Merge pull request #5199 from solgenomics/topic/tracking_transformation

Tracking transformation workflow

Author: lukasmueller

db/00187/AddTransformationAndTrackingCvterms.pm

@@ -0,0 +1,94 @@
+#!/usr/bin/env perl
+
+=head1 NAME
+
+AddTransformationAndTrackingCvterms.pm
+
+=head1 SYNOPSIS
+
+mx-run ThisPackageName [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 autogenerated_name_metadata, autogenerated_name_format, default_plant_material project_property cvterms, progress_of project_relationship cvterm, tracking_transformation_json, completed_metadata stock_property cvterms.
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Titima Tantikanjana<[email protected]>
+
+=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 AddTransformationAndTrackingCvterms;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+Description of this patch goes here
+
+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 CV TERMS...\n";
+
+    my $terms = {
+        'project_property' => [
+            'autogenerated_name_metadata',
+            'autogenerated_name_format',
+            'default_plant_material',
+        ],
+        'project_relationship' => [
+            'progress_of',
+        ],
+        'stock_property' => [
+            'tracking_transformation_json',
+            'completed_metadata',
+        ]
+    };
+
+    foreach my $t (keys %$terms){
+        foreach (@{$terms->{$t}}){
+            $schema->resultset("Cv::Cvterm")->create_with({
+                name => $_,
+                cv => $t
+            });
+        }
+    }
+
+    print "You're done!\n";
+
+}
+
+
+####
+1; #
+####

lib/CXGN/BreedersToolbox/Projects.pm

@@ -253,7 +253,7 @@ sub get_trials_by_breeding_program {
     my @sorted_by_year_keys = sort { $project_year{$a} cmp $project_year{$b} } keys(%project_year);
 
     foreach my $id_key (@sorted_by_year_keys) {
-        if (!$projects_that_are_crosses{$id_key} && !$projects_that_are_genotyping_trials{$id_key} && !$projects_that_are_genotyping_trials{$id_key} && !$projects_that_are_treatment_trials{$id_key} && !$projects_that_are_genotyping_data_projects{$id_key} && !$projects_that_are_drone_run_projects{$id_key} && !$projects_that_are_drone_run_band_projects{$id_key} && !$projects_that_are_analyses{$id_key} && !$projects_that_are_sampling_trials{$id_key} && !$projects_that_are_tracking_projects{$id_key}) {
+        if (!$projects_that_are_crosses{$id_key} && !$projects_that_are_genotyping_trials{$id_key} && !$projects_that_are_genotyping_trials{$id_key} && !$projects_that_are_treatment_trials{$id_key} && !$projects_that_are_genotyping_data_projects{$id_key} && !$projects_that_are_drone_run_projects{$id_key} && !$projects_that_are_drone_run_band_projects{$id_key} && !$projects_that_are_analyses{$id_key} && !$projects_that_are_sampling_trials{$id_key} && !$projects_that_are_tracking_projects{$id_key} && !$projects_that_are_transformation_projects{$id_key}) {
             push @$field_trials, [ $id_key, $project_name{$id_key}, $project_description{$id_key}];
         } elsif ($projects_that_are_crosses{$id_key}) {
             push @$cross_trials, [ $id_key, $project_name{$id_key}, $project_description{$id_key}];
@@ -852,4 +852,26 @@ sub get_related_treatments {
 }
 
 
+sub get_autogenerated_name_metadata_by_breeding_program {
+    my $self = shift;
+    my $schema = $self->schema;
+    my $breeding_program_id = shift;
+
+    my $autogenerated_name_metadata_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_metadata', 'project_property');
+    my $program = $schema->resultset('Project::Project')->find({ project_id => $breeding_program_id});
+
+    my $name_metadata_hashes;
+    my $name_metadata_projectprop_rs = $program->projectprops({type_id => $autogenerated_name_metadata_cvterm->cvterm_id});
+    if ($name_metadata_projectprop_rs->count == 1){
+        my $name_metadata_string = $name_metadata_projectprop_rs->first->value();
+        $name_metadata_hashes = decode_json $name_metadata_string;
+    } else {
+        return {error => "Error retrieving autogenerated name metadata!\n"};
+    }
+
+    return {name_metadata => $name_metadata_hashes};
+
+}
+
+
 1;

lib/CXGN/Project.pm

@@ -265,7 +265,7 @@ sub get_year {
     my $rs = $self->bcs_schema->resultset('Project::Project')->search( { 'me.project_id' => $self->get_trial_id() })->search_related('projectprops', { 'projectprops.type_id' => $type_id } );
 
     if ($rs->count() == 0) {
-	return undef;
+	return;
     }
     else {
 	return $rs->first()->value();
@@ -944,7 +944,7 @@ sub get_project_type {
 	    }
 	}
     }
-    return undef;
+    return;
 
 }
 
@@ -1029,21 +1029,21 @@ sub get_breeding_program {
     my $self = shift;
 
     my $rs = $self->bcs_schema()->resultset("Project::ProjectRelationship")->search({
-			subject_project_id => $self->get_trial_id(),
-	    type_id => $self->get_breeding_program_trial_relationship_cvterm_id(),
-		});
+        subject_project_id => $self->get_trial_id(),
+        type_id => $self->get_breeding_program_trial_relationship_cvterm_id(),
+    });
     if ($rs->count() == 0) {
-			return undef;
+        return;
     }
 
     my $bp_rs = $self->bcs_schema()->resultset("Project::Project")->search({
-			project_id => $rs->first()->object_project_id()
-		});
+        project_id => $rs->first()->object_project_id()
+    });
     if ($bp_rs->count > 0) {
-			return $bp_rs->first()->name();
+        return $bp_rs->first()->name();
     }
 
-    return undef;
+    return;
 }
 
 sub set_breeding_program {
@@ -1344,7 +1344,7 @@ sub get_transplanting_date {
     if ($row){
         my $harvest_date = $calendar_funcs->display_start_date($row->value());
         return $harvest_date;
-    } 
+    }
     else {
         return;
     }
@@ -1363,7 +1363,7 @@ sub set_transplanting_date {
         });
         $row->value($transplanting_event);
         $row->update();
-    } 
+    }
     else{
         print STDERR "date format did not pass check while preparing to set transplanting date: $transplanting_date \n";
     }
@@ -1377,14 +1377,14 @@ sub remove_transplanting_date {
         my $transplanting_date_cvterm_id = $self->get_transplanting_date_cvterm_id();
         my $row = $self->bcs_schema->resultset('Project::Projectprop')->find_or_create({
             project_id => $self->get_trial_id(),
-            type_id => $transplanting_date_cvterm_id,  
+            type_id => $transplanting_date_cvterm_id,
             value => $transplanting_event,
         });
         if ($row){
             print STDERR "Removing transplanting date $transplanting_event from trial ".$self->get_trial_id()."\n";
             $row->delete();
-        }   
-    } 
+        }
+    }
     else {
         print STDERR "date format did not pass check while preparing to delete transplanting date: $transplanting_date  \n";
     }
@@ -5385,6 +5385,71 @@ sub genotyping_protocol_count {
 }
 
 
+=head2 function delete_empty_transformation_project()
+
+ Usage:
+ Desc:
+ Ret:
+ Args:
+ Side Effects:
+ Example:
+
+=cut
+
+sub delete_empty_transformation_project {
+    my $self = shift;
+    my $project_id = $self->get_trial_id();
+
+    if ($self->transformation_id_count() > 0) {
+        return 'Cannot delete transformation project with associated transformation IDs.';
+    }
+
+    my $project_owner_schema = CXGN::Phenome::Schema->connect( sub {$self->bcs_schema->storage->dbh()},{on_connect_do => ['SET search_path TO public,phenome;']});
+    my $project_owner_row = $project_owner_schema->resultset('ProjectOwner')->find( { project_id=> $project_id });
+    if ($project_owner_row) {
+        $project_owner_row->delete();
+    }
+
+    eval {
+        my $row = $self->bcs_schema->resultset("Project::Project")->find( { project_id=> $project_id });
+        $row->delete();
+        print STDERR "deleted project ".$project_id."\n";
+    };
+    if ($@) {
+        print STDERR "An error occurred during deletion: $@\n";
+        return $@;
+    }
+}
+
+=head2 function transformation_id_count()
+
+ Usage:
+ Desc:    The number of transformation ids associated with this transformation project
+ Ret:
+ Args:
+ Side Effects:
+ Example:
+
+=cut
+
+sub transformation_id_count {
+    my $self = shift;
+    my $schema = $self->bcs_schema;
+    my $project_id = $self->get_trial_id();
+    my $transformation_experiment_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "transformation_experiment", "experiment_type")->cvterm_id();
+
+    my $q = "SELECT count(nd_experiment_project.nd_experiment_id)
+        FROM nd_experiment_project
+        JOIN nd_experiment on (nd_experiment_project.nd_experiment_id = nd_experiment.nd_experiment_id)
+        WHERE nd_experiment.type_id = ?
+        AND nd_experiment_project.project_id = ?";
+    my $h = $self->bcs_schema->storage->dbh()->prepare($q);
+    $h->execute($transformation_experiment_type_id, $project_id);
+    my ($count) = $h->fetchrow_array();
+    return $count;
+}
+
+
 
 
 1;