Merge branch 'devel' into view_traces_manousos

Changes

@@ -1,5 +1,20 @@
 {{$NEXT}}
 
+0.341     2015-10-08 15:18:51 Europe/London
+
+0.340     2015-10-07 15:27:03 Europe/London
+    Sequencing project 96 plate creation added
+    Download sequencing project xlsx added
+    Sequencing project view and create interfaces added 
+0.339     2015-10-01 11:50:37 Europe/London
+
+    Cell line added to projects
+    Experiments linked to genes rather than projects
+
+0.337     2015-09-17 16:50:11 Europe/London
+    Added create design and crispr plates function
+    Added experiments to summarys table
+
 0.336     2015-09-03 12:59:33 Europe/London
 
     Removed dependancy on lustre file system

bin/add_cell_lines_to_projects.pl

@@ -113,8 +113,4 @@ sub sponsor_cell_line{
 	}
 
 	return 'kolf';
-<<<<<<< HEAD
 }
-=======
-}
->>>>>>> devel

bin/lims2_setup.sh

@@ -239,6 +239,7 @@ function lims2_devel {
     export SHARED_WEBAPP_TT_DIR=$LIMS2_SHARED/WebApp-Common/shared_templates
     export WGE_REST_CLIENT_CONFIG=/nfs/team87/farm3_lims2_vms/conf/wge-devel-rest-client.conf
     export LIMS2_PRIMER_DIR=/lustre/scratch109/sanger/team87/lims2_primer_generation/
+    export LIMS2_TEMP=/opt/t87/local/tmp
 }
 
 function lims2_pg9.3 {
@@ -270,6 +271,7 @@ LIMS2 useful environment variables:
 \$PGUSER                       : $PGUSER
 
 \$LIMS2_PRIMER_DIR             : $LIMS2_PRIMER_DIR
+\$LIMS2_TEMP                   : $LIMS2_TEMP
 \$DEFAULT_CRISPR_ES_QC_DIR     : $DEFAULT_CRISPR_ES_QC_DIR
 \$VEP_CACHE_DIR                : $VEP_CACHE_DIR
 \$DESIGN_CREATION_HUMAN_FA     : $DESIGN_CREATION_HUMAN_FA

ddl/versions/101/audit-up.sql

@@ -5,7 +5,6 @@ audit_stamp TIMESTAMP NOT NULL,
 audit_txid INTEGER NOT NULL,
 id integer,
 name text,
-qc_template_id integer,
 created_by_id integer,
 created_at timestamp without time zone,
 sub_projects integer,
@@ -54,6 +53,30 @@ $sequencing_project_primers_audit$ LANGUAGE plpgsql;
 CREATE TRIGGER sequencing_project_primers_audit
 AFTER INSERT OR UPDATE OR DELETE ON public.sequencing_project_primers
     FOR EACH ROW EXECUTE PROCEDURE public.process_sequencing_project_primers_audit();
+CREATE TABLE audit.sequencing_project_templates (
+audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
+audit_user TEXT NOT NULL,
+audit_stamp TIMESTAMP NOT NULL,
+audit_txid INTEGER NOT NULL,
+seq_project_id integer,
+qc_template_id integer
+);
+CREATE OR REPLACE FUNCTION public.process_sequencing_project_templates_audit()
+RETURNS TRIGGER AS $sequencing_project_templates_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.sequencing_project_templates SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.sequencing_project_templates SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.sequencing_project_templates SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$sequencing_project_templates_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER sequencing_project_templates_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.sequencing_project_templates
+    FOR EACH ROW EXECUTE PROCEDURE public.process_sequencing_project_templates_audit();
 CREATE TABLE audit.sequencing_primer_types (
 audit_op CHAR(1) NOT NULL CHECK (audit_op IN ('D','I','U')),
 audit_user TEXT NOT NULL,

ddl/versions/101/up.sql

@@ -1,7 +1,6 @@
 CREATE TABLE sequencing_projects(
     id serial primary key not null,
     name text not null,
-    qc_template_id integer references qc_templates(id),
     created_by_id integer references users(id) not null,
     created_at timestamp without time zone default now() not null,
     sub_projects integer not null,
@@ -10,13 +9,12 @@ CREATE TABLE sequencing_projects(
     abandoned boolean default false, 
     is_384 boolean default false);
 
+CREATE TABLE sequencing_primer_types( id text primary key not null );
+
 CREATE TABLE sequencing_project_primers(
     seq_project_id integer references sequencing_projects(id) not null,
     primer_id text references sequencing_primer_types(id) not null);
 
 CREATE TABLE sequencing_project_templates(
     seq_project_id integer references sequencing_projects(id) not null,
     qc_template_id integer references qc_templates(id) not null);
-
-
-CREATE TABLE sequencing_primer_types( id text primary key not null );

lib/LIMS2/Model/Util/SequencingProject.pm

@@ -14,6 +14,9 @@ use namespace::autoclean;
 use Try::Tiny;
 use Excel::Writer::XLSX;
 use File::Slurp;
+use Carp;
+use Path::Class;
+use MooseX::Types::Path::Class::MoreCoercions qw/AbsDir/;
 
 sub build_seq_data {
     my ( $self, $c, $id, $primer_req, $sub_number) = @_;
@@ -58,8 +61,9 @@ sub build_seq_data {
     else {
         return "Primers not found.";
     }
-    my $base = $ENV{ 'LIMS2_SEQ_DIR' } // '/var/tmp/seq/';
-    my $body = read_file( $base . $file_name, {binmode => ':raw'} );
+
+    my $dir = dir_build($file_name);
+    my $body = read_file( $dir, {binmode => ':raw'} );
 
     my $file_contents = ({
         body    => $body,
@@ -74,8 +78,9 @@ sub build_xlsx_file {
     my $project = $wells->{project_data};
     my $file_name = $project->{name} . '_' . $sub_num . '_' . $primer_name . '.xlsx';
 
-    my $base = $ENV{ 'LIMS2_SEQ_DIR' } // '/var/tmp/seq/';
-    my $workbook = Excel::Writer::XLSX->new( $base . $file_name );
+    my $dir = dir_build($file_name);
+    my $workbook = Excel::Writer::XLSX->new($dir);
+
     my $worksheet = $workbook->add_worksheet();
 
     #Create Headers
@@ -94,5 +99,11 @@ sub build_xlsx_file {
     return $file_name;
 }
 
+sub dir_build{
+    my ($file_name) = @_;
+    my $base = $ENV{LIMS2_TEMP}
+        or die "LIMS2_TEMP not set";
+    return $base . '/' . $file_name;
+}
 
 1;

root/site/user/crisprqc/crispr_es_qc_runs.tt

@@ -16,7 +16,7 @@
         [% FOR run IN runs %]
         <tr>
             <td><a href="[% c.uri_for('es_qc_run', run.id) %]">[% run.id.substr(0, 8) %]</a></td>
-            <td>[% run.plate_name %]</dt>
+            <td><a href="[% c.uri_for('/user/view_plate', { name => run.plate_name}) %]">[% run.plate_name %]</a></dt>
             <td>[% run.sequencing_project %]</td>
             <td>
                 [% IF run.validated %]

root/static/test/fixtures/00-clean-db.sql

@@ -51,8 +51,12 @@ DELETE FROM qc_template_well_cassette;
 DELETE FROM qc_template_well_backbone;
 DELETE FROM qc_template_well_recombinase;
 DELETE FROM qc_template_wells;
+DELETE FROM sequencing_project_templates;
 DELETE FROM qc_templates;
 DELETE FROM qc_eng_seqs;
+DELETE FROM sequencing_project_primers;
+DELETE FROM sequencing_primer_types;
+DELETE FROM sequencing_projects;
 DELETE FROM well_accepted_override;
 DELETE FROM well_comments;
 DELETE FROM well_chromosome_fail;