[Biopython-dev] Setting the NCBI Entrez tool parameter globally

[Michiel de Hoon]

Basically I think that this patch is OK, but why do tool and email need to be global inside the _open function?

--Michiel

--- On Mon, 3/29/10, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Setting the NCBI Entrez tool parameter globally
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>, "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
> Date: Monday, March 29, 2010, 7:05 AM
> Hi Michiel et al,
> 
> The NCBI looks to be encouraging more use of the email and
> tool
> parameters in their revised guidelines. To make this easy
> to use
> we have a global setting for the email - I think we should
> do the
> same for the tool (for when users are building their own
> application
> or script on top of Biopython). Something like this patch?
> 
> What do you think?
> 
> Peter
> 
> ------------------------
> 
> diff --git a/Bio/Entrez/__init__.py
> b/Bio/Entrez/__init__.py
> index 33d8d14..f64015c 100644
> --- a/Bio/Entrez/__init__.py
> +++ b/Bio/Entrez/__init__.py
> @@ -12,6 +12,9 @@ http://www.ncbi.nlm.nih.gov/Entrez/
>  A list of the Entrez utilities is available at:
>  http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
> 
> +Variables:
> +email        Set the Entrez email
> parameter globally (default is not set).
> +tool         Set the Entrez
> tool parameter globally (defaults to biopython).
> 
>  Functions:
>  efetch       Retrieves records in
> the requested format from a list of one or
> @@ -50,7 +53,7 @@ from Bio import File
> 
> 
>  email = None
> -
> +tool = "biopython"
> 
>  # XXX retmode?
>  def epost(db, **keywds):
> @@ -275,6 +278,7 @@ def _open(cgi, params={}, post=False):
>      This function also enforces the
> "up to three queries per second rule"
>      to avoid abusing the NCBI
> servers.
>      """
> +    global tool, email
>      # NCBI requirement: At most three
> queries per second.
>      # Equivalently, at least a third
> of second between queries
>      delay = 0.333333334
> @@ -291,7 +295,7 @@ def _open(cgi, params={}, post=False):
>              del
> params[key]
>      # Tell Entrez that we are using
> Biopython
>      if not "tool" in params:
> -        params["tool"] = "biopython"
> +        params["tool"] = tool
>      # Tell Entrez who we are
>      if not "email" in params:
>          if email!=None:
>