hicsail / clotho Goto Github PK

Run npm run lint and fix these issues. npm run lint should be used before every commit

Many models don't have indexes, all models must have at least one

Allow user to reset password

Transfer over Clotho HTML

On Update Part and Device By ID, allow toDelete: true to be removed

In API branch, createPart method requires the sequence field, which was not a required field in the previous iteration of Clotho.

Please refer here for documentation regarding convenience methods

• Create a POST Route /api/blast
• Have route create temp directory mkdir -p /blast/temp####
• Create FASTA File on Sequences based on payload
• Read FASTA File and reply with the results
• Delete the Temp Folder After replying results

Reference : child_process

FASTA File should have extension .fasta

> Sequence Name-SequenceID
TAGDTAGDTdnalettersTSGAGTA

> Sequence Name2-SequenceID2
TAGSTGATGSATAGSTAGTSGA

Create UI to Run Clotho Functions

If you have reached the max auth attempts, be directed to update your password.

On password update, delete all auth attempts from your ip and username

These roles are possible for create convenience methods

• Glycerol
• Vector
• RBS
• Gene
• FP

• Install Blast on Docker
• Save Blast FASTA file on server
• Run BLAST on FASTA file with given sequence
• Parse results
• return results
• delete FASTA file

after Clotho is installed, we need a root user. Create a setup page that creates this root user and inserts it into the database.

• Provided instructions after is running to go to /setup
• Create an API route to insert root user, only if there is no root user
• Create /setup to get root users info if there is already a root user, return setup complete

When a user calls delete part or device, an attribute toDelete: true is added, and removed from search queries. Create a route to delete theses objects.

• route must only be run by admin user
• must go through each collection and delete instances
• return success / failure message

finish the create function page

Here is a List of Java Models that need to be converted, other can be added based on dependencies
other Java models

Please update what models you are working on

• Annotation - @jgyou-bu
• Assembly
• BasicModule
• BioDesign - @ibrahims123457
• CompositeModule
• Feature - @jgyou-bu
• Sequence - @jgyou-bu
• Part - @jgyou-bu
• Parameter - @ibrahims123457

Create A Model that keep track of version control history for BioDesign.

Version: Number
Application Used to Update: Get From Current Session
OldBioDesignId:
NewBioDesignId:

Implementation and proper testing

Create API to Update Bio Design and make a new version

Create Model to Store Custom Javascript Functions

Model Attributes

• Function Name - String
• UserID - String
• Code - String
• Example Input - Array
• Example Output - Array
• Pass Test - Boolean

Use the $isolated attribute on MongoDB on update functions to support concurrent interaction by multiple users

MongoDB Docs $isolated

Confirm If all DNA Charters are included before making function

Create A Pre-Function to check whether DNA Sequence is valid.
Use Bio Node checkType to see if it returns a valid sequence

create a page to allow users to edit account settings

• Change username
• Change email
• Change full name
• Change password

Build an API to Create A Clotho Function
The function should be tested in the browser.

Create an API to execute custom functions

Getting no response with the following payload:

{
	"createSeqFromParts":"true",
	"name":"pBAD_betIBFP_EF",
	"partIds":["59772f52844cd13aefd11935","59772f54844cd13aefd11953","59772f54844cd13aefd11959","59772f55844cd13aefd11971"],
	"displayId":"pBAD_betIBFP_EF"
}

api/Get Part/{:filter}
will only return Biodesign with the filtered object

Example:
api/Get Part/parameters

will only return the Biodesign with the parameters object, parts and modules not included

[
  {
    "_id":"BioDesignID",
    "Others": "Bio Designs Attrubtes",
    "parameters": [
      {"parameter object"}
    ]
  }
]

Get Part/parts
will only return the bodyDesign with the parts object, parameters and modules not included

[
  {
    "_id":"BioDesignID",
    "Others": "Bio Designs Attrubtes",
    "parts": [
      {"part object"}
    ]
  }
]

This route will have the same payload as Get Part

Call Server.inject(request, response) with the same request as Get Part and loop parse the output

Same Routes for the Device

Add optional attribute to include deleted objects and as only deleted devices

On search for Part and Device add a boolean parameter default to be false,
if false return all part/devices
if true return your part/device

• Part
• Device

Create A Model Roles that is a List Of Part And Device Roles that is used, Role Often Change or be added.

• No assembly

• No subAnnotations

• No superSequence

• No superAnnotation

• Move all client side javascript to a folder.
• Create a script to minify javascript
• Reference all scripts to minified javascript

Use node-minify

get___ and findBy___Id functions do not all except lists of ids.
This interferes with the get Functions.
Either resolve this, or create 2 separate routes accordingly.

Get Access to AWS from CIDER lab and set up Docker and CI on Master Branch
Switch Out out CI Server to Staging Branch

Error: ENOENT: no such file or directory, open './server/web/public/mini-js/register.min.js'

minify script has to make ./server/web/public/mini-js/ dirctory

Make logout API call be more descriptive on it responses.

some of the models have attribute author and author_id. these must be changed to userId to match current pattern in frame

Use BioNode to create clotho functions

• checkType
• reverse
• complement
• reversecomplement
• removeIntrons
• transcribe
• translate - not used, unable to store proteins in database

Add docker to the application as well as documentation on how to install, setup and run application using docker.

Two payloads:

{
	"name":"testpart5",
	"displayId":"testpart5",
	"role":"FP",
	"sequence":"ACTGACTGACTG",
}

Role and Sequence are not being stored in the database. In screenshot, middle left is database output.

{
	"name":"testpart6",
	"displayId":"testpart6",
	"role":"FP",
	"sequence":"ACTGACTGACTG",
	"parameters":[
		{
			"name":"toxic metric",
			"value":"0.5",
			"units":"mmol",
			"variable":"toxicity"
			
		}
	]
}

Role, Sequence and Parameters are not being stored in the database. In screenshot, bottom left is database output

GET-ting either with .../api/part/{_id} returns 404

Some models have 2 create statements

class CompositeModule extends MongoModels {

  static create(name, role, submodules, author, callback) {
    return create(name, null, role, submodules, author, callback);
  }

  static create(name, description, role, submodules, author_id, callback) {

remove first create statement since api method will insert default | null when approprate

 static create(name, role, submodules, author, callback) {
    return create(name, null, role, submodules, author, callback);
  }

• Retrieve superPart with BioDesignId
• Retrieve subparts though bioDesign
• Retrieve Assembly
• Retrieve subAnnotations

Slate has a better system to document the API, which includes multi-language support, better search functionality

• Get Slate Up And Running
• Customize It to Include Favicon And Logo
• Add Slate Requirements to documentation
• Add Slate Requirements to Docker
• Change API Docs to point to Slate

View scale as an example