New Decision Meeting Tool

.gitignore

@@ -29,6 +29,7 @@ logfile*.txt
 MANIFEST*
 ./cgi-bin/secretom
 MYMETA.json
+db/delete_nd_experiment_ids/
 tags
 .prove
 .Rhistory

db/00200/AddPopulationToWizard.pm

@@ -0,0 +1,259 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+AddPopulationToWizard.pm
+
+
+=head1 SYNOPSIS
+
+mx-run AddPopulationUser [options] -H hostname -D dbname -u username [-F]
+
+this is a subclass of L<CXGN::Metadata::Dbpatch>
+see the perldoc of parent class for more details.
+
+=head1 DESCRIPTION
+
+This patch:
+ - Add populations to materilized view
+
+=head1 AUTHOR
+
+Chris Simoes <ccs263@cornell.edu>
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2010 Boyce Thompson Institute for Plant Research
+
+This program is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+package AddPopulationToWizard;
+
+use Moose;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch updates the materialized_phenoview by adding tissue sample to the view
+
+
+sub patch {
+    my $self=shift;
+
+    print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
+
+    print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
+
+    print STDOUT "\nExecuting the SQL commands.\n";
+
+    $self->dbh->do(<<EOSQL);
+--do your SQL here
+
+-- ADDING Populations searh --
+
+DROP VIEW IF EXISTS public.populations CASCADE;
+CREATE VIEW public.populations AS
+  SELECT stock.stock_id AS population_id,
+  stock.uniquename AS population_name
+  FROM stock
+  WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'population') AND is_obsolete = 'f'
+  GROUP BY 1,2;
+ALTER VIEW populations OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.accessionsXpopulations CASCADE;
+CREATE VIEW public.accessionsXpopulations AS
+SELECT s2.stock_id as accession_id,
+    stock.stock_id AS population_id
+   FROM stock
+   JOIN stock_relationship sr on sr.object_id = stock.stock_id
+   JOIN stock s2 on s2.stock_id = sr.subject_id
+   WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'population') AND stock.is_obsolete = 'f'
+   AND s2.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'accession') AND s2.is_obsolete = 'f'
+  GROUP BY 1,2;
+ALTER VIEW public.accessionsXpopulations OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXaccessions_ids CASCADE;
+CREATE VIEW public.populationsXaccessions_ids AS
+SELECT ap.population_id,
+    stock.stock_id AS accessions_id_id
+   FROM accessionsXpopulations ap
+   join stock on stock.stock_id = ap.accession_id
+   WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'accession') AND is_obsolete = 'f'
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXaccessions_ids OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXseedlots CASCADE;
+CREATE VIEW public.populationsXseedlots AS
+SELECT ap.population_id,
+    s.stock_id as seedlot_id
+FROM accessionsXpopulations ap
+JOIN stock_relationship sr on sr.subject_id = ap.accession_id
+JOIN stock s on s.stock_id = sr.object_id 
+WHERE sr.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'collection_of')
+AND s.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'seedlot')
+GROUP BY 1,2;
+ALTER VIEW public.populationsXseedlots OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.breeding_programsXpopulations CASCADE;
+CREATE VIEW public.breeding_programsXpopulations AS
+SELECT mp.breeding_program_id,
+       ap.population_id
+   from accessionsXpopulations ap 
+   join public.materialized_phenoview mp on mp.accession_id = ap.accession_id
+  GROUP BY 1,2;
+ALTER VIEW public.breeding_programsXpopulations OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.genotyping_protocolsXpopulations CASCADE;
+CREATE VIEW public.genotyping_protocolsXpopulations AS
+SELECT ap.population_id,
+    mg.genotyping_protocol_id
+   FROM public.accessionsXpopulations ap
+   JOIN public.materialized_genoview mg on mg.accession_id = ap.accession_id
+  GROUP BY 1,2;
+ ALTER VIEW public.genotyping_protocolsXpopulations OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXlocations CASCADE;
+CREATE VIEW public.populationsXlocations AS
+select ap.population_id, 
+    mp.location_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview mp on mp.accession_id = ap.accession_id
+  GROUP BY 1,2;
+  ALTER VIEW populationsXlocations OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXplants CASCADE;
+CREATE VIEW public.populationsXplants AS
+SELECT ap.population_id, 
+    public.stock.stock_id AS plant_id
+   FROM public.accessionsXpopulations ap 
+   JOIN public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN  public.stock ON(public.materialized_phenoview.stock_id = public.stock.stock_id AND public.stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'plant'))
+  GROUP BY 1,2;
+  ALTER VIEW public.populationsXplants OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXtissue_sample CASCADE;
+CREATE VIEW public.populationsXtissue_sample AS
+select ap.population_id, 
+    public.stock.stock_id AS tissue_sample_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id 
+   JOIN public.stock ON(public.materialized_phenoview.stock_id = public.stock.stock_id AND public.stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'tissue_sample'))
+  GROUP BY 1,2;
+ALTER view populationsXtissue_sample OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXplots CASCADE;
+CREATE VIEW public.populationsXplots AS
+SELECT ap.population_id,
+    public.stock.stock_id AS plot_id
+   FROM public.accessionsxpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN public.stock ON(public.materialized_phenoview.stock_id = public.stock.stock_id AND public.stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'plot'))
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXplots OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXsubplots CASCADE;
+CREATE VIEW public.populationsXsubplots AS
+SELECT ap.population_id,
+    public.stock.stock_id AS subplot_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN public.stock ON(public.materialized_phenoview.stock_id = public.stock.stock_id AND public.stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'subplot'))
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXsubplots OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXtrial_designs CASCADE;
+CREATE VIEW public.populationsXtrial_designs AS
+SELECT ap.population_id,
+    trialdesign.value AS trial_design_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN public.projectprop trialdesign ON materialized_phenoview.trial_id = trialdesign.project_id AND trialdesign.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'design' )
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXtrial_designs OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXtrial_types CASCADE;
+CREATE VIEW public.populationsXtrial_types AS
+SELECT ap.population_id,
+    trialterm.cvterm_id AS trial_type_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN projectprop trialprop ON materialized_phenoview.trial_id = trialprop.project_id AND trialprop.type_id IN (SELECT cvterm_id from cvterm JOIN cv USING(cv_id) WHERE cv.name = 'project_type' )
+   JOIN cvterm trialterm ON trialprop.type_id = trialterm.cvterm_id
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXtrial_types OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXtrials CASCADE;
+CREATE VIEW public.populationsXtrials AS
+SELECT ap.population_id,
+    public.materialized_phenoview.trial_id
+   FROM public.accessionsxpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXtrials OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXyears CASCADE;
+CREATE VIEW public.populationsXyears AS
+SELECT ap.population_id,
+      public.materialized_phenoview.year_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXyears OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXgenotyping_projects CASCADE;
+CREATE VIEW public.populationsXgenotyping_projects AS 
+    SELECT ap.population_id,
+           genotyping_project_id
+    FROM public.accessionsXpopulations ap
+    join materialized_genoview on materialized_genoview.accession_id = ap.accession_id
+    GROUP BY 1,2;
+ALTER VIEW public.populationsXgenotyping_projects OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXorganisms CASCADE;
+CREATE VIEW public.populationsXorganisms AS
+select ap.population_id,
+       s.organism_id
+from public.accessionsXpopulations ap
+join stock s on s.stock_id = ap.accession_id
+group by 1,2;
+ALTER VIEW public.populationsXorganisms OWNER TO web_usr;
+
+
+DROP VIEW IF EXISTS public.populationsXtraits CASCADE;
+CREATE VIEW public.populationsXtraits as
+SELECT ap.population_id,
+    public.materialized_phenoview.trait_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXtraits OWNER TO web_usr;
+
+DROP VIEW IF EXISTS public.populationsXtrait_components CASCADE;
+CREATE VIEW public.populationsXtrait_components AS
+SELECT ap.population_id,
+    trait_component.cvterm_id AS trait_component_id
+   FROM public.accessionsXpopulations ap
+   join public.materialized_phenoview on public.materialized_phenoview.accession_id = ap.accession_id
+   JOIN cvterm trait ON(materialized_phenoview.trait_id = trait.cvterm_id)
+   JOIN cvterm_relationship ON(trait.cvterm_id = cvterm_relationship.object_id AND cvterm_relationship.type_id = (SELECT cvterm_id from cvterm where name = 'contains'))
+   JOIN cvterm trait_component ON(cvterm_relationship.subject_id = trait_component.cvterm_id)
+  GROUP BY 1,2;
+ALTER VIEW public.populationsXtrait_components OWNER TO web_usr;
+
+-- ADDING User --
+
+
+
+EOSQL
+
+print "You're done!\n";
+}
+
+
+####
+1; #
+####

db/00204/AddExperimentMeetingCvterms.pm

@@ -0,0 +1,117 @@
+#!/usr/bin/env perl
+
+=head1 NAME
+
+ AddExperimentMeetingCvterms
+
+=head1 SYNOPSIS
+
+mx-run AddExperimentMeetingCvterms [options] -H hostname -D dbname -u username [-F]
+
+this is a subclass of L<CXGN::Metadata::Dbpatch>
+see the perldoc of parent class for more details.
+
+=head1 DESCRIPTION
+
+This patch adds:
+- the cv 'experiment_meeting'
+- the cvterm 'meeting_project' in cv 'experiment_meeting'
+- the cvterm 'meeting_json' in cv 'project_property'
+
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Chris Simoes
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2010 Boyce Thompson Institute for Plant Research
+
+This program is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+package AddExperimentMeetingCvterms;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+use SGN::Model::Cvterm;
+
+extends 'CXGN::Metadata::Dbpatch';
+
+has '+description' => ( default => <<'' );
+This patch adds the cv 'experiment_meeting', the cvterm 'meeting_project' in cv 'experiment_meeting', and the cvterm 'meeting_json' in cv 'project_property'
+
+has '+prereq' => (
+    default => sub {
+        [],
+    },
+);
+
+sub patch {
+    my $self = shift;
+
+    print STDOUT "Executing the patch:\n " . $self->name . ".\n\nDescription:\n  " . $self->description . ".\n\nExecuted by:\n " . $self->username . " .";
+
+    print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
+    print STDOUT "\nExecuting the SQL commands.\n";
+
+    my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
+
+    print STDERR "INSERTING CVS AND CV TERMS...\n";
+
+    my $cv_name = 'experiment_meeting';
+
+    my $cv = $schema->resultset('Cv::Cv')->find({ name => $cv_name });
+    if (!$cv) {
+        $cv = $schema->resultset('Cv::Cv')->create({ name => $cv_name });
+        print STDERR "Created cv '$cv_name'\n";
+    }
+    else {
+        print STDERR "cv '$cv_name' already exists\n";
+    }
+
+    my $meeting_project = $schema->resultset('Cv::Cvterm')->find({
+        name  => 'meeting_project',
+        cv_id => $cv->cv_id
+    });
+
+    if (!$meeting_project) {
+        $schema->resultset('Cv::Cvterm')->create_with({
+            name => 'meeting_project',
+            cv   => $cv_name
+        });
+        print STDERR "Created cvterm 'meeting_project' in cv '$cv_name'\n";
+    }
+    else {
+        print STDERR "cvterm 'meeting_project' already exists in cv '$cv_name'\n";
+    }
+
+    my $project_property_cv = $schema->resultset('Cv::Cv')->find({ name => 'project_property' });
+    die "cv 'project_property' does not exist\n" unless $project_property_cv;
+
+    my $meeting_json = $schema->resultset('Cv::Cvterm')->find({
+        name  => 'meeting_json',
+        cv_id => $project_property_cv->cv_id
+    });
+
+    if (!$meeting_json) {
+        $schema->resultset('Cv::Cvterm')->create_with({
+            name => 'meeting_json',
+            cv   => 'project_property'
+        });
+        print STDERR "Created cvterm 'meeting_json' in cv 'project_property'\n";
+    }
+    else {
+        print STDERR "cvterm 'meeting_json' already exists in cv 'project_property'\n";
+    }
+
+    print "You're done!\n";
+}
+
+####
+1; #
+####