Add TenX Assemblies

db/mysql/deploy/create_tenx_assemblies.sql

@@ -0,0 +1,16 @@
+-- Deploy tenx:create_tenx_assemblies to sqlite
+-- requires tenx_reads
+
+BEGIN;
+
+CREATE TABLE IF NOT EXISTS tenx_assemblies (
+        id VARCHAR(32),
+	directory VARCHAR(256),
+	reads_id VARCHAR(256),
+	status VARCHAR(16),
+
+	CONSTRAINT tenxassemblies_pk PRIMARY KEY(id),
+	CONSTRAINT tenxassemblies_reference_fk FOREIGN KEY(reads_id) REFERENCES tenx_reads(id)
+);
+
+COMMIT;

db/mysql/revert/create_tenx_assemblies.sql

@@ -0,0 +1,7 @@
+-- Revert tenx:create_tenx_assemblies from sqlite
+
+BEGIN;
+
+DROP TABLE IF EXISTS tenx_assemblies;
+
+COMMIT;

db/mysql/sqitch.plan

@@ -5,3 +5,4 @@
 create_tenx_references 2017-06-07T21:31:02Z Eddie Belter <ebelter@mullis.local> # Create TenX References!
 create_tenx_reads 2017-06-07T21:40:30Z Eddie Belter <ebelter@mullis.local> # Create TenX Reads!
 create_tenx_alignments 2017-06-07T21:42:54Z Eddie Belter <ebelter@mullis.local> # Add TenX Alignments!
+create_tenx_assemblies 2018-01-16T22:31:39Z ebelter <ebelter@dev-perl> # Create 10X Assemblies!

db/mysql/verify/create_tenx_assemblies.sql

@@ -0,0 +1,10 @@
+-- Verify tenx:create_tenx_assemblies on sqlite
+
+BEGIN;
+
+SELECT
+	id, directory, reads_id, status
+FROM tenx_assemblies
+WHERE 0;
+
+ROLLBACK;

db/sqlite/deploy/create_tenx_assemblies.sql

@@ -0,0 +1,16 @@
+-- Deploy tenx:create_tenx_assemblies to sqlite
+-- requires tenx_reads
+
+BEGIN;
+
+CREATE TABLE IF NOT EXISTS tenx_assemblies (
+        id VARCHAR(32),
+	directory VARCHAR(256),
+	reads_id VARCHAR(256),
+	status VARCHAR(16),
+
+	CONSTRAINT tenxassemblies_pk PRIMARY KEY(id),
+	CONSTRAINT tenxassemblies_reference_fk FOREIGN KEY(reads_id) REFERENCES tenx_reads(id)
+);
+
+COMMIT;

db/sqlite/revert/create_tenx_assemblies.sql

@@ -0,0 +1,7 @@
+-- Revert tenx:create_tenx_assemblies from sqlite
+
+BEGIN;
+
+DROP TABLE IF EXISTS tenx_assemblies;
+
+COMMIT;

db/sqlite/sqitch.plan

@@ -5,3 +5,4 @@
 create_tenx_references 2017-06-06T18:45:22Z Eddie Belter <ebelter@mullis.local> # Create TenX References!
 create_tenx_reads 2017-06-06T23:25:06Z Eddie Belter <ebelter@mullis.local> # Create TenX Reads!
 create_tenx_alignments 2017-06-06T23:27:18Z Eddie Belter <ebelter@mullis.local> # Add TenX Alignments!
+create_tenx_assemblies 2018-01-16T22:00:59Z ebelter <ebelter@dev-perl> # Create TenX Assemblies!

db/sqlite/verify/create_tenx_assemblies.sql

@@ -0,0 +1,10 @@
+-- Verify tenx:create_tenx_assemblies on sqlite
+
+BEGIN;
+
+SELECT
+	id, directory, reads_id, status
+FROM tenx_assemblies
+WHERE 0;
+
+ROLLBACK;

lib/Tenx/Assembly.pm

@@ -0,0 +1,29 @@
+package Tenx::Assembly;
+
+use strict;
+use warnings 'FATAL';
+
+class Tenx::Assembly {
+    table_name => 'tenx_assemblies',
+    id_generator => '-uuid',
+    id_by => {
+        id => { is => 'Text', },
+    },
+    has => {
+        directory => { is => 'Text', doc => 'File system location.', },
+        reads => {
+            is => 'Tenx::Reads',
+            id_by => 'reads_id',
+            doc => 'The reads that are assembled.',
+        },
+    },
+    has_optional => {
+        status => {
+            is => 'Text',
+            doc => 'The status of the assembly: running, succeeded, failed, etc.',
+        },
+    },
+    data_source => Tenx::Config::get('tenx_ds'),
+};
+
+1;

lib/Tenx/Assembly/Command.pm

@@ -0,0 +1,16 @@
+package Tenx::Assembly::Command;
+
+use strict;
+use warnings 'FATAL';
+
+use UR::Object::Command::Crud;
+UR::Object::Command::Crud->create_command_subclasses(
+    target_class => 'Tenx::Assembly',
+    target_name => 'alignment',
+    namespace => 'Tenx::Assembly::Command',
+    sub_command_configs => {
+        copy => { skip => 1, },
+    },
+);
+
+1;

t/Tenx-Assembly.t

@@ -0,0 +1,33 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings 'FATAL';
+
+use TenxTestEnv;
+
+use Test::More tests => 1;
+
+subtest "create" => sub{
+    plan tests => 8;
+
+    my $pkg = 'Tenx::Assembly';
+    use_ok($pkg) or die;
+    use_ok('Tenx::Reads') or die;
+
+    my $assembly = $pkg->create(
+        directory => '/tmp',
+        reads => Tenx::Reads->__define__(directory => '/tmp/', sample_name => 'TEST-TESTY-MCTESTERSON'),
+        status => 'running',
+    );
+    ok($assembly, 'create tenx assembly');
+
+    ok($assembly->id, 'assembly id');
+    ok($assembly->directory, 'assembly directory');
+    is($assembly->reads_id, $assembly->reads->id, 'assembly reads');
+    ok($assembly->status, 'assembly status');
+
+    ok(UR::Context->commit, 'commit');
+
+};
+
+done_testing();