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 = 'AU=BRATKO, D';
$q = 'CA=BRATKO, D';
#$q = 'AD=(croat* OR hrvat*)';

my $range_size = 100;
my $overlap    = 3; # between previous and this range

my $results = 0;
my $citations = 0;
my $cited_reference = 1; # 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://www.webofknowledge.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";
                save_mech;

                $mech->submit_form(
                        form_name => 'output_form',
                        fields => {
                                'value(record_select_type)' => 'range',
                                markFrom => $from,
                                markTo => $to,

                                mark_from => $from,
                                mark_to => $to,
                                mark_id => 'WOS',

                                fields_selection => 'ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS',
                                filters => 'ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS CITREF',
                                fullrec_fields_option => 'CITREF',

                                save_options => 'fieldtagged',
                                format => 'saveToFile',

                        },
                        button => 'saveToFile',
                );
                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: expecting processing request";
                }


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

                warn "save $from - $to into $path\n";
                $mech->submit_form(
                        form_name => 'etsForm',
                );
                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();
                $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 $q = 'AD=Croatia';
15	dpavlin	1370	#$q = 'AU=BRATKO, D';
16			$q = 'CA=BRATKO, D';
17	dpavlin	1369	#$q = 'AD=(croat* OR hrvat*)';
18	dpavlin	1335
19	dpavlin	1369	my $range_size = 100;
20	dpavlin	1294	my $overlap = 3; # between previous and this range
21	dpavlin	1335
22	dpavlin	1370	my $results = 0;
23	dpavlin	1334	my $citations = 0;
24	dpavlin	1370	my $cited_reference = 1; # html tables
25			my $citing_articles = 1; # as many files as cited articles
26	dpavlin	1335
27	dpavlin	1332	my $cites_by_year = 0;
28	dpavlin	1280
29	dpavlin	1292	my $max_cites = 5000; # ISI limit to get cites
30	dpavlin	1282
31	dpavlin	1332	$q = unac_string( 'utf-8', join(' ', @ARGV) ) if @ARGV;
32	dpavlin	1331
33	dpavlin	1335	warn "QUERY: $q\n";
34
35	dpavlin	1289	our $mech = WWW::Mechanize->new(
36	dpavlin	1333	autocheck => 0, # it dies in reference download with it!
37	dpavlin	1280	cookie_jar => undef,
38			);
39
40	dpavlin	1281	our $step = 0;
41	dpavlin	1294	our @ranges;
42	dpavlin	1280
43	dpavlin	1291	my $dir = '/tmp/isi/';
44	dpavlin	1331	#rmtree $dir if -e $dir;
45			mkdir $dir unless -d $dir;
46	dpavlin	1291
47	dpavlin	1280	sub save_mech {
48	dpavlin	1292	my $path = shift;
49	dpavlin	1281	$step++;
50	dpavlin	1291	my $base_path = sprintf('%s/%04d', $dir,$step);
51	dpavlin	1292	$path \|\|= $base_path;
52			$path .= $mech->{ct} =~ m{html}i ? '.html' : '.txt';
53	dpavlin	1281	$mech->save_content( $path );
54	dpavlin	1290	warn "# [$step] $path ", -s $path, " ", $mech->ct, "\n";
55			open(my $dump, '>', "$base_path.dump.txt");
56			$mech->dump_all($dump);
57	dpavlin	1280	}
58
59			warn "# get session";
60	dpavlin	1369	$mech->get( 'http://www.webofknowledge.com/?DestApp=WOS' );
61	dpavlin	1292	save_mech;
62	dpavlin	1280
63	dpavlin	1290	sub search {
64			warn "# advanced serach";
65			$mech->follow_link( url_regex => qr/AdvancedSearch/ );
66	dpavlin	1292	save_mech;
67	dpavlin	1280
68	dpavlin	1290	warn "# cookie_jar ", dump $mech->cookie_jar;
69	dpavlin	1280
70	dpavlin	1292	my $q_this = $q;
71
72			if ( @ranges ) {
73			$q_this .= ' AND (' . join(' OR ', map { "PY=$_" } @{ shift @ranges } ) . ')';
74			}
75
76			warn "# submit_form search: $q_this\n";
77	dpavlin	1290	$mech->submit_form(
78			fields => {
79	dpavlin	1292	'value(input1)' => $q_this,
80			},
81	dpavlin	1290	);
82	dpavlin	1292	save_mech;
83	dpavlin	1280
84	dpavlin	1290	warn "# summary";
85			$mech->follow_link( url_regex => qr/summary/ );
86	dpavlin	1292	save_mech;
87	dpavlin	1290	}
88
89	dpavlin	1289	sub get_results {
90	dpavlin	1292	my $desc = shift;
91	dpavlin	1289	my $from = 1;
92	dpavlin	1280
93	dpavlin	1289	while ( 1 ) {
94	dpavlin	1280
95	dpavlin	1289	my $to = $from + $range_size;
96	dpavlin	1280
97	dpavlin	1292	warn "# submit_form results $from - $to\n";
98	dpavlin	1369	save_mech;
99	dpavlin	1292
100	dpavlin	1289	$mech->submit_form(
101	dpavlin	1369	form_name => 'output_form',
102	dpavlin	1289	fields => {
103	dpavlin	1369	'value(record_select_type)' => 'range',
104			markFrom => $from,
105			markTo => $to,
106
107	dpavlin	1289	mark_from => $from,
108			mark_to => $to,
109			mark_id => 'WOS',
110	dpavlin	1280
111	dpavlin	1369	fields_selection => 'ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS',
112			filters => 'ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS CITREF',
113			fullrec_fields_option => 'CITREF',
114	dpavlin	1280
115	dpavlin	1369	save_options => 'fieldtagged',
116			format => 'saveToFile',
117	dpavlin	1280
118	dpavlin	1289	},
119	dpavlin	1369	button => 'saveToFile',
120	dpavlin	1289	);
121	dpavlin	1292	save_mech;
122	dpavlin	1281
123	dpavlin	1292
124	dpavlin	1289	if ( $mech->content =~ m{invalid API call} ) {
125			$mech->back;
126	dpavlin	1290	last;
127	dpavlin	1289	}
128	dpavlin	1281
129	dpavlin	1338	if ( $mech->content !~ m{Please wait while your request is processed} ) {
130			warn "WARNING: expecting processing request";
131	dpavlin	1336	}
132	dpavlin	1292
133	dpavlin	1336
134	dpavlin	1292	my $path = "/tmp/isi.$q.$from-$to";
135			$path .= '.' . $desc if $desc;
136
137			warn "save $from - $to into $path\n";
138	dpavlin	1369	$mech->submit_form(
139			form_name => 'etsForm',
140			);
141	dpavlin	1292	save_mech $path;
142	dpavlin	1281
143	dpavlin	1292	$from += $range_size - $overlap;
144	dpavlin	1281
145	dpavlin	1289	$mech->back;
146			$mech->back;
147	dpavlin	1369	save_mech;
148	dpavlin	1290	}
149	dpavlin	1281	}
150	dpavlin	1289
151
152	dpavlin	1290	sub citations {
153			warn "# citation report";
154			$mech->follow_link( url_regex => qr/search_mode=CitationReport/ );
155	dpavlin	1292	save_mech;
156	dpavlin	1289
157	dpavlin	1290	warn "view citing articles";
158			$mech->follow_link( url_regex => qr/search_mode=TotalCitingArticles/ );
159	dpavlin	1292	save_mech;
160	dpavlin	1290	}
161	dpavlin	1289
162	dpavlin	1290	sub years {
163	dpavlin	1292	my $years_url = $mech->find_link( url_regex => qr/ra_name=/ );
164	dpavlin	1291	if ( ! $years_url ) {
165	dpavlin	1292	warn "W: can't find ra_name link\n";
166	dpavlin	1291	return;
167			}
168			$years_url = $years_url->url_abs;
169	dpavlin	1290	warn "## $years_url";
170	dpavlin	1291	if ( $years_url !~ s{ra_name=\w+}{ra_name=PublicationYear} ) {
171	dpavlin	1292	warn "W: no ra_name in $years_url\n";
172	dpavlin	1291	return;
173			}
174	dpavlin	1290	warn "# refine years (hidden by javascript)";
175	dpavlin	1292	# warn "http://apps.isiknowledge.com/RAMore.do?product=WOS&search_mode=TotalCitingArticles&SID=T1o6bChdN9PGP1LN1Nh&qid=3&ra_mode=more&ra_name=PublicationYear&db_id=WOS&viewType=raMore\n$years_url\n";
176	dpavlin	1290	$mech->get( $years_url );
177	dpavlin	1292	save_mech;
178	dpavlin	1290
179			my $html = $mech->content;
180	dpavlin	1291	my $years;
181	dpavlin	1292	while ( $html =~ s{<label.+?PublicationYear.+?>(\d{4})\s\(([\d,]+)\)</label>}{} ) {
182			my ( $year, $count ) = ( $1, $2 );
183			$count =~ s{,}{}g;
184			$years->{$year} = $count;
185	dpavlin	1290	}
186	dpavlin	1291	warn "# years ",dump $years;
187	dpavlin	1290	$mech->back;
188	dpavlin	1292
189			my @y = sort keys %$years;
190
191	dpavlin	1300	@ranges = ();
192
193			if ( $cites_by_year ) {
194			push @ranges, [ $_ ] foreach @y;
195			warn "# cites_by_year ranges ", dump @ranges;
196			return;
197			}
198
199	dpavlin	1292	my $y = shift @y;
200			my $size = $years->{$y};
201
202			my $cites_range;
203			$cites_range = [$y] if $y;
204
205			foreach my $y ( @y ) {
206			if ( $size + $years->{$y} > $max_cites ) {
207			push @ranges, $cites_range;
208			warn "# cites_range $size years ",dump( $cites_range ),$/;
209
210			$cites_range = [];
211			$size = 0;
212			}
213			$size += $years->{$y};
214			push @$cites_range, $y;
215			}
216
217			if ( $cites_range ) {
218			push @ranges, $cites_range;
219			warn "# cites_range $size years ",dump( $cites_range ), " FINAL\n"
220			}
221
222			warn '# ranges ', dump @ranges;
223			@ranges = () if $#ranges == 1; # just take all
224
225	dpavlin	1291	return $years;
226	dpavlin	1290	}
227
228	dpavlin	1337
229			our $page = 1;
230			sub next_page {
231			$page++;
232			warn "next_page $page\n";
233
234			$mech->submit_form(
235			form_name => 'summary_navigation',
236			fields => {
237			'page' => $page,
238			},
239			);
240
241			save_mech;
242
243			$mech->form_name( 'summary_navigation' );
244			my $is_next_page = $mech->value('page') == $page;
245			warn "no next_page" unless $is_next_page;
246			return $is_next_page;
247			}
248
249	dpavlin	1335	if ( $results ) {
250			search;
251			years;
252			get_results;
253			}
254	dpavlin	1290
255	dpavlin	1334	if ( $citations ) {
256	dpavlin	1291
257	dpavlin	1334	citations;
258	dpavlin	1335	years unless @ranges;
259	dpavlin	1289
260	dpavlin	1334	do {
261			my $part;
262			if ( @ranges ) {
263			$part .= $ranges[0]->[0] . '.';
264			search;
265			citations;
266			}
267			$part .= 'citing';
268			get_results $part;
269			} while ( @ranges );
270	dpavlin	1292
271	dpavlin	1334	}
272	dpavlin	1335
273	dpavlin	1337
274
275	dpavlin	1336	if ( $q =~ m{CA=(.+)} && $cited_reference ) {
276	dpavlin	1335
277			my $CA = $1;
278
279			warn "# citated reference search";
280			$mech->follow_link( url_regex => qr/CitedReferenceSearch/ );
281			save_mech;
282
283
284			$mech->submit_form(
285			form_name => 'WOS_CitedReferenceSearch_input_form',
286			fields => {
287			'value(input1)' => $CA,
288			},
289			);
290
291			my $page = 1;
292			my $records = $1 if $mech->content =~ m/(\d+)\s+records/;
293			warn "# found $records records\n";
294			my $last_span = 'fake';
295
296			while (1) {
297			save_mech "/tmp/isi.$q.citedref.$page";
298
299	dpavlin	1337	last unless next_page();
300	dpavlin	1370	$page++;
301	dpavlin	1335
302			if ( $mech->content =~ m/(\d+\s-\s(\d+))/ ) {
303			warn "span: $1\n";
304			last if $2 == $records;
305			last if $1 == $last_span;
306			$last_span = $1;
307			} elsif ( $page > 5 ) {
308			warn "ARTIFICALLY LIMITED TO 5 PAGES WITHOUT VALID SPAN!";
309			last;
310			}
311
312			}
313
314			}
315
316	dpavlin	1336	if ( $q =~ m{CA=(.+)} && $citing_articles ) {
317
318			search;
319
320			my $orig_q = $q;
321			my $nr = 0;
322
323	dpavlin	1337	do {
324
325	dpavlin	1336	foreach my $link ( $mech->find_all_links( url_regex => qr/CitingArticles.do/ ) ) {
326			$nr++;
327			warn "link $nr\n";
328			$mech->get( $link->url );
329			save_mech;
330			$q = $orig_q . '.citing_article.' . $nr;
331			get_results;
332			$mech->back;
333			$mech->back;
334	dpavlin	1337
335			#last if $nr > 3; # FIXME only for development
336	dpavlin	1336	}
337
338	dpavlin	1337	} while next_page;
339
340	dpavlin	1336	$q = $orig_q;
341			}
342
343	dpavlin	1335	warn "OVER\n";