feat: Show RCSB metadata on frontend.

fissoreg commented 3 years ago

PR type

🏆 Enhancements

Getting some metadata from rcsb.org to show on the frontend.

Purpose

To actually understand if the results are meaningful (i.e. to evaluate the model) we need more details then the PDB ID.

Why?

Make the prototype more usable and user-friendly.

Feedback required over

A quick pair of :eyes: on the code
Discussion on what to add. For now we can merge this and deploy, but we will probably want to add/remove information. We can open an issue to discuss this.

Mentions

@georgeamccarthy

georgeamccarthy commented 3 years ago

Spinning proteins is an epic feature. I'm gonna edit the title to make the purpose a little more specific.

georgeamccarthy commented 3 years ago

Really cool stuff! I'll test it out and see what it looks like.

georgeamccarthy commented 3 years ago

I'm getting errors trying to use gql

➜ pip install gql
WARNING: Value for scheme.platlib does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/lib/python3.9/site-packages
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/lib/python3.9/site-packages
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/include/python3.9/UNKNOWN
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/UNKNOWN
WARNING: Value for scheme.scripts does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/bin
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9
WARNING: Additional context:
user = False
home = None
root = None
prefix = None
Requirement already satisfied: gql in /opt/homebrew/lib/python3.9/site-packages (2.0.0)
Requirement already satisfied: graphql-core<3,>=2.3.2 in /opt/homebrew/lib/python3.9/site-packages (from gql) (2.3.2)
Requirement already satisfied: promise<3,>=2.3 in /opt/homebrew/lib/python3.9/site-packages (from gql) (2.3)
Requirement already satisfied: six>=1.10.0 in /opt/homebrew/lib/python3.9/site-packages (from gql) (1.16.0)
Requirement already satisfied: requests<3,>=2.12 in /opt/homebrew/lib/python3.9/site-packages (from gql) (2.26.0)
Requirement already satisfied: rx<2,>=1.6 in /opt/homebrew/lib/python3.9/site-packages (from graphql-core<3,>=2.3.2->gql) (1.6.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/homebrew/lib/python3.9/site-packages (from requests<3,>=2.12->gql) (1.26.6)
Requirement already satisfied: certifi>=2017.4.17 in /opt/homebrew/lib/python3.9/site-packages (from requests<3,>=2.12->gql) (2021.5.30)
Requirement already satisfied: idna<4,>=2.5 in /opt/homebrew/lib/python3.9/site-packages (from requests<3,>=2.12->gql) (3.2)
Requirement already satisfied: charset-normalizer~=2.0.0 in /opt/homebrew/lib/python3.9/site-packages (from requests<3,>=2.12->gql) (2.0.3)

➜ pip uninstall gql
Found existing installation: gql 2.0.0
Uninstalling gql-2.0.0:
  Would remove:
    /opt/homebrew/lib/python3.9/site-packages/gql-2.0.0.dist-info/*
    /opt/homebrew/lib/python3.9/site-packages/gql/*
Proceed (Y/n)? Y
  Successfully uninstalled gql-2.0.0

➜ pip install --pre gql[all]
zsh: no matches found: gql[all]

➜ pip install --pre gql
WARNING: Value for scheme.platlib does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/lib/python3.9/site-packages
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/lib/python3.9/site-packages
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/include/python3.9/UNKNOWN
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/UNKNOWN
WARNING: Value for scheme.scripts does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew/bin
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /opt/homebrew
sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9
WARNING: Additional context:
user = False
home = None
root = None
prefix = None
Collecting gql
  Downloading gql-3.0.0a6.tar.gz (86 kB)
     |████████████████████████████████| 86 kB 1.3 MB/s
Collecting graphql-core<3.2,>=3.1.5
  Downloading graphql_core-3.1.5-py3-none-any.whl (188 kB)
     |████████████████████████████████| 188 kB 1.6 MB/s
Collecting yarl<2.0,>=1.6
  Downloading yarl-1.6.3.tar.gz (176 kB)
     |████████████████████████████████| 176 kB 3.4 MB/s
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting multidict>=4.0
  Downloading multidict-5.1.0.tar.gz (53 kB)
     |████████████████████████████████| 53 kB 1.9 MB/s
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: idna>=2.0 in /opt/homebrew/lib/python3.9/site-packages (from yarl<2.0,>=1.6->gql) (3.2)
Building wheels for collected packages: gql, yarl, multidict
  Building wheel for gql (setup.py) ... done
  Created wheel for gql: filename=gql-3.0.0a6-py2.py3-none-any.whl size=34862 sha256=4a777de53ec0eddcbb36e6dbb66dc099437de3e6eb92d5cf98ebd915a7ec5363
  Stored in directory: /Users/georgeamccarthy/Library/Caches/pip/wheels/a7/29/1a/9709f3b2c98a2d811d8be839cba15af7e578815f0e8f87d96e
  Building wheel for yarl (PEP 517) ... done
  Created wheel for yarl: filename=yarl-1.6.3-cp39-cp39-macosx_11_0_arm64.whl size=121303 sha256=40d5164419a32cae8dd1b5c5da4149a463fadd6ab1b9fae585088cf272836285
  Stored in directory: /Users/georgeamccarthy/Library/Caches/pip/wheels/c2/03/d3/a7ea30efd0c84c03fd1caf7757949a1dedf797361267741ef0
  Building wheel for multidict (PEP 517) ... done
  Created wheel for multidict: filename=multidict-5.1.0-cp39-cp39-macosx_11_0_arm64.whl size=49478 sha256=ef34625338e4f47ac7ba120ca105c7a9d089edfff53a85f820c00098a0f54789
  Stored in directory: /Users/georgeamccarthy/Library/Caches/pip/wheels/30/e1/1c/e049eab71b71df690ef505f2c3d5ef4d0c583346bd22f5a85f
Successfully built gql yarl multidict
Installing collected packages: multidict, yarl, graphql-core, gql
  WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
  distutils: /opt/homebrew/include/python3.9/multidict
  sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/multidict
  WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
  distutils: /opt/homebrew/include/python3.9/yarl
  sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/yarl
  Attempting uninstall: graphql-core
    Found existing installation: graphql-core 2.3.2
    Uninstalling graphql-core-2.3.2:
      Successfully uninstalled graphql-core-2.3.2
  WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
  distutils: /opt/homebrew/include/python3.9/graphql-core
  sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/graphql-core
  WARNING: Value for scheme.headers does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
  distutils: /opt/homebrew/include/python3.9/gql
  sysconfig: /opt/homebrew/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9/gql
Successfully installed gql-3.0.0a6 graphql-core-3.1.5 multidict-5.1.0 yarl-1.6.3

➜ streamlit run frontend/app.py
2021-07-29 17:13:43.685 Traceback (most recent call last):
  File "/Users/georgeamccarthy/opt/anaconda3/envs/jina/lib/python3.8/site-packages/streamlit/script_runner.py", line 349, in _run_script
    exec(code, module.__dict__)
  File "/Users/georgeamccarthy/Documents/workspace/python/protein_search/frontend/app.py", line 4, in <module>
    from gql import gql, Client
ModuleNotFoundError: No module named 'gql'

fissoreg commented 3 years ago

My bad, I didn't update the requirements. Can you try the following line?

pip install --pre "gql[aiohttp]"

I'll try to update the requirements.txt in the meanwhile.

georgeamccarthy commented 3 years ago

No worries, I tried that but I was facing issues because my pip version was for python 3.9 and my python was 3.8! I've corrected that and the install has worked!

georgeamccarthy commented 3 years ago

The metadata is great! Good job. I'm noticing that the proteins aren't loading for me. Are they for you?

georgeamccarthy commented 3 years ago

Also getting a big dump on the frontend

georgeamccarthy commented 3 years ago

I just had to disable my add blocker! Looks great, loving the spinning and gonna merge :)

fissoreg commented 3 years ago

The dump on the frontend is a problem indeed. I ignored it for now, I think it is some logging from gql. We can probably disable it using the right arguments.

georgeamccarthy / protein_search