From: Tara L Andrews <tla@mit.edu>
Date: Fri, 14 Sep 2012 13:16:03 +0000 (+0200)
Subject: split out persistence / DB functionality
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=ed5b9b7019c32c126faecf339bef3a98928f9f31;p=scpubgit%2Fstemmatology.git

split out persistence / DB functionality
---

diff --git a/base/Makefile.PL b/base/Makefile.PL
index 2bedd72..86e7613 100644
--- a/base/Makefile.PL
+++ b/base/Makefile.PL
@@ -6,18 +6,10 @@ license( 'perl' );
 perl_version( '5.012' );
 all_from( 'lib/Text/Tradition.pm' );
 requires( 'Algorithm::Diff' );
-requires( 'Class::Load' );
-requires( 'DBI' );
 requires( 'File::Which' );
 requires( 'Graph' );
 requires( 'IPC::Run' );
 requires( 'JSON' );
-requires( 'KiokuDB::Backend::DBI' );
-requires( 'KiokuDB::GC::Naive' );
-requires( 'KiokuDB::TypeMap' );
-requires( 'KiokuDB::TypeMap::Entry::Naive' );
-requires( 'KiokuX::Model' );
-requires( 'KiokuX::User::Util' );
 requires( 'Module::Load' );
 requires( 'Moose' );
 requires( 'Moose::Util' );
@@ -33,9 +25,6 @@ requires( 'TryCatch' );
 requires( 'XML::Easy::Syntax' );
 requires( 'XML::LibXML' );
 requires( 'XML::LibXML::XPathContext' );
-requires( 'YAML::XS' );
-requires( 'namespace::clean' );
 build_requires( 'Data::Dump' );
 build_requires( 'Test::Warn' );
-build_requires( 'Test::Memory::Cycle' );
 &WriteAll;
diff --git a/base/lib/Text/Tradition.pm b/base/lib/Text/Tradition.pm
index fda7b3c..e85f366 100644
--- a/base/lib/Text/Tradition.pm
+++ b/base/lib/Text/Tradition.pm
@@ -15,9 +15,10 @@ $VERSION = "1.1";
 
 # Enable plugin(s) if available
 eval { with 'Text::Tradition::HasStemma'; };
-if( $@ ) {
-	warn "Text::Tradition::Analysis not found. Disabling stemma analysis functionality";
-};
+# Don't warn normally
+# if( $@ ) {
+# 	warn "Text::Tradition::Analysis not found. Disabling stemma analysis functionality";
+# };
 eval { with 'Text::Tradition::Language'; };
 
 has 'collation' => (
diff --git a/base/lib/Text/Tradition/Parser/Self.pm b/base/lib/Text/Tradition/Parser/Self.pm
index 4ca6e63..55ec769 100644
--- a/base/lib/Text/Tradition/Parser/Self.pm
+++ b/base/lib/Text/Tradition/Parser/Self.pm
@@ -95,11 +95,9 @@ source of the XML to be parsed.
 
 =begin testing
 
-use File::Temp;
 use Safe::Isa;
 use Test::Warn;
 use Text::Tradition;
-use Text::Tradition::Directory;
 use TryCatch;
 binmode STDOUT, ":utf8";
 binmode STDERR, ":utf8";
@@ -154,28 +152,6 @@ if( $newt ) {
     }
 }
 
-# Test user save / restore
-my $fh = File::Temp->new();
-my $file = $fh->filename;
-$fh->close;
-my $dsn = "dbi:SQLite:dbname=$file";
-my $userstore = Text::Tradition::Directory->new( { dsn => $dsn,
-	extra_args => { create => 1 } } );
-my $scope = $userstore->new_scope();
-my $testuser = $userstore->create_user( { url => 'http://example.com' } );
-ok( $testuser->$_isa('Text::Tradition::User'), "Created test user via userstore" );
-$testuser->add_tradition( $newt );
-is( $newt->user->id, $testuser->id, "Assigned tradition to test user" );
-$graphml_str = $newt->collation->as_graphml;
-my $usert;
-warning_is {
-	$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str );
-} 'DROPPING user assignment without a specified userstore',
-	"Got expected user drop warning on parse";
-$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str,
-	'userstore' => $userstore );
-is( $usert->user->id, $testuser->id, "Parsed tradition with userstore points to correct user" );
-
 # Test warning if we can
 unless( $stemma_enabled ) {
 	my $nst;
diff --git a/base/t/text_tradition_parser_self.t b/base/t/text_tradition_parser_self.t
index ed921aa..df36d06 100644
--- a/base/t/text_tradition_parser_self.t
+++ b/base/t/text_tradition_parser_self.t
@@ -8,11 +8,9 @@ $| = 1;
 
 # =begin testing
 {
-use File::Temp;
 use Safe::Isa;
 use Test::Warn;
 use Text::Tradition;
-use Text::Tradition::Directory;
 use TryCatch;
 binmode STDOUT, ":utf8";
 binmode STDERR, ":utf8";
@@ -67,28 +65,6 @@ if( $newt ) {
     }
 }
 
-# Test user save / restore
-my $fh = File::Temp->new();
-my $file = $fh->filename;
-$fh->close;
-my $dsn = "dbi:SQLite:dbname=$file";
-my $userstore = Text::Tradition::Directory->new( { dsn => $dsn,
-	extra_args => { create => 1 } } );
-my $scope = $userstore->new_scope();
-my $testuser = $userstore->create_user( { url => 'http://example.com' } );
-ok( $testuser->$_isa('Text::Tradition::User'), "Created test user via userstore" );
-$testuser->add_tradition( $newt );
-is( $newt->user->id, $testuser->id, "Assigned tradition to test user" );
-$graphml_str = $newt->collation->as_graphml;
-my $usert;
-warning_is {
-	$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str );
-} 'DROPPING user assignment without a specified userstore',
-	"Got expected user drop warning on parse";
-$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str,
-	'userstore' => $userstore );
-is( $usert->user->id, $testuser->id, "Parsed tradition with userstore points to correct user" );
-
 # Test warning if we can
 unless( $stemma_enabled ) {
 	my $nst;
diff --git a/persistence/Makefile.PL b/persistence/Makefile.PL
new file mode 100644
index 0000000..e5dadc7
--- /dev/null
+++ b/persistence/Makefile.PL
@@ -0,0 +1,24 @@
+#!/usr/bin/env perl
+
+use inc::Module::Install;
+author( 'Tara L Andrews <aurum@cpan.org>' );
+license( 'perl' );
+perl_version( '5.012' );
+all_from( 'lib/Text/Tradition/Directory.pm' );
+requires( 'Class::Load' );
+requires( 'DBI' );
+requires( 'JSON' );
+requires( 'KiokuDB::Backend::DBI' );
+requires( 'KiokuDB::GC::Naive' );
+requires( 'KiokuDB::TypeMap' );
+requires( 'KiokuDB::TypeMap::Entry::Naive' );
+requires( 'KiokuX::Model' );
+requires( 'KiokuX::User::Util' );
+requires( 'Moose' );
+requires( 'Safe::Isa' );
+requires( 'TryCatch' );
+requires( 'YAML::XS' );
+requires( 'namespace::clean' );
+build_requires( 'Test::Warn' );
+build_requires( 'Test::Memory::Cycle' );
+&WriteAll;
diff --git a/base/lib/Text/Tradition/Directory.pm b/persistence/lib/Text/Tradition/Directory.pm
similarity index 100%
rename from base/lib/Text/Tradition/Directory.pm
rename to persistence/lib/Text/Tradition/Directory.pm
diff --git a/base/lib/Text/Tradition/Store.pm b/persistence/lib/Text/Tradition/Store.pm
similarity index 100%
rename from base/lib/Text/Tradition/Store.pm
rename to persistence/lib/Text/Tradition/Store.pm
diff --git a/base/lib/Text/Tradition/TypeMap/Entry.pm b/persistence/lib/Text/Tradition/TypeMap/Entry.pm
similarity index 100%
rename from base/lib/Text/Tradition/TypeMap/Entry.pm
rename to persistence/lib/Text/Tradition/TypeMap/Entry.pm
diff --git a/base/lib/Text/Tradition/User.pm b/persistence/lib/Text/Tradition/User.pm
similarity index 100%
rename from base/lib/Text/Tradition/User.pm
rename to persistence/lib/Text/Tradition/User.pm
diff --git a/persistence/t/00dependencies.t b/persistence/t/00dependencies.t
new file mode 100644
index 0000000..e70a616
--- /dev/null
+++ b/persistence/t/00dependencies.t
@@ -0,0 +1,95 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+=head1 DESCRIPTION
+
+Makes sure that all of the modules that are 'use'd are listed in the
+Makefile.PL as dependencies.  Also as long as we are source filtering,
+make sure there are no $DB::single statements in the code.
+
+=cut
+
+use Test::More;
+use File::Find;
+eval 'use Module::CoreList';
+if ($@) { plan skip_all => 'Module::CoreList not installed' }
+
+plan 'no_plan';
+
+my %skipped;
+if( -f 'MANIFEST.SKIP' ) {
+	# We don't want these
+	open( SKIP, 'MANIFEST.SKIP' ) or die "Could not open manifest skip file";
+	while(<SKIP>) {
+		chomp;
+		$skipped{$_} = 1;
+	}
+	close SKIP;
+}
+my %used;
+find( \&wanted, qw/ lib t / );
+
+sub wanted {
+    return unless -f $_;
+    return if $File::Find::dir  =~ m!/.git($|/)!;
+    return if $File::Find::name =~ /~$/;
+    return if $File::Find::name =~ /\.(pod|html)$/;
+    return if $skipped{$File::Find::name};
+
+    # read in the file from disk
+    my $filename = $_;
+    local $/;
+    open( FILE, $filename ) or return;
+    my $data = <FILE>;
+    close(FILE);
+
+    # strip pod, in a really idiotic way.  Good enough though
+    $data =~ s/^=(begin|head).+?(^=cut|\Z)//gms;
+
+    # look for use and use base statements
+    $used{$1}{$File::Find::name}++ while $data =~ /^\s*use\s+([\w:]+)/gm;
+    while ( $data =~ m|^\s*use base qw.([\w\s:]+)|gm ) {
+        $used{$_}{$File::Find::name}++ for split ' ', $1;
+    }
+    # look for DB statements while we are here
+    while( $data =~ /^\s*\$DB::single/gm ) {
+    	fail( "DB::single statement present in source " . $File::Find::name );
+    }
+}
+
+my %required;
+{
+    local $/;
+    ok( open( MAKEFILE, "Makefile.PL" ), "Opened Makefile" );
+    my $data = <MAKEFILE>;
+    close(FILE);
+    while ( $data =~ /^\s*?(?:requires|recommends|).*?([\w:]+)'(?:\s*=>\s*['"]?([\d\.]+)['"]?)?.*?(?:#(.*))?$/gm ) {
+        $required{$1} = $2;
+        if ( defined $3 and length $3 ) {
+            $required{$_} = undef for split ' ', $3;
+        }
+    }
+}
+
+for ( sort keys %used ) {
+    my $first_in = Module::CoreList->first_release($_);
+    next if defined $first_in and $first_in <= 5.00803;
+    next if /^(Text::Tradition|inc|t|feature|parent)(::|$)/;
+
+    #warn $_;
+    ok( exists $required{$_}, "$_ in Makefile.PL" )
+        or diag( "used in ", join ", ", sort keys %{ $used{$_} } );
+    delete $used{$_};
+    delete $required{$_};
+}
+
+for ( sort keys %required ) {
+    my $first_in = Module::CoreList->first_release( $_, $required{$_} );
+    fail("Required module $_ (v. $required{$_}) is in core since $first_in")
+        if defined $first_in and $first_in <= 5.008003;
+}
+
+1;
+
diff --git a/persistence/t/02pod.t b/persistence/t/02pod.t
new file mode 100644
index 0000000..32b6d9f
--- /dev/null
+++ b/persistence/t/02pod.t
@@ -0,0 +1,10 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Test::More;
+
+eval "use Test::Pod 1.14";
+plan skip_all => 'Test::Pod 1.14 required' if $@;
+# plan skip_all => 'set TEST_POD to enable this test' unless $ENV{TEST_POD};
+
+all_pod_files_ok();
diff --git a/persistence/t/03podcoverage.t b/persistence/t/03podcoverage.t
new file mode 100644
index 0000000..d58a539
--- /dev/null
+++ b/persistence/t/03podcoverage.t
@@ -0,0 +1,32 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Test::More;
+
+eval "use Test::Pod::Coverage 1.04";
+plan skip_all => 'Test::Pod::Coverage 1.04 required' if $@;
+plan skip_all => 'set TEST_POD to enable this test' unless $ENV{TEST_POD};
+
+my @exclude = qw/ Store Collation::Data TypeMap::Entry /;
+
+my %mods;
+map { $mods{$_} = 1 } all_modules();
+map { delete $mods{'Text::Tradition::'.$_} } @exclude;
+if( -e 'MANIFEST.SKIP' ) {
+	open( SKIP, 'MANIFEST.SKIP' ) or die "Could not open skip file";
+	while(<SKIP>) {
+		chomp;
+		next unless /^lib/;
+		s/^lib\///;
+		s/\.pm//;
+		s/\//::/g;
+		delete $mods{$_};
+	}
+	close SKIP;
+}
+		
+foreach my $mod ( keys %mods ) {
+	pod_coverage_ok( $mod, { also_private => [ qw/ TO_JSON BUILD throw / ] } );
+}
+
+done_testing();
diff --git a/base/t/bin/make-load-test.pl b/persistence/t/bin/make-load-test.pl
similarity index 100%
rename from base/t/bin/make-load-test.pl
rename to persistence/t/bin/make-load-test.pl
diff --git a/base/t/bin/update-load-test.pl b/persistence/t/bin/update-load-test.pl
similarity index 100%
rename from base/t/bin/update-load-test.pl
rename to persistence/t/bin/update-load-test.pl
diff --git a/persistence/t/data/Collatex-16.xml b/persistence/t/data/Collatex-16.xml
new file mode 100644
index 0000000..869d665
--- /dev/null
+++ b/persistence/t/data/Collatex-16.xml
@@ -0,0 +1,294 @@
+<?xml version="1.0" ?>
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
+    xmlns:xsi="http://www.C.org/2001/XMLSchema-instance"
+        xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+    <key id="d0" for="node" attr.name="number" attr.type="int"/>
+    <key id="d1" for="node" attr.name="tokens" attr.type="string"/>
+    <key id="d2" for="edge" attr.name="number" attr.type="int"/>
+    <key id="d3" for="edge" attr.name="type" attr.type="string"/>
+    <key id="d4" for="edge" attr.name="witnesses" attr.type="string"/>
+    <graph id="g0" edgedefault="directed" parse.nodeids="canonical" parse.edgeids="canonical"
+        parse.order="nodesfirst">
+        <node id="n0">
+            <data key="d0">0</data>
+            <data key="d1"/>
+        </node>
+        <node id="n1">
+            <data key="d0">1</data>
+            <data key="d1">when</data>
+        </node>
+        <node id="n2">
+            <data key="d0">2</data>
+            <data key="d1">april</data>
+        </node>
+        <node id="n3">
+            <data key="d0">3</data>
+            <data key="d1">with</data>
+        </node>
+        <node id="n4">
+            <data key="d0">4</data>
+            <data key="d1">his</data>
+        </node>
+        <node id="n5">
+            <data key="d0">5</data>
+            <data key="d1">showers</data>
+        </node>
+        <node id="n6">
+            <data key="d0">6</data>
+            <data key="d1">sweet</data>
+        </node>
+        <node id="n7">
+            <data key="d0">7</data>
+            <data key="d1">with</data>
+        </node>
+        <node id="n8">
+            <data key="d0">8</data>
+            <data key="d1">april</data>
+        </node>
+        <node id="n9">
+            <data key="d0">11</data>
+            <data key="d1">fruit</data>
+        </node>
+        <node id="n10">
+            <data key="d0">12</data>
+            <data key="d1">the</data>
+        </node>
+        <node id="n11">
+            <data key="d0">13</data>
+            <data key="d1">teh</data>
+        </node>
+        <node id="n12">
+            <data key="d0">14</data>
+            <data key="d1">march</data>
+        </node>
+        <node id="n13">
+            <data key="d0">15</data>
+            <data key="d1">drought</data>
+        </node>
+        <node id="n14">
+            <data key="d0">16</data>
+            <data key="d1">of</data>
+        </node>
+        <node id="n15">
+            <data key="d0">17</data>
+            <data key="d1">march</data>
+        </node>
+        <node id="n16">
+            <data key="d0">18</data>
+            <data key="d1">drought</data>
+        </node>
+        <node id="n17">
+            <data key="d0">19</data>
+            <data key="d1">has</data>
+        </node>
+        <node id="n18">
+            <data key="d0">20</data>
+            <data key="d1">pierced</data>
+        </node>
+        <node id="n19">
+            <data key="d0">21</data>
+            <data key="d1">unto</data>
+        </node>
+        <node id="n20">
+            <data key="d0">22</data>
+            <data key="d1">to</data>
+        </node>
+        <node id="n21">
+            <data key="d0">23</data>
+            <data key="d1">teh</data>
+        </node>
+        <node id="n22">
+            <data key="d0">24</data>
+            <data key="d1">the</data>
+        </node>
+        <node id="n23">
+            <data key="d0">9</data>
+            <data key="d1">rood</data>
+        </node>
+        <node id="n24">
+            <data key="d0">10</data>
+            <data key="d1">root</data>
+        </node>
+        <node id="n25">
+            <data key="d0">25</data>
+            <data key="d1"/>
+        </node>
+        <edge id="e0" source="n0" target="n1">
+            <data key="d2">0</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B, C</data>
+        </edge>
+        <edge id="e1" source="n1" target="n2">
+            <data key="d2">1</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e2" source="n1" target="n5">
+            <data key="d2">2</data>
+            <data key="d3">path</data>
+            <data key="d4">B, C</data>
+        </edge>
+        <edge id="e3" source="n2" target="n3">
+            <data key="d2">3</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e4" source="n8" target="n9">
+            <data key="d2">4</data>
+            <data key="d3">path</data>
+            <data key="d4">B, C</data>
+        </edge>
+        <edge id="e5" source="n5" target="n6">
+            <data key="d2">5</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B, C</data>
+        </edge>
+        <edge id="e6" source="n3" target="n4">
+            <data key="d2">6</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e7" source="n9" target="n10">
+            <data key="d2">7</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B</data>
+        </edge>
+        <edge id="e8" source="n9" target="n11">
+            <data key="d2">8</data>
+            <data key="d3">path</data>
+            <data key="d4">C</data>
+        </edge>
+        <edge id="e9" source="n6" target="n7">
+            <data key="d2">9</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B, C</data>
+        </edge>
+        <edge id="e10" source="n7" target="n8">
+            <data key="d2">10</data>
+            <data key="d3">path</data>
+            <data key="d4">B, C</data>
+        </edge>
+        <edge id="e11" source="n10" target="n13">
+            <data key="d2">11</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e12" source="n10" target="n12">
+            <data key="d2">12</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e13" source="n11" target="n13">
+            <data key="d2">13</data>
+            <data key="d3">path</data>
+            <data key="d4">C</data>
+        </edge>
+        <edge id="e14" source="n7" target="n9">
+            <data key="d2">14</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e15" source="n3" target="n4">
+            <data key="d2">15</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e16" source="n13" target="n14">
+            <data key="d2">16</data>
+            <data key="d3">path</data>
+            <data key="d4">A, C</data>
+        </edge>
+        <edge id="e17" source="n12" target="n14">
+            <data key="d2">17</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e18" source="n4" target="n5">
+            <data key="d2">18</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e19" source="n14" target="n15">
+            <data key="d2">19</data>
+            <data key="d3">path</data>
+            <data key="d4">A, C</data>
+        </edge>
+        <edge id="e20" source="n14" target="n16">
+            <data key="d2">20</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e22" source="n15" target="n17">
+            <data key="d2">22</data>
+            <data key="d3">path</data>
+            <data key="d4">A, C</data>
+        </edge>
+        <edge id="e23" source="n16" target="n17">
+            <data key="d2">23</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e24" source="n17" target="n18">
+            <data key="d2">24</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B, C</data>
+        </edge>
+        <edge id="e25" source="n18" target="n19">
+            <data key="d2">25</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e26" source="n18" target="n20">
+            <data key="d2">26</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e27" source="n18" target="n21">
+            <data key="d2">27</data>
+            <data key="d3">path</data>
+            <data key="d4">C</data>
+        </edge>
+        <edge id="e28" source="n19" target="n22">
+            <data key="d2">28</data>
+            <data key="d3">path</data>
+            <data key="d4">A</data>
+        </edge>
+        <edge id="e29" source="n20" target="n22">
+            <data key="d2">29</data>
+            <data key="d3">path</data>
+            <data key="d4">B</data>
+        </edge>
+        <edge id="e30" source="n21" target="n23">
+            <data key="d2">30</data>
+            <data key="d3">path</data>
+            <data key="d4">C</data>
+        </edge>
+        <edge id="e31" source="n22" target="n24">
+            <data key="d2">31</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B</data>
+        </edge>
+        <edge id="e32" source="n23" target="n25">
+            <data key="d2">32</data>
+            <data key="d3">path</data>
+            <data key="d4">C</data>
+        </edge>
+        <edge id="e33" source="n24" target="n25">
+            <data key="d2">33</data>
+            <data key="d3">path</data>
+            <data key="d4">A, B</data>
+        </edge>
+        <edge id="e36" source="n8" target="n2">
+            <data key="d2">36</data>
+            <data key="d3">transposition</data>
+        </edge>
+        <edge id="e37" source="n13" target="n16">
+            <data key="d2">37</data>
+            <data key="d3">transposition</data>
+        </edge>
+        <edge id="e38" source="n15" target="n12">
+            <data key="d2">38</data>
+            <data key="d3">transposition</data>
+        </edge>
+    </graph>
+</graphml>
diff --git a/persistence/t/data/florilegium_graphml.xml b/persistence/t/data/florilegium_graphml.xml
new file mode 100644
index 0000000..f5ddc1d
--- /dev/null
+++ b/persistence/t/data/florilegium_graphml.xml
@@ -0,0 +1,13066 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
+  <key attr.name="version" attr.type="string" for="graph" id="dg0"/>
+  <key attr.name="wit_list_separator" attr.type="string" for="graph" id="dg1"/>
+  <key attr.name="baselabel" attr.type="string" for="graph" id="dg2"/>
+  <key attr.name="linear" attr.type="string" for="graph" id="dg3"/>
+  <key attr.name="ac_label" attr.type="string" for="graph" id="dg4"/>
+  <key attr.name="public" attr.type="boolean" for="graph" id="dg5"/>
+  <key attr.name="text" attr.type="string" for="node" id="dn0"/>
+  <key attr.name="is_end" attr.type="boolean" for="node" id="dn1"/>
+  <key attr.name="is_start" attr.type="boolean" for="node" id="dn2"/>
+  <key attr.name="id" attr.type="string" for="node" id="dn3"/>
+  <key attr.name="rank" attr.type="string" for="node" id="dn4"/>
+  <key attr.name="is_lacuna" attr.type="boolean" for="node" id="dn5"/>
+  <key attr.name="witness" attr.type="string" for="edge" id="de0"/>
+  <key attr.name="non_correctable" attr.type="boolean" for="edge" id="de1"/>
+  <key attr.name="relationship" attr.type="string" for="edge" id="de2"/>
+  <key attr.name="non_independent" attr.type="boolean" for="edge" id="de3"/>
+  <key attr.name="extra" attr.type="boolean" for="edge" id="de4"/>
+  <key attr.name="class" attr.type="string" for="edge" id="de5"/>
+  <key attr.name="colocated" attr.type="boolean" for="edge" id="de6"/>
+  <graph edgedefault="directed" id="Tradition" parse.edgeids="canonical" parse.edges="376" parse.nodeids="canonical" parse.nodes="319" parse.order="nodesfirst">
+    <data key="dg0">2.0</data>
+    <data key="dg1">, </data>
+    <data key="dg2">base text</data>
+    <data key="dg3">1</data>
+    <data key="dg4"> (a.c.)</data>
+    <data key="dg5">1</data>
+    <node id="n0">
+      <data key="dn0">#END#</data>
+      <data key="dn1">1</data>
+      <data key="dn3">#END#</data>
+      <data key="dn4">281</data>
+    </node>
+    <node id="n1">
+      <data key="dn0">#LACUNA_a1.42_0#</data>
+      <data key="dn3">#LACUNA_a1.42_0#</data>
+      <data key="dn4">101</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n2">
+      <data key="dn0">#LACUNA_a1_0#</data>
+      <data key="dn3">#LACUNA_a1_0#</data>
+      <data key="dn4">1</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n3">
+      <data key="dn0">#LACUNA_a1_1#</data>
+      <data key="dn3">#LACUNA_a1_1#</data>
+      <data key="dn4">1</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n4">
+      <data key="dn0">#LACUNA_a9.31_0#</data>
+      <data key="dn3">#LACUNA_a9.31_0#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n5">
+      <data key="dn0">#LACUNA_a9.31_1#</data>
+      <data key="dn3">#LACUNA_a9.31_1#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n6">
+      <data key="dn0">#LACUNA_a9.31_2#</data>
+      <data key="dn3">#LACUNA_a9.31_2#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n7">
+      <data key="dn0">#LACUNA_a9.31_3#</data>
+      <data key="dn3">#LACUNA_a9.31_3#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n8">
+      <data key="dn0">#LACUNA_a9.31_4#</data>
+      <data key="dn3">#LACUNA_a9.31_4#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n9">
+      <data key="dn0">#LACUNA_a9.31_5#</data>
+      <data key="dn3">#LACUNA_a9.31_5#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n10">
+      <data key="dn0">#LACUNA_a9.31_6#</data>
+      <data key="dn3">#LACUNA_a9.31_6#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n11">
+      <data key="dn0">#LACUNA_a9.31_7#</data>
+      <data key="dn3">#LACUNA_a9.31_7#</data>
+      <data key="dn4">228</data>
+      <data key="dn5">1</data>
+    </node>
+    <node id="n12">
+      <data key="dn0">#START#</data>
+      <data key="dn2">1</data>
+      <data key="dn3">#START#</data>
+      <data key="dn4">0</data>
+    </node>
+    <node id="n13">
+      <data key="dn0">Μαξίμου</data>
+      <data key="dn3">w0</data>
+      <data key="dn4">1</data>
+    </node>
+    <node id="n14">
+      <data key="dn0">καταλύσαντι</data>
+      <data key="dn3">w100</data>
+      <data key="dn4">87</data>
+    </node>
+    <node id="n15">
+      <data key="dn0">κατακλύσαντι</data>
+      <data key="dn3">w103</data>
+      <data key="dn4">87</data>
+    </node>
+    <node id="n16">
+      <data key="dn0">οὔτε</data>
+      <data key="dn3">w105</data>
+      <data key="dn4">88</data>
+    </node>
+    <node id="n17">
+      <data key="dn0">ἐνταῦθα</data>
+      <data key="dn3">w106</data>
+      <data key="dn4">89</data>
+    </node>
+    <node id="n18">
+      <data key="dn0">οὔτε</data>
+      <data key="dn3">w107</data>
+      <data key="dn4">90</data>
+    </node>
+    <node id="n19">
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+      <data key="dn3">w108</data>
+      <data key="dn4">91</data>
+    </node>
+    <node id="n20">
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+      <data key="dn3">w11</data>
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+    <node id="n22">
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+    <node id="n23">
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+      <data key="dn3">w111</data>
+      <data key="dn4">94</data>
+    </node>
+    <node id="n24">
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+      <data key="dn3">w112</data>
+      <data key="dn4">95</data>
+    </node>
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+      <data key="dn3">w113</data>
+      <data key="dn4">96</data>
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+    <node id="n26">
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+      <data key="dn3">w114</data>
+      <data key="dn4">97</data>
+    </node>
+    <node id="n27">
+      <data key="dn0">ἀθεΐας</data>
+      <data key="dn3">w115</data>
+      <data key="dn4">98</data>
+    </node>
+    <node id="n28">
+      <data key="dn0">ἡ</data>
+      <data key="dn3">w116</data>
+      <data key="dn4">99</data>
+    </node>
+    <node id="n29">
+      <data key="dn0">ἁμαρτία.</data>
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+      <data key="dn4">100</data>
+    </node>
+    <node id="n30">
+      <data key="dn0">Ἰσιδώρου</data>
+      <data key="dn3">w118</data>
+      <data key="dn4">101</data>
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+    <node id="n31">
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+      <data key="dn3">w119</data>
+      <data key="dn4">102</data>
+    </node>
+    <node id="n32">
+      <data key="dn0">βλασφημία</data>
+      <data key="dn3">w12</data>
+      <data key="dn4">11</data>
+    </node>
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+      <data key="dn4">102</data>
+    </node>
+    <node id="n34">
+      <data key="dn0">νείλου</data>
+      <data key="dn3">w121</data>
+      <data key="dn4">101</data>
+    </node>
+    <node id="n35">
+      <data key="dn0">Γρηγορίου</data>
+      <data key="dn3">w122</data>
+      <data key="dn4">103</data>
+    </node>
+    <node id="n36">
+      <data key="dn0">Νύσης</data>
+      <data key="dn3">w123</data>
+      <data key="dn4">104</data>
+    </node>
+    <node id="n37">
+      <data key="dn0">τοῦ</data>
+      <data key="dn3">w124</data>
+      <data key="dn4">102</data>
+    </node>
+    <node id="n38">
+      <data key="dn0">νύσσης</data>
+      <data key="dn3">w125</data>
+      <data key="dn4">103</data>
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+    <node id="n39">
+      <data key="dn0">Ἤκουσά</data>
+      <data key="dn3">w126</data>
+      <data key="dn4">105</data>
+    </node>
+    <node id="n40">
+      <data key="dn0">που</data>
+      <data key="dn3">w127</data>
+      <data key="dn4">106</data>
+    </node>
+    <node id="n41">
+      <data key="dn0">τῆς</data>
+      <data key="dn3">w128</data>
+      <data key="dn4">107</data>
+    </node>
+    <node id="n42">
+      <data key="dn0">ἁγίας</data>
+      <data key="dn3">w129</data>
+      <data key="dn4">108</data>
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+      <data key="dn3">w13</data>
+      <data key="dn4">11</data>
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+    <node id="n44">
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+      <data key="dn3">w130</data>
+      <data key="dn4">109</data>
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+    <node id="n45">
+      <data key="dn0">κατακινούσης</data>
+      <data key="dn3">w131</data>
+      <data key="dn4">110</data>
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+    <node id="n46">
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+      <data key="dn3">w132</data>
+      <data key="dn4">110</data>
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+    <node id="n47">
+      <data key="dn0">ἐκείνους,</data>
+      <data key="dn3">w133</data>
+      <data key="dn4">111</data>
+    </node>
+    <node id="n48">
+      <data key="dn0">οἳ</data>
+      <data key="dn3">w134</data>
+      <data key="dn4">112</data>
+    </node>
+    <node id="n49">
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+      <data key="dn3">w135</data>
+      <data key="dn4">113</data>
+    </node>
+    <node id="n50">
+      <data key="dn0">τῆς</data>
+      <data key="dn3">w136</data>
+      <data key="dn4">114</data>
+    </node>
+    <node id="n51">
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+      <data key="dn3">w137</data>
+      <data key="dn4">115</data>
+    </node>
+    <node id="n52">
+      <data key="dn0">θεοῦ</data>
+      <data key="dn3">w138</data>
+      <data key="dn4">116</data>
+    </node>
+    <node id="n53">
+      <data key="dn0">βλασφημίας</data>
+      <data key="dn3">w139</data>
+      <data key="dn4">117</data>
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+    <node id="n54">
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+      <data key="dn3">w14</data>
+      <data key="dn4">12</data>
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+      <data key="dn3">w140</data>
+      <data key="dn4">118</data>
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+      <data key="dn3">w141</data>
+      <data key="dn4">119</data>
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+      <data key="dn3">w142</data>
+      <data key="dn4">120</data>
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+    <node id="n58">
+      <data key="dn0">γὰρ</data>
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+      <data key="dn4">121</data>
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+      <data key="dn4">122</data>
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+      <data key="dn3">w145</data>
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+      <data key="dn3">w146</data>
+      <data key="dn4">124</data>
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+      <data key="dn3">w148</data>
+      <data key="dn4">126</data>
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+    <node id="n64">
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+      <data key="dn3">w149</data>
+      <data key="dn4">127</data>
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+      <data key="dn3">w15</data>
+      <data key="dn4">13</data>
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+      <data key="dn4">128</data>
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+      <data key="dn4">129</data>
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+      <data key="dn4">130</data>
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+      <data key="dn4">131</data>
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+      <data key="dn4">132</data>
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+      <data key="dn4">133</data>
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+      <data key="dn3">w156</data>
+      <data key="dn4">134</data>
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+      <data key="dn3">w158</data>
+      <data key="dn4">135</data>
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+      <data key="dn3">w159</data>
+      <data key="dn4">136</data>
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+      <data key="dn3">w16</data>
+      <data key="dn4">13</data>
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+    <node id="n76">
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+      <data key="dn3">w160</data>
+      <data key="dn4">137</data>
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+    <node id="n77">
+      <data key="dn0">ἀπειλὴν</data>
+      <data key="dn3">w161</data>
+      <data key="dn4">138</data>
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+      <data key="dn3">w162</data>
+      <data key="dn4">139</data>
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+      <data key="dn3">w163</data>
+      <data key="dn4">140</data>
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+      <data key="dn3">w164</data>
+      <data key="dn4">141</data>
+    </node>
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+      <data key="dn0">λέγων</data>
+      <data key="dn3">w165</data>
+      <data key="dn4">142</data>
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+      <data key="dn3">w166</data>
+      <data key="dn4">143</data>
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+      <data key="dn3">w167</data>
+      <data key="dn4">144</data>
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+      <data key="dn3">w168</data>
+      <data key="dn4">145</data>
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+      <data key="dn3">w169</data>
+      <data key="dn4">146</data>
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+    <node id="n86">
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+      <data key="dn4">14</data>
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+      <data key="dn3">w170</data>
+      <data key="dn4">147</data>
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diff --git a/base/t/data/load-save-benchmark.json b/persistence/t/data/load-save-benchmark.json
similarity index 100%
rename from base/t/data/load-save-benchmark.json
rename to persistence/t/data/load-save-benchmark.json
diff --git a/persistence/t/data/simple.dot b/persistence/t/data/simple.dot
new file mode 100644
index 0000000..193e356
--- /dev/null
+++ b/persistence/t/data/simple.dot
@@ -0,0 +1,11 @@
+digraph Stemma {
+	1 [ class="hypothetical" ];
+	2 [ class="hypothetical" ];
+	A [ class="extant" ];
+	B [ class="extant" ];
+	C [ class="extant" ];
+	1 -> A;
+	1 -> 2;
+	2 -> B;
+	2 -> C;
+}
\ No newline at end of file
diff --git a/persistence/t/data/simple.txt b/persistence/t/data/simple.txt
new file mode 100644
index 0000000..8be9717
--- /dev/null
+++ b/persistence/t/data/simple.txt
@@ -0,0 +1,23 @@
+A	B	C
+Je	Je	Je
+suis	suis	suis
+dépourvu	dépourvu	depourvu
+de	de	de
+foi	foi	foi
+et	et	et
+ne	ne	ne
+puis	puis	puis
+donc	donc	donc
+être	être	être
+"heureux,"	"heureux,"	"heureux,"
+l'être	le lézard	l'être
+humain		humain
+doit	doit	doit
+mettre	mettre	mettre
+des	des	des
+millions	millions	millions
+d'années	d'années	d'années
+pour	pour	pour
+devenir	devenir	devenir
+un	un	un
+lézard!	être humain	lézard!
\ No newline at end of file
diff --git a/base/t/data/speed_test_load.sql b/persistence/t/data/speed_test_load.sql
similarity index 100%
rename from base/t/data/speed_test_load.sql
rename to persistence/t/data/speed_test_load.sql
diff --git a/base/t/load-save-speed.t b/persistence/t/load-save-speed.t
similarity index 100%
rename from base/t/load-save-speed.t
rename to persistence/t/load-save-speed.t
diff --git a/base/t/text_tradition_directory.t b/persistence/t/text_tradition_directory.t
similarity index 100%
rename from base/t/text_tradition_directory.t
rename to persistence/t/text_tradition_directory.t
diff --git a/base/t/text_tradition_user.t b/persistence/t/text_tradition_user.t
similarity index 100%
rename from base/t/text_tradition_user.t
rename to persistence/t/text_tradition_user.t
diff --git a/base/t/text_tradition_user_collapse.t b/persistence/t/text_tradition_user_collapse.t
similarity index 100%
rename from base/t/text_tradition_user_collapse.t
rename to persistence/t/text_tradition_user_collapse.t
diff --git a/persistence/t/userrestore.t b/persistence/t/userrestore.t
new file mode 100644
index 0000000..3c734b1
--- /dev/null
+++ b/persistence/t/userrestore.t
@@ -0,0 +1,36 @@
+#!/usr/bin/env perl;
+
+use strict;
+use warnings;
+use File::Temp;
+use Safe::Isa;
+use Test::More;
+use Test::Warn;
+use Text::Tradition;
+use Text::Tradition::Directory;
+
+my $newt = Text::Tradition->new( 'input' => 'Self', 
+	'file' => 't/data/florilegium_graphml.xml' );
+
+my $fh = File::Temp->new();
+my $file = $fh->filename;
+$fh->close;
+my $dsn = "dbi:SQLite:dbname=$file";
+my $userstore = Text::Tradition::Directory->new( { dsn => $dsn,
+	extra_args => { create => 1 } } );
+my $scope = $userstore->new_scope();
+my $testuser = $userstore->create_user( { url => 'http://example.com' } );
+ok( $testuser->$_isa('Text::Tradition::User'), "Created test user via userstore" );
+$testuser->add_tradition( $newt );
+is( $newt->user->id, $testuser->id, "Assigned tradition to test user" );
+my $graphml_str = $newt->collation->as_graphml;
+my $usert;
+warning_is {
+	$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str );
+} 'DROPPING user assignment without a specified userstore',
+	"Got expected user drop warning on parse";
+$usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str,
+	'userstore' => $userstore );
+is( $usert->user->id, $testuser->id, "Parsed tradition with userstore points to correct user" );
+
+done_testing();