Anweshi Anavadya

Thanks for the input @JohnGiorgi, is there anything else required?

Sure, sounds good. Thanks, @JohnGiorgi. Will merge after all the tests.

I'm not sure how to go about doing that. Do you think you could show me sometime? Would this be a `pytest` test?

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....

Set up an environment variable for the file path so the user can provide (optional). https://github.com/PathwayCommons/semantic-search/blob/6e3c35dda63f89b71373b017adbc85a8a73e66c6/semantic_search/main.py#L19 If they do provide then use that file to read the index. Look below...

By the way, all the situations you suggested I check out, work. Except for when the `uid` provided doesn't exist. This breaks the code producing an `Internal Server error`, trying...

Hey @JohnGiorgi, had a question regarding displaying the message. I pinpointed the location to fix the problem where uid is not valid to this place in the `ncbi.py` file: https://github.com/PathwayCommons/semantic-search/blob/a52492f00d63c81b3554c787607e7571a2469198/semantic_search/ncbi.py#L101-L103...

Line 102 where it states `logging.warn`, when changed to `logging.error` shows this: `ERROR:root:No PMID for {"id:": ["8463928683 Error occurred: The following PMID is not available: 938463928683"]}` So, when the `record`...

Essentially, that `if` block only triggers when we have a case of an invalid `uid`, so we don't actually need the `continue` here. We had the `continue` for the `pubmed-dl`...