Bio::Tools::EUtilities::EUtilParameters - Manipulation of NCBI eutil-based parameters for remote database requests.
# Bio::Tools::EUtilities::EUtilParameters implements Bio::ParameterBaseI my @params = (-eutil => 'efetch', db => 'nucleotide', id => \@ids, email => 'me@foo.bar', retmode => 'xml'); my $p = Bio::Tools::EUtilities::EUtilParameters->new(@params); if ($p->parameters_changed) { # ... } # state information $p->set_parameters(@extra_params); # set new NCBI parameters, leaves others preset $p->reset_parameters(@new_params); # reset NCBI parameters to original state $p->to_string(); # get a URI-encoded string representation of the URL address $p->to_request(); # get an HTTP::Request object (to pass on to LWP::UserAgent)
Bio::Tools::EUtilities::EUtilParameters is-a Bio::ParameterBaseI implementation that allows simple manipulation of NCBI eutil parameters for CGI-based queries. SOAP-based methods may be added in the future.
For simplicity parameters do not require dashes when passed and do not need URI encoding (spaces are converted to '+', symbols encoded, etc). Also, the following extra parameters can be passed to the new() constructor or via set_parameters() or reset_parameters():
eutil - the eutil to be used. The default is 'efetch' if not set. correspondence - Flag for how IDs are treated. Default is undef (none). history - a Bio::Tools::EUtilities::HistoryI object. Default is undef (none).
At this point minimal checking is done for potential errors in parameter passing, though these should be easily added in the future when necessary.
Possibly integrate SOAP-compliant methods. SOAP::Lite may be undergoing an complete rewrite so I'm hesitant about adding this in immediately.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : set_parameters Usage : $pobj->set_parameters(@params); Function: sets the NCBI parameters listed in the hash or array Returns : None Args : [optional] hash or array of parameter/values. Note : This sets any parameter passed but leaves previously set data alone. In addition to regular eutil-specific parameters, you can set the following: -eutil - the eUtil to be used (default 'efetch') -history - pass a HistoryI-implementing object, which sets the WebEnv, query_key, and possibly db and linkname (the latter two only for LinkSets) -correspondence - Boolean flag, set to TRUE or FALSE; indicates how IDs are to be added together for elink request where ID correspondence might be needed (default 0)
Title : reset_parameters Usage : resets values Function: resets parameters to either undef or value in passed hash Returns : none Args : [optional] hash of parameter-value pairs Note : This sets any parameter passed, but resets all others (deletes them). In addition to regular eutil-specific parameters, you can set the following: -eutil - the eUtil to be used (default 'efetch') -history - pass a HistoryI-implementing object, which sets the WebEnv, query_key, and possibly db and linkname (the latter two only for LinkSets) -correspondence - Boolean flag, set to TRUE or FALSE; indicates how IDs are to be added together for elink request where ID correspondence might be needed (default 0)
Title : parameters_changed Usage : if ($pobj->parameters_changed) {...} Function: Returns TRUE if parameters have changed Returns : Boolean (0 or 1) Args : [optional] Boolean
Title : available_parameters Usage : @params = $pobj->available_parameters() Function: Returns a list of the available parameters Returns : Array of available parameters (no values) Args : [optional] A string with the eutil name (for returning eutil-specific parameters)
Title : get_parameters Usage : @params = $pobj->get_parameters; %params = $pobj->get_parameters; Function: Returns list of key/value pairs, parameter => value Returns : Flattened list of key-value pairs. All key-value pairs returned, though subsets can be returned based on the '-type' parameter. Data originally set as an array ref are returned based on whether the '-join_id' flag is set (default is the same array ref). Args : -type : the eutil name (Default: returns all). Use of '-list' supercedes this -list : array ref of specific parameters -join_ids : Boolean; join IDs based on correspondence (Default: no join)
Title : to_string Usage : $string = $pobj->to_string; Function: Returns string (URL only in this case) Returns : String (URL only for now) Args : [optional] 'all'; build URI::http using all parameters Default : Builds based on allowed parameters (presence of history data or eutil type in %MODE). Note : Changes state of object. Absolute string
Title : to_request Usage : $uri = $pobj->to_request; Function: Returns HTTP::Request object Returns : HTTP::Request Args : [optional] 'all'; builds request using all parameters Default : Builds based on allowed parameters (presence of history data or eutil type in %MODE). Note : Changes state of object (to boolean FALSE). Used for CGI-based GET/POST
Title : eutil Usage : $p->eutil('efetch') Function: gets/sets the eutil for this set of parameters Returns : string (eutil) Args : [optional] string (eutil) Throws : '$eutil not supported' if eutil not present Note : This does not reset retmode to the default if called directly.
Title : history Usage : $p->history($history); Function: gets/sets the history object to be used for these parameters Returns : Bio::Tools::EUtilities::HistoryI (if set) Args : [optional] Bio::Tools::EUtilities::HistoryI Throws : Passed something other than a Bio::Tools::EUtilities::HistoryI Note : This overrides WebEnv() and query_key() settings when set. This caches the last history object passed and returns like a Get/Set
Title : correspondence Usage : $p->correspondence(1); Function: Sets flag for posting IDs for one-to-one correspondence Returns : Boolean Args : [optional] boolean value
Title : id_file Usage : $p->id_file('<foo'); Function: convenience method; passes in file containing a list of IDs for searches (one per line), sets id() to list Returns : none Args : either string indicating file to use, a file handle, or an IO::Handle object Note : use of this overrides concurrent use of the '-id' parameter when both are passed. The filename is not retained, merely parsed for IDs.
Title : url_base_address Usage : $address = $p->url_base_address(); Function: Get URL base address Returns : String Args : None in this implementation; the URL is fixed
Title : set_default_retmode Usage : $p->set_default_retmode(); Function: sets retmode to default value specified by the eutil() and the value in %NCBI_DATABASE (for efetch only) if called Returns : none Args : none
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