1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
|
#!/usr/local/bin/perl -w
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
# Author: Oleg Khovayko
#
# File Description: eSearch/eFetch calling example
#
# ---------------------------------------------------------------------------
# Subroutine to prompt user for variables in the next section
sub ask_user {
print "$_[0] [$_[1]]: ";
my $rc = <>;
chomp $rc;
if($rc eq "") { $rc = $_[1]; }
return $rc;
}
# ---------------------------------------------------------------------------
# Define library for the 'get' function used in the next section.
# $utils contains route for the utilities.
# $db, $query, and $report may be supplied by the user when prompted;
# if not answered, default values, will be assigned as shown below.
use LWP::Simple;
my $utils = "http://www.ncbi.nlm.nih.gov/entrez/eutils";
my $db = ask_user("Database", "Pubmed");
my $query = ask_user("Query", "zanzibar");
my $report = ask_user("Report", "abstract");
# ---------------------------------------------------------------------------
# $esearch contins the PATH & parameters for the ESearch call
# $esearch_result containts the result of the ESearch call
# the results are displayed nd parsed into variables
# $Count, $QueryKey, and $WebEnv for later use and then displayed.
my $esearch = "$utils/esearch.fcgi?" .
"db=$db&retmax=1&usehistory=y&term=";
my $esearch_result = get($esearch . $query);
print "\nESEARCH RESULT: $esearch_result\n";
$esearch_result =~
m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;
my $Count = $1;
my $QueryKey = $2;
my $WebEnv = $3;
print "Count = $Count; QueryKey = $QueryKey; WebEnv = $WebEnv\n";
# ---------------------------------------------------------------------------
# this area defines a loop which will display $retmax citation results from
# Efetch each time the the Enter Key is pressed, after a prompt.
my $retstart;
my $retmax=3;
for($retstart = 0; $retstart < $Count; $retstart += $retmax) {
my $efetch = "$utils/efetch.fcgi?" .
"rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" .
"db=$db&query_key=$QueryKey&WebEnv=$WebEnv";
print "\nEF_QUERY=$efetch\n";
my $efetch_result = get($efetch);
print "---------\nEFETCH RESULT(".
($retstart + 1) . ".." . ($retstart + $retmax) . "): ".
"[$efetch_result]\n-----PRESS ENTER!!!-------\n";
<>;
}
|
