Merge branch 'genotyping_results' of github.com:htgt/LIMS2-WebApp int…

…o genotyping_results

ddl/templates/versions/14/audit-up.sql

@@ -1,56 +1,58 @@
-CREATE TABLE audit.well_chromosome_fail (
+
+CREATE TABLE audit.well_genotyping_results (
 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,
 well_id integer,
-result text,
+genotyping_result_type_id text,
+call text,
+copy_number double precision,
+copy_number_range double precision,
+confidence double precision,
 created_at timestamp without time zone,
 created_by_id integer
 );
-GRANT SELECT ON audit.well_chromosome_fail TO [% ro_role %];
-GRANT SELECT,INSERT ON audit.well_chromosome_fail TO [% rw_role %];
-CREATE OR REPLACE FUNCTION public.process_well_chromosome_fail_audit()
-RETURNS TRIGGER AS $well_chromosome_fail_audit$
+GRANT SELECT ON audit.well_genotyping_results TO [% ro_role %];
+GRANT SELECT,INSERT ON audit.well_genotyping_results TO [% rw_role %];
+CREATE OR REPLACE FUNCTION public.process_well_genotyping_results_audit()
+RETURNS TRIGGER AS $well_genotyping_results_audit$
     BEGIN
         IF (TG_OP = 'DELETE') THEN
-           INSERT INTO audit.well_chromosome_fail SELECT 'D', user, now(), txid_current(), OLD.*;
+           INSERT INTO audit.well_genotyping_results SELECT 'D', user, now(), txid_current(), OLD.*;
         ELSIF (TG_OP = 'UPDATE') THEN
-           INSERT INTO audit.well_chromosome_fail SELECT 'U', user, now(), txid_current(), NEW.*;
+           INSERT INTO audit.well_genotyping_results SELECT 'U', user, now(), txid_current(), NEW.*;
         ELSIF (TG_OP = 'INSERT') THEN
-           INSERT INTO audit.well_chromosome_fail SELECT 'I', user, now(), txid_current(), NEW.*;
+           INSERT INTO audit.well_genotyping_results SELECT 'I', user, now(), txid_current(), NEW.*;
         END IF;
         RETURN NULL;
     END;
-$well_chromosome_fail_audit$ LANGUAGE plpgsql;
-CREATE TRIGGER well_chromosome_fail_audit
-AFTER INSERT OR UPDATE OR DELETE ON public.well_chromosome_fail
-    FOR EACH ROW EXECUTE PROCEDURE public.process_well_chromosome_fail_audit();
-CREATE TABLE audit.well_targeting_pass (
+$well_genotyping_results_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER well_genotyping_results_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.well_genotyping_results
+    FOR EACH ROW EXECUTE PROCEDURE public.process_well_genotyping_results_audit();
+CREATE TABLE audit.genotyping_result_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,
-well_id integer,
-result text,
-created_at timestamp without time zone,
-created_by_id integer
+id text
 );
-GRANT SELECT ON audit.well_targeting_pass TO [% ro_role %];
-GRANT SELECT,INSERT ON audit.well_targeting_pass TO [% rw_role %];
-CREATE OR REPLACE FUNCTION public.process_well_targeting_pass_audit()
-RETURNS TRIGGER AS $well_targeting_pass_audit$
+GRANT SELECT ON audit.genotyping_result_types TO [% ro_role %];
+GRANT SELECT,INSERT ON audit.genotyping_result_types TO [% rw_role %];
+CREATE OR REPLACE FUNCTION public.process_genotyping_result_types_audit()
+RETURNS TRIGGER AS $genotyping_result_types_audit$
     BEGIN
         IF (TG_OP = 'DELETE') THEN
-           INSERT INTO audit.well_targeting_pass SELECT 'D', user, now(), txid_current(), OLD.*;
+           INSERT INTO audit.genotyping_result_types SELECT 'D', user, now(), txid_current(), OLD.*;
         ELSIF (TG_OP = 'UPDATE') THEN
-           INSERT INTO audit.well_targeting_pass SELECT 'U', user, now(), txid_current(), NEW.*;
+           INSERT INTO audit.genotyping_result_types SELECT 'U', user, now(), txid_current(), NEW.*;
         ELSIF (TG_OP = 'INSERT') THEN
-           INSERT INTO audit.well_targeting_pass SELECT 'I', user, now(), txid_current(), NEW.*;
+           INSERT INTO audit.genotyping_result_types SELECT 'I', user, now(), txid_current(), NEW.*;
         END IF;
         RETURN NULL;
     END;
-$well_targeting_pass_audit$ LANGUAGE plpgsql;
-CREATE TRIGGER well_targeting_pass_audit
-AFTER INSERT OR UPDATE OR DELETE ON public.well_targeting_pass
-    FOR EACH ROW EXECUTE PROCEDURE public.process_well_targeting_pass_audit();
+$genotyping_result_types_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER genotyping_result_types_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.genotyping_result_types
+    FOR EACH ROW EXECUTE PROCEDURE public.process_genotyping_result_types_audit();

ddl/templates/versions/14/fixtures.sql

@@ -1,3 +1,6 @@
 INSERT INTO schema_versions(version)
 VALUES (14);
 
+INSERT INTO genotyping_result_types(id)
+values ('loacrit'), ('loatam'), ('loxp'),('lacz'),('neo'),('en2-int'),('cre'),('puro'),('chry'),('chr1'),('chr8a'),('chr11b'),('bsd');
+

ddl/templates/versions/14/up.sql

@@ -1,20 +1,20 @@
-CREATE TABLE well_targeting_pass (
-       well_id integer NOT NULL REFERENCES wells(id),
-       result TEXT NOT NULL,
-       created_at timestamp without time zone NOT NULL DEFAULT now(),
-       created_by_id integer NOT NULL REFERENCES users(id),
-       PRIMARY KEY(well_id)
+CREATE TABLE genotyping_result_types (
+       id  TEXT NOT NULL, 
+       PRIMARY KEY(id)
 );
-GRANT SELECT ON well_targeting_pass TO "[% ro_role %]";
-GRANT SELECT, INSERT, UPDATE, DELETE ON well_targeting_pass TO "[% rw_role %]";
+GRANT SELECT ON genotyping_result_types TO "[% ro_role %]";
+GRANT SELECT, INSERT, UPDATE, DELETE ON genotyping_result_types TO "[% rw_role %]";
 
-CREATE TABLE well_chromosome_fail (
-       well_id integer NOT NULL REFERENCES wells(id),
-       result TEXT NOT NULL,
-       created_at timestamp without time zone NOT NULL DEFAULT now(),
-       created_by_id integer NOT NULL REFERENCES users(id),
-       PRIMARY KEY(well_id)
+CREATE TABLE well_genotyping_results (
+       well_id                    INTEGER NOT NULL REFERENCES wells(id),
+       genotyping_result_type_id  TEXT NOT NULL REFERENCES genotyping_result_types(id),
+       call                       TEXT NOT NULL,
+       copy_number                FLOAT,
+       copy_number_range          FLOAT,
+       confidence                 FLOAT,
+       created_at                 TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
+       created_by_id              INTEGER NOT NULL REFERENCES users(id),
+       PRIMARY KEY(well_id, genotyping_result_type_id)
 );
-GRANT SELECT ON well_chromosome_fail TO "[% ro_role %]";
-GRANT SELECT, INSERT, UPDATE, DELETE ON well_chromosome_fail TO "[% rw_role %]";
-
+GRANT SELECT ON well_genotyping_results TO "[% ro_role %]";
+GRANT SELECT, INSERT, UPDATE, DELETE ON well_genotyping_results TO "[% rw_role %]";

ddl/templates/versions/15/audit-up.sql

@@ -0,0 +1,56 @@
+CREATE TABLE audit.well_chromosome_fail (
+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,
+well_id integer,
+result text,
+created_at timestamp without time zone,
+created_by_id integer
+);
+GRANT SELECT ON audit.well_chromosome_fail TO [% ro_role %];
+GRANT SELECT,INSERT ON audit.well_chromosome_fail TO [% rw_role %];
+CREATE OR REPLACE FUNCTION public.process_well_chromosome_fail_audit()
+RETURNS TRIGGER AS $well_chromosome_fail_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.well_chromosome_fail SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.well_chromosome_fail SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.well_chromosome_fail SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$well_chromosome_fail_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER well_chromosome_fail_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.well_chromosome_fail
+    FOR EACH ROW EXECUTE PROCEDURE public.process_well_chromosome_fail_audit();
+CREATE TABLE audit.well_targeting_pass (
+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,
+well_id integer,
+result text,
+created_at timestamp without time zone,
+created_by_id integer
+);
+GRANT SELECT ON audit.well_targeting_pass TO [% ro_role %];
+GRANT SELECT,INSERT ON audit.well_targeting_pass TO [% rw_role %];
+CREATE OR REPLACE FUNCTION public.process_well_targeting_pass_audit()
+RETURNS TRIGGER AS $well_targeting_pass_audit$
+    BEGIN
+        IF (TG_OP = 'DELETE') THEN
+           INSERT INTO audit.well_targeting_pass SELECT 'D', user, now(), txid_current(), OLD.*;
+        ELSIF (TG_OP = 'UPDATE') THEN
+           INSERT INTO audit.well_targeting_pass SELECT 'U', user, now(), txid_current(), NEW.*;
+        ELSIF (TG_OP = 'INSERT') THEN
+           INSERT INTO audit.well_targeting_pass SELECT 'I', user, now(), txid_current(), NEW.*;
+        END IF;
+        RETURN NULL;
+    END;
+$well_targeting_pass_audit$ LANGUAGE plpgsql;
+CREATE TRIGGER well_targeting_pass_audit
+AFTER INSERT OR UPDATE OR DELETE ON public.well_targeting_pass
+    FOR EACH ROW EXECUTE PROCEDURE public.process_well_targeting_pass_audit();

ddl/templates/versions/15/fixtures.sql

@@ -0,0 +1,3 @@
+INSERT INTO schema_versions(version)
+VALUES (15);
+

ddl/templates/versions/15/up.sql

@@ -0,0 +1,20 @@
+CREATE TABLE well_targeting_pass (
+       well_id integer NOT NULL REFERENCES wells(id),
+       result TEXT NOT NULL,
+       created_at timestamp without time zone NOT NULL DEFAULT now(),
+       created_by_id integer NOT NULL REFERENCES users(id),
+       PRIMARY KEY(well_id)
+);
+GRANT SELECT ON well_targeting_pass TO "[% ro_role %]";
+GRANT SELECT, INSERT, UPDATE, DELETE ON well_targeting_pass TO "[% rw_role %]";
+
+CREATE TABLE well_chromosome_fail (
+       well_id integer NOT NULL REFERENCES wells(id),
+       result TEXT NOT NULL,
+       created_at timestamp without time zone NOT NULL DEFAULT now(),
+       created_by_id integer NOT NULL REFERENCES users(id),
+       PRIMARY KEY(well_id)
+);
+GRANT SELECT ON well_chromosome_fail TO "[% ro_role %]";
+GRANT SELECT, INSERT, UPDATE, DELETE ON well_chromosome_fail TO "[% rw_role %]";
+

lib/LIMS2/Model/FormValidator/Constraint.pm

@@ -109,6 +109,20 @@ sub integer {
     }
 }
 
+sub confidence_float {
+    return sub {
+        my $val = shift;
+        return $val =~ qr/^\d+\.\d+$/ ;
+    }
+}
+
+sub copy_float {
+    return sub {
+        my $val = shift;
+        return $val =~ qr/^\d+\.\d+$/ ;
+    }
+}
+
 sub alphanumeric_string {
     return regexp_matches(qr/^\w+$/);
 }
@@ -244,6 +258,11 @@ sub existing_genotyping_primer_type {
     return in_resultset( $model, 'GenotypingPrimerType', 'id' );
 }
 
+sub existing_genotyping_result_type {
+    my ( $class, $model ) = @_;
+    return in_resultset( $model, 'GenotypingResultType', 'id' );
+}
+
 sub existing_user {
     my ( $class, $model ) = @_;
     return in_resultset( $model, 'User', 'name' );