker:27
+  services:
+    - docker:27-dind
+  only:
+    - staging
+    - main
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login "$CI_REGISTRY" -u "$CI_REGISTRY_USER" --password-stdin
+  script:
+    - cd packages/server
+    - docker build
+      --tag $SERVER_PREPRODUCTION.$CI_COMMIT_SHA
+      --tag $SERVER_PREPRODUCTION.latest
+      -f Dockerfile-production .
+    - docker push $SERVER_PREPRODUCTION.$CI_COMMIT_SHA
+    - docker push $SERVER_PREPRODUCTION.latest
+
+deploy fly staging:
+  stage: Deploy staging
+  interruptible: false
+  image: cokoapps/fly
+  only:
+    - staging
+  script:
+    - FLY_API_TOKEN=$FLY_SERVER_TEST_TOKEN flyctl deploy --config .fly/kotahi-server-test.toml --image $SERVER_PREPRODUCTION.$CI_COMMIT_SHA
+    - FLY_API_TOKEN=$FLY_CLIENT_TEST_TOKEN flyctl deploy --config .fly/kotahi-client-test.toml --image $CLIENT_PREPRODUCTION.$CI_COMMIT_SHA
+
+deploy fly main:
+  stage: Deploy staging
+  interruptible: false
+  image: cokoapps/fly
+  only:
+    - main
+  script:
+    - FLY_API_TOKEN=$FLY_SERVER_MAIN_TOKEN flyctl deploy --config .fly/kotahi-server-main.toml --image $SERVER_PREPRODUCTION.$CI_COMMIT_SHA
+    - FLY_API_TOKEN=$FLY_CLIENT_MAIN_TOKEN flyctl deploy --config .fly/kotahi-client-main.toml --image $CLIENT_PREPRODUCTION.$CI_COMMIT_SHA
+
+release:
+  stage: Release
+  interruptible: false
+  image: node:18
+  when: manual
+  only:
+    - main
+  before_script:
+    - git remote set-url --push origin "https://gitlab-ci-token:$CI_RELEASE_TOKEN@gitlab.coko.foundation/kotahi/kotahi.git"
+    - git config user.email "$CI_RELEASE_BOT_EMAIL"
+    - git config user.name "kotahi release bot"
+  script:
+    - node scripts/updatePackageJson.js
+    - VERSION=$(node -e "const packageJson = require('./package.json'); console.log(packageJson.version);")
+    - echo VERSION set to $VERSION
+    - git add -A
+    - git commit -m "release version $VERSION [skip ci]"
+    - git show-ref --tags "$VERSION" > /dev/null 2>&1 && git tag -d "$VERSION" || echo "Tag '$VERSION' does not exist."
+    - git tag $VERSION
+    - git push origin HEAD:$CI_COMMIT_REF_NAME --verbose
+    - git push origin $VERSION
+    - echo RELEASE_VERSION=$VERSION >> version.env
+  artifacts:
+    reports:
+      dotenv: version.env
+
+production client:
+  stage: Publish
+  interruptible: false
+  image: docker:27
+  services:
+    - docker:27-dind
+  needs:
+    - release
+  only:
+    - main
+  before_script:
+    - '[ -z "$RELEASE_VERSION" ] && exit 1'
+    - docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD
+  script:
+    - git fetch origin $CI_COMMIT_REF_NAME
+    - git reset --hard origin/$CI_COMMIT_REF_NAME
+    - cd packages/client
+    - docker build --tag $CLIENT_PRODUCTION:$RELEASE_VERSION -f Dockerfile-production .
+    - docker push $CLIENT_PRODUCTION:$RELEASE_VERSION
+
+production server:
+  stage: Publish
+  interruptible: false
+  image: docker:27
+  services:
+    - docker:27-dind
+  needs:
+    - release
+  only:
+    - main
+  before_script:
+    - '[ -z "$RELEASE_VERSION" ] && exit 1'
+    - docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD
+  script:
+    - git fetch origin $CI_COMMIT_REF_NAME
+    - git reset --hard origin/$CI_COMMIT_REF_NAME
+    - cd packages/server
+    - docker build --tag $SERVER_PRODUCTION:$RELEASE_VERSION -f Dockerfile-production .
+    - docker push $SERVER_PRODUCTION:$RELEASE_VERSION
+
+build docs:
+  stage: Publish
+  interruptible: false
+  image: docker:27
+  services:
+    - docker:27-dind
+  needs:
+    - release
+  only:
+    - main
+  before_script:
+    - echo "$CI_REGISTRY_PASSWORD" | docker login "$CI_REGISTRY" -u "$CI_REGISTRY_USER" --password-stdin
+  script:
+    - cd packages/devdocs
+    - docker build -f Dockerfile-production -t $DEV_DOCS.$CI_COMMIT_SHA .
+    - docker push $DEV_DOCS.$CI_COMMIT_SHA
+
+deploy docs:
+  stage: Deploy production
+  interruptible: false
+  image: cokoapps/fly
+  needs:
+    - build docs
+  only:
+    - main
+  script:
+    - FLY_API_TOKEN=$FLY_DEV_DOCS_TOKEN flyctl deploy --config .fly/kotahi-dev-docs.toml --image $DEV_DOCS.$CI_COMMIT_SHA

.gitlab/issue_templates/bug-report.md

+<!-- Required. Provide a general summary of the issue in the title above -->
+
+## Expected behaviour
+
+<!-- Required. Tell us what should happen -->
+
+## Current behaviour
+
+<!-- Required. Tell us what happens instead of the expected behaviour -->
+
+## Steps to reproduce
+
+<!-- Required. Provide a link to a live example or screenshots, and the steps to reproduce this bug.]-->
+
+1.
+2.
+3.
+4.
+
+## Environment
+
+<!-- Required. Provide relevant information such as browser name and version, PC or Mac use, internet speed, etc.]-->
+
+## Possible solution
+
+<!-- If known, provide details on how to fix the bug.-->
+
+<!-- After creating this issue you can link other related or blocking issues with the Gitlab's Linked issues functionality. -->

.gitlab/issue_templates/dev_issue.md

+---
+name: Developer issue
+about: Issue with description, learning objectives, todo, and useful links
+title: ''
+labels: ''
+assignees: ''
+---
+
+## Description
+
+## Learning objectives
+
+- Objective
+
+## Todo
+
+These points are a rough guideline. **Please** feel free to discuss with others on the team about the best way to design this component!
+
+- Todo
+
+## Useful links
+
+- Useful link
+
+<!--
+Template sourced from https://github.com/hack4impact-uiuc/falling-fruit
+Shoutout to the wonderful FF team!
+-->

.husky/commit-msg

+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+yarn commitlint --edit