mapsidebar-12labours v1.0.0-beta.0

map-side-bar

This project aims to provide a sidebar for searching capability for SPARC portal.

Project installation

npm i @abi-software/map-side-bar

Project setup

npm install
npm run serve

Compiles and minifies for production

npm run build-bundle

How to use

Include the package in your script.

import '@abi-software/map-side-bar'
import '@abi-software/map-side-bar/dist/map-side-bar.css'

#Template The code should looks like this

<SideBar :envVars="envVars"
         :visible="sideBarVisibility"
         @actionClick="actionClick">
</SideBar>

envVars contains environment varibables like so:

{
  API_LOCATION: 'http://localhost:5000/',
  ALGOLIA_KEY: 'xxxxxxxxxxxxxxxxxxxxxxxxx',
  ALGOLIA_ID: 'xxxxx',
  ALGOLIA_INDEX: 'k-core_dev_published_time_desc',
}

actionClick event is called when an action button has benn clicked on.

Sidebar Data formats

Algolia

Data retrieved from Algolia can be found here: https://github.com/ABI-Software/map-sidebar/blob/3310b165489b10901f50a21e5689ef046251dbd9/src/algolia/algolia.js#L136

           [
            'pennsieve.publishDate',  // optional
            'pennsieve.updatedAt', // optional
            'Item.curie', //contains the DOI for the dataset (required)
            'Item.name', // dataset title (required)
            'Item.description', // dataset description (required)
            'objectID', // Pennsieve discover ID (required)
          ],

Scicrunch

Data retrieved from scicrunch can be found here: https://github.com/nih-sparc/sparc-api/blob/f3444a32964f5340e0ee1f10a08a05839620d098/app/scicrunch_processing_common.py#L25

And mimetypes can be viewed here https://github.com/nih-sparc/sparc-api/blob/f3444a32964f5340e0ee1f10a08a05839620d098/app/scicrunch_processing_common.py#L28

ADDITIONAL_LINKS = 'additionalLinks'
BIOLUCIDA_2D = 'biolucida-2d'
BIOLUCIDA_3D = 'biolucida-3d'
COMMON_IMAGES = 'common-images'
CONTEXT_FILE = 'abi-context-file'
CSV = 'csv'
NAME = 'name'
ORGANS = 'organs'
PLOT_FILE = 'abi-plot'
SEGMENTATION_FILES = 'mbf-segmentation'
SCAFFOLD_DIR = 'abi-scaffold-dir'
SCAFFOLD_FILE = 'abi-scaffold-metadata-file'
THUMBNAIL_IMAGE = 'abi-thumbnail'
SCAFFOLD_VIEW_FILE = 'abi-scaffold-view-file'
SIMULATION_FILE = 'abi-simulation-file'
VIDEO = 'video'
VERSION = 'version'
README = 'readme'
TITLE = 'title'

Note: All are optional except for ‘name’

Sidebar input processing

Sidebar input processing can be viewed here: https://github.com/ABI-Software/map-sidebar/blob/3310b165489b10901f50a21e5689ef046251dbd9/src/components/SidebarContent.vue#L318

It is used to keep the code from attempting to access an object property that does not exist

Context card data format

All fields are strings:

{
  "description": required ,
  "id": optional,
  "samples": [ // array required here (can be empty)
    {
      "annotation": optional,
      "description": required,
      "doi": optional // Doi will be used to link sample to a separate dataset,
      "heading": required,
      "id": required,
      "path": optional // path will be used to link to file location,
      "view": optional // Will be used to link to “views[i].id”
    }
  ],
  "version": // not currently used,
  "views": [ // array required here (can be empty)
    {
      "annotation": optional,
      "description": required,
      "id": requried,
      "path": required // relative path to the view file, eg "derivative\\Scaffolds\\scaffoldMap_tenial_view.json",
      "sample": optional // used to link to views to samples
      "thumbnail": optional // technically optional but it won’t look great
    } 
  ]
}

An example context card file can be viewed here: https://drive.google.com/file/d/15NVRBny7WGltpMSRbsgMglXo0xOC3-Q9/view?usp=sharing