/
bibfmt
executable file
·146 lines (120 loc) · 3.56 KB
/
bibfmt
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
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
#! /usr/bin/perl
# bibfmt <bibkey>
#
# Looks up .bib entry corresponding to <bibkey> and
# formats it in HTML.
#
# SRE, Mon Nov 3 10:07:47 1997
# RCS $Header$
require "importenv.pl";
$master = "/nfs/wol2/people/eddy/lib/bib/master.bib";
$key = shift;
&get_bibfiles();
&process_macros($master);
$entry = &get_entry($key);
($author, $title, $journal, $year, $volume, $pages, $pmid) = &parse_entry($entry);
output_html($author, $title, $journal, $year, $volume, $pages, $pmid);
#print $entry;
# get_bibfiles()
#
# Sets up the global list @bibfiles, given a correctly set
# environment variable $BIBINPUTS.
#
sub get_bibfiles {
local(@bibpaths, $bibpath, @newfiles, $newfile);
@bibpaths = split(':',$BIBINPUTS);
foreach $bibpath (@bibpaths) {
if ($bibpath eq "") { $bibpath = "."; }
opendir(BIBDIR,$bibpath) || die;
@newfiles = grep(/\.bib$/, readdir(BIBDIR));
foreach $newfile (@newfiles) {
$newfile = $bibpath . "/" . $newfile;
push(@bibfiles, $newfile);
}
}
}
# get_entry($key)
#
# Retrieves the .bib text for $key;
# assumes that global @bibfiles contains list of valid .bib databases.
#
sub get_entry {
local($findkey) = @_;
local($entry, $foundone, $thiskey);
foreach $bibfile (@bibfiles) {
open(BIBFILE,$bibfile) || die "$!\n";
while (<BIBFILE>) {
if (/^@\S+\{(\S+),/) {
$thiskey = $1;
if ($findkey eq $thiskey) {
$foundone = 1;
$entry = $_;
while (<BIBFILE>) {
if (/^@/) { last; }
$entry = $entry . $_;
}
close BIBFILE;
return $entry;
}
}
}
close BIBFILE;
}
die ("didn't find $findkey");
}
# parse_entry($entry)
#
# Parse an entry and return
# ($author, $title, $journal, $year, $volume, $pages, $pmid)
#
sub parse_entry {
local($entry) = @_;
local ($author, $title, $journal, $year, $volume, $pages, $pmid);
@lines = split(", *\n", $entry);
foreach $line (@lines) {
$line =~ s/\n//g;
$line =~ s/ +/ /g;
# print $line, "\n";
if ($line =~ /^\s*author\s*=\s*[\"{](.+)[\"}]/) { $author = $1; }
if ($line =~ /^\s*title\s*=\s*[\"{](.+)[\"}]/) { $title = $1; }
if ($line =~ /^\s*journal\s*=\s*[\"{]?(\S.+[^\" }])[\"}]?\s*$/) { $journal = $1; }
if ($line =~ /^\s*year\s*=\s*(\d+)/) { $year = $1; }
if ($line =~ /^\s*volume\s*=\s*(\d+)/) { $volume = $1; }
if ($line =~ /^\s*pages\s*=\s*[\"{](.+)[\"}]/) { $pages = $1; }
if ($line =~ /^\s*pmid\s*=\s*(\d+)/) { $pmid = $1; }
}
return ($author, $title, $journal, $year, $volume, $pages, $pmid);
}
# output_html($author, $title, $journal, $year, $volume, $pages, $pmid)
#
# output in HTML format
#
sub output_html {
local($author, $title, $journal, $year, $volume, $pages, $pmid) = @_;
$author =~ s/ and/,/g;
$author =~ s/[{}]//g;
$pages =~ s/--/-/;
if ($is_abbrev{$journal}) { $journal = $fulljournal{$journal}; }
$title =~ s/[{}]//g;
# print "<p>\n";
print "$author.<br>\n" ;
if ($pmid) {
print "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=retrieve&list_uids=$pmid&dopt=abstract\">\n $title. </a><br>\n";
} else {
print "$title.\n";
}
print "<em> $journal</em> <strong>$volume:</strong>$pages, $year\n";
}
sub process_macros {
local ($master) = @_;
my ($abbrev, $full);
open(MASTER, $master) || die ("couldn't open master bib file $master\n");
while (<MASTER>) {
if (/^\@string\{(\S+)\s*=\s*\"(.+)\"\}/) {
$abbrev = $1;
$full = $2;
$is_abbrev{$abbrev} = 1;
$fulljournal{$abbrev} = $full;
}
}
}