requirements.txt

[Bancherd-DeLong]

HI: I am fairly new to Knowledge Graph, and totally new to biomedical KGs. Thank you very much for sharing your work.

I am having problems installing requirements.txt, with "responses==0.10.12". I am using ubuntu 20.04, with anaconda for virtual environment. It appears that conda only has version 0.10.8. Can I use 0.10.8?

Best Regards, Bancherd DeLong

[callahantiff]

Hi @Bancherd-DeLong. Thanks for your comment and for using PheKnowLator! I'd be very happy to try and help troubleshoot this. I can't initially see any issues with using the version of responses that you mention. Are you able to fork the PheKnowLator GitHub repo and use it in your environment? If so, this might be the quickest way to get things running for you. Let me know if that seems reasonable I can let you know exactly which scripts/files would need to be changed.

In the meantime, I can implement some tests and meet with my team to think through whether or not we will be able to support releasing a version on PyPI that extends the versions required for responses.

[Bancherd-DeLong]

HI:

Thank you for a very quick response.

I tried to run the notebook(Data_Preparation.ipynb) and received the following error : The strange thing is that when I manually executed the code, I did not have problems with "rdflib".

Thank you. PS. I am using a conda-env with python=3.6, and installed using "pip install pkt_kg"

[callahantiff]

Hi @Bancherd-DeLong -

Hmmm 🤔 I am sorry you are hitting this error. Did you by chance uncomment and run the first two code chunks in this notebook? The one that looks like the screenshot below? Please see note below before running these chunks.

BEFORE RUNNING THOSE CHUNKS: Please note that I just pushed a PR to the master branch to update notebooks/requirements.txt that you will need to make sure you pull changes from origin from your fork to get. The test suit takes about ~20 minutes to run and then it should be available. Otherwise, you will get an error like the one shown below.

In case you need this file to be updated immediately, can open the file and remove line 15 (i.e., "urllib") or you can replace the original content of this file with the text shown in the snippet below.

updated content: notebooks/requirements.txt

Cython>=0.29.14
more-itertools>=8.6.0
networkx>=2.4
numpy>=1.18.1
openpyxl>=3.0.3
pandas>=1.0.5
psutil>=5.6.3
python-json-logger>=2.0.1
ray>=1.1.0
rdflib>=4.2.2
reactome2py>=0.0.8
requests>=2.22.0
responses==0.10.12
tqdm>=4.47.0
urllib3>=1.25.3

With the updated requirements.txt file and kernel restarted in the Jupyter Notebook you should not (hopefully) not hit any errors.

One last question -- did you end up forking the library rather than installing it directly from PyPI? Just trying to think through why this error might be occurring.

[Bancherd-DeLong]

Hi: Sorry, I finally forked the repo(about 24 hours ago?) and installed from git. I manually installed the files in the requirements.txt and got to the downloading section. I am now in the downloading section trying to populate /resources/.

Please note that I received an error during "quality check" after the fork. I will refork the repo and try using the notebook again.

Thanks.

[Bancherd-DeLong]

Sorry, I think I had just committed a major faux pas, by committing changes to "master".
With the updated version, I still had errors(ray<=1.0.1, and did not find "networkx"). I am not sure if "conda" was causing the problem. I will try with "venv"

[Bancherd-DeLong]

Let me wrestle with this a little more, the problems might be on my side. I will close this for now. Thank you.

[callahantiff]

Sounds good @Bancherd-DeLong! Don't hesitate to let me know if there is anything that I can help with! 😄