Initial commit

.babelrc

+{
+  "presets": ["env", "react", "stage-2"]
+}
\ No newline at end of file

.dockerignore

+node_modules

.envrc

+#https://github.com/direnv/direnv/wiki/Node#load-nodejs-version-from-a-node-version-or-nvmrc-file
+set -e
+use node 8

.eslintignore

+_build
+node_modules

.eslintrc

+{
+  "env": {
+    "es6": true,
+    "browser": true
+  },
+  "extends": [
+    "pubsweet"
+  ],
+  "parser": "babel-eslint",
+  "rules": {
+    "camelcase": 0,
+    "consistent-return": 0,
+    "global-require": 0,
+    "jsx-a11y/anchor-is-valid": 0,
+    "jsx-a11y/click-events-have-key-events": 0,
+    "jsx-a11y/label-has-for": 0,
+    "jsx-a11y/no-static-element-interactions": 0,
+    "import/extensions": 0,
+    "import/no-dynamic-require": 0,
+    "import/no-extraneous-dependencies": 0,
+    "import/no-named-as-default": 0,
+    "import/no-named-as-default-member": 0,
+    "import/prefer-default-export": 0,
+    "no-console": ["error", { "allow": ["warn", "error"] }],
+    "no-param-reassign": 0,
+    "no-shadow": 0,
+    "no-underscore-dangle": 0,
+    "react/no-did-mount-set-state": 0,
+    "react/prop-types": 0,
+    "sort-keys": 0
+  }
+}

.gitignore

+*.log
+.bash_history
+.env
+.env.*
+.cache
+dist/
+node_modules
+coverage/
+api/db/*
+logs/*
+log.txt
+config.json
+_build/
+uploads/
+config/local*.*

.gitlab-ci.yml

+variables:
+  IMAGE_ORG: xpub
+  IMAGE_NAME: xpub
+  BASE_DOMAIN: gateway.xpub.semioticsquares.com
+  CONFIGURATION_REPOSITORY: https://gitlab.coko.foundation/yld/xpub-deployment-config-postgres.git 
+
+stages:
+  - build
+  - test
+  - review
+  - staging
+  - production
+  - demo
+
+build:
+  image: docker:latest
+  stage: build
+  script:
+    - docker version
+    - docker build -t $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA .
+    - if [ -z "$DOCKERHUB_USERNAME" ] || [ -z "$DOCKERHUB_PASSWORD" ]; then echo "Not pushing" && exit 0; fi
+    - docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD
+    - echo "Ignore warning! Cannot perform an interactive login from a non TTY device"
+    - docker push $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
+
+lint:
+  image: $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
+  stage: test
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd ${HOME}
+    - npm run lint
+
+# disable this job to make it clear we're not running any tests
+.test:
+  image: $IMAGE_ORG/$IMAGE_NAME:$CI_COMMIT_SHA
+  stage: test
+  variables:
+    GIT_STRATEGY: none
+    # setup data for postgres image
+    POSTGRES_USER: test
+    POSTGRES_PASSWORD: pw
+    # connection details for tests
+    PGUSER: test
+    PGPASSWORD: pw
+    NODE_ENV: test
+  services:
+    - postgres
+  script:
+    - cd ${HOME}
+    # specify host here else it confuses the linked postgres image
+    - PGHOST=postgres npm run test
+
+push:latest:
+  image: docker:latest
+  stage: staging
+  script:
+    - if [ -z "$DOCKERHUB_USERNAME" ] || [ -z "$DOCKERHUB_PASSWORD" ]; then echo "Not pushing" && exit 0; fi
+    - docker login -u $DOCKERHUB_USERNAME -p $DOCKERHUB_PASSWORD
+    - echo "Ignore warning! Cannot perform an interactive login from a non TTY device"
+    - docker build -t $IMAGE_ORG/$IMAGE_NAME:latest --label COMMIT_SHA=$CI_COMMIT_SHA .
+    - docker push $IMAGE_ORG/$IMAGE_NAME:latest
+  only:
+  - master
+
+review:xpub-collabra:
+  image: pubsweet/deployer:latest
+  stage: review
+  variables:
+    PACKAGE_NAME: xpub-collabra
+    FORCE_FRESH_DB: "yes"
+    REQUIRES_PROVISIONING: "yes"
+  environment:
+    name: $PACKAGE_NAME/review/$CI_COMMIT_REF_NAME
+    # !! kube-lego will fail if domain > 64 chars
+    url: "http://${CI_ENVIRONMENT_SLUG}.${BASE_DOMAIN}"
+    on_stop: stop_review:xpub-collabra
+  except:
+  - master
+  script:
+    - source deploy.sh
+    - create_deployment
+
+stop_review:xpub-collabra:
+  image: pubsweet/deployer:latest
+  stage: review
+  variables:
+    PACKAGE_NAME: xpub-collabra
+    REQUIRES_PROVISIONING: "yes"
+    GIT_STRATEGY: none
+  environment:
+    name: $PACKAGE_NAME/review/$CI_COMMIT_REF_NAME
+    action: stop
+  when: manual
+  except:
+  - master
+  script:
+    - source deploy.sh
+    - delete_deployment
+    - delete_objects_in_environment pvc
+
+staging:xpub-collabra:
+  image: pubsweet/deployer:latest
+  stage: staging
+  variables:
+    PACKAGE_NAME: xpub-collabra
+  environment:
+    name: $PACKAGE_NAME/staging
+    url: "https://${CI_ENVIRONMENT_SLUG}.${BASE_DOMAIN}"
+  only:
+  - master
+  script:
+    - source deploy.sh
+    - create_deployment
+
+production:xpub-collabra:
+  image: pubsweet/deployer:latest
+  stage: production
+  variables:
+    PACKAGE_NAME: xpub-collabra
+  environment:
+    name: $PACKAGE_NAME/production
+    url: "https://${CI_ENVIRONMENT_SLUG}.${BASE_DOMAIN}"
+  when: manual
+  only:
+  - master
+  script:
+    - source deploy.sh
+    - create_deployment
+
+demo:xpub-collabra:
+  image: pubsweet/deployer:latest
+  stage: demo
+  variables:
+    PACKAGE_NAME: xpub-collabra
+  environment:
+    name: $PACKAGE_NAME/demo
+    url: "https://${CI_ENVIRONMENT_SLUG}.${BASE_DOMAIN}"
+  when: manual
+  script:
+    - source deploy.sh
+    - create_deployment

.prettierrc

+{
+  "semi": false,
+  "singleQuote": true,
+  "trailingComma": "all"
+}

.stylelintignore

+**/_build
+**/node_modules

.stylelintrc

+{
+  "extends": "stylelint-config-pubsweet"
+}

Dockerfile

+FROM xpub/xpub:base
+
+WORKDIR ${HOME}
+COPY package.json yarn.lock ./
+
+# We do a development install because react-styleguidist is a dev dependency
+RUN [ "yarn", "install", "--frozen-lockfile" ]
+
+# Remove cache and offline mirror
+RUN [ "yarn", "cache", "clean"]
+RUN [ "rm", "-rf", "/npm-packages-offline-cache"]
+
+COPY app.js .babelrc .eslintignore .eslintrc .prettierrc .stylelintignore .stylelintrc ./
+
+COPY static static
+COPY api api
+COPY webpack webpack
+COPY config config
+COPY app app
+
+ENV NODE_ENV "production"
+
+RUN [ "npx", "pubsweet", "build"]
+
+EXPOSE 3000
+
+CMD []

Dockerfile-development

+FROM xpub/xpub:base
+
+WORKDIR ${HOME}
+
+COPY package.json yarn.lock app.js .babelrc .eslintignore .eslintrc .prettierrc .stylelintignore .stylelintrc ./
+COPY static static
+COPY api api
+COPY webpack webpack
+COPY config config
+COPY app app
+
+EXPOSE 3000
+
+CMD []

LICENSE

+Copyright (c) 2017 Adam Hyde
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

+# xpub-elife
+
+## Quickstart
+
+```
+npm start # or docker-compose up
+```
+
+**Note**: yarn will be run automatically inside the container to install dependencies. If dependencies were already installed on the host, this may cause problems as the binaries are compiled for the wrong platform. If you encounter errors about "invalid ELF header", do `npm run clean` and then `npm start` again.
+
+See `pubsweet-cli` for detailed documentation on running the app
+
+## Installing
+
+In the root directory, run `yarn` to install all the dependencies.
+
+## Configuration
+
+To enable manuscript conversion via INK, add the following values to `config/local-development.json` (ask in [the xpub channel](https://mattermost.coko.foundation/coko/channels/xpub) if you need an account):
+
+```json
+{
+  "pubsweet-server": {
+    "secret": "__EDIT_THIS__"
+  },
+  "pubsweet-component-ink-backend": {
+    "inkEndpoint": "__EDIT_THIS__",
+    "email": "__EDIT_THIS__",
+    "password": "__EDIT_THIS__"
+  }
+}
+```
+
+## Running the app
+
+1. The first time you run the app, initialise the database with `yarn run setupdb` (press Enter when asked for a collection title, to skip that step).
+2. `yarn start`
+
+## CI
+
+CI requires a Kubernetes cluster, resources for which can be found in [`pubsweet/infra`](https://gitlab.coko.foundation/pubsweet/infra). In order to set up a Kubernetes cluster (using AWS) you need to follow the instructions there. Templates for deploying to this cluster with [`pubsweet/deployer`](https://gitlab.coko.foundation/pubsweet/deployer) are located in [`xpub/deployment-config`](https://gitlab.coko.foundation/xpub/deployment-config).
+
+## Community
+
+Join [the Mattermost channel](https://mattermost.coko.foundation/coko/channels/xpub) for discussion of xpub.

app.js

+const logger = require('@pubsweet/logger')
+const startServer = require('pubsweet-server')
+
+startServer().catch(err => {
+  logger.error('FATAL ERROR, SHUTTING DOWN:', err)
+  process.exit(1)
+})

app/app.js

+import React from 'react'
+import ReactDOM from 'react-dom'
+import { AppContainer } from 'react-hot-loader'
+import createHistory from 'history/createBrowserHistory'
+
+import { configureStore, Root } from 'pubsweet-client'
+
+import theme from '@pubsweet/default-theme'
+
+import Routes from './routes'
+
+const history = createHistory()
+const store = configureStore(history, {})
+
+const render = () => {
+  ReactDOM.render(
+    <AppContainer>
+      <Root history={history} routes={<Routes />} store={store} theme={theme} />
+    </AppContainer>,
+    document.getElementById('root'),
+  )
+}
+
+render()
+
+if (module.hot) {
+  module.hot.accept('./routes', () => {
+    render()
+  })
+}

app/index-production.html

+<!DOCTYPE html>
+<html>
+<head>
+    <meta charset=utf-8>
+    <title><%= htmlWebpackPlugin.options.title %></title>
+</head>
+<body>
+<div id="root"></div>
+</body>
+</html>

app/index.html

+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+</head>
+<body>
+  <div id="root"></div>
+  <script src="/assets/app.js"></script>
+</body>
+</html>

app/routes.js

+import React from 'react'
+
+const Routes = () => <div>TODO</div>
+
+export default Routes

config/authsome.js

+module.exports = (user, operation, project, version) =>
+  // console.log({ user, operation, project, version })
+  true // TODO