use strict;
use warnings;
-use vars qw/%DB %OWNS %PARENT %CURR $last_field $debugmatch $debugparse $key $owner $parent $ref $note_rest $printdupl $maxsize $fileno $fileid $filename/;
+use Cwd;
+use Data::Dumper;
+use DBI;
+
+my(%DB,%OWNS,$debugmatch,$D,$key,$owner,$ref,$filename,$doimport,$import_xlate);
-$maxsize=0x40000;
%DB=();
-%CURR=();
-$debugparse=0;
-$printdupl=0;
+$D=0;
$debugmatch=0;
-
-sub name_to_key
-{
-my( $r )=@_;
-
- $r=~tr/A-Z/a-z/;
- $r=~tr/a-z0-9//cd;
- return $r;
-}
-
-sub rec_to_name
-{
-my( %rec )=@_;
-my( @list )=("Genus","Species");
-my( $item,$r );
-
- $r="";
- while ($item=shift @list)
- { $r.=" ".$rec{$item} if exists $rec{$item}; }
- $r=~s/^ //;
- return $r;
-}
-
-sub htmlquote
-{
-($_)=@_;
-
- s/&/&/g;
- s/</</g;
- s/>/>/g;
- s/\n/&nl;/g;
- s/"/"/g;
- return $_;
-}
-
-sub format_record
-{
-my( $preinsert,$postinsert,%rec )=@_;
-
- my($r)="<p><span class=\"name\">".$preinsert.&htmlquote(&rec_to_name(%rec)).$postinsert."</span>";
- $r.="\n".htmlquote($rec{"Publ. Author"}) if (exists($rec{"Publ. Author"}));
- $r.="<br />\n".htmlquote($rec{"Publication"}) if (exists($rec{"Publication"}));
- $r.="<br />\n".htmlquote($rec{"Notes"}) if (exists($rec{"Notes"}));
- $r.="</p>\n";
- return($r);
-}
+$doimport=1;
+$import_xlate=1;
sub extract_year
{
$_=$';
}
}
- return(-1);
+ return -1;
}
-sub flush_CURR
+sub failed
{
-my( $key );
-
- $key=&name_to_key(&rec_to_name(%CURR));
- return if (!$key);
- delete $CURR{"Family"};
- if (exists $DB{$key})
- { print STDERR "Key \"$key\" is duplicated!\n" if $printdupl; }
- else {
- print STDERR "ADDKEY: $key\n" if $debugparse;
- %{$DB{$key}}=%CURR;
-# my($year)=&extract_year($CURR{"Notes"});
-# %{$DB{$key}}{"year"}=$year if (defined($year));
- }
- %CURR=();
- @{$OWNS{$key}}=();
+my($file)=@_;
+
+ print("-$file----------------$'--------------\n");
+ warn "Unable to match file \"".getcwd()."/$file\".";
}
-%OWNS=();
+sub process_file
+{
+my($file)=@_;
-while (<>) {
- tr/\r\n//d;
- if (/^ *\304\301\304/) {
- &flush_CURR();
- print STDERR "---\n" if $debugparse;
+ if (!open(FI,$file)) {
+ warn("Unable to open file \"$file\" in dir \"".getcwd()."\": $!");
+ return;
}
- elsif (/^([^³]*[^ ]) *³ *(.*)$/) {
- print STDERR "FIELD: $1, VALUE: $2\n" if $debugparse;
- $last_field=$1;
- $CURR{$1}=$2;
+ undef $/;
+ my($fi)=<FI>;
+ close(FI);
+ my($word)='[^<]*';
+ my($bigword)='[^<]*(?:<IT>)?[^<]*(?:<RO>)?[^<]*(?:<1000 m)?[^<]*';
+ my($idone)='[-\d]';
+ my($id)="$idone+";
+ my($any)='[\x00-\xFF]*';
+ my($ipniservletword)="<a href=\"\\./IpniServlet\\?id=($id)&query_type=by_id\">($word)</a>";
+ my($idquoted)=$id; $idquoted=~s%\W%\\$&%g;
+ my($ipniservletwordthree)=$ipniservletword; $ipniservletwordthree=~s%\($idquoted\)%((?:$idone){3})$&%os or die;
+ my($attrpat)="<p>nomenclatural synonym(\\(Main Record\\))?:$ipniservletword</p>|<p>basionym(\\(\\d+\\))?:$ipniservletword</p>|<p>basionym:($word)|<p>replaced synonym:$ipniservletword</p>|<p>replaced synonym:($word)|<p>Is a replaced synonym of:$ipniservletword</p>|<p>Is a basionym of:$ipniservletword</p>|<p>later publication of(\\(\\d+\\))?:$ipniservletword</p>|<p>Is a later publication of of:$ipniservletword</p>";
+ $|=1;
+ "<undef>"=~/^/;
+ if ($fi!~m%^<html>
+<head>
+<title>IPNI Query Results</title>
+</head>
+<body bgcolor="#ffffff" text="#000000" link="#006666" vlink="#008080" alink="#008080">
+<HR><b><i>Orchidaceae</i> ($word)</b> ($word) <br>
+((?:<a href="\./PublicationServlet\?id=($id)&query_type=by_id"> ($word)</a> ($word)|$bigword(?:<br>\n$word)*)?<p>($bigword)?</p><p>($word)?</p>(?:
+remarks: .*)?(<HR><h4>Type</h4>)?(<table $any</table>)?(?:
+<h4>Linked Records</h2>
+((?:$attrpat)*))?(<br>
+
+<h4>Original Data</h2>
+(?:basionym: ($word)<br>
+)?(?:hybrid parentage: ($word)<br>
+)?(?:replaced synonym: ($word)<br>
+)?(?:distribution: ($word)<br>
+)?(?:Notes: ($word))?)?)(?:<p><a href="\./query_ipni.html">Back to Search Page</a></p>
+</body>
+</html>)$%os) {
+ failed($file);
+ return;
}
- elsif (/^ *³ *(.*)$/) {
- print STDERR "APPEND: $1\n" if $debugparse;
- $CURR{$last_field}.=" ".$1;
+ my(%rec);
+ $rec{"name"}=$1;
+ $rec{"Publ. Author"}=$2;
+ $rec{"Publication"}="$5 $6" if defined($5) && defined($6);
+ $rec{"html"}=$3 if defined $3;
+ my($attrsbody)=$11;
+ ($rec{"id"}=$file)=~s#^($id)\.html$#$1#os or failed($file);
+ $rec{"html"}=~s#$ipniservletwordthree#<a href="$1/$1$2.html">$3</a>#osg if $import_xlate && exists $rec{"html"};
+ my $score=0; # -: upper, +: lower
+ while (defined($attrsbody) && $attrsbody=~s%^(?:$attrpat)%%os) {
+ # nomenclatural synonym: id=$2
+ # basionym: id=$5
+ # replaced synonym: id=$8
+ # Is a replaced synonym: id=$11
+ # Is a basionym: id=$13
+ # later publication: id=$16
+ # Is a later publication: id=$18
+ my(@refs)=($2,$5,$8,$11,$13,$16,$18);
+ $rec{"refs"}=[];
+ while (@refs) {
+ push(@{$rec{"refs"}},$_) if defined ($_=shift @refs);
+ }
+ $score+=-10 if defined $5; # basionym: id=$5
+ $score+=+10 if defined $13; # Is a basionym: id=$13
+ $score+=+10 if defined $16; # later publication: id=$16
+ $score+=-10 if defined $18; # Is a later publication: id=$18
}
- else {
- print STDERR "DISCARD: $_\n" if $debugparse;
+ $rec{"score"}=$score;
+ if ($attrsbody) {
+ failed($file);
+ return;
}
- }
-&flush_CURR();
-undef %CURR;
+ $DB{$rec{"id"}}=\%rec;
+}
-%PARENT=();
-sub try_reparent
+sub process_dir
{
-my( $reparent,$refkey );
-
- $refkey=&name_to_key($ref);
- return 0 if ($refkey eq "");
- return 0 if ($parent eq $refkey);
- return 0 if !exists $DB{$refkey};
- print STDERR "try_reparent: SUCCESS: key=\"$key\", refkey=\"$refkey\"\n" if $debugmatch;
- if ($note_rest)
- { $DB{$key}{"Notes"}=$note_rest; }
- else
- { delete $DB{$key}{"Notes"}; }
-
- foreach $reparent (@{$OWNS{$parent}}) {
- $PARENT{$reparent}=$refkey;
+my( $dir )=@_;
+my( $old )=getcwd();
+
+ if (!chdir($dir)) {
+ warn("Unable to change to dir \"$dir\" from dir \"$old\": $!");
+ return;
+ }
+ opendir(DIR,".") or die("Cannot open . in \"".getcwd()."\": $!");
+ foreach (sort readdir(DIR)) {
+ process_entry($_) if ($_!~/^\./);
}
- @{$OWNS{$parent}}=() if (!exists $OWNS{$parent});
- @{$OWNS{$refkey}}=() if (!exists $OWNS{$refkey});
- @{$OWNS{$refkey}}=(@{$OWNS{$refkey}},$parent,@{$OWNS{$parent}});
- delete $OWNS{$parent};
+ closedir(DIR);
+ chdir($old) or warn("Unable to retreat to dir \"$old\": $!");
+}
- return 1;
+sub process_entry
+{
+my( $entry )=@_;
+
+ process_dir ($entry) if -d $entry;
+ process_file($entry) if -f $entry;
}
-MATCH: foreach $key (keys %DB) {
- $parent=$PARENT{$key};
- $parent=$key if (!defined $parent);
- $ref=$DB{$key}{"Notes"};
- next MATCH if (!defined $ref);
- $ref=~tr/()//d;
- $ref=~s/^=//;
- $ref=~s/^O\. *//i;
- $ref=~s/^Orchidaceae *//i;
- $ref=~s/\. *(.*)$//;
- $note_rest=$1;
- next MATCH if &try_reparent();
- $ref=$DB{$key}{"Rank"}." $ref" if exists $DB{$key}{"Rank"};
- next MATCH if &try_reparent();
- $ref=$DB{$key}{"Genus"}." $ref" if exists $DB{$key}{"Genus"};
- next MATCH if &try_reparent();
+%OWNS=();
+
+foreach (@ARGV)
+ { process_entry($_); }
+
+my($id);
+for $id (keys %DB) {
+ my($refid);
+ my(@refs);
+ for $refid (@{$DB{$id}{"refs"}}) {
+ if (!exists $DB{$refid}) {
+ warn "Undefined ref id \"$refid\" from id \"$id\"" if $D;
+ next;
+ }
+ next if $id eq $refid; # self-ref
+# push(@refs,$DB{$refid});
+ push(@refs,$refid);
+ }
+ $DB{$id}{"refs"}=\@refs;
+ }
+
+print Data::Dumper->Dump([\%DB],["%DB"]) if $D;
+
+%OWNS=map { $_=>[] } keys(%DB);
+
+for $id (keys %OWNS) {
+ next if !exists $OWNS{$id};
+ for my $refid (@{$DB{$id}{"refs"}}) {
+ next if !exists $OWNS{$refid};
+ push(@{$OWNS{$id}},$refid,@{$OWNS{$refid}});
+ delete $OWNS{$refid};
+ print "connected: id=$id,refid=$refid\n" if $D;
+ }
}
-undef %PARENT;
-#foreach $key (keys %DB) {
-# $DB{$key}{"Publication"}=&extract_year($DB{$key}{"Publication"})." ::: ".$DB{$key}{"Publication"}
-# if (exists($DB{$key}{"Publication"}));
-# }
+print Data::Dumper->Dump([\%OWNS],["%OWNS"]) if $D;
foreach $key (keys %OWNS) {
my(@keys)=@{$OWNS{$key}};
delete($OWNS{$key});
unshift(@keys,$key);
- @keys=sort { &extract_year($DB{$b}{"Publication"}) <=> &extract_year($DB{$a}{"Publication"}); } @keys;
+ @keys=sort { $DB{$a}{"score"} <=> $DB{$b}{"score"}
+ || extract_year($DB{$b}{"Publication"}) <=> extract_year($DB{$a}{"Publication"}); } @keys;
my($pkey)=shift(@keys);
- @{$OWNS{$pkey}}=@keys;
+ $OWNS{$pkey}=\@keys;
}
-sub print_header
-{
-my($header)=@_;
-
- print OUT
-"<?xml version=\"1.0\" encoding=\"iso-8859-1\"?>
-<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.1//EN\" \"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd\">
-<html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\">
-<head><title>Kewensis $header</title>
-<style type=\"text/css\"><!--
-.name { font-weight: bold; }
---></style>
-</head><body>
-\n";
-}
-
-$fileno=-1;
-
-sub OUT_flush
-{
- print OUT "</body></html>\n";
- close(OUT);
-}
+my($db_driver,$db_host,$db_user,$db_pwd,$DB_PWD,$db_name,$db);
+my($tb_tree);
-my( $filename );
-foreach $owner (sort keys %OWNS) {
-my( $child );
+$db_driver="mysql";
+$db_host="";
+#$db_user="short";
+#$DB_PWD=$ENV{"HOME"}."/priv/mysql.${db_user}.pwd";
+$db_name="short";
+$tb_tree="kewensis_tree";
- if ($fileno<0 || tell(OUT)>=$maxsize) {
- &OUT_flush() if ($fileno>=0);
- $fileid=sprintf("%04d",++$fileno);
- $filename="kew-$fileid.html";
- open(OUT,">$filename") or die "Cannot open \"$filename\": $!";
- &print_header("chunk $fileid");
- }
+$db=DBI->connect("DBI:$db_driver:database=$db_name;host=$db_host",$db_user,$db_pwd) or die "Database open fail: $!";
- if ($debugmatch) {
- print STDERR "($owner):";
- foreach $child (@{$OWNS{$owner}})
- { print STDERR " ($child)"; }
- print STDERR "\n";
- }
- print OUT &format_record("<a id=\"".&htmlquote($owner)."\">","</a>",%{$DB{$owner}});
- if (@{$OWNS{$owner}}) {
- print OUT "<blockquote>\n";
- foreach $child (@{$OWNS{$owner}})
- { print OUT &format_record("","",%{$DB{$child}}); }
- print OUT "</blockquote>\n";
- }
- print OUT "\n";
- $DB{$owner}{"_filename"}=$filename;
- }
-&OUT_flush();
-open(OUT,">kew-index.html") or die "Cannot open \"kew-index.html\": $!";
-&print_header("Index");
-
-sub print_href
+sub db_do
{
-my($owner)=@_;
-my(%rec)=%{$DB{$owner}};
+my( $cmd )=@_;
- print OUT &htmlquote(&rec_to_name(%rec));
+ $db->do($cmd) or die("SQL command \"$cmd\" failed: $!");
}
-foreach $owner (sort keys %OWNS) {
-my( $child );
-
- print OUT "<p><a href=\"".$DB{$owner}{"_filename"}."#$owner\">";
- &print_href($owner);
- print OUT "</a></p>";
- if (@{$OWNS{$owner}}) {
- print OUT "<ul>\n";
- foreach $child (@{$OWNS{$owner}}) {
- print OUT "<li>";
- &print_href($child);
- print OUT "</li>\n";
- }
- print OUT "</ul>";
+eval { &db_do("drop table $tb_tree") };
+
+&db_do("create table $tb_tree ("
+ ."id char(10) not null,"
+ ."family_id char(10) not null,"
+ ."family_order int not null,"
+ ."name varchar(100) not null,"
+ ."Publication text null,"
+ ."Notes text null,"
+ ."html text null"
+ .")");
+
+&db_do("alter table $tb_tree add unique (id)");
+&db_do("alter table $tb_tree add index (name)");
+&db_do("alter table $tb_tree add unique (family_id,family_order)");
+
+my $insert_tb_tree=$db->prepare("insert into $tb_tree (id,family_id,family_order,name,Publication,Notes,html) values (?,?,?,?,?,?,?)")
+ or die "Prepare fail: $!";
+
+foreach $owner (sort { $DB{$b}{"name"} cmp $DB{$a}{"name"}; } keys %OWNS) {
+ my @family=@{$OWNS{$owner}};
+ unshift(@family,$owner);
+ my $family_id=$DB{$owner}{"id"};
+ for my $family_order (0..$#family) {
+ my $id=$family[$family_order];
+ print "insert:$id,".$DB{$id}{"name"}."\n" if $D;
+ $insert_tb_tree->execute($id,$family_id,$family_order,
+ $DB{$id}{"name"},$DB{$id}{"Publication"},$DB{$id}{"Notes"},$DB{$id}{"html"}
+ ) or die "SQL insert failure: $!";
}
- print OUT "\n";
}
-OUT_flush();
git://git.jankratochvil.net / kewensis.git / blobdiff