class Bio::NCBI
Constants
- ENTREZ_DEFAULT_PARAMETERS
(Hash) Default parameters for Entrez (eUtils). They may also be used for other
NCBI
services.
Public Class Methods
Gets default email address for Entrez (eUtils).
- Returns
-
String or nil
# File lib/bio/io/ncbirest.rb 50 def self.default_email 51 ENTREZ_DEFAULT_PARAMETERS['email'] 52 end
Sets default email address used for Entrez (eUtils). It may also be used for other NCBI
services.
In www.ncbi.nlm.nih.gov/books/NBK25497/ NCBI
says: “The value of email should be a complete and valid e-mail address of the software developer and not that of a third-party end user.”
By default, email address of BioRuby staffs is set.
From the above NCBI
documentation, the tool and email value is used only for unblocking IP addresses blocked by NCBI
due to excess requests. For the purpose, NCBI
says: “Please be aware that merely providing values for tool and email in requests is not sufficient to comply with this policy; these values must be registered with NCBI
.”
Please use your own email address and tool name when registering tool and email values to NCBI
.
Arguments:
-
(required) str: (String) email address
- Returns
-
same as given argument
# File lib/bio/io/ncbirest.rb 78 def self.default_email=(str) 79 ENTREZ_DEFAULT_PARAMETERS['email'] = str 80 end
Gets default tool name for Entrez (eUtils).
- Returns
-
String or nil
# File lib/bio/io/ncbirest.rb 85 def self.default_tool 86 ENTREZ_DEFAULT_PARAMETERS['tool'] 87 end
Sets default tool name for Entrez (eUtils). It may also be used for other NCBI
services.
In www.ncbi.nlm.nih.gov/books/NBK25497/ NCBI
says: “The value of tool should be a string with no internal spaces that uniquely identifies the software producing the request.”
“bioruby” is set by default. Please use your own tool name when registering to NCBI
.
See the document of default_email
= for more information.
Arguments:
-
(required) str: (String) tool name
- Returns
-
same as given argument
# File lib/bio/io/ncbirest.rb 106 def self.default_tool=(str) 107 ENTREZ_DEFAULT_PARAMETERS['tool'] = str 108 end
Resets Entrez (eUtils) default parameters.
- Returns
-
(Hash) default parameters
# File lib/bio/io/ncbirest.rb 38 def self.reset_entrez_default_parameters 39 h = { 40 'tool' => "bioruby", 41 'email' => 'staff@bioruby.org', 42 } 43 ENTREZ_DEFAULT_PARAMETERS.clear 44 ENTREZ_DEFAULT_PARAMETERS.update(h) 45 end