From bf24bf9e31a3688bc5c8dc35a8a627eea9570664 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Mon, 27 Jan 2014 11:12:52 -0800
Subject: [PATCH] switch to sqlite for bibtex_to_paper; default cache location;
 actually kind of works now

---
 bibtex_to_paper | 309 +++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 267 insertions(+), 42 deletions(-)

diff --git a/bibtex_to_paper b/bibtex_to_paper
index f6ac661..9d9cf7c 100755
--- a/bibtex_to_paper
+++ b/bibtex_to_paper
@@ -13,11 +13,14 @@ use Getopt::Long;
 use Pod::Usage;
 
 use File::Find;
-use Text::BibTex;
+use File::Basename qw(basename);
+use File::Spec qw(rel2abs);
+use Text::BibTeX;
+use User;
+use Data::Printer;
 
-use DB_File;
-use MLDBM qw(DB_FILE Storable);
-use Fcntl qw/O_RDWR O_CREAT O_TRUNC/;
+use DBI;
+use Tie::DBI;
 
 =head1 NAME
 
@@ -80,13 +83,15 @@ use vars qw($DEBUG);
 my %options = (debug           => 0,
                help            => 0,
                man             => 0,
+               'bibtex_cache'  => File::Spec->catfile(User->Home,'.bibtex_to_paper_cache'),
               );
 
 GetOptions(\%options,
            'build_cache|build-cache|B!',
-           'bibtex|b=s',
+           'bibtex|b=s@',
            'bibtex_cache|bibtex-cache|c=s',
            'pdfviewer|p=s',
+           'papers_directory|papers-directory=s@',
            'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -104,50 +109,221 @@ if (not exists $options{bibtex} and
 
 pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
 
+main();
+
+sub main{
+
+    my $dbh;
+    my $sth;
+    if (exists $options{bibtex_cache}) {
+        my $initialize = 0;
+        if (-e $options{bibtex_cache}) {
+            ($dbh,$sth) = open_cache($options{bibtex_cache});
+        } else {
+            ($dbh,$sth) = initialize_database($options{bibtex_cache});
+        }
+    }
+
+    my %entries;
+    if (exists $options{build_cache}) {
+        $options{bibtex} //= [];
+        $options{bibtex} =
+            [@ARGV,
+             @{ref $options{bibtex}?$options{bibtex}:[$options{bibtex}]},
+            ];
+    }
+    if (exists $options{bibtex}) {
+        for my $bibtex_file (@{ref $options{bibtex}?$options{bibtex}:[$options{bibtex}]}) {
+            parse_bibtex_file($bibtex_file,\%entries);
+        }
+    }
+
+    if (exists $options{papers_directory} and
+        defined $dbh
+       ) {
+        load_papers_into_database($dbh,$sth,$options{papers_directory});
+    }
+
+    p %entries if $DEBUG;
+    if (keys %entries and
+        defined $dbh) {
+        load_bibtex_entries_into_database($dbh,$sth,\%entries);
+    }
+
+    for my $bibtex_key (@ARGV) {
+        open_bibtex_key(\%options,$dbh,$sth,\%entries,$bibtex_key);
+    }
+
+}
+
+sub load_papers_into_database {
+    my ($dbh,$sth,$dir) = @_;
+
+    my @dirs = ref($dir)?@{$dir}:$dir;
+
+    my $actually_load_it = sub {
+        return unless /\.pdf$/;
+        my $xoj = 0;
+        if (-e "${_}.xoj") {
+            $xoj = 1;
+        }
+        insert_or_replace_papers($dbh,$sth,basename($File::Find::name),File::Spec->rel2abs($File::Find::name),$xoj);
+    };
+
+    my @pdfs;
+    find($actually_load_it,@dirs);
+}
+
+sub insert_or_replace_papers {
+    my ($dbh,$sth,$file_name,$file_loc,$has_xoj) = @_;
+    $sth->{insert_papers}->execute($file_name,$file_loc,$has_xoj);
+    $sth->{insert_papers}->finish();
+}
+
+sub load_bibtex_entries_into_database {
+    my ($dbh,$sth,$entries) = @_;
+    for my $entry (keys %{$entries}) {
+        next unless defined $entries->{$entry};
+        $sth->{insert_bibtex}->execute($entry,@{$entries->{$entry}}{qw(file_name doi html)});
+        $sth->{insert_bibtex}->finish();
+        print STDERR "inserted $entry $entries->{$entry}\n" if $DEBUG;
+    }
+}
+
+sub open_bibtex_key {
+    my ($options,$dbh,$sth,$entries,$bibtex_key) = @_;
+    if (not defined $dbh) {
+        open_entry($dbh,$sth,$entries->{$bibtex_key},$options);
+    } else {
+        my $entry = select_entry_from_bibtex_key($dbh,$sth,$bibtex_key);
+        p $entry if $DEBUG;
+        open_entry($dbh,$sth,$entry,$options);
+    }
+}
+
+sub fork_exec {
+    my (@cmd) = @_;
+    my $child = fork();
+    if (not defined $child) {
+        die "Unable to fork for some reason: $!";
+    }
+    if ($child == 0) {
+        exec(@cmd);
+    } else {
+        return $child;
+    }
+
+}
+
+sub open_pdf {
+    my ($file_name,$options,$has_xoj) = @_;
+    print STDERR "opening $file_name\n" if $DEBUG;
+    if ($has_xoj) {
+        fork_exec('xournal',$file_name);
+    } else {
+        fork_exec('evince',$file_name)
+    }
+}
+
+sub open_browser{
+    my ($file) = @_;
+    fork_exec('sensible-browser',$file);
+}
+
+sub open_entry{
+    my ($dbh,$sth,$entry,$options) = @_;
+
+    return unless defined $entry and ref $entry and keys %{$entry};
+    if (defined $entry->{file_name} and length $entry->{file_name}) {
+        my $paper = select_one($dbh,$sth->{select_papers_by_name},$entry->{file_name});
+        p $paper if $DEBUG;
+        print STDERR $entry->{file_name} if $DEBUG;
+        if (defined $paper) {
+            open_pdf($paper->{file_name},$options,$paper->{xoj});
+            return;
+        }
+    }
+    if (defined $entry->{doi}) {
+        my $url = $entry->{doi};
+        $url =~ s{^doi://}{http://dx.doi.org/};
+        open_browser($url,$options);
+        return;
+    }
+    if (defined $entry->{html}) {
+        open_browser($entry->{html},$options);
+        return;
+    }
+}
+
+sub select_entry_from_bibtex_key{
+    my ($dbh,$sth,$bibtex_key) = @_;
+
+    my $entry = select_one($dbh,$sth->{select_bibtex_by_key},$bibtex_key);
+    return $entry;
+}
+
+sub select_one{
+    my ($dbh,$sth,@bind_vals) = @_;
+    $sth->execute(@bind_vals) or
+        die "Unable to select one: ".$dbh->errstr();
+    my $results = $sth->fetchall_arrayref({});
+    $sth->finish();
+    return ref($results)?$results->[0]:undef;
+}
+
 sub parse_bibtex_file {
     my ($file,$entries) = @_;
 
-    my $bibfile = Text::BibTex::File->new($file)
-        or die "Unable to open $bibfile for reading: $!";
+    my $bibfile = Text::BibTeX::File->new($file)
+        or die "Unable to open $file for reading: $!";
     my @entry_comments;
     my $entry;
-    while ($entry = Text::BibTex::Entry->new($bibfile)) {
-        if ($entry->metatype() eq 'BTE_COMMENT') {
+    while ($entry = Text::BibTeX::Entry->new($bibfile)) {
+        print STDERR "In Entry ".$entry->metatype() if $DEBUG;
+        if ($entry->metatype() == BTE_COMMENT) {
             push @entry_comments,$entry->value();
-        } elsif ($entry->metatype() eq 'BTE_REGULAR') {
+        } elsif ($entry->metatype() == BTE_REGULAR) {
             my $entry_key = $entry->key();
-            my $link_name;
-            if (defined $entry_key) {
-                # if there is a file comment, use it as the file name
-                for my $comment (@entry_comments) {
-                    next unless $comment =~ /^\s*file(?:name)?:?\s*(.+?)\s*$/i;
-                    $link_name = $1;
-                    last;
-                }
-                # if there is a file key, use that as the file name
-                # if there is a doi, then use that
-                # if there is a html, then use that
-                if (not defined $link_name) {
-                    my @possible_fields = $entry->get(qw(file doi html));
-                    for my $possible_field (@possible_fields) {
-                        if (defined $possible_field and length $possible_field) {
-                            $link_name = $possible_field;
-                            last;
-                        }
-                    }
+            if (not defined $entry_key) {
+                @entry_comments = ();
+                next;
+            }
+            my %entry_data;
+            # if there is a file comment, use it as the file name
+            for my $comment (@entry_comments) {
+                next unless $comment =~ /^\s*file(?:name)?:?\s*(.+?)\s*$/i;
+                next unless length $1;
+                $entry_data{file_name} = $1.'.pdf';
+                last;
+            }
+            my %field_prefix = (doi => 'doi://',
+                                html => 'http://',
+                                file => '',
+                               );
+            my %field_name = (doi => 'doi',
+                              html => 'html',
+                              file => 'file_name',);
+            for my $field (qw(file doi html)) {
+                my $field_value = $entry->get($field);
+                if (defined $field_value and $field_value =~ /\S+/) {
+                    $entry_data{$field_name{$field}} =
+                        $field_prefix{$field}.$field_value if
+                        not defined $entry_data{$field_name{$field}};
                 }
             }
-            if (not exists $entries->{$entry_key} or
-                defined $link_name;
-               ) {
-                $entries->{$entry_key} = $link_name
+            $entries->{$entry_key} = {} if not defined $entries->{$entry_key};
+            for my $field (keys %entry_data) {
+                $entries->{$entry_key}{$field} = $entry_data{$field} if
+                    defined $entry_data{$field};
             }
             # reset the entry comments
             @entry_comments = ();
         } else {
             # do nothing
         }
+        print STDERR "\n" if $DEBUG;
     }
+    return $entries;
 }
 
 
@@ -157,17 +333,66 @@ sub initialize_database {
 }
 
 sub open_cache {
-    my ($cache,$initialize) @_;
-    my $open_flags = O_RDWR|O_CREAT;
+    my ($cache,$initialize) = @_;
+    my $dbh = DBI->connect("dbi:SQLite:dbname=$cache","","") or
+        die "Unable to open/create database $cache";
     if ($initialize) {
-        $open_flags = $open_flags | O_TRUNC;
+        $dbh->do("DROP TABLE IF EXISTS bibtex;");
+        $dbh->do("DROP TABLE IF EXISTS papers;");
+        $dbh->do(<<EOF);
+CREATE TABLE bibtex (
+bibtex_key TEXT PRIMARY KEY,
+file_name TEXT,
+doi TEXT,
+html TEXT
+);
+EOF
+        $dbh->do(<<EOF);
+CREATE UNIQUE INDEX bibtex_file_name ON bibtex(file_name);
+EOF
+        $dbh->do(<<EOF);
+CREATE UNIQUE INDEX bibtex_bibtex_key ON bibtex(bibtex_key);
+EOF
+        $dbh->do(<<EOF);
+CREATE TABLE papers (
+file_name TEXT PRIMARY KEY,
+path TEXT,
+has_xoj BOOLEAN
+);
+EOF
+        $dbh->do(<<EOF);
+CREATE UNIQUE INDEX papers_path ON papers(path);
+EOF
+        $dbh->do(<<EOF);
+CREATE UNIQUE INDEX papers_file_name ON papers(file_name);
+EOF
     }
-
-    my %entries;
-    tie %entries, MLDBM => $cache
-        $open_flags, 0666
-        or die "Unable to create create/truncate $cache: $!";
-    return \%entries;
+    my %s =
+        (insert_papers => <<'EOF',
+INSERT OR REPLACE INTO papers(file_name,path,has_xoj) VALUES (?,?,?);
+EOF
+         insert_bibtex => <<'EOF',
+INSERT OR REPLACE INTO bibtex (bibtex_key,file_name,doi,html) VALUES (?,?,?,?);
+EOF
+         select_papers_by_name => <<'EOF',
+SELECT * FROM papers WHERE file_name = ?;
+EOF
+         select_papers_by_path => <<'EOF',
+SELECT * FROM papers WHERE path = ?;
+EOF
+         select_bibtex_by_key => <<'EOF',
+SELECT * FROM bibtex WHERE bibtex_key = ?;
+EOF
+         select_bibtex_by_file_name => <<'EOF',
+SELECT * FROM bibtex WHERE file_name = ?;
+EOF
+        );
+    my $st;
+    for my $key (keys %s) {
+        $st->{$key}=$dbh->prepare($s{$key}) //
+            die "Unable to prepare sql statement: ".$dbh->errstr;
+    }
+    return ($dbh,$st);
 }
 
 
-- 
2.39.5