Portal Setup

Learn about Portals and how to set up and use them for your organization.

A license is required to set up and use a Portal. Contact DNAnexus Sales for more information.

About Portals

A Portal is an org with special privileges that serves two purposes. First, it provides a space for your organization to showcase projects with special data sets, tools that you’ve published, news and highlights or other important links. Second, the Portal has customized branding that will follow the end-user throughout the site with a curated view of projects and tools.

Portal Home

Initial Portal Setup by DNAnexus

To configure a new Portal for your org you will work with the DNAnexus xVantage team. First, the Partner will need to specify the org that will host the Portal. The Portal is tied to exactly one org.

We will ask you to provide the initial configuration requirements and assets (logos or other images, brand colors, text, and links) listed below.

Once all configuration requirements and assets have been provided, the Portal will be ready to test. At this point the xVantage team will provide a link to the Portal along with a brief training to orient the Org Admin to using the portal.

Features of a Portal and Configuration Options

This section describes configurations that the Org Admin can make by editing and uploading new .json files or new images.

Login Page (branding.json)

• Logo (no size limit, but it’s recommended to stay under 200px high)

• (Optional) Login button color; must be conducive to white text

• (Optional) Whether to hide the registration link

• (Optional) Text to display under login button

Register Page (branding.json)

• Logo (max 100x100px)

• (Optional) Register button color; must be conducive to white text

• (Optional) Can disable registration page, redirecting directly back to login

• (Optional) Markdown text to display under register buttons

• (Optional) Add default region for users who register with this page

• (Optional) Add short sentence indicating terms of acceptance

Header (branding.json and navigation.json)

The branding.json controls the colors in the Header. The navigation.json controls the navigation links and menus (with the exception of the logo navigation).

These are the items you can configure:

• Header corner Logo (min 15x15px, max 50x30px)

• (Optional) Logo link destination, defaults to Home page (configure in the branding.json file)

• (Optional) Whether the logo link opens in a new tab (configure in the branding.json file)

• (Optional) Support page (used when the user clicks on “Get Help” in the Help menu, default is DNAnexus Support Form)

• (Optional) Color for the nav underbar, text, background, nav hover background color, landing page button color and color array for the user bubble. Currently icons do NOT change color, so do not make the background bar a dark color or text will not be visible.

• (Optional) Navigation customization. You can add custom items to the ends of our Projects, Tools, and Help menus, remove those menus entirely, or add new menus and links to the nav header.

Example of adding items to the Tools menu

Example of adding extra navigational links or menus. Also shows recoloring text and highlight.

• (Optional) Filters for the projects list (i.e. when the user clicks on “All Projects” in the Projects menu)

• (Optional) Whether to hide the community switcher (this will “lock” the user into the current community)

Landing Page (home.json)

The main page is a customizable landing page with the ability to showcase in any order with any amount of widgets:

• Specific projects

• Specific tools

• Links to external websites

• Images (PNG, JPEG, TIFF, BMP, etc)

• Markdown text

The home.json file contains a list of widgets to display, and the order in which to display them.

Text Widget

• Title

• id property of “markdown”

• Minimum width

• Markdown text

Image Widget

• Minimum width

• id property of “image”

• Image resource or location (image can be any type, e.g. PNG, JPEG, TIFF, BMP)

• Alt text (when image can’t be displayed)

Link List Widget

• Title

• id property of “link”

• Minimum width

• List of link destinations and their titles

Project List Widget

• Title

• id property of “project” or “projectCards”

• Minimum width

• Project filter criteria - To have projects displayed here, set up a search using the system/findProjects API method. Note that if you want all projects to be visible to all users who can access the Portal, set the level parameter to "VIEW."

• Project sub-page destination

Tool List Widget

• Title

• id property of “tool”

• Minimum width

• Tool filter criteria - To have available tools displayed here, set up a search using the /system/findApps API method.

A list of icons available to use on home.json is available here. DNAnexus supports the use of icons introduced in version 4.3 and earlier.

Managing, Modifying, and Updating Portal Assets

Portal assets are stored with the json files. You can easily upload json and PNG files using the GUI on the main portal home page. The sections for each json file describe the access permissions that each file requires.

The UI can become disabled if a flawed json is inadvertently uploaded. Review the section below on how to validate json files.

File Upload

Validating JSON files Before Upload

JSON (JavaScript Object Notation) is a lightweight data-interchange format. Most of the time, it is easy for humans to read and write but sometimes, it is extremely difficult to actually read and make sense of. We highly recommend validating your portal asset using tools such as jsonlint or jsonformatter, before using them to update the community portal.

Viewing changes in the browser

It is mandatory to clear your browser cache after updating your portal assets with a revised JSON file.

In most browsers, you can clear the cache from the Privacy or History area in the Settings or Options menu, depending on the browser. The hotkey combination Ctrl+Shift+Del (or Cmd-Shift-Del on a Mac) works with most browsers as well.

While that hotkey combo works in most non-mobile browsers, the exact steps involved in clearing your browser's cache depend entirely on what web browser you're using. If these suggested steps do not work please refer to your browser’s documentation.

As an alternative to clearing your cache, it is possible to use ‘private’ browsing (a.k.a ‘privacy’ mode or ‘incognito’ mode) to view the asset updates. This is a privacy feature in some web browsers to disable browsing history and the web cache allowing a person to browse the Web without storing local data that could be retrieved at a later date. To launch your browser in ‘incognito’ mode, please refer to your browser's documentation.

Making Updates via the Command-Line Interface (CLI)

DNAnexus can also provide you with CLI scripts to update your assets. This provides an alternative to the UI, which can become disabled if a flawed json is inadvertently uploaded. Contact [e-mail] for more information and to request access to the scripts for CLI updating.

Compiling Portal Assets

Portal assets are split into many different files, all loaded at different times by different components. Below are samples of each file. Note that several of these files contain references to images; for communities, you can either prepend a pound sign (#) to denote an image fetched from the community assets (e.g. “#logo.png” would fetch the file “logo.png” stored in the community), or you can use a normal URL to fetch an image from an external source.

branding.json

This file must be public (viewable by all users) Applies to the header and community selector, as well as the login and registration pages. colors is optional in each section and contains information about how to change the colors of various elements in the given section.

Earlier versions of Portals had two additional files -- login.json and register.json' -- you do not need to remove those, but all of their information will need to be transferred to branding.json.

In the header, logoOpensNewTab is optional and if true will open a new tab when the user clicks on the logo in the upper left. hideCommunitySwitch is also optional and, if true, will hide the community selector in the upper left (essentially locking the user into the current community).

In the login and registration sections, logo specifies a logo to be used at the top of the given page and text can be Markdown which will be rendered at the bottom of the page (below the button but above the footer).

The registration section has several optional attributes. First, disable, which if true will hide the “Create Account” link on the login page and redirect the user to the login page if they try to manually visit the registration page. There’s also an optional agreeToText attribute, which will be a plain text string (not Markdown) with a checkbox which the user needs to agree to before they can register. It also has an optional region attribute which, if set, will force any user created with this login page to have the given default region instead of presenting them with an option.

homeURL and supportURL are optional and are the URLs used for the main community site (destination when clicking on the logo in the upper left) and support pages (destination when a user selects “Get Help” from the Help menu), respectively. description is shown in the community selector menu.

Note that any logo images defined here must be uploaded with public permissions--logos for the login and registration pages in particular will need to be downloaded by unauthenticated users.

{
 "header": {
   "logo": "#logo_header.png",
   "logoOpensNewTab": true,
   "hideCommunitySwitch": true,
   "colors": {
     "background": "#123456",
     "border": "#123456",
     "text": "#123456",
     "hoverBackground": "#123456",
     "userColors": ["#123456", "#234567", "#345678"],
     "button": {"success": {"border-color": "green", "background":
      "pink", "hover": {"background": "dusk"}}}
   }
 },
 "login": {
   "logo": "#logo_login.png",
   "text": "#Title\n\nThis is Markdown text.",
   "colors": {
     "loginButton": "#123456"
   }
 },
 "register": {
   "disable": true,
   "logo": "#logo_register.png",
   "text": "#Title\n\nThis is more Markdown text.",
   "agreeToText": "Plain text you need to agree to before registering",
   "region": "aws:us-east-1",
   "colors": {
     "registerButton": "#123456"
   }
 },
 "homeURL": "http://example.com",
 "supportURL": "http://example.com/support",
 "hideCommunitySwitch": true,
 "description": "A short description of two or three lines for the community selector"
}

home.json

This file must be at least accessible to community members.

{
 "order": ["hero-image", "featured-projects", "featured-tools", "reference-links", "help-text"],
 "components": {
   "help-text": {
     "type": "markdown",
     "id": "help-text",
     "title": "Useful Advice",
     "content": "# Always wear sunscreen\nIt’s really important.",
     "minWidth": "400px"
   },
   "unused-table-component": {
     "type": "markdown",
     "id": "unused-table-component",
     "title": "A table for you",
     "content": "| Tables | Are | Cool  |\n| --- | --- | --- |\n| a | b | $1600 |\n| c | d | $12 |\n| e | f | $1 |",
     "minWidth": "100px"
   },
   "hero-image": {
     "type": "image",
     "id": "hero-image",
     "src": "#my_awesome_image.png",
     "alt": "Heroes are great"
   },
   "unused-image": {
     "type": "image",
     "id": "unused-image",
     "src": "https://example.com/image.png",
     "alt": "Alt text"
   },
   "reference-links": {
     "type": "link",
     "id": "reference-links",
     "title": "Help and News",
     "links": [
       {
         "name": "Getting Started",
         "subname": "First steps with your new account",
         "href": "https://www.dnanexus.com",
         "icon": "fa-question-circle"
       },
       {
         "name": "Some Helpful News or Docs Link",
         "subname": "Come here for useful information",
         "href": "https://www.dnanexus.com",
         "icon": "fa-question-circle"
       }
     ],
     "footer": {
       "name": "Visit Help Center...",
       "href": "https://www.dnanexus.com/help"
     },
     "minWidth": "300px"
   },
   "featured-projects": {
     "type": "project",
     "id": "featured-projects",
     "title": "Featured Projects",
     "query": {
       "tags": "community-tag",
       "limit": 5
     },
     "columns": [
       {
         "property": "name",
         "label": "Name"
       },
       {
         "property": "modified",
         "formatter": "date",
         "label": "Modified"
       },
       {
         "property": "createdBy.user",
         "formatter": "userHandle",
         "label": "Created By"
       }
     ],
     "viewMore": "/panx/communities/communityname-without-org/projects",
     "minWidth": "400px"
   },
   "featured-tools": {
     "type": "tool",
     "id": "featured-tools",
     "title": "Featured Tools",
     "query": {
       "category": "community-tag"
     }
   },
   "project-destination": {
     "type": "projectCards",
     "id": "project-destination",
     "title": "Project Destinations (Samples)",
     "destination": "samples",
     "query": {
       "properties": {
         "dashboard_config_project": true
       }
     },
     "minWidth": "400px"
   },
 }
}

navigation.json

This file must be at least accessible to community members. Applies to the header. _filters is optional and contains information about how to alter the query sent to the server to fetch the main and featured lists of projects. _projects, _tools, and supportURL are all optional and can be:

• null to remove the item from the header

• An array of objects with the following format to add items to the end of the corresponding menu:

  • text is the text of the menu item

  • url is the destination to take the user to

  • newTab is optional and indicates that the link should be opened in a new tab

Any other entries in this file will indicate new navigation items to be added. These are defined by a key (in the example below, “A New Menu” and “A New Link”), and can be either an object with url and optional newTab values (in which case it will be rendered as a simple link in the navigation header), or as an array of objects with keys text, url, and optionally newTab (in which case it will be rendered as a dropdown menu with the listed items).

{
 "_filters": {
  "projects": {
    "featured": {
      "id": ["project-1234", "project-2345"]
    },
    "all": {
      "tags": "community-demo",
      "billTo": "org-demo"
  }
 },
 "_projects": null,
 "_tools": [
  {"text": "Custom Menu Item", "url": "http://example.com"},
  {"text": "Opens in New Tab", "url": "http://example.com", "newTab": true}
 ],
 "_help": null,
 "A New Menu": [
  {"text": "New Menu Item", "url": "http://example.com"},
 ],
 "A New Link": {"url": "http://example.com", "newTab": true}
}