Add a command 'pubmed-annotate' to retrieve PMIDs for a search term, then apply a template to all of them to extract info #127
Conversation
…apply a template to extract info
| @@ -280,6 +280,26 @@ def pubmed_extract(pmid, template, output, output_format, **kwargs): | |||
| write_extraction(results, output, output_format) | |||
|
|
|||
|
|
|||
| @main.command() | |||
There was a problem hiding this comment.
note we already have pubmed-extract which I think does the same thing...?
There was a problem hiding this comment.
I'm open to suggestions here, but pubmed-extract (IIUC) takes a list of PMIDs and extracts info
The idea here is to take a search term, retrieve PMIDs, then extract info on all of them
Glad to refactor if there is a better way to do this
There was a problem hiding this comment.
It may be more intuitive to modify pubmed-extract to accept more than one PMID
There was a problem hiding this comment.
though that also assumes you already have the PMIDs, so maybe more like providing a flag to do the search, output the PMID list, then pass that to extract
While making the distinction that there's also a use case for search -> get PMIDs -> extract keywords -> new search -> new PMIDs -> extract/summarize
There was a problem hiding this comment.
my $0.02 I'd say why not make a command to do this in one go, rather than making the user run two commands (one to get PMIDs and another to extract info)
@AgranyaGitHub @caufieldjh @pnrobinson along the lines of what we discussed today