New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Entrez journal examples fixes #735 #736
Conversation
Current coverage is
|
@@ -263,12 +265,11 @@ \section{ESummary: Retrieving summaries from primary IDs} | |||
>>> Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are | |||
>>> handle = Entrez.esummary(db="journals", id="30367") |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Shouldn't this line be changed too?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I am too dyslexic for this.
@@ -200,18 +200,20 @@ \section{ESearch: Searching the Entrez databases} | |||
|
|||
As a final example, let's get a list of computational journal titles: | |||
\begin{verbatim} | |||
>>> handle = Entrez.esearch(db="journals", term="computational") | |||
print("{} computational Journals found".format(record["Count"])) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
That should have three leading >>>
signs and the expected result if you want it to be part of the "doctest".
However, since this appears later I think this is more likely an accident and this line should be removed?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Correct, it needed to be removed.
@peterjc Would you like me to refactor this pull request to be more like the previous example? |
@@ -200,18 +200,19 @@ \section{ESearch: Searching the Entrez databases} | |||
|
|||
As a final example, let's get a list of computational journal titles: | |||
\begin{verbatim} | |||
>>> handle = Entrez.esearch(db="journals", term="computational") | |||
>>> handle = Entrez.esearch(db="nlmcatalog", term="computational[Journal]", , RetMax='20') |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
The extra comma in there is a glitch, and I will remove it...
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Also it should be retmax
not RetMax
although it "works" and the case is carried forward to the URL.
I was going to merge this (using
|
, term="[journal]", --> , (i.e. remove this argment) |
Squashed commit of GitHub pull request #736
Applied as squashed commit 05ee639 - thanks! |
Entrez journal examples fixes #735
Fixed two (all) examples, still searches journals but finds them via the nlmcatalog.