diff --git a/README.md b/README.md index bd84e80..baa852a 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,9 @@ The PAML Editor (PAMLED) is a web application that supports the authoring and sharing of PAML protocols. PAMLED consists of two components: `frontend` and `backend`. The frontend is a React-based server for handling the graphical interface. The backend is a Django REST server that handles persistent storage (protocols, user accounts, and primitives), and access to the pyPAML library. +# **User Guide** + +See the user guide at: [User Guide](frontend/web/src/USERGUIDE.md) # **Running the PAML Editor in Development** diff --git a/frontend/web/package-lock.json b/frontend/web/package-lock.json index bfe03d5..022a560 100644 --- a/frontend/web/package-lock.json +++ b/frontend/web/package-lock.json @@ -15,10 +15,13 @@ "bootstrap": "^5.1.3", "eslint-plugin-react": "^7.28.0", "history": "^5.1.0", + "marked": "^4.0.12", "react-bootstrap": "^2.0.2", "react-icons": "^4.3.1", + "react-markdown": "^8.0.0", "react-router-dom": "^6.0.2", "react-scripts": "^3.4.4", + "remark-gfm": "^3.0.1", "rete": "^1.3.0", "rete-area-plugin": "^0.2.1", "rete-connection-plugin": "^0.9.0", @@ -2920,6 +2923,14 @@ "@babel/types": "^7.3.0" } }, + "node_modules/@types/debug": { + "version": "4.1.7", + "resolved": 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"@types/unist": "^2.0.0", + "unist-util-stringify-position": "^3.0.0" + } + }, "vm-browserify": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/vm-browserify/-/vm-browserify-1.1.2.tgz", @@ -36549,6 +38587,11 @@ "camelcase": "^5.0.0", "decamelize": "^1.2.0" } + }, + "zwitch": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.2.tgz", + "integrity": "sha512-JZxotl7SxAJH0j7dN4pxsTV6ZLXoLdGME+PsjkL/DaBrVryK9kTGq06GfKrwcSOqypP+fdXGoCHE36b99fWVoA==" } } } diff --git a/frontend/web/package.json b/frontend/web/package.json index 4e62854..d64d35b 100644 --- a/frontend/web/package.json +++ b/frontend/web/package.json @@ -11,10 +11,13 @@ "bootstrap": "^5.1.3", "eslint-plugin-react": "^7.28.0", "history": "^5.1.0", + "marked": "^4.0.12", "react-bootstrap": "^2.0.2", "react-icons": "^4.3.1", + "react-markdown": "^8.0.0", "react-router-dom": "^6.0.2", "react-scripts": "^3.4.4", + "remark-gfm": "^3.0.1", "rete": "^1.3.0", "rete-area-plugin": "^0.2.1", "rete-connection-plugin": "^0.9.0", diff --git a/frontend/web/src/USERGUIDE.md b/frontend/web/src/USERGUIDE.md new file mode 100644 index 0000000..11b0c23 --- /dev/null +++ b/frontend/web/src/USERGUIDE.md @@ -0,0 +1,39 @@ +# PAML User Guide + +- Getting Started + - From the homepage, login with existing credentials (registering if needed). + - Start editing a protocol. (See below) +- Loading Protocols + - If you have a graph file (json) that you previously downloaded, or were given (see `examples`), then click the triangle dropdown button next to the `+` button, and select `Load Rete Graph`. + - Your saved protocols will also be listed across the top of the screen and can be selected by clicking on the name. +- Saving Protocols + - Click the triangle dropdown next to the protocol name and select `Save`. This will save the protocol to the PAMLED database and it will be available when you login in at a later time. +- Downloading Protocols + - Click the triangle dropdown next to the protocol name and select `Download Protocol` to save the PAML RDF. Similarly, click `Download Rete Graph` to save the visual script graph representing the protocol. This file can also be used later to upload the protocol into PAMLED for other users or yourself. +- Create a new Protocol + - Click the "+" button at the top of the screen in the list of protocols. +- Edit a Protocol + - Add Activities + - Drag and drop from the palette on the left side. + - Or, right click on the workspace to bring up a context menu with the list of primitives and protocols. + - Clone Activities + - Right click on activity and select `Clone`. + - Deleting Activities + - Right click on activity and select `Delete`. + - Linking ports + - Click on a port and drag the connector to another port. + - Unlinking ports + - Click on port and drag connector off the port, then release the click. + - Adding Paramters + - Add a Parameter node in the same manner as an Activity. + - Configure the name (text), type (dropdown), and value (text). + - Protocol Inputs and Outputs + - Add an Input or Output node in the same manner as an Activity. + - Link the node's port to another Activity port. + - Saving the protocol will update the node for the protocol so that the protocol can be used as a sub-protocol in another protocol. + - Creating Primitives + - Create a protocol and only use Input and Output nodes to define its interface. This protocol can be used as a new primitive. + +# Getting Help +- Create an issue on the Github project: https://github.com/Bioprotocols/pamled +- Contact dbryce@sift.net diff --git a/frontend/web/src/editor/UserGuideModal.jsx b/frontend/web/src/editor/UserGuideModal.jsx new file mode 100644 index 0000000..f5fa88d --- /dev/null +++ b/frontend/web/src/editor/UserGuideModal.jsx @@ -0,0 +1,56 @@ +import React, { Component } from 'react'; +import { Modal, Button, Alert, Spinner, Row, Col } from 'react-bootstrap'; +import ReactMarkdown from 'react-markdown'; +import remarkGfm from 'remark-gfm'; +import marked from "marked"; +//import ug from "USERGUIDE.md" + +export default class UserGuideModal extends Component { + + state = {}; + + componentDidMount() { + const readmePath = require("../USERGUIDE.md"); + + fetch(readmePath) + .then(response => { + return response.text() + }) + .then(text => { + this.setState({ + markdown: text + }) + }) + } + + + render() { + + const { markdown } = this.state; + return ( + + + + {/* + PAMLED User Guide + */} + + + + + + + + + + ); + } +} + diff --git a/frontend/web/src/editor/components/ProtocolInspector.jsx b/frontend/web/src/editor/components/ProtocolInspector.jsx index ae8833b..ddf404f 100644 --- a/frontend/web/src/editor/components/ProtocolInspector.jsx +++ b/frontend/web/src/editor/components/ProtocolInspector.jsx @@ -85,11 +85,11 @@ export class ProtocolInspectorGroup extends React.Component { - + {/*

HI

*/} {this.props.workspaceComponent()} - + {/* {Object.entries(this.props.protocols).map( @@ -105,7 +105,7 @@ export class ProtocolInspectorGroup extends React.Component { - + */} {/* */} diff --git a/frontend/web/src/editor/editor.css b/frontend/web/src/editor/editor.css index 4737622..04d9924 100644 --- a/frontend/web/src/editor/editor.css +++ b/frontend/web/src/editor/editor.css @@ -31,7 +31,7 @@ } .editor-workspace-inspector-row { - height: 85%; + height: 100%; } .editor-workspace-column { @@ -55,6 +55,10 @@ background-image: radial-gradient(circle, #000000 2px, rgba(0, 0, 0, 0) 1px); } +.context-menu { + width: unset !important; +} + /* Hide bootstrap outline around focused buttons */ .btn:focus:not(:focus-visible) { outline: 0; diff --git a/frontend/web/src/editor/editor.jsx b/frontend/web/src/editor/editor.jsx index 5157d16..ee92c3d 100644 --- a/frontend/web/src/editor/editor.jsx +++ b/frontend/web/src/editor/editor.jsx @@ -20,7 +20,7 @@ import { ProtocolInspectorGroup } from "./components/ProtocolInspector"; import RenameProtocolModal from "./RenameProtocolModal"; import DownloadProtocolModal from "./DownloadProtocolModal"; import RebuildPrimitivesModal from "./RebuildPrimitivesModal"; - +import UserGuideModal from "./UserGuideModal"; function downloadStringAsFile(data, filename) { let url = window.URL.createObjectURL(new Blob([data])) @@ -52,7 +52,8 @@ export default class Editor extends Component { portTypes: {}, isRebuildingPrimitives: true, download: null, - renameProtocol: null + renameProtocol: null, + userGuideVisible: null } this.dataTypes = new Set(); @@ -68,6 +69,8 @@ export default class Editor extends Component { this.handleProtocolDownload = this.handleProtocolDownload.bind(this); this.displayAnyProtocol = this.displayAnyProtocol.bind(this); this.rebuildPrimitives = this.rebuildPrimitives.bind(this); + this.onUserGuide = this.onUserGuide.bind(this); + this.onUserGuideDone = this.onUserGuideDone.bind(this); } componentDidMount() { @@ -653,6 +656,13 @@ export default class Editor extends Component { this.setState({ download: null }) } + onUserGuideDone(){ + this.setState({ userGuideVisible: null }) + } + onUserGuide(){ + this.setState({ userGuideVisible: true }) + } + render() { let workspaceComponent = () => ( @@ -664,10 +674,6 @@ export default class Editor extends Component { @@ -698,6 +704,10 @@ export default class Editor extends Component { handleCancel={() => this.onCancelDownload()} handleDone={() => this.onDoneDownload()} /> + this.onUserGuideDone()} + /> diff --git a/frontend/web/src/editor/menu.jsx b/frontend/web/src/editor/menu.jsx index d6db732..f587e42 100644 --- a/frontend/web/src/editor/menu.jsx +++ b/frontend/web/src/editor/menu.jsx @@ -10,9 +10,6 @@ export default class Menu extends Component { constructor(props){ super(props); this.editor = props.editor; - // this.handleSave = props.handleSave; - // this.getProtocols = props.getProtocols; - // this.setProtocol = props.setProtocol; } render() { @@ -43,6 +40,11 @@ export default class Menu extends Component { Logout +