Class: Bio::NCBI
Defined Under Namespace
Classes: REST
Constant Summary collapse
- ENTREZ_DEFAULT_PARAMETERS =
(Hash) Default parameters for Entrez (eUtils). They may also be used for other NCBI services.
{ # Cited from # http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.Release_Notes # tool: # Name of application making the E-utility call. # Value must be a string with no internal spaces. 'tool' => "bioruby", # Cited from # http://www.ncbi.nlm.nih.gov/books/NBK25497/ # 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. 'email' => '[email protected]', }
Class Method Summary collapse
-
.default_email ⇒ Object
Gets default email address for Entrez (eUtils).
-
.default_email=(str) ⇒ Object
Sets default email address used for Entrez (eUtils).
-
.default_tool ⇒ Object
Gets default tool name for Entrez (eUtils).
-
.default_tool=(str) ⇒ Object
Sets default tool name for Entrez (eUtils).
-
.reset_entrez_default_parameters ⇒ Object
Resets Entrez (eUtils) default parameters.
Class Method Details
.default_email ⇒ Object
Gets default email address for Entrez (eUtils).
- Returns
-
String or nil
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# File 'lib/bio/io/ncbirest.rb', line 50 def self.default_email ENTREZ_DEFAULT_PARAMETERS['email'] end |
.default_email=(str) ⇒ Object
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
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# File 'lib/bio/io/ncbirest.rb', line 78 def self.default_email=(str) ENTREZ_DEFAULT_PARAMETERS['email'] = str end |
.default_tool ⇒ Object
Gets default tool name for Entrez (eUtils).
- Returns
-
String or nil
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# File 'lib/bio/io/ncbirest.rb', line 85 def self.default_tool ENTREZ_DEFAULT_PARAMETERS['tool'] end |
.default_tool=(str) ⇒ Object
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
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# File 'lib/bio/io/ncbirest.rb', line 106 def self.default_tool=(str) ENTREZ_DEFAULT_PARAMETERS['tool'] = str end |
.reset_entrez_default_parameters ⇒ Object
Resets Entrez (eUtils) default parameters.
- Returns
-
(Hash) default parameters
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# File 'lib/bio/io/ncbirest.rb', line 38 def self.reset_entrez_default_parameters h = { 'tool' => "bioruby", 'email' => '[email protected]', } ENTREZ_DEFAULT_PARAMETERS.clear ENTREZ_DEFAULT_PARAMETERS.update(h) end |