PathwayCommons
Load index
Overview
I think this allows users to pass in a file path for an already existing index on their drive.
I tried testing it by having the program write the index to a file and on the next run I passed in the file path for that file and it seemed to work. When it loaded from an index I could see the significant speed boost instead of the original method.
Let me know if you guys see any issues, otherwise, we can merge.
PS: There are 2 commits, the first one has all the code updates, the second one was a minor flake8 fix.
Closes
Closes #56.
@Anwesh1 Looks good.
One thing, I changed the base branch from master to develop. The reason being that we are moving fast here (good) but that increases the chances we will break something. Let's keep master clean for now. At some point, we can merge develop into master.
~~Otherwise, LGTM.~~
@Anwesh1 Actually, it would be great if we could add a test to see if the server works as expected when an index is loaded from disk. Think you can handle that or would you rather I take it?
I'm not sure how to go about doing that. Do you think you could show me sometime?
Would this be a pytest test?
@Anwesh1 No problem, it is rather complicated so I will take it.
It would be good (for this project and beyond) to start getting familiar with pytest, though. They have great documentation, and there are lots of tutorials online. Unit testing is an important part of software engineering and pytest is the tool of choice of unit testing python code.
Okay sounds good, I'll definitely do that. Sure go ahead and tackle it when you can and then feel free to merge
Importing @jvwong code from pubmed-dl for the ncbi.py file works perfectly. However, the only issue is that one of the pytest tests is failing. Otherwise, the code works as intended.
@Anwesh1 Can you do the copy and paste in a new (fresh) branch off of develop, and open a PR? We can discuss this issue there.