Fixed docker, single sample endpoint, matrix calculation, documentation

[Fattigman]

(sc2rep2) ➜  backend git:(fix-single-sample) python -m pytest .
===================================== test session starts ======================================
platform darwin -- Python 3.10.9, pytest-7.4.2, pluggy-1.3.0
rootdir: /Users/jacobkarlstrom/Projects/SarsCov2/docker-sc2reporter/backend
plugins: anyio-3.5.0, asyncio-0.21.1
asyncio: mode=strict
collected 13 items                                                                             

tests/test_authentication.py .........                                                   [ 69%]
tests/test_dashboard.py ..                                                               [ 84%]
tests/test_db.py .                                                                       [ 92%]
tests/test_root.py .                                                                     [100%]

======================================= warnings summary =======================================
../../../../miniconda3/envs/sc2rep2/lib/python3.10/site-packages/tornado/ioloop.py:263
  /Users/jacobkarlstrom/miniconda3/envs/sc2rep2/lib/python3.10/site-packages/tornado/ioloop.py:263: DeprecationWarning: There is no current event loop
    loop = asyncio.get_event_loop()

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================ 13 passed, 1 warning in 15.23s ================================

[Fattigman]

What I have done

* Documented the code

• Wrote tests for the backend
• Formatted the code
• Parallelised phylogenetic calculations
• Formatted external links to CoVariants
• Fixed local log in from docker

[Fattigman]

dup is an alias for docker-compose up

(sc2rep2) ➜  docker-sc2reporter git:(fix-single-sample) dup -d --build
WARNING: Found orphan containers (docker-sc2reporter_mongo_seed_1) for this project. If you removed or renamed this service in your compose file, you can run this command with the --remove-orphans flag to clean it up.
Building fastapi
[+] Building 546.2s (13/13) FINISHED                                                            
 => [internal] load build definition from Dockerfile                                       0.0s
 => => transferring dockerfile: 37B                                                        0.0s
 => [internal] load .dockerignore                                                          0.0s
 => => transferring context: 2B                                                            0.0s
 => [internal] load metadata for docker.io/library/python:3.10-slim-bullseye               2.4s
 => [auth] library/python:pull token for registry-1.docker.io                              0.0s
 => [internal] load build context                                                          0.0s
 => => transferring context: 11.70kB                                                       0.0s
 => [1/7] FROM docker.io/library/python:3.10-slim-bullseye@sha256:3b3c97a489c2321c92f08b6  3.1s
 => => resolve docker.io/library/python:3.10-slim-bullseye@sha256:3b3c97a489c2321c92f08b6  0.0s
 => => sha256:3b3c97a489c2321c92f08b6b12523435e9cfa02c84c820f3f14efd94d70 1.65kB / 1.65kB  0.0s
 => => sha256:fc88130496455176d24d3f613445abcee3732576060e14afa61e7f6daa1 1.37kB / 1.37kB  0.0s
 => => sha256:416b2ef9606d7e24b3307b5107efb5786cc7974ebd08e094d3c23eba174 6.93kB / 6.93kB  0.0s
 => => sha256:e67fdae3559346105027c63e7fb032bba57e62b1fe9f2da23e6fdfb56 31.42MB / 31.42MB  1.2s
 => => sha256:a970ffaebef6fd07818bd49400c57484158e1665c80c51d70eac2080012 1.08MB / 1.08MB  0.3s
 => => sha256:f19835c73b0e5e58fe6e0ef70e2119e31fd0f459c9d569fd2845d194e 11.54MB / 11.54MB  0.8s
 => => sha256:da1214bed9aa273d3be4a2db0c2e622a54f5c4e66c9af766ce2d9fbae914d1a 244B / 244B  0.5s
 => => sha256:19fcedbbd72d418019ea480656dfd0ee0a0a5a5ffd87e540613c82936c2 3.37MB / 3.37MB  0.8s
 => => extracting sha256:e67fdae3559346105027c63e7fb032bba57e62b1fe9f2da23e6fdfb56384e00b  1.0s
 => => extracting sha256:a970ffaebef6fd07818bd49400c57484158e1665c80c51d70eac2080012d73ef  0.1s
 => => extracting sha256:f19835c73b0e5e58fe6e0ef70e2119e31fd0f459c9d569fd2845d194e26fd066  0.3s
 => => extracting sha256:da1214bed9aa273d3be4a2db0c2e622a54f5c4e66c9af766ce2d9fbae914d1ab  0.0s
 => => extracting sha256:19fcedbbd72d418019ea480656dfd0ee0a0a5a5ffd87e540613c82936c2fdae4  0.1s
 => [2/7] RUN apt-get update &&     apt-get install -y         gcc                        48.5s
 => [3/7] RUN python -m pip install --upgrade pip                                         16.8s
 => [4/7] COPY ./requirements.txt /requirements.txt                                        0.0s 
 => [5/7] RUN pip install -r requirements.txt                                            469.4s 
 => [6/7] COPY ./ /app                                                                     0.1s 
 => [7/7] WORKDIR /app                                                                     0.0s 
 => exporting to image                                                                     5.6s 
 => => exporting layers                                                                    5.6s 
 => => writing image sha256:540bb5ccd9320c0f14a4b67beacebbcbe0cc06138a8f3f5c3f6d3077d0ebe  0.0s 
 => => naming to docker.io/library/docker-sc2reporter_fastapi                              0.0s
Building frontend
[+] Building 129.2s (11/11) FINISHED                                                            
 => [internal] load build definition from Dockerfile                                       0.0s
 => => transferring dockerfile: 37B                                                        0.0s
 => [internal] load .dockerignore                                                          0.0s
 => => transferring context: 34B                                                           0.0s
 => [internal] load metadata for docker.io/library/node:18-alpine                          1.8s
 => [auth] library/node:pull token for registry-1.docker.io                                0.0s
 => [1/5] FROM docker.io/library/node:18-alpine@sha256:435dcad253bb5b7f347ebc69c8cc52de7c  3.1s
 => => resolve docker.io/library/node:18-alpine@sha256:435dcad253bb5b7f347ebc69c8cc52de7c  0.0s
 => => sha256:435dcad253bb5b7f347ebc69c8cc52de7c912eb7241098b920f2fc2d784 1.43kB / 1.43kB  0.0s
 => => sha256:f439e9091207d478bf7cf8ce3967ea08f3ef357f08eb264dd14eac7f4da 1.16kB / 1.16kB  0.0s
 => => sha256:f5a5f92010157c0e38d5611b97eb473f6f95fd583c8bf45a2fca5cddd98 6.79kB / 6.79kB  0.0s
 => => sha256:579b34f0a95bb83b3acd6b3249ddc52c3d80f5c84b13c944e9e324feb86 3.33MB / 3.33MB  0.2s
 => => sha256:193dce5f4a0cf83f577b68c70b4e91199f39f88aac032b21359a13314 48.02MB / 48.02MB  1.3s
 => => sha256:78d1fe6b9b44fc9c132c16332d54041ac771dc5e65e8fee11bba0ee306c 2.34MB / 2.34MB  0.6s
 => => extracting sha256:579b34f0a95bb83b3acd6b3249ddc52c3d80f5c84b13c944e9e324feb86dd329  0.3s
 => => sha256:18c854bc80eaceb8b8e4e799cc9955831ea8355d0b61a08b80b3a5226ea1da5 450B / 450B  0.5s
 => => extracting sha256:193dce5f4a0cf83f577b68c70b4e91199f39f88aac032b21359a13314f7dc6f5  1.5s
 => => extracting sha256:78d1fe6b9b44fc9c132c16332d54041ac771dc5e65e8fee11bba0ee306c9b04e  0.1s
 => => extracting sha256:18c854bc80eaceb8b8e4e799cc9955831ea8355d0b61a08b80b3a5226ea1da55  0.0s
 => [internal] load build context                                                          0.0s
 => => transferring context: 2.07kB                                                        0.0s
 => [2/5] WORKDIR /app                                                                     0.0s
 => [3/5] COPY package.json yarn.lock ./                                                   0.0s
 => [4/5] RUN yarn install                                                                85.1s
 => [5/5] COPY . .                                                                         0.0s
 => exporting to image                                                                    39.0s 
 => => exporting layers                                                                   39.0s 
 => => writing image sha256:d5cacc89269bcae61a756149cfea673080b05a6d2ef051fda4942c156b476  0.0s 
 => => naming to docker.io/library/docker-sc2reporter_frontend                             0.0s 
Building grapetree                                                                              
[+] Building 178.8s (11/11) FINISHED                                                            
 => [internal] load build definition from Dockerfile                                       0.0s
 => => transferring dockerfile: 37B                                                        0.0s
 => [internal] load .dockerignore                                                          0.0s
 => => transferring context: 2B                                                            0.0s
 => [internal] load metadata for docker.io/library/python:3.7-slim-bullseye                1.9s
 => [auth] library/python:pull token for registry-1.docker.io                              0.0s
 => [internal] load build context                                                          0.0s
 => => transferring context: 29.08kB                                                       0.0s
 => [1/5] FROM docker.io/library/python:3.7-slim-bullseye@sha256:603879aeff06df23f0d392a1  2.7s
 => => resolve docker.io/library/python:3.7-slim-bullseye@sha256:603879aeff06df23f0d392a1  0.0s
 => => sha256:603879aeff06df23f0d392a19f7ce02aa85e14e6b4d25fd9647b116e0cb 1.86kB / 1.86kB  0.0s
 => => sha256:ea8897698c0955ba96144bd2b7310ef7884ccce4db7a1f97ffc21fb8b89 1.37kB / 1.37kB  0.0s
 => => sha256:b5b0a67a91504c733095fdc8785063e5732d19237524be91c600d1608f1 7.54kB / 7.54kB  0.0s
 => => sha256:7dbc1adf280e1aa588c033eaa746aa6db327ee16be705740f81741f5e 31.42MB / 31.42MB  0.8s
 => => sha256:4171d440ff028644f6d5b9862d500def1778bccd4495d24c3183acde409 1.08MB / 1.08MB  0.4s
 => => sha256:747d3e54f9105492033c0319688ed162eea0268626d66be15f866683e 10.57MB / 10.57MB  0.8s
 => => sha256:329353726c169e287f3a2cc0742d55a8070921975b04cdc166ab9c54efeecfa 244B / 244B  0.7s
 => => sha256:13d0722ff7000ee3431f398ef35fb6f2060172a5ae6d327fff764040d16 3.14MB / 3.14MB  1.0s
 => => extracting sha256:7dbc1adf280e1aa588c033eaa746aa6db327ee16be705740f81741f5e6945c86  1.0s
 => => extracting sha256:4171d440ff028644f6d5b9862d500def1778bccd4495d24c3183acde40950a9f  0.1s
 => => extracting sha256:747d3e54f9105492033c0319688ed162eea0268626d66be15f866683e6158789  0.3s
 => => extracting sha256:329353726c169e287f3a2cc0742d55a8070921975b04cdc166ab9c54efeecfad  0.0s
 => => extracting sha256:13d0722ff7000ee3431f398ef35fb6f2060172a5ae6d327fff764040d1644968  0.2s
 => [2/5] COPY . /app                                                                      0.4s
 => [3/5] WORKDIR /app                                                                     0.0s
 => [4/5] RUN apt-get update &&     apt-get install -y         gcc                        57.6s
 => [5/5] RUN pip3 install . &&     pip3 install pandas requests gunicorn                114.4s
 => exporting to image                                                                     1.7s 
 => => exporting layers                                                                    1.7s 
 => => writing image sha256:6b68949695e50aeb4f973e7801438b798b89bfc2f0d67ff02841c742145e5  0.0s 
 => => naming to docker.io/library/docker-sc2reporter_grapetree                            0.0s 
docker-sc2reporter_mongodb_1 is up-to-date                                                      
Recreating sc2reporter-api ... 
Recreating sc2reporter-api ... done
Recreating sc2reporter-grapetree ... done
Recreating sc2reporter-frontend  ... done