trunk/bin/isi-download-results.pl

#!/usr/bin/perl

use warnings;
use strict;

use WWW::Mechanize;
use Data::Dump qw(dump);
use File::Path;
use Text::Unaccent;

# Advanced search syntax:
# http://images.isiknowledge.com/WOK46/help/WOS/h_advanced_examples.html

our $q = 'AD=Croatia';
$q = 'CA=BRATKO, D';

my $range_size = 500;
my $overlap    = 3; # between previous and this range

my $results = 0;
my $citations = 0;
my $cited_reference = 0; # html tables
my $citing_articles = 1; # as many files as cited articles

my $cites_by_year = 0;

my $max_cites = 5000; # ISI limit to get cites

$q = unac_string( 'utf-8', join(' ', @ARGV) ) if @ARGV;

warn "QUERY: $q\n";

our $mech = WWW::Mechanize->new(
        autocheck => 0, # it dies in reference download with it!
        cookie_jar => undef,
);

our $step = 0;
our @ranges;

my $dir = '/tmp/isi/';
#rmtree $dir if -e $dir;
mkdir $dir unless -d $dir;

sub save_mech {
        my $path = shift;
        $step++;
        my $base_path = sprintf('%s/%04d', $dir,$step);
        $path ||= $base_path;
        $path .= $mech->{ct} =~ m{html}i ? '.html' : '.txt';
        $mech->save_content( $path );
        warn "# [$step] $path ", -s $path, " ", $mech->ct, "\n";
        open(my $dump, '>', "$base_path.dump.txt");
        $mech->dump_all($dump);
}

warn "# get session";
$mech->get( 'http://isiknowledge.com/?DestApp=WOS' );
save_mech;

sub search {
        warn "# advanced serach";
        $mech->follow_link( url_regex => qr/AdvancedSearch/ );
        save_mech;

        warn "# cookie_jar ", dump $mech->cookie_jar;

        my $q_this = $q;

        if ( @ranges ) {
                $q_this .= ' AND (' . join(' OR ', map { "PY=$_" } @{ shift @ranges } ) . ')';
        }

        warn "# submit_form search: $q_this\n";
        $mech->submit_form(
                fields => {
                        'value(input1)' => $q_this,
                },
        );
        save_mech;

        warn "# summary";
        $mech->follow_link( url_regex => qr/summary/ );
        save_mech;
}

sub get_results {
        my $desc = shift;
        my $from = 1;

        while ( 1 ) {

                my $to = $from + $range_size;

                warn "# submit_form results $from - $to\n";

                $mech->submit_form(
                        form_name => 'summary_output_form',
                        fields => {
                                record_select_type => 'range',
                                mark_from => $from,
                                mark_to => $to,
                                mark_id => 'WOS',

                                qo_fields => 'fullrecord',
                                citedref => 'citedref',

                                save_options => 'plain_text',

                                fields => 'Full',
                                format => 'save',
                        },
                        button => 'save',
                );
                save_mech;


                if ( $mech->content =~ m{invalid API call} ) {
                        $mech->back;
                        last;
                }

                if ( $mech->content =~ m{Please wait while your request is processed} ) {
                        warn "WARNING: processing request";
                }


                my $path = "/tmp/isi.$q.$from-$to";
                $path .= '.' . $desc if $desc;

                warn "save $from - $to into $path\n";
                $mech->follow_link( url_regex => qr/save_file/ );
                save_mech $path;

                $from += $range_size - $overlap;

                $mech->back;
                $mech->back;
                #save_mech;
        }
}


sub citations {
        warn "# citation report";
        $mech->follow_link( url_regex => qr/search_mode=CitationReport/ );
        save_mech;

        warn "view citing articles";
        $mech->follow_link( url_regex => qr/search_mode=TotalCitingArticles/ );
        save_mech;
}

sub years {
        my $years_url = $mech->find_link( url_regex => qr/ra_name=/ );
        if ( ! $years_url ) {
                warn "W: can't find ra_name link\n";
                return;
        }
        $years_url = $years_url->url_abs;
        warn "## $years_url";
        if ( $years_url !~ s{ra_name=\w+}{ra_name=PublicationYear} ) {
                warn "W: no ra_name in $years_url\n";
                return;
        }
        warn "# refine years (hidden by javascript)";
#       warn "http://apps.isiknowledge.com/RAMore.do?product=WOS&search_mode=TotalCitingArticles&SID=T1o6bChdN9PGP1LN1Nh&qid=3&ra_mode=more&ra_name=PublicationYear&db_id=WOS&viewType=raMore\n$years_url\n";
        $mech->get( $years_url );
        save_mech;

        my $html = $mech->content;
        my $years;
        while ( $html =~ s{<label.+?PublicationYear.+?>(\d{4})\s\(([\d,]+)\)</label>}{} ) {
                my ( $year, $count ) = ( $1, $2 );
                $count =~ s{,}{}g;
                $years->{$year} = $count;
        }
        warn "# years ",dump $years;
        $mech->back;

        my @y = sort keys %$years;

        @ranges = ();

        if ( $cites_by_year ) {
                push @ranges, [ $_ ] foreach @y;
                warn "# cites_by_year ranges ", dump @ranges;
                return;
        }

        my $y = shift @y;
        my $size = $years->{$y};

        my $cites_range;
        $cites_range = [$y] if $y;

        foreach my $y ( @y ) {
                if ( $size + $years->{$y} > $max_cites ) {
                        push @ranges, $cites_range;
                        warn "# cites_range $size years ",dump( $cites_range ),$/;

                        $cites_range = [];
                        $size = 0;
                }
                $size += $years->{$y};
                push @$cites_range, $y;
        }

        if ( $cites_range ) {
                push @ranges, $cites_range;
                warn "# cites_range $size years ",dump( $cites_range ), " FINAL\n"
        }

        warn '# ranges ', dump @ranges;
        @ranges = () if $#ranges == 1; # just take all

        return $years;
}


our $page = 1;
sub next_page {
        $page++;
        warn "next_page $page\n";

        $mech->submit_form(
                form_name => 'summary_navigation',
                fields => {
                        'page' => $page,
                },
        );

        save_mech;

        $mech->form_name( 'summary_navigation' );
        my $is_next_page = $mech->value('page') == $page;
        warn "no next_page" unless $is_next_page;
        return $is_next_page;
}

if ( $results ) {
        search;
        years;
        get_results;
}

if ( $citations ) {

        citations;
        years unless @ranges;

        do {
                my $part;
                if ( @ranges ) {
                        $part .= $ranges[0]->[0] . '.';
                        search;
                        citations;
                }
                $part .= 'citing';
                get_results $part;
        } while ( @ranges );

}


if ( $q =~ m{CA=(.+)} && $cited_reference ) {

        my $CA = $1;

        warn "# citated reference search";
        $mech->follow_link( url_regex => qr/CitedReferenceSearch/ );
        save_mech;


        $mech->submit_form(
                form_name => 'WOS_CitedReferenceSearch_input_form',
                fields => {
                        'value(input1)' => $CA,
                },
        );

        my $page = 1;
        my $records = $1 if $mech->content =~ m/(\d+)\s+records/;
        warn "# found $records records\n";
        my $last_span = 'fake';

        while (1) {
                save_mech "/tmp/isi.$q.citedref.$page";

                last unless next_page();

                if ( $mech->content =~ m/(\d+\s*-\s*(\d+))/ ) {
                        warn "span: $1\n";
                        last if $2 == $records;
                        last if $1 == $last_span;
                        $last_span = $1;
                } elsif ( $page > 5 ) {
                        warn "ARTIFICALLY LIMITED TO 5 PAGES WITHOUT VALID SPAN!";
                        last;
                }

        }

}

if ( $q =~ m{CA=(.+)} && $citing_articles ) {

        search;

        my $orig_q = $q;
        my $nr = 0;

        do {

        foreach my $link ( $mech->find_all_links( url_regex => qr/CitingArticles.do/ ) ) {
                $nr++;
                warn "link $nr\n";
                $mech->get( $link->url );
                save_mech;
                $q = $orig_q . '.citing_article.' . $nr;
                get_results;
                $mech->back;
                $mech->back;

                #last if $nr > 3; # FIXME only for development
        }

        } while next_page;

        $q = $orig_q;
}

warn "OVER\n";
1	dpavlin	1280	#!/usr/bin/perl
2
3			use warnings;
4			use strict;
5
6	dpavlin	1332	use WWW::Mechanize;
7			use Data::Dump qw(dump);
8			use File::Path;
9			use Text::Unaccent;
10
11	dpavlin	1292	# Advanced search syntax:
12			# http://images.isiknowledge.com/WOK46/help/WOS/h_advanced_examples.html
13
14	dpavlin	1291	our $q = 'AD=Croatia';
15	dpavlin	1335	$q = 'CA=BRATKO, D';
16
17	dpavlin	1289	my $range_size = 500;
18	dpavlin	1294	my $overlap = 3; # between previous and this range
19	dpavlin	1335
20	dpavlin	1334	my $results = 0;
21			my $citations = 0;
22	dpavlin	1336	my $cited_reference = 0; # html tables
23			my $citing_articles = 1; # as many files as cited articles
24	dpavlin	1335
25	dpavlin	1332	my $cites_by_year = 0;
26	dpavlin	1280
27	dpavlin	1292	my $max_cites = 5000; # ISI limit to get cites
28	dpavlin	1282
29	dpavlin	1332	$q = unac_string( 'utf-8', join(' ', @ARGV) ) if @ARGV;
30	dpavlin	1331
31	dpavlin	1335	warn "QUERY: $q\n";
32
33	dpavlin	1289	our $mech = WWW::Mechanize->new(
34	dpavlin	1333	autocheck => 0, # it dies in reference download with it!
35	dpavlin	1280	cookie_jar => undef,
36			);
37
38	dpavlin	1281	our $step = 0;
39	dpavlin	1294	our @ranges;
40	dpavlin	1280
41	dpavlin	1291	my $dir = '/tmp/isi/';
42	dpavlin	1331	#rmtree $dir if -e $dir;
43			mkdir $dir unless -d $dir;
44	dpavlin	1291
45	dpavlin	1280	sub save_mech {
46	dpavlin	1292	my $path = shift;
47	dpavlin	1281	$step++;
48	dpavlin	1291	my $base_path = sprintf('%s/%04d', $dir,$step);
49	dpavlin	1292	$path \|\|= $base_path;
50			$path .= $mech->{ct} =~ m{html}i ? '.html' : '.txt';
51	dpavlin	1281	$mech->save_content( $path );
52	dpavlin	1290	warn "# [$step] $path ", -s $path, " ", $mech->ct, "\n";
53			open(my $dump, '>', "$base_path.dump.txt");
54			$mech->dump_all($dump);
55	dpavlin	1280	}
56
57			warn "# get session";
58			$mech->get( 'http://isiknowledge.com/?DestApp=WOS' );
59	dpavlin	1292	save_mech;
60	dpavlin	1280
61	dpavlin	1290	sub search {
62			warn "# advanced serach";
63			$mech->follow_link( url_regex => qr/AdvancedSearch/ );
64	dpavlin	1292	save_mech;
65	dpavlin	1280
66	dpavlin	1290	warn "# cookie_jar ", dump $mech->cookie_jar;
67	dpavlin	1280
68	dpavlin	1292	my $q_this = $q;
69
70			if ( @ranges ) {
71			$q_this .= ' AND (' . join(' OR ', map { "PY=$_" } @{ shift @ranges } ) . ')';
72			}
73
74			warn "# submit_form search: $q_this\n";
75	dpavlin	1290	$mech->submit_form(
76			fields => {
77	dpavlin	1292	'value(input1)' => $q_this,
78			},
79	dpavlin	1290	);
80	dpavlin	1292	save_mech;
81	dpavlin	1280
82	dpavlin	1290	warn "# summary";
83			$mech->follow_link( url_regex => qr/summary/ );
84	dpavlin	1292	save_mech;
85	dpavlin	1290	}
86
87	dpavlin	1289	sub get_results {
88	dpavlin	1292	my $desc = shift;
89	dpavlin	1289	my $from = 1;
90	dpavlin	1280
91	dpavlin	1289	while ( 1 ) {
92	dpavlin	1280
93	dpavlin	1289	my $to = $from + $range_size;
94	dpavlin	1280
95	dpavlin	1292	warn "# submit_form results $from - $to\n";
96
97	dpavlin	1289	$mech->submit_form(
98			form_name => 'summary_output_form',
99			fields => {
100			record_select_type => 'range',
101			mark_from => $from,
102			mark_to => $to,
103			mark_id => 'WOS',
104	dpavlin	1280
105	dpavlin	1289	qo_fields => 'fullrecord',
106			citedref => 'citedref',
107	dpavlin	1280
108	dpavlin	1289	save_options => 'plain_text',
109	dpavlin	1280
110	dpavlin	1289	fields => 'Full',
111			format => 'save',
112			},
113			button => 'save',
114			);
115	dpavlin	1292	save_mech;
116	dpavlin	1281
117	dpavlin	1292
118	dpavlin	1289	if ( $mech->content =~ m{invalid API call} ) {
119			$mech->back;
120	dpavlin	1290	last;
121	dpavlin	1289	}
122	dpavlin	1281
123	dpavlin	1336	if ( $mech->content =~ m{Please wait while your request is processed} ) {
124			warn "WARNING: processing request";
125			}
126	dpavlin	1292
127	dpavlin	1336
128	dpavlin	1292	my $path = "/tmp/isi.$q.$from-$to";
129			$path .= '.' . $desc if $desc;
130
131			warn "save $from - $to into $path\n";
132	dpavlin	1289	$mech->follow_link( url_regex => qr/save_file/ );
133	dpavlin	1292	save_mech $path;
134	dpavlin	1281
135	dpavlin	1292	$from += $range_size - $overlap;
136	dpavlin	1281
137	dpavlin	1289	$mech->back;
138			$mech->back;
139	dpavlin	1292	#save_mech;
140	dpavlin	1290	}
141	dpavlin	1281	}
142	dpavlin	1289
143
144	dpavlin	1290	sub citations {
145			warn "# citation report";
146			$mech->follow_link( url_regex => qr/search_mode=CitationReport/ );
147	dpavlin	1292	save_mech;
148	dpavlin	1289
149	dpavlin	1290	warn "view citing articles";
150			$mech->follow_link( url_regex => qr/search_mode=TotalCitingArticles/ );
151	dpavlin	1292	save_mech;
152	dpavlin	1290	}
153	dpavlin	1289
154	dpavlin	1290	sub years {
155	dpavlin	1292	my $years_url = $mech->find_link( url_regex => qr/ra_name=/ );
156	dpavlin	1291	if ( ! $years_url ) {
157	dpavlin	1292	warn "W: can't find ra_name link\n";
158	dpavlin	1291	return;
159			}
160			$years_url = $years_url->url_abs;
161	dpavlin	1290	warn "## $years_url";
162	dpavlin	1291	if ( $years_url !~ s{ra_name=\w+}{ra_name=PublicationYear} ) {
163	dpavlin	1292	warn "W: no ra_name in $years_url\n";
164	dpavlin	1291	return;
165			}
166	dpavlin	1290	warn "# refine years (hidden by javascript)";
167	dpavlin	1292	# warn "http://apps.isiknowledge.com/RAMore.do?product=WOS&search_mode=TotalCitingArticles&SID=T1o6bChdN9PGP1LN1Nh&qid=3&ra_mode=more&ra_name=PublicationYear&db_id=WOS&viewType=raMore\n$years_url\n";
168	dpavlin	1290	$mech->get( $years_url );
169	dpavlin	1292	save_mech;
170	dpavlin	1290
171			my $html = $mech->content;
172	dpavlin	1291	my $years;
173	dpavlin	1292	while ( $html =~ s{<label.+?PublicationYear.+?>(\d{4})\s\(([\d,]+)\)</label>}{} ) {
174			my ( $year, $count ) = ( $1, $2 );
175			$count =~ s{,}{}g;
176			$years->{$year} = $count;
177	dpavlin	1290	}
178	dpavlin	1291	warn "# years ",dump $years;
179	dpavlin	1290	$mech->back;
180	dpavlin	1292
181			my @y = sort keys %$years;
182
183	dpavlin	1300	@ranges = ();
184
185			if ( $cites_by_year ) {
186			push @ranges, [ $_ ] foreach @y;
187			warn "# cites_by_year ranges ", dump @ranges;
188			return;
189			}
190
191	dpavlin	1292	my $y = shift @y;
192			my $size = $years->{$y};
193
194			my $cites_range;
195			$cites_range = [$y] if $y;
196
197			foreach my $y ( @y ) {
198			if ( $size + $years->{$y} > $max_cites ) {
199			push @ranges, $cites_range;
200			warn "# cites_range $size years ",dump( $cites_range ),$/;
201
202			$cites_range = [];
203			$size = 0;
204			}
205			$size += $years->{$y};
206			push @$cites_range, $y;
207			}
208
209			if ( $cites_range ) {
210			push @ranges, $cites_range;
211			warn "# cites_range $size years ",dump( $cites_range ), " FINAL\n"
212			}
213
214			warn '# ranges ', dump @ranges;
215			@ranges = () if $#ranges == 1; # just take all
216
217	dpavlin	1291	return $years;
218	dpavlin	1290	}
219
220	dpavlin	1337
221			our $page = 1;
222			sub next_page {
223			$page++;
224			warn "next_page $page\n";
225
226			$mech->submit_form(
227			form_name => 'summary_navigation',
228			fields => {
229			'page' => $page,
230			},
231			);
232
233			save_mech;
234
235			$mech->form_name( 'summary_navigation' );
236			my $is_next_page = $mech->value('page') == $page;
237			warn "no next_page" unless $is_next_page;
238			return $is_next_page;
239			}
240
241	dpavlin	1335	if ( $results ) {
242			search;
243			years;
244			get_results;
245			}
246	dpavlin	1290
247	dpavlin	1334	if ( $citations ) {
248	dpavlin	1291
249	dpavlin	1334	citations;
250	dpavlin	1335	years unless @ranges;
251	dpavlin	1289
252	dpavlin	1334	do {
253			my $part;
254			if ( @ranges ) {
255			$part .= $ranges[0]->[0] . '.';
256			search;
257			citations;
258			}
259			$part .= 'citing';
260			get_results $part;
261			} while ( @ranges );
262	dpavlin	1292
263	dpavlin	1334	}
264	dpavlin	1335
265	dpavlin	1337
266
267	dpavlin	1336	if ( $q =~ m{CA=(.+)} && $cited_reference ) {
268	dpavlin	1335
269			my $CA = $1;
270
271			warn "# citated reference search";
272			$mech->follow_link( url_regex => qr/CitedReferenceSearch/ );
273			save_mech;
274
275
276			$mech->submit_form(
277			form_name => 'WOS_CitedReferenceSearch_input_form',
278			fields => {
279			'value(input1)' => $CA,
280			},
281			);
282
283			my $page = 1;
284			my $records = $1 if $mech->content =~ m/(\d+)\s+records/;
285			warn "# found $records records\n";
286			my $last_span = 'fake';
287
288			while (1) {
289			save_mech "/tmp/isi.$q.citedref.$page";
290
291	dpavlin	1337	last unless next_page();
292	dpavlin	1335
293			if ( $mech->content =~ m/(\d+\s-\s(\d+))/ ) {
294			warn "span: $1\n";
295			last if $2 == $records;
296			last if $1 == $last_span;
297			$last_span = $1;
298			} elsif ( $page > 5 ) {
299			warn "ARTIFICALLY LIMITED TO 5 PAGES WITHOUT VALID SPAN!";
300			last;
301			}
302
303			}
304
305			}
306
307	dpavlin	1336	if ( $q =~ m{CA=(.+)} && $citing_articles ) {
308
309			search;
310
311			my $orig_q = $q;
312			my $nr = 0;
313
314	dpavlin	1337	do {
315
316	dpavlin	1336	foreach my $link ( $mech->find_all_links( url_regex => qr/CitingArticles.do/ ) ) {
317			$nr++;
318			warn "link $nr\n";
319			$mech->get( $link->url );
320			save_mech;
321			$q = $orig_q . '.citing_article.' . $nr;
322			get_results;
323			$mech->back;
324			$mech->back;
325	dpavlin	1337
326			#last if $nr > 3; # FIXME only for development
327	dpavlin	1336	}
328
329	dpavlin	1337	} while next_page;
330
331	dpavlin	1336	$q = $orig_q;
332			}
333
334	dpavlin	1335	warn "OVER\n";