SOAPLab Backend

DJANGO-Assembly-Methods 🔬

Docs: https://imperial-igem.github.io/DJANGO-Assembly-Methods/

hosted and available at: http://app.soaplab.io/graphql

A django restframework with 2 endpoints /Basic and /Moclo to provide OT2 lab automation python scripts for the respective asembly methods from formatted CSV files

getting set up 👨‍💻

Open your command line and create a directory in which you would like to work

Make a directory (recommended DJANGO-ASSEMBLY-METHODS)

$ mkdir DJANGO-ASSEMBLY-METHODS

change directory into your new directory

$ cd DJANGO-ASSEMBLY-METHODS

clone our repositry

$ git clone https://github.com/Imperial-iGEM/DJANGO-Assembly-Methods.git

create a venv inside root folder

$ cd ..
$ pip3 install virtualenv
$ virtualenv -p $(which python3.7) venv

activate the virtual enviroment

$ source venv/bin/activate

Install our repositry dependencies inside requirements.txt

$ cd DJANGO-Assembly-Methods

$ pip install -r requirements.txt

Run server

$ python manage.py migrate

$ python manage.py collectstatic

$ python manage.py runserver

Continuous Intergration and Unittests ✅

For our Ci we use Github Actions, to check progress of you pull request click on the actions folder. Every push request is tested against a build on python 3.6, 3.7 and 3.8.

For out unit tests we use Django's built in offering, before making a pull request trying running this command in the root folder to initiate unit tests

python manage.py test

Ensure PEP8 Code Style Compatability 📚

Before submitting a pull request to ensure high code quality navigate to the root folder of the project and run

$ cd ..
$ autopep8 -r --diff DJANGO-Assembly-Methods/

testing the RESTAPI 🧬

Once your server in running as we left our machine in the previous stage, we can use the GUI django rest framework provides to test out our two end points!

Graphql

We implemented graphql technologies into our Django Backend with the python library graphene. Because of this we only have 1 endpoint "/graphql"

linkerList

Note Full docs are available by clicking docs at top right of http://app.soaplab.io/graphql

One graphql mutation present at this endpoint is:

linkerList(sbolFileString: String): LinkerList

The only argument sbolFileString is of type String; contains the contents of the SBOL file base64 Encoded in a string format. The only output is an array LinkerList; an array containing strings of each Part/Linker name inside the SBOL file

Final Spec

Note Full docs are available by clicking docs at top right of http://app.soaplab.io/graphql

The only other mutation present at the graphql endpoint is:

finalSpec(
  assemblyType: String
  linkerTypes: [LinkerInType]
  sbolFileString: String
  specificationsBasic: InputSpecsBASIC
  specificationsBioBricks: InputSpecsBioBricks
  specificationsMoClo: InputSpecsMoClo
): FinalSpec

AssemblyType

The first argument specifies the assembly type 'basic', 'moclo' or 'biobricks'

example

'basic'

linkerTypes

The second argument is a json object specifiying partid, concentration, well and location

example

[{ "linkerId": "BBa_J23100", "concentration": 50, "plateNumber": 1, "well": "A1" }, {"linkerId": "BBa_J23106", "concentration": 50, "plateNumber": 1, "well": "A2" }, {"linkerId": "BBa_J23114", "concentration": 50, "plateNumber": 1, "well": "A3" }, }]

sbolFileString

The third argument is the same as the only argument at the linkerList mutation, a string with the contents of the SBOL file base64 Encoded.

example

https://github.com/Imperial-iGEM/DJANGO-Assembly-Methods/blob/master/examples/sbol/basic_linkers_standard.xml

specificationsBasic 🦠

The fourth argument is a object called InputSpecsBASIC which has the format displayed withing the example input

"specificationsBasic": {
    "ethanolWellForStage2": "A1",
		"deepWellPlateStage4": "A11",
		"labwareDict": {
			"commonLabware": {
        "p10Mount": "right",
        "p300Mount": "left",
        "p10Type": "p10_single",
        "p300Type": "p300_single",
        "wellPlate": "biorad_96_wellplate_200ul_pcr"
      },
      "wellPlate": 1,
      "reagentPlate": "2",
      "magPlate": "String",
      "tubeRack": "String",
      "aluminumBlock": "String",
      "beadContainer": "String",
      "socPlate": "String",
      "agarPlate": "String"
    }
  },

specificationsBioBricks 🧑‍🔬

The fifth argument is a object called InputSpecsBioBricks which has the format displayed withing the example input

"specificationsBioBricks": {
    "labwareDict": {
      "commonLabware": {
        "p10Mount": "right",
        "p300Mount": "left",
        "p10Type": "p10_single",
        "p300Type": "p300_single",
        "wellPlate": "biorad_96_wellplate_200ul_pcr"
      },
      "tubeRack": "opentrons_24_tuberack_nest_1.5ml_snapcap",
      "socPlate": "usascientific_96_wellplate_2.4ml_deep",
      "transformationPlate": "corning_96_wellplate_360ul_flat"
    },
    "thermocycle": true
  }

specificationsMoClo 🧑‍🔬

The sixth argument is a object called InputSpecsMoClo which has the format displayed withing the example input

"specificationsMoClo": {
    "thermocycle": false, 
    "labwareDict": {
      "commonLabware": {
        "p10Mount": "right",
        "p300Mount": "left",
        "p10Type": "p10_single",
        "p300Type": "p300_single",
        "wellPlate": "4ti_0960_framestar"
      },
      "trough": "4ti-0131",
      "reagentPlate": "4ti_0960_framestar",
      "agarPlate": "thermofisher_96_wellplate_180ul"
    } 
  }

Interested in Contributing 🤔💡

We welcome everyone interested in contrubuting if your a seasoned open source professional or interested in learning something new fell free to open issues and pull requests.

If you have any specific questions feel free to send an email to the 2020 imperial igem team 🚀

imperialigem2020@gmail.com