resolved merge conflict

htgt · Oct 13, 2015 · 9fc96fd · 9fc96fd
2 parents 4ce01e0 + c3ea436
commit 9fc96fd
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Showing 44 changed files with 2,060 additions and 363 deletions.
diff --git a/Changes b/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

diff --git a/bin/add_cell_lines_to_projects.pl b/bin/add_cell_lines_to_projects.pl
@@ -36,8 +36,10 @@
     open (my $fh, ">", "new_projects.csv") or die $!;
     process_projects($projects_rs,$fh);
     close $fh;
+
 	ERROR "Rolling back!";
 	$model->schema->txn_rollback();
+
 });
 
 sub process_projects{
@@ -111,4 +113,4 @@ sub sponsor_cell_line{
 	}
 
 	return 'kolf';
-}
+}
diff --git a/bin/extract_eurofins_data.pl b/bin/extract_eurofins_data.pl
@@ -0,0 +1,153 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Archive::Zip qw( :ERROR_CODES );
+use Path::Class;
+use POSIX;
+use File::Path qw(remove_tree);
+
+my ($archive) = @ARGV;
+
+# Unpack zip archive
+my $tmp_dir_name = $archive;
+$tmp_dir_name =~ s/\.zip$//g;
+
+if ($tmp_dir_name eq $archive){
+	die "Archive $archive is not a .zip file";
+}
+
+my $archive_file = file($archive);
+
+my $temp_dir = dir($tmp_dir_name);
+$temp_dir->mkpath;
+
+print "Unzipping archive..";
+my $zip = Archive::Zip->new();
+unless( $zip->read("$archive_file") == AZ_OK ){
+	die "Could not inflate zip $archive_file - $!";
+}
+$zip->extractTree( '', $temp_dir );
+print "Done\n";
+
+my $STRING_TO_REMOVE = qr/_premix-w\.-temp/;
+my $PROJECT_NAME_RX = qr/^(.*)_\d+[a-z]{1}\d{2}\./;
+
+# Keep track of which project we have found in archive
+my %projects;
+
+# One directory per plate, e.g. plate_CGaP_EDQ0034_SF
+# For each directory find scf and seq.clipped files
+# Work out project name from root of file names
+# Create project directory in warehouse (LIMS2_SEQ_FILE_DIR) if not exists
+# Move fixed files to this directory
+while( my $plate_dir = $temp_dir->next ){
+	next unless -d $plate_dir;
+	while(my $data_file = $plate_dir->next){
+		my ($project_name, $fixed_file);
+        #if ($data_file =~ /\.seq\.clipped$/){
+        if($data_file =~ /\.seq$/){
+        	($project_name, $fixed_file) = fix_seq_file($data_file);
+        }
+        elsif($data_file =~ /\.scf$/){
+        	($project_name, $fixed_file) = fix_scf_file($data_file);
+        }
+        else{
+        	next;
+        }
+
+        # Sometimes we get reads called Empty Well so no project name
+        # Ignore them
+        next unless $project_name;
+
+        my $project_dir = $projects{ $project_name };
+        unless($project_dir){
+        	$project_dir = dir($ENV{LIMS2_SEQ_FILE_DIR},$project_name);
+        	$project_dir->mkpath;
+        	$projects{$project_name} = $project_dir;
+        }
+
+        $fixed_file->move_to($project_dir) or die "Could not move $fixed_file to $project_dir - $!";
+	}
+
+}
+
+# Remove "premic-w.-temp" from file names and read names:
+# e.g. EDQ0034_1a03.p1kSF_premix-w.-temp.scf
+sub fix_scf_file{
+    my $file = shift;
+
+print "SCF file name: $file\n";
+    my $new_name = "$file";
+    $new_name =~ s/$STRING_TO_REMOVE//;
+
+    # tmp fix to convert SF -> SF1
+    $new_name =~ s/p1kSF\./p1kSF1./;
+    $new_name =~ s/p1kSR\./p1kSR1./;
+
+    my $new_file = file($new_name);
+    $file->move_to( $new_file ) or die "Could not move $file to $new_file";
+
+    my ($project_name) = ( $new_file->basename =~ /$PROJECT_NAME_RX/g );
+
+print "New SCF file name: $new_file\n";
+print "Project name: $project_name\n\n";
+    return ($project_name, $new_file);
+}
+
+# EDQ0034_1a03.p1kSF_premix-w.-temp.seq.clipped
+# >EDQ0034_1a05.p1kSF_premix-w.-temp -- 17..634 of sequence
+sub fix_seq_file{
+    my $file = shift;
+print "Seq file name: $file\n";
+    my @lines = $file->slurp;
+
+    my $new_name = "$file";
+    $new_name =~ s/$STRING_TO_REMOVE//;
+    $new_name =~ s/\.clipped$//;
+
+    # tmp fix to convert SF -> SF1
+    $new_name =~ s/p1kSF\./p1kSF1./;
+    $new_name =~ s/p1kSR\./p1kSR1./;
+
+    my $new_file = file($new_name);
+    my $fh = $new_file->openw or die "Can't open $new_file for writing - $!";
+
+    foreach my $line (@lines){
+    	$line =~ s/$STRING_TO_REMOVE//;
+        # tmp fix to convert SF -> SF1
+        $line =~ s/p1kSF\b/p1kSF1/;
+        $line =~ s/p1kSR\b/p1kSR1/;
+
+    	print $fh $line;
+    }
+
+    close $fh;
+
+    my ($project_name) = ( $new_file->basename =~ /$PROJECT_NAME_RX/g );
+print "New seq file name: $new_file\n";
+print "Project name: $project_name\n\n";
+    return ($project_name, $new_file);
+}
+
+# Create file archive_names.txt in this dir if not exists
+# Append archive name to this file
+my $time_stamp = strftime("%Y-%m-%d %H:%M:%S", localtime(time));
+foreach my $project_dir (values %projects){
+	my $project_list = $project_dir->file('archive_names.txt');
+    my $fh = $project_list->opena or die "Cannot open $project_list for appending - $!";
+    print $fh "$time_stamp,$archive\n";
+    close $fh;
+    print "Sequencing data in project directory $project_dir updated\n";
+}
+
+
+# Store orig archives in warehouse too
+# FIXME: put this in environment variable
+my $archive_dir = dir('/warehouse/team87_wh01/eurofins_order_archive_data');
+my $archive_to = $archive_dir->file( $archive_file->basename );
+$archive_file->move_to( $archive_to ) or die "Cannot move archive file $archive_file to $archive_to - $!";
+
+# Tidy up temporarily unpacked files
+remove_tree($temp_dir->stringify) or die "Could not remove $temp_dir - $!";
diff --git a/bin/lims2_setup.sh b/bin/lims2_setup.sh
@@ -239,6 +239,7 @@ function lims2_devel {
     export SHARED_WEBAPP_TT_DIR=$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

diff --git a/ddl/versions/101/audit-up.sql b/ddl/versions/101/audit-up.sql
@@ -0,0 +1,102 @@
+CREATE TABLE audit.sequencing_projects (
+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,
+id integer,
+name text,
+created_by_id integer,
+created_at timestamp without time zone,
+sub_projects integer,
+qc boolean,
+available_results boolean,
+abandoned boolean,
+is_384 boolean
+);
+CREATE OR REPLACE FUNCTION public.process_sequencing_projects_audit()
+RETURNS TRIGGER AS $sequencing_projects_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.sequencing_projects SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.sequencing_projects SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.sequencing_projects SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$sequencing_projects_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER sequencing_projects_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.sequencing_projects
+    FOR EACH ROW EXECUTE PROCEDURE public.process_sequencing_projects_audit();
+CREATE TABLE audit.sequencing_project_primers (
+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,
+primer_id text
+);
+CREATE OR REPLACE FUNCTION public.process_sequencing_project_primers_audit()
+RETURNS TRIGGER AS $sequencing_project_primers_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.sequencing_project_primers SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.sequencing_project_primers SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.sequencing_project_primers SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$sequencing_project_primers_audit$ 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,
+audit_stamp TIMESTAMP NOT NULL,
+audit_txid INTEGER NOT NULL,
+id text
+);
+CREATE OR REPLACE FUNCTION public.process_sequencing_primer_types_audit()
+RETURNS TRIGGER AS $sequencing_primer_types_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.sequencing_primer_types SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.sequencing_primer_types SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.sequencing_primer_types SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$sequencing_primer_types_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER sequencing_primer_types_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.sequencing_primer_types
+    FOR EACH ROW EXECUTE PROCEDURE public.process_sequencing_primer_types_audit();
diff --git a/ddl/versions/101/fixtures.sql b/ddl/versions/101/fixtures.sql
@@ -0,0 +1,6 @@
+INSERT INTO schema_versions(version) VALUES (101);
+
+INSERT INTO sequencing_primer_types(id)
+    VALUES ('L1'),('LR'),('PNF'),('R1R'),('R2R'),('R3'),('Z1'),('Z2'),('PGO'),('FCHK'),('SP6R'),('LU6F'),('T3'),('T7gRNA_F'),('R4'),('NF'),('BACT3'),('BBR'),('EF1'),
+    ('SP6'),('PPA1'),('rox_SV40'),('Z1a'),('Z2a'),('hBac'),('IRNA5'),('IRNA3'),('LFR'),('LRR'),('bpA'),('En2'),('CRF'),('ERT'),('HPF'),('HPR'),('3ARM'),('IRES_B1'),('IRES_right'),
+    ('A2'),('A5'),('P19F'),('P19R'),('EF1aR1'),('betaR1'),('LFREV'),('p15A_Rev2'),('p15A_For2');
diff --git a/ddl/versions/101/up.sql b/ddl/versions/101/up.sql
@@ -0,0 +1,20 @@
+CREATE TABLE sequencing_projects(
+    id serial primary key not null,
+    name text not null,
+    created_by_id integer references users(id) not null,
+    created_at timestamp without time zone default now() not null,
+    sub_projects integer not null,
+    qc boolean default false,
+    available_results boolean default false,
+    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);
diff --git a/lib/LIMS2/Model/FormValidator/Constraint.pm b/lib/LIMS2/Model/FormValidator/Constraint.pm
@@ -303,6 +303,13 @@ sub existing_experiment_id {
     return shift->in_resultset( 'Experiment', 'id' );
 }
 
+sub primer_array {
+    my $self = shift;
+    return sub {
+        ref $_[0] eq 'ARRAY';
+    }
+}
+
 =head2 in_enum_column
 
   Use enum from database schema as set, e.g. value column from WellAssemblyQc