https://github.com/digital-science/physiome-coko
Journal article submission system for the Physiome Journal.
https://github.com/digital-science/physiome-coko
bpm camunda camunda-modeller figshare pegjs postgres
Last synced: 3 months ago
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Journal article submission system for the Physiome Journal.
- Host: GitHub
- URL: https://github.com/digital-science/physiome-coko
- Owner: digital-science
- Created: 2019-06-21T14:28:13.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-04-26T02:53:08.000Z (about 5 years ago)
- Last Synced: 2024-12-23T18:25:30.448Z (5 months ago)
- Topics: bpm, camunda, camunda-modeller, figshare, pegjs, postgres
- Language: JavaScript
- Homepage: https://journal.physiomeproject.org
- Size: 3.31 MB
- Stars: 2
- Watchers: 5
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Physiome Submission System
_Physiome_ publishes reproducible and reusable mathematical models of physiological processes where the experimental details and model validation have been published or accepted for publication in a recognised 'primary' peer-reviewed journal.
Physiome curators will help authors ensure that models and simulation experiments are made available using appropriate community standards prior to acceptance for publication in Physiome.
More details about the Physiome Journal itself can be found here:
The piece of software held in this repository is designed to facilitate the submission of manuscripts to the Physiome journal. Submitters
are able to upload their manuscript file, specify additional metadata such as authors, funding etc. and then submit
these to the journal for consideration. Subsequently, the journals curators able to use the administrative functions within the software
platform to manage submissions, make editorial modifications and finally publish accepted manuscripts and models through
into the Physiome figshare instance.
Videos showing briefly the functions of the software can be found on figshare here:
This development utilises and builds upon the PubSweet application core managed by the Coko Foundation and wider PubSweet community.
PubSweet Project:
Coko Foundation:
## Getting Started
### Prerequisites
For local development the easiest way to get started is to have Docker installed and run the following services on Docker to link to the Physiome submission system instance.
* NodeJS
* Yarn
* Docker (for local development ease)
* Camunda BPM ([camunda/camunda-bpm-platform:latest](https://hub.docker.com/r/camunda/camunda-bpm-platform/))
* Postgres ([postgres:latest](https://hub.docker.com/r/camunda/camunda-bpm-platform/))
* Camunda Modeller ([download](https://camunda.com/download/modeler/)) - for viewing/modifying BPM model documents
### Services (local development)
Create a new Postgres instance
```console
docker run -d --name physiome-postgres -p 5432:5432 postgres:latest
```
Create a new Camunda BPM Engine instance
```console
docker run -d --name physiome-camunda -p 8080:8080 camunda/camunda-bpm-platform:latest
```
### Setup
From the root project directory perform the following
```console
yarn install
yarn dsl-compile
```
### Configuration
The application itself pulls configuration from several different locations:
* Within the file /packages/app/config/default.js an overview and the default values utilised within the application can be found.
* Run-time environment can also effect the aggregated configuration. The default configuration
noted above is then supplemented with /packages/app/config/test.js for example when running
in the "test" environment.
* Environment variables for the NodeJS application are utilised in certain defaults. These
environment variables can be provided at run-time or via the .env located /packages/app/.env
Example ".env" file for local development:
```
PUBSWEET_SERVER_SECRET=
WORKFLOW_FILE_IDENTIFIER_DOMAIN=physiome-submission-dev.ds-innovation-experiments.com
AWS_S3_ACCESS_KEY=
AWS_S3_SECRET_KEY=
AWS_S3_REGION=
AWS_S3_BUCKET=
ORCID_CLIENT_ID=
ORCID_CLIENT_SECRET=
AWS_SES_ACCESS_KEY=
AWS_SES_SECRET_KEY=
AWS_SES_REGION=
FIGSHARE_API_BASE=https://api.figsh.com/v2/
FIGSHARE_API_TOKEN=
PUBLISH_FIGSHARE_TYPE="journal contribution"
PUBLISH_FIGSHARE_GROUP_ID=
PUBLISH_FIGSHARE_CATEGORIES=4,12,135
DIMENSIONS_API_BASE=https://app.dimensions.ai/api
DIMENSIONS_API_USERNAME=
DIMENSIONS_API_PASSWORD=
STRIPE_IS_PRODUCTION=false
STRIPE_SECRET_KEY=
STRIPE_PUBLISHABLE_KEY=
STRIPE_WEBHOOK_SECRET_KEY=
IDENTITY_ADMIN_USERS=
EMAIL_SEND_FROM=Physiome Journal
EMAIL_SUBJECT_PREFIX="Physiome submission system:"
EMAIL_SIGNATURE="Kind regards,\nPhysiome curation team\[email protected]"
EMAIL_RESTRICTED_TO=
EMAIL_EDITORS_MAILING_LIST="[email protected]"
```
* The business logic is described within /definitions/physiome-submission-v2.bpmn. This file
can be opened using the Camunda Modeler application. It describes the tasks and steps a submission
goes through, including any "external tasks" such as sending an email or publishing to figshare.
* The description of how these components all fit together (the glue so to speak) is defined within the file
/definitions/physiome-submission.wfd. This contains a custom domain-specific language that
is "compiled" via PegJS into a JSON file representation. The compiled representation can be found
within /packages/app/config/description.json
The minimum required to get this configured locally for testing things out is to create the .env
file and provide it with the required values for S3, SES and ORCID. The figshare options do
not need to be specified for local development purposes (unless you have access to a test figshare instance).
For deployment purposes or to utilise a database/BPM from another machine, it is also possible
to define a Postgres database and Camunda engine located elsewhere using the following environment
variables:
```
DATABASE=
DB_USER=
DB_PASS=
DB_HOST=
WORKFLOW_API_URI=http://:8080/engine-rest
```
## Deployment
We need to compile the current "Workflow Description". This will use the PegJS created processor to
read in the file /definitions/award-submission.wfd and process it into the description JSON
file located within /packages/app/config/description.json
```console
yarn desc
```
In order for Camunda to know about the business logic model we wish to use, it needs to be deployed to the Camunda instance.
This will happen automatically as part of a Knex database migration script.
## Running
With all of the above configured and deployed it is now possible to run the application.
From the root directory of the project, run the following command:
```console
yarn start
```
This will kick off the initial database setup steps (including BPM deployments) and then run the backend GraphQL endpoint. It will also run webpack
over the front-end application and expose it for testing.
Navigate in your local browser of preference to: [http://localhost:3000](http://localhost:3000)
## Notes
The BPMN workflow (as seen above from the Camunda Modeller) describes the workflow and possible actions at each stage a submission
may go through during its lifetime. It also describes any third-party integrations, defining where and when they are enacted
during the process of a submission. Each task within the BPM definition has specific attributes which tie into the workflow description
(expressed in our custom DSL) which defines what form is associated with a task. The workflow description also includes
details relating to user interface elements, data models, validations and access control restrictions on data.
The above example workflow description shows validations that are applied during the manuscript submission phase, including
the end-user warnings that are displayed when a validation fails. The example layout also shows how the
submission form itself is generated, including the links between a form element and the data model it targets.
The code relating to how the DSL language takes the data model and transforms this into a representation
used within the PubSweet core is in need of a refactoring, so please ignore the code smell that lingers in these parts.
## Videos/Screenshots
Screenshot: Manuscript submission form
Screenshot: Administration view with submissions listing
Screenshot: Administration view, submission details
Videos of functionality can be seen here:
## Contact
Please feel free to contact Jared Watts ([email protected]) about this project. To contact the Physiome journal, [email protected].