Swab 'n Seq Application

Application to show sequencing results for IGO's open house

Dev

Frontend

cd frontend && npm install && npm run start

Backend

cd backend && make init && make run

Loading Data

Currently, no "DB" is used and instead two files are written swab_n_seq_results.py & download.py. Use this setup by formatting Qiime results like below,

• swab_n_seq_results.py - Contains visualized data in the following format,

data = {
   "results":{
      "user_id":[
         {
            "count":698.0,
            "org":{                 # fullest taxonomic identification from Kingdom -> Species ("" if couldn't specify)
               "":"",
               "k":"Bacteria"
            }
         },
         ...
      ],
      ...
   },
   "summary":{
      "c":[                         # Taxonomic (e.g. "c" - Phylum, "f" - "Family")
         {
            "count":44.0,
            "org":{
               "c":"Elusimicrobia"
            }
         },
      

• download.py - Contains same information as swab_n_seq_results.py, but in downloadable csv form that comes in a dense-matrix format like below,

data = {
   "headers":[
      "index",
      "k__Archaea;p__Crenarchaeota;c__Thaumarchaeota;o__Nitrososphaerales;f__Nitrososphaeraceae;g__Candidatus Nitrososphaera;s__SCA1145",
      ...
   "data":{
      "user_id": [
        user_id,
        (int),
        ...
      ]
  }
}

• headers are the identified taxonomies in semicolon-separated groups
• data are the counts for a given user_id

Deploy

make HOST=dlviigoweb1  ENV=prod deploy

Notes:

• This DELETES the existing application on the HOST specified. It then copies the packaged application created locally to the new location.
• This creates and copies a build directory to the backend directory in your home on the HOST specified. Make sure your ~/deployments exists on that HOST!
• make deploy is a Makefile command. If there are issues w/ this step, please review the deploy step of the Makefile
• Expect to enter your password four times - once to scp the packaged application, once to remotely send the install command, and twice to run dzdo remotely (dzdo allows for root access on our VM's and is needed so you can re-deploy if another user was the last to deploy)