@manuscripts/manuscript-article-editor

manuscripts-article-editor

This repository contains the editor package of Manuscripts app to be used in a react application.

Dependencies

Manuscripts is highly modular: it is composed out of a series of NPM published modules following a few different themes.

Data model

• @manuscripts/manuscripts-json-schema (source code at gitlab.com/mpapp-public/manuscripts-json-schema): a JSON schema describing the application's data model used in this and other manuscripts.io based applications, plus browser, Node.js and Couchbase Sync Gateway executable validator functions.
• @manuscripts/manuscripts-json-schema-utils (source at gitlab.com/mpapp-public/manuscripts-json-schema-utils/): a set of utility functions for working with Manuscripts JSON schema formatted data.

Data synchronisation

• @manuscripts/manuscripts-sync (source at gitlab.com/mpapp-public/manuscripts-sync/): this repository contains a build script, a Dockerfile, and a sync function definition and associated tests for a Couchbase Sync Gateway instance configured to act as a realtime synchronisation backend, from the frontend application interacted with using RxDB / PouchDB. The Sync Gateway used is currently a mildly forked version tracking the stable versions of Sync Gateway.
• @manuscripts/sync-client (source at gitlab.com/mpapp-public/manuscripts-sync-client): client-side business logic for merging Manuscripts data model revisions: implementations of conflict detection and merging strategies relevant for different model types in the schema.

Editor components

• @manuscripts/manuscript-editor (source at gitlab.com/mpapp-public/manuscripts-manuscript-editor): the article body editor as a React component – this is where the great majority of this frontend application's logic is actually found from.
• @manuscripts/title-editor (source at gitlab.com/mpapp-public/manuscripts-title-editor: a React editor component for headings, titles and other title-like short stretches of text. In practice, the title editor component is mostly a ProseMirror schema.
• @manuscripts/comment-editor (source at gitlab.com/mpapp-public/manuscripts-comment-editor): a React editor component for editing and viewing manuscript comments. Like the title editor component, the abstract editor is mostly a wrapper for a ProseMirror schema.
• @manuscripts/abstract-editor (source at gitlab.com/mpapp-public/manuscripts-abstract-editor): a React editor component for editing and viewing abstracts. Like the title editor component, the abstract editor is mostly a wrapper for a ProseMirror schema.

ProseMirror specifics

• @manuscripts/prosemirror-recreate-steps (source at gitlab.com/mpapp-public/prosemirror-recreate-steps): an extension to the ProseMirror word processing library that the Manuscripts editor is based on, used to find and merge changes between two documents without access to the precise history of steps.
• @manuscripts/manuscript-transform (source at gitlab.com/mpapp-public/manuscripts-manuscript-transform: the definition of the ProseMirror schema used by @manuscripts/manuscript-editor, plus modules for converting to and from the Manuscripts data model and exporting to HTML or JATS XML.

Export

• @manuscripts/sachs (source at gitlab.com/mpapp-public/sachs): command-line utility for Manuscripts format conversion, used by the Pressroom web service, in particular at the time of writing, JATS XML conversions. A thin wrapper for the actual conversion code in @manuscripts/manuscript-transform.
• Pressroom: a web service for importing and exporting Manuscripts formatted data, wrapping sachs and other open source document transformation tools and libraries into a REST web service. Source at gitlab.com/mpapp-public/pressroom, documentation at pressroom.manuscripts.io/v1/docs?html.

Reusable UI components

• @manuscripts/style-guide (source at gitlab.com/mpapp-public/manuscripts-style-guide): a set of reusable UI controls and theme definitions used by this application and other Manuscripts based applications.
• @manuscripts/resizer (source at gitlab.com/mpapp-public/manuscripts-resizer): a React component providing a resize handle for panels, based on an AtlasKit component.
• @manuscripts/assets (source at gitlab.com/mpapp-private/manuscripts-gfx-assets/): shared graphical assets used across Manuscripts projects in bitmap image, SVG and PDF vector form as well as React components built into the NPM package, based on Sketch originals.

Datasets

• @manuscripts/data (source at gitlab.com/mpapp-public/manuscripts-data): source data such as document templates for use by Manuscripts client applications, plus scripts for building and deploying the data to npm.
• @manuscripts/examples (source at gitlab.com/mpapp-public/manuscripts-examples): example Manuscripts documents for reference and test purposes.

Utilities

• @manuscripts/eslint-config (source at gitlab.com/mpapp-public/manuscripts-eslint-config): as the name suggests, the ESLint configuration used by other Manuscripts TypeScript repositories.
• @manuscripts/publish (source at gitlab.com/mpapp-public/manuscripts-publish): a command-line utility to assist publishing other Manuscripts NPM packages to an NPM registry (publishes a package if the current version hasn't already been published).

Installation

Run yarn install @manuscripts/article-editor in your application.

Build (for production)

The variables listed in .env.example must all be defined as environment variables in your project.

Run yarn build to build the app to the dist folder.

Deploy the files to S3 with scripts/deploy.sh.

Running the client in development mode

1. cp .env.example .env. The variables listed in .env.example have appropriate default values for running in a mode where the backend API server is running locally (this is optional, and you can complete local development tasks in the absence of the backend services). See steps below under "Running the backend API in Docker" for steps to launch the API server locally.
2. Run docker volume create --name=yarn-cache to create a yarn cache for the backend services that you will launch in the next step. This step is only needed once.
3. docker-compose up jupyter to start the services needed for development.
4. yarn start to start the app in development mode (using webpack-dev-server and react-hot-loader).
5. To avoid signing up an account, open http://localhost:8080/developer to create a dummy user profile. Now you're good to go.

Running the backend API in Docker

1. Add any environment variables needed for the API server in docker/server/.env.
2. docker login registry.gitlab.com to log in to GitLab’s Container Registry using your GitLab username and password (or a deploy token for read-only access to the registry images).
3. Run docker-compose pull to pull the latest server Docker images.
4. [first run] Initialize the backend services: scripts/api/initialize.sh. If running on Windows or MacOS, it may be necessary to increase the RAM allocated to Docker. (This can be done through Docker Desktop > Preferences > Resources > Advanced > Memory.)
5. [subsequent runs] Start the backend services: docker-compose up api
6. Run docker-compose up jupyter to start the additional services.
7. Open chrome://flags/#cookies-without-same-site-must-be-secure and set to Disabled.
8. Run yarn start to start the frontend.
9. Open Chrome, and enter http://localhost:8080/signup to create a user account. Confirmation emails generally won't be sent from a locally-running API, but you can ignore that message (see APP_SKIP_ACCOUNT_VERIFICATION in docker/server/defaults.env)
10. To stop the service, run docker-compose down. Add an optional -v flag to delete the data volumes.

Running the Manuscripts stack in Kubernetes via Docker Desktop

1. Make sure kubectl is using the appropriate context:
   1. Run kubectl config current-context to show the current context.
   2. Run kubectl config get-contexts to list the available contexts.
   3. Run kubectl config set-context docker-desktop to set the context.
2. To build the client image, run docker-compose build client
3. To start the services, run docker stack deploy --compose-file <(docker-compose config) manuscripts
4. To stop the services, run docker stack rm manuscripts

Template publishing

1. Make sure you are using the test environment. (@manuscripts/data fetch published templates from the test environment: https://gitlab.com/mpapp-public/manuscripts-data/-/blob/master/scripts/fetch-published-templates.js#L6)
2. Make sure you are logged in as a user who is allowed to publish templates (APP_COUCHBASE_ALLOWED_OWNERS) or you are using (have access to) one of the projects which is allowed to publish templates (APP_COUCHBASE_ALLOWED_PROJECTS).
3. Create a manuscript, edit the title (will be used as the template title), and specify requirements. Then publish the template (This can be done through Project menu > Publish Template).
4. Release new version of manuscripts-data. (The build process will fetch published, user-generated template data from a manuscripts-api endpoint and adds it to the data published as @manuscripts/data)
5. Release new version of manuscripts-requirements after updating the @manuscripts/data dependency version. (Essential for the validation process and building the quality report.)
6. Upgrade pressroom-js after updating @manuscripts/data and @manuscripts/requirements dependencies.
7. Update fusion-kubernetes-env with the new pressroom-js image tag.
8. Upgrade this repository dependencies (@manuscripts/data and @manuscripts/requirements).

Testing

Unit tests

Run yarn test to run the unit tests in Jest.

Running tests with Cypress

1. Run yarn run cypress:open to launch the Cypress runner.
2. From the Cypress runner, select an individual test to run or select Run all specs

Development

See the manuscripts-frontend wiki for more information.

Developing manuscripts-api

1. If needed, initialize the backend services: scripts/api/initialize.sh
2. Start the other backend services in Docker: docker-compose up sync-gateway jupyter
3. Start the API: scripts/api/start-local.sh

Developing @manuscripts/style-guide

1. Clone @manuscripts/style-guide to a folder alongside this one, run yarn install to install its dependencies, run yarn link to make it available as a local dependency, then run yarn dev in that folder to start building it.
2. In this folder, run yarn link @manuscripts/style-guide to use the linked module as a local dependency.

Analysis

Run yarn stats to generate a stats.json file, then yarn analyze to open webpack-bundle-analyzer's visualization of the webpack bundle.

Configuration

The service is configured using environment variables, .env.example file placed at the root of the repository.

API_APPLICATION_ID

The application ID acceptable by the server (manuscripts-api).

API_BASE_URL

The *server* app base URL (the manuscripts-api instance) corresponding to this service.

BACKUP_REPLICATION_PATH

Backup replication URL.

BASE_URL

The base URL of this service (the manuscripts-frontend instance).

BEACON_HTTP_URL

The URL of a service that tracks the user presence on a manuscript.

BEACON_WS_URL

The URL of WebSocket. Required for tracking users presence on a manuscript.

COMMENTING

If set to '1', enables commenting on a manuscript.

DERIVED_DATA_BUCKET

The name of a database bucket for derived data.

DISABLE_ATTACH_CODE

If set to '1', disables the ability to attach code with figure.

DISCOURSE_HOST

The base URL of the Discourse host (used to show updates).

ENABLE_CONNECT_LOGIN_OPTION

If set to '1', enables auth using connect.

EXPORT_LITERATUM

If set to '1', enables the ability to export manuscript as Literatum Digital Object.

EXPORT_STS

If set to '1', enables the ability to export manuscript as STS.

EXPORT_TO_REVIEW

If set to '1', show Submissions tab and enable submit to review option.

EXTYLES_ARC_SECRET

Secret used as part of pressroom request to import docx/doc via eXtyles Arc.

FEATURE_FILE_MANAGEMENT

If set to '1', enables the ability to manage files. Specially made for lean workflow purposes.

FEATURE_PRODUCTION_NOTES

If set to '1', enables the ability to manipulate notes on a manuscript. Specially made for lean workflow purposes.

FEATURE_PROJECT_MANAGEMENT

If set to '1', provide project management tools to users. Allow users to tag and track the status of parts of a manuscript, and assign work to collaborators.

FEATURE_QUALITY_CONTROL

If set to '1', enables the ability to display quality reports. Specially made for lean workflow purposes.

FEATURE_SWITCH_TEMPLATE

If set to '1', enables the ability to change the manuscript's template.

FOOTNOTES_ENABLED

If set to '1', allow providing footnotes.

FRONTMATTER_URI

The URL of the login or about page (generated by manuscripts-io-www)

IAM_BASE_URL

The base URL of the IAM server. Used when auth using Connect.

JUPYTER_URL

The base URL of Jupyter notebook server.

JUPYTER_TOKEN

Token used to authenticate requests to Jupyter notebook server.

LEAN_WORKFLOW

If set to '1', enables lean workflow mode (This mode include some UI changes and load the manuscript differently so that it can be tracked).

LEAN_WORKFLOW_MANAGER_URL

The base URL of lean workflow server.

LEAN_WORKFLOW_GRAPHQL_ENDPOINT

The endPoint for the graphql.

LOG_SYNC_EVENTS

If set to '1', console log sync events.

NATIVE

If set to '1', the build of manuscripts-frontend is intended for the native (Mac) app

PICKER_ORIGINS

List of acceptable security origins where the Manuscripts document picker is presented at

PRESSROOM_URL

The base URL of pressroom service (used for importing/exporting).

PRODUCTION

If set to 0, include a "Develop" menu in the menu bar.

PROJECTS_BUCKET

The name of a database bucket for projects data.

PUBLISH_TEMPLATES

If set to '1', enables the ability to publish template.

SERVICEWORKER_ENABLED

When set to '1', application is built with its [service worker](https://developer.mozilla.org/en-US/docs/Web/API/Service_Worker_API/Using_Service_Workers) enabled. Essential for offline support.

SHACKLES_ENABLED

If set to '1', enables the ability to show history (snapshots).

SHACKLES_URL

The base URL of shackles service (used to create/retrieve snapshots).

SUPPORT_EMAIL

The email address used to contact support.

SUBMISSION_SERIES_CODE

Required for export as a "Literatum bundle".

SUBMISSION_GROUP_DOI

Required for export as a "Literatum bundle".

SUBMISSION_ID

The ID of submission does exist in the lean workflow server. To be used for local development (to workaround the association between submission/manuscript to load manuscript properly) when lean workflow mode enabled.

SYNC_GATEWAY_URL

The base URL of Sync Gateway.

ZOTERO_TRANSLATION_SERVER

URL used as a citation search source.

FEATURE_KEYWORDS_CATEGORIES

Allow categories for the keywords.

RXDB

Enable RxDb Database.