Refex

Build Setup

# install dependencies
$ npm install

# serve with hot reload at localhost:3000
$ npm run dev

# build for production and launch server
$ npm run build
$ npm run start

# generate static project
$ npm run generate

For detailed explanation on how things work, check out Nuxt.js docs.

Naming rules for variables

• JS variables

  camelCase

  ---

• Vuex variables

  snake_case

  ---

• CSS classes

  snakecase _but can sometimes be kebab-case due to use of plugin

  ---

• json / config files

  snake_case

Maintenance for filters(eg. sample / gene)

A filter consists of the following attributes:

1. an object in the `static/filters.json'

  {
    // name of the filter. This name should correspond to the API prefix
    "name": "gene",


    // columns to be shown in the results on the index page & project page.
    // in case of 'sample', these filters are set by the backend hence not in this file
    // column: parameter refers to the key of the object in the API results
    // label: label of column
    // note: sub label of column
    // is_checkbox: if true, the value cannot be freely set by the user but is a choice of preset options
    // is_displayed: if true, the column is shown by default
    // is_ontology: if true, the column has note as sublabel at the project table
    "filter": [
      {
        "column": "symbol",
        "label": "GeneSymbol",
        "note": "",
        "is_checkbox": false,
        "is_displayed": true,
        "is_ontology": false
      },
    ],
  }

2. a dedicated screenerView in components/screener named as ScreenerView{filterName}

Maintenance for species (eg. human/ mouse)

A specie consists of the following attributes:

1. an object in `refex-sample/datasets.json'

  {
    // name of specie. `_` characters will be parsed to ` `
    "species": "Human",
    // search examples shown in searchBar component
    "search_conditions": [
      {
        "label": "Gene Name",
        "examples": ["transcription factor"]
      },
      { "label": "Symbol", "examples": ["ITG"] },
      { "label": "Summary", "examples": ["Breast cancer"] }
    ],
    // array of info by dataset
    "datasets": [
      // dataset: dataset name
      // label: label of dataset
      // gene: Information for gene filter which is different by dataset
      //       info that does not differ by dataset is set in static/filters.json
      // sample: Infromation for sample filter which is different by dataset
      //       includes filter array since the columns used in tables are different per dataset
      {
        "dataset": "humanFantom5",
        "label": "FANTOM5",
        "gene": {
          "key": "ncbiGeneId",
          "header": "NCBI Gene ID",
          "item_comparison_example": [
            {
              "route": "5460,6657,9314,4609",
              "label": "Yamanaka Factors (OCT3/4, SOX2, KLF4 and C-MYC-OSKM)"
            }
          ]
        },
        "sample": {
          "filter": [
            {
              "column": "SampleTypeCategory",
              "label": "Sample type",
              "note": "FANTOM5",
              "is_checkbox": true,
              "is_displayed": true,
              "is_ontology": false
            },
          ],
          "item_comparison_example": [
            {
              "route": "RES00001676,RES00001677,RES00001678",
              "label": "Adipocyte differentiation"
            },
          ],
          "search_conditions": [
            {
              "label": "Sample Name",
              "examples": ["liver", "lung"]
            }
          ]
        }
      }
    ]
  }

2. an SVG icon in components/icons by the name of Icon{SpecieName} . The name of the specie should be in PascalCase without _

Main API callings in front-end app

＊all API callings are done by Axios and have a default base of 'https://refex2-api.dbcls.jp/' as set in nuxt.config.js

1. Auto suggestions - upon creation

   api

    // GET API call
    `api/cv`

   ---

   parameters

   n/a

   ---

   response

   Object with dataset names are parameters. These then contain the fixed options for the screener & column filters

   gtexV8: {
    Age: ["20-29", "20-79", "30-39", "40-49", "50-59", "60-69", "70-79"],
    Sex: ["F", "M", "Mixed"]
    }

   ---

   place of usage

   used in components/ScreenerView/ScreenerViewSample.vue upon creation to set autocomplete items. The API is only called on creation and not updated afterwards.

2. Auto suggestions - real time API fetch for GO terms

   api

    // POST API graphQI call
    `gql`

   parameters

    - `query`
      - object containing the following
      ```JavaScript
        `{ goSuggest (text: ${SEARCH_TERM}, dataset: ${DATASET_NAME}) { goId, goTerm }}`
      ```
    - `SEARCH_TERM`
      - string reffering to the search key inputted by the user
    - `DATASET_NAME`
      - string reffering to the dataset name as set in `datasets.json`
   

   response

   Object with data and goSuggest array in that.

   // example of Genes with GO terms auto completion list.
   {
       "data": {
         "goSuggest": [
           {
             "goId": "GO:0022900",
             "goTerm": "electron transport chain"
           }
         ]
       }
   }

   place of usage

   used in components/ScreenerView/ScreenerViewGene.vue when the input for temporaryParameters.go_term has been changed. This process is done by the vue-tags-input external plugin.

3. Results and Estimated results number fetch of Index page

   api

    // POST API call
    `gql`

   see more and test[https://refex2-api.dbcls.jp/gql]

   ---

   parameters

   • query

     // string with the following structure
     `${SPECIE}${DATASET}${FILTERTYPE}${NUMFOUND}(${FILTER_PARAMETERS}){${RESPONSE_PARAMETERS}}`
     
     // SPECIE - specie selected by user.
     // Uses`suggestions_key` property of `static/species.json`
     
     // DATASET - dataset selected by user.
     // Uses a single item of `projects` of `static/species.json`
     
     // FILTERTYPE - filtertype selected by user.
     // Uses `name` property of  `static/filters.json`
     
     // NUMFOUND - suffix in case the API is called to get the estimated result count.
     // In this case, `Numfound` is attached to the string.
     
     // RESPONSE_PARAMETERS - properties that should be included in response separated by spaces.
     
     // FILTER_PARAMETERS - filters set by user on the `index` page.
     // Contains each key and value of the filter
     
     
     // example calling both `response` and `numfound` API
     `humanFantom5Sample(UBERON: "skin epidermi", )
         {
             Description
             biosample
             UBERON
             CL
             NCIT
         } humanFantom5SampleNumfound }"`

   ---

   response

   Object with data property containing dynamic result properties based on ${SPECIE}${DATASET}${FILTERTYPE}.

       {
         data:
          {
            // only available in case `${SPECIE}${DATASET}${FILTERTYPE}` was part of the POST calling
            // contains result data shown in `components/ResultsWrapper.vue`
            // array contains objects with keys set at `columns` of the FILTERTYPE as set in`static/filters.json`
            `${SPECIE}${DATASET}${FILTERTYPE}`: [],
   
            // only available in case `${SPECIE}${DATASET}${FILTERTYPE}${NUMFOUND}` was part of the POST calling
            // only counts amount of results as number
            `${SPECIE}${DATASET}${FILTERTYPE}${NUMFOUND}`: 0
          }
       }
   
        // example of API response with both `response` and `numfound`
        {
            data:
                {
                    humanFantom5Sample:
                    [
                        {
                            Description: "basal cell carcinoma cell line:TE 354.T",
                            biosample: "SAMD00004671",
                            UBERON: "skin epidermis"
                            ,CL: "basal cell of epidermis",
                            NCIT: "Skin basal cell carcinoma"
                        }...
                    ]
                    humanFantom5SampleNumfound :19
                }
        }

   ---

   place of usage

   used in components/SearchBar.vue when

   1. a filter has changed value, triggering a Numfound search to update the estimated results.
   2. the search button has been clicked, triggering a results and Numfound API call. The query itself is formed in the suggest_query method.

4. Result data for project page

   api

   // GET API call
   `api/${FILTER_TYPE}/${ID}?dataset=${DATASET_NAME}`

   parameters

   • FILTER_TYPE
     • one of the filters as set in static/filters.json. In case of sample, columns of gene are used and vice versa
   • ID
     • array of IDS to get. Either sample or Gene ids
   • DATASET_NAME
     • name of dataset to get information from

   response

   object with table results and details of the id.

   {
     // contains details about requested id. `sample_info` in case of sample data.
     "gene_info": {
       alias: '[\"AOF2\", \"BHC110\", \"CPRF\", \"KDM1\", \"LSD1\"]',
       id: 23028
       name: "lysine demethylase 1A"
       symbol: "KDM1A",
     },
     // contains results for table
     "refex_info": []
   }

   place of usage

   used in pages/_organism/_project.vue in asyncData. Upon opening the page, the info in the URL is used to make this API call. In this way, one can use the URL directly to go the project page without having to pass index page.

5. Gene information with information icon

   api

   // GET API call
   `https://mygene.info/v3/gene/${GENE_ID}`

   parameters

   • GENE_ID
   • id of gene info to get

   response

   Object with detailed information about the gene.

      HGNC: "56187"
      accession: {genomic: ["AC078778.34", "AC079313.35", "CP068266.2", "KF459780.1", "NC_000012.12", "NC_060936.1"],...}]
      ...

   place of usage

   used in components/ModalView/ModalViewGene.vue to get detailed information about specific gene to show when user clicks on information icon.

Icons

Font awesome icons

• pro icons are used in this project so it is neccesary to set a token. See official documentation for more info

SVG icons

• all SVG icons should be set in components/icons by the name of Icon{NameOfIconInPascalCase}.
• When using the icon, import the components/icons/IconBase and pass the icon-name of NameOfIconInPascalCase.
• the color can be optionally set by icon-color. If it is not set, it will default to currentColor(inherits parents color)
• make sure all SVG icons do not have a fill color set otherwise the components/icons/IconBase will not be able to alter the color.
• if the SVG icon makes use of stroke, set strokeColor as a prop and use it for all strokes of the icon. (see components/icons/IconOryzasativa for an example)

Folders

components

For the component folder, find the preferred structure below:

1. Simple, dynamic components to be used all throughout the app

   • Stored inside the components folder
   • name of single component consist of 2 words in PascalCase eg LoadingSpinner
   • Should be small-scale modals to be imported to other components regardless of their parent

2. Complex components with specific purpose and child components

   • name of parent component should consist of 2 words in PascalCase eg FilterSection
   • folder name should be identical to the parent component name eg @/components/FilterSection/FilterSection.vue
   • child components should start with the same name as parent + child name in 1 word eg FilterSectionCondition.vue
   • children/siblings can be directly imported in the parent component by using PascalCase in the vue template

   <!-- template of FilterSection (parent component) -->
   <template>
       <FilterSectionSearch />
       <FilterSectionButtons />
   </template>
   

3. Components that belong to a similair group but do not neccesarily have a parent/child relationship

   • grouped together in folder
   • folder name should be a single word like search

pages

This directory contains your application views and routes. Nuxt will read all the *.vue files inside this directory and setup Vue Router automatically. More information about the usage of this directory in the documentation.

plugins

The plugins directory contains JavaScript plugins that you want to run before instantiating the root Vue.js Application. This is the place to add Vue plugins and to inject functions or constants. Every time you need to use Vue.use(), you should create a file in plugins/ and add its path to plugins in nuxt.config.js. More information about the usage of this directory in the documentation.

static

This directory contains your static files. Each file inside this directory is mapped to /. Example: /static/robots.txt is mapped as /robots.txt. More information about the usage of this directory in the documentation.

store

This directory contains your Vuex store files. Creating a file in this directory automatically activates Vuex. More information about the usage of this directory in the documentation.