Skip to content

Add HDPs to to the search wizard #6141

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
bm743 wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Add HDPs to to the search wizard #6141

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c8cfeab
Add HDP protocols and instance ids to search wizard
bm743 May 22, 2026
80c86c7
Create HDP phenotype download for CSV and excel
bm743 Jun 4, 2026
79344d4
Add hdp download section to wizard page
bm743 Jun 4, 2026
32bc999
Merge remote-tracking branch 'origin/master' into topic/hdp_search_wi…
bm743 Jun 4, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
307 changes: 307 additions & 0 deletions db/00206/AddInstanceToMaterializedViews.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,307 @@
#!/usr/bin/env perl

=head1 NAME

AddInstanceToMaterializedViews.pm

=head1 SYNOPSIS

mx-run AddInstanceToMaterializedViews [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 a new instances view based on metadata.md_files
- Adds cross-reference views between instances and other search wizard categories
including protocols, trials, accessions, breeding programs, locations, and years

=head1 AUTHOR

Ben Maza

=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 AddInstanceToMaterializedViews;

use Moose;
extends 'CXGN::Metadata::Dbpatch';

has '+description' => ( default => <<'' );
This patch adds instance file ids to the search wizard materialized views

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

-- Add instances view
-- instances are files in metadata.md_files connected to protocols
-- via nd_experiment_protocol and phenome.nd_experiment_md_files
DROP VIEW IF EXISTS public.instances CASCADE;
CREATE VIEW public.instances AS
SELECT
m.file_id AS instance_id,
m.file_id::text AS instance_name
FROM metadata.md_files m
GROUP BY m.file_id, m.basename;
ALTER VIEW public.instances OWNER TO web_usr;

-- instancesXprotocols
-- connects instances to protocols via the experiment chain
DROP VIEW IF EXISTS public.instancesXprotocols CASCADE;
CREATE VIEW public.instancesXprotocols AS
SELECT DISTINCT
ef.file_id AS instance_id,
ep.nd_protocol_id AS protocol_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_protocol ep ON ef.nd_experiment_id = ep.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.instancesXprotocols OWNER TO web_usr;

-- protocolsXinstances
DROP VIEW IF EXISTS public.protocolsXinstances CASCADE;
CREATE VIEW public.protocolsXinstances AS
SELECT DISTINCT
ep.nd_protocol_id AS protocol_id,
ef.file_id AS instance_id
FROM nd_experiment_protocol ep
JOIN phenome.nd_experiment_md_files ef ON ep.nd_experiment_id = ef.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.protocolsXinstances OWNER TO web_usr;

-- instancesXtrials
-- connects instances to trials via experiment chain
DROP VIEW IF EXISTS public.instancesXtrials CASCADE;
CREATE VIEW public.instancesXtrials AS
SELECT DISTINCT
ef.file_id AS instance_id,
ep.project_id AS trial_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_project ep ON ef.nd_experiment_id = ep.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.instancesXtrials OWNER TO web_usr;

-- trialsXinstances
DROP VIEW IF EXISTS public.trialsXinstances CASCADE;
CREATE VIEW public.trialsXinstances AS
SELECT DISTINCT
ep.project_id AS trial_id,
ef.file_id AS instance_id
FROM nd_experiment_project ep
JOIN phenome.nd_experiment_md_files ef ON ep.nd_experiment_id = ef.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.trialsXinstances OWNER TO web_usr;

-- instancesXaccessions
-- connects instances to accessions via experiment stock chain
DROP VIEW IF EXISTS public.instancesXaccessions CASCADE;
CREATE VIEW public.instancesXaccessions AS
SELECT DISTINCT
ef.file_id AS instance_id,
stock.stock_id AS accession_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_stock nes ON ef.nd_experiment_id = nes.nd_experiment_id
JOIN stock ON nes.stock_id = stock.stock_id
AND stock.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'accession')
GROUP BY 1, 2;
ALTER VIEW public.instancesXaccessions OWNER TO web_usr;

-- accessionsXinstances
DROP VIEW IF EXISTS public.accessionsXinstances CASCADE;
CREATE VIEW public.accessionsXinstances AS
SELECT DISTINCT
stock.stock_id AS accession_id,
ef.file_id AS instance_id
FROM nd_experiment_stock nes
JOIN stock ON nes.stock_id = stock.stock_id
AND stock.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'accession')
JOIN phenome.nd_experiment_md_files ef ON nes.nd_experiment_id = ef.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.accessionsXinstances OWNER TO web_usr;

-- instancesXtissue_sample
DROP VIEW IF EXISTS public.instancesXtissue_sample CASCADE;
CREATE VIEW public.instancesXtissue_sample AS
SELECT DISTINCT
ef.file_id AS instance_id,
nes.stock_id AS tissue_sample_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_stock nes ON ef.nd_experiment_id = nes.nd_experiment_id
JOIN stock ON nes.stock_id = stock.stock_id
AND stock.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'tissue_sample')
GROUP BY 1, 2;
ALTER VIEW public.instancesXtissue_sample OWNER TO web_usr;

-- tissue_sampleXinstances
DROP VIEW IF EXISTS public.tissue_sampleXinstances CASCADE;
CREATE VIEW public.tissue_sampleXinstances AS
SELECT DISTINCT
nes.stock_id AS tissue_sample_id,
ef.file_id AS instance_id
FROM nd_experiment_stock nes
JOIN stock ON nes.stock_id = stock.stock_id
AND stock.type_id = (SELECT cvterm_id FROM cvterm WHERE cvterm.name = 'tissue_sample')
JOIN phenome.nd_experiment_md_files ef ON nes.nd_experiment_id = ef.nd_experiment_id
GROUP BY 1, 2;
ALTER VIEW public.tissue_sampleXinstances OWNER TO web_usr;

-- instancesXbreeding_programs
-- connects instances to breeding programs via trial chain in matview
DROP VIEW IF EXISTS public.instancesXbreeding_programs CASCADE;
CREATE VIEW public.instancesXbreeding_programs AS
SELECT DISTINCT
ef.file_id AS instance_id,
mpv.breeding_program_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_project ep ON ef.nd_experiment_id = ep.nd_experiment_id
JOIN public.materialized_phenoview mpv ON ep.project_id = mpv.trial_id
WHERE mpv.breeding_program_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.instancesXbreeding_programs OWNER TO web_usr;

-- breeding_programsXinstances
DROP VIEW IF EXISTS public.breeding_programsXinstances CASCADE;
CREATE VIEW public.breeding_programsXinstances AS
SELECT DISTINCT
mpv.breeding_program_id,
ef.file_id AS instance_id
FROM public.materialized_phenoview mpv
JOIN nd_experiment_project ep ON mpv.trial_id = ep.project_id
JOIN phenome.nd_experiment_md_files ef ON ep.nd_experiment_id = ef.nd_experiment_id
WHERE mpv.breeding_program_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.breeding_programsXinstances OWNER TO web_usr;

-- instancesXlocations
-- connects instances to locations via trial chain in matview
DROP VIEW IF EXISTS public.instancesXlocations CASCADE;
CREATE VIEW public.instancesXlocations AS
SELECT DISTINCT
ef.file_id AS instance_id,
mpv.location_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_project ep ON ef.nd_experiment_id = ep.nd_experiment_id
JOIN public.materialized_phenoview mpv ON ep.project_id = mpv.trial_id
WHERE mpv.location_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.instancesXlocations OWNER TO web_usr;

-- locationsXinstances
DROP VIEW IF EXISTS public.locationsXinstances CASCADE;
CREATE VIEW public.locationsXinstances AS
SELECT DISTINCT
mpv.location_id,
ef.file_id AS instance_id
FROM public.materialized_phenoview mpv
JOIN nd_experiment_project ep ON mpv.trial_id = ep.project_id
JOIN phenome.nd_experiment_md_files ef ON ep.nd_experiment_id = ef.nd_experiment_id
WHERE mpv.location_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.locationsXinstances OWNER TO web_usr;

-- instancesXyears
-- connects instances to years via trial chain in matview
DROP VIEW IF EXISTS public.instancesXyears CASCADE;
CREATE VIEW public.instancesXyears AS
SELECT DISTINCT
ef.file_id AS instance_id,
mpv.year_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_project ep ON ef.nd_experiment_id = ep.nd_experiment_id
JOIN public.materialized_phenoview mpv ON ep.project_id = mpv.trial_id
WHERE mpv.year_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.instancesXyears OWNER TO web_usr;

-- yearsXinstances
DROP VIEW IF EXISTS public.yearsXinstances CASCADE;
CREATE VIEW public.yearsXinstances AS
SELECT DISTINCT
mpv.year_id,
ef.file_id AS instance_id
FROM public.materialized_phenoview mpv
JOIN nd_experiment_project ep ON mpv.trial_id = ep.project_id
JOIN phenome.nd_experiment_md_files ef ON ep.nd_experiment_id = ef.nd_experiment_id
WHERE mpv.year_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.yearsXinstances OWNER TO web_usr;

-- instancesXtraits
-- connects instances to traits via phenotype observations in same experiment
DROP VIEW IF EXISTS public.instancesXtraits CASCADE;
CREATE VIEW public.instancesXtraits AS
SELECT DISTINCT
ef.file_id AS instance_id,
phenotype.cvalue_id AS trait_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_phenotype nep ON ef.nd_experiment_id = nep.nd_experiment_id
JOIN phenotype ON nep.phenotype_id = phenotype.phenotype_id
WHERE phenotype.cvalue_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.instancesXtraits OWNER TO web_usr;

-- traitsXinstances
DROP VIEW IF EXISTS public.traitsXinstances CASCADE;
CREATE VIEW public.traitsXinstances AS
SELECT DISTINCT
phenotype.cvalue_id AS trait_id,
ef.file_id AS instance_id
FROM nd_experiment_phenotype nep
JOIN phenotype ON nep.phenotype_id = phenotype.phenotype_id
JOIN phenome.nd_experiment_md_files ef ON nep.nd_experiment_id = ef.nd_experiment_id
WHERE phenotype.cvalue_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.traitsXinstances OWNER TO web_usr;

-- instancesXorganisms
-- connects instances to organisms via stock in the experiment
DROP VIEW IF EXISTS public.instancesXorganisms CASCADE;
CREATE VIEW public.instancesXorganisms AS
SELECT DISTINCT
ef.file_id AS instance_id,
stock.organism_id
FROM phenome.nd_experiment_md_files ef
JOIN nd_experiment_stock nes ON ef.nd_experiment_id = nes.nd_experiment_id
JOIN stock ON nes.stock_id = stock.stock_id
WHERE stock.organism_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.instancesXorganisms OWNER TO web_usr;

-- organismsXinstances
DROP VIEW IF EXISTS public.organismsXinstances CASCADE;
CREATE VIEW public.organismsXinstances AS
SELECT DISTINCT
stock.organism_id,
ef.file_id AS instance_id
FROM nd_experiment_stock nes
JOIN stock ON nes.stock_id = stock.stock_id
JOIN phenome.nd_experiment_md_files ef ON nes.nd_experiment_id = ef.nd_experiment_id
WHERE stock.organism_id IS NOT NULL
GROUP BY 1, 2;
ALTER VIEW public.organismsXinstances OWNER TO web_usr;

EOSQL

print "You're done!\n";
}

####
1; #
####
Loading
Loading