Environment stratification tool #6093
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,324 @@ | ||
| use strict; | ||
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| package SGN::Controller::AJAX::EnvironmentStratification; | ||
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| use Moose; | ||
| use File::Temp qw | tempfile |; | ||
| use File::Slurp qw | read_file |; | ||
| use File::Basename qw | basename |; | ||
| use File::Copy; | ||
| use File::Spec qw | catfile |; | ||
| use CXGN::Dataset; | ||
| use CXGN::Dataset::File; | ||
| use CXGN::Job; | ||
| use JSON::Any; | ||
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| BEGIN { extends 'Catalyst::Controller::REST' } | ||
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| __PACKAGE__->config( | ||
| default => 'application/json', | ||
| stash_key => 'rest', | ||
| map => { 'application/json' => 'JSON' }, | ||
| ); | ||
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| sub shared_phenotypes : Path('/ajax/environment_stratification/shared_phenotypes') : { | ||
|
Member
There was a problem hiding this comment. Should these functions be only available to logged in users? |
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| my $self = shift; | ||
| my $c = shift; | ||
| my $dataset_id = $c->req->param('dataset_id'); | ||
| my $exclude_outliers = $c->req->param('dataset_trait_outliers') || 0; | ||
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| if (!$dataset_id) { | ||
| $c->stash->{rest} = { error => 'Dataset id is required.' }; | ||
| return; | ||
| } | ||
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| my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef; | ||
| my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id); | ||
| my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado", $sp_person_id); | ||
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| my $ds = CXGN::Dataset->new( | ||
| people_schema => $people_schema, | ||
| schema => $schema, | ||
| sp_dataset_id => $dataset_id, | ||
| ); | ||
| my $traits = $ds->retrieve_traits(); | ||
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| $c->tempfiles_subdir("environment_stratification_files"); | ||
| my ($fh, $tempfile) = $c->tempfile(TEMPLATE => "environment_stratification_files/trait_XXXXX"); | ||
| my $temppath = $c->config->{basepath} . "/" . $tempfile; | ||
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| my $ds_file = CXGN::Dataset::File->new( | ||
| people_schema => $people_schema, | ||
| schema => $schema, | ||
| sp_dataset_id => $dataset_id, | ||
| exclude_dataset_outliers => $exclude_outliers, | ||
| exclude_phenotype_outlier => $exclude_outliers, | ||
| file_name => $temppath, | ||
| quotes => 0, | ||
| ); | ||
| $ds_file->retrieve_phenotypes(); | ||
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| $c->stash->{rest} = { | ||
| options => $traits, | ||
| tempfile => $tempfile . "_phenotype.txt", | ||
| }; | ||
| } | ||
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| sub extract_trait_data : Path('/ajax/environment_stratification/getdata') Args(0) { | ||
| my $self = shift; | ||
| my $c = shift; | ||
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| my $file = basename($c->req->param("file") || ''); | ||
| my $trait = $c->req->param("trait"); | ||
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| if (!$file) { | ||
| $c->stash->{rest} = { error => "Phenotype file is required." }; | ||
| return; | ||
| } | ||
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| my $temppath = File::Spec->catfile($c->config->{basepath}, "static/documents/tempfiles/environment_stratification_files/" . $file); | ||
| my $F; | ||
| if (!open($F, "<", $temppath)) { | ||
| $c->stash->{rest} = { error => "Can't find data." }; | ||
| return; | ||
| } | ||
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| my $header = <$F>; | ||
| chomp($header); | ||
| my @keys = split("\t", $header); | ||
| for (my $n = 0; $n < @keys; $n++) { | ||
| $keys[$n] =~ s/\|CO_.*// if $keys[$n] =~ /\|CO_/; | ||
| } | ||
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| my @data; | ||
| while (<$F>) { | ||
| chomp; | ||
| my @fields = split "\t"; | ||
| my %line; | ||
| for (my $n = 0; $n < @keys; $n++) { | ||
| $line{$keys[$n]} = $fields[$n] if exists($fields[$n]) && defined($fields[$n]); | ||
| } | ||
| push @data, \%line; | ||
| } | ||
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| $c->stash->{rest} = { data => \@data, trait => $trait }; | ||
| } | ||
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| sub generate_results : Path('/ajax/environment_stratification/generate_results') : { | ||
| my $self = shift; | ||
| my $c = shift; | ||
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| my $dataset_id = $c->req->param('dataset_id'); | ||
| my $trait_id = $c->req->param('trait_id'); | ||
| my $alpha = $c->req->param('alpha') || 0.05; | ||
| my $exclude_outliers = $c->req->param('dataset_trait_outliers') || 0; | ||
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| if (!$dataset_id || !$trait_id) { | ||
| $c->stash->{rest} = { error => 'Dataset and trait are required.' }; | ||
| return; | ||
| } | ||
| if ($alpha !~ /^\d*\.?\d+$/ || $alpha <= 0 || $alpha >= 1) { | ||
| $c->stash->{rest} = { error => 'Alpha must be a number between 0 and 1.' }; | ||
| return; | ||
| } | ||
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| $c->tempfiles_subdir("environment_stratification_files"); | ||
| my $tmp_output_dir = $c->config->{cluster_shared_tempdir} . "/environment_stratification_files"; | ||
| mkdir $tmp_output_dir if !-d $tmp_output_dir; | ||
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| my ($tmp_fh, $tempfile) = tempfile( | ||
| "environment_stratification_XXXXX", | ||
| DIR => $tmp_output_dir, | ||
| ); | ||
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| my $pheno_filepath = $tempfile . "_phenotype.txt"; | ||
| my $pairwise_file = $tempfile . "_pairwise.json"; | ||
| my $group_summary_file = $tempfile . "_group_summary.json"; | ||
| my $group_membership_file = $tempfile . "_group_membership.json"; | ||
| my $ungrouped_file = $tempfile . "_ungrouped.json"; | ||
| my $summary_file = $tempfile . "_summary.json"; | ||
| my $anova_file = $tempfile . "_anova.json"; | ||
| my $message_file = $tempfile . "_message.txt"; | ||
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| my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef; | ||
| my $people_schema = $c->dbic_schema("CXGN::People::Schema", undef, $sp_person_id); | ||
| my $schema = $c->dbic_schema("Bio::Chado::Schema", "sgn_chado", $sp_person_id); | ||
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| my $ds = CXGN::Dataset::File->new( | ||
| people_schema => $people_schema, | ||
| schema => $schema, | ||
| sp_dataset_id => $dataset_id, | ||
| exclude_dataset_outliers => $exclude_outliers, | ||
| exclude_phenotype_outlier => $exclude_outliers, | ||
| file_name => $tempfile, | ||
| quotes => 0, | ||
| ); | ||
| $ds->retrieve_phenotypes($pheno_filepath); | ||
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| my $r_trait = $trait_id; | ||
| $r_trait =~ tr/ /\./; | ||
| $r_trait =~ tr/\//\./; | ||
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| my $cxgn_tools_run_config = { | ||
| backend => $c->config->{backend}, | ||
| submit_host => $c->config->{cluster_host}, | ||
| temp_base => $tmp_output_dir, | ||
| queue => $c->config->{'web_cluster_queue'}, | ||
| do_cleanup => 0, | ||
| max_cluster_jobs => 1_000_000_000, | ||
| }; | ||
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| my $cmd_str = join(" ", ( | ||
| "Rscript", | ||
| map { _shell_quote($_) } ( | ||
| $c->config->{basepath} . "/R/environment_stratification.R", | ||
| $pheno_filepath, | ||
| $r_trait, | ||
| $alpha, | ||
| $pairwise_file, | ||
| $group_summary_file, | ||
| $group_membership_file, | ||
| $ungrouped_file, | ||
| $summary_file, | ||
| $anova_file, | ||
| $message_file, | ||
| ) | ||
| )); | ||
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| my $user = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef; | ||
| my $job = CXGN::Job->new({ | ||
| schema => $schema, | ||
| people_schema => $people_schema, | ||
| sp_person_id => $user, | ||
| name => $ds->name() . " environment stratification", | ||
| job_type => 'environment_stratification', | ||
| cmd => $cmd_str, | ||
| cxgn_tools_run_config => $cxgn_tools_run_config, | ||
| finish_logfile => $c->config->{job_finish_log}, | ||
| }); | ||
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| $job->submit(); | ||
| while ($job->alive()) { | ||
| sleep(1); | ||
| } | ||
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| my $finished = $job->read_finish_timestamp(); | ||
| if (!$finished) { | ||
| $job->update_status("failed"); | ||
| my $message = -e $message_file ? read_file($message_file) : 'Environment stratification failed before producing results.'; | ||
| $c->stash->{rest} = { error => $message }; | ||
| return; | ||
| } | ||
| $job->update_status("finished"); | ||
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| my $public_dir = $c->config->{basepath} . "/static/documents/tempfiles/environment_stratification_files"; | ||
| mkdir $public_dir if !-d $public_dir; | ||
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| foreach my $file ($pairwise_file, $group_summary_file, $group_membership_file, $ungrouped_file, $summary_file, $anova_file, $message_file) { | ||
| copy($file, $public_dir) if -e $file; | ||
| } | ||
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| my $json = JSON::Any->new; | ||
| my $message = -e $message_file ? read_file($message_file) : 'Analysis finished.'; | ||
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| my $pairwise = _read_json_file($json, $pairwise_file); | ||
| my $group_summary = _read_json_file($json, $group_summary_file); | ||
| my $group_membership = _read_json_file($json, $group_membership_file); | ||
| my $ungrouped = _read_json_file($json, $ungrouped_file); | ||
| my $summary = _read_json_file($json, $summary_file); | ||
| my $anova = _read_json_file($json, $anova_file); | ||
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| $c->stash->{rest} = { | ||
| message => $message, | ||
| pairwise => $pairwise, | ||
| group_summary => $group_summary, | ||
| group_membership => $group_membership, | ||
| ungrouped => $ungrouped, | ||
| summary => $summary, | ||
| anova => $anova, | ||
| map_locations => _build_map_locations($schema, $group_membership, $ungrouped), | ||
| files => { | ||
| pairwise => "/documents/tempfiles/environment_stratification_files/" . basename($pairwise_file), | ||
| group_summary => "/documents/tempfiles/environment_stratification_files/" . basename($group_summary_file), | ||
| group_membership => "/documents/tempfiles/environment_stratification_files/" . basename($group_membership_file), | ||
| ungrouped => "/documents/tempfiles/environment_stratification_files/" . basename($ungrouped_file), | ||
| summary => "/documents/tempfiles/environment_stratification_files/" . basename($summary_file), | ||
| anova => "/documents/tempfiles/environment_stratification_files/" . basename($anova_file), | ||
| }, | ||
| }; | ||
| } | ||
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| sub _read_json_file { | ||
| my $json = shift; | ||
| my $file = shift; | ||
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| return [] if !$file || !-e $file; | ||
| my $contents = read_file($file); | ||
| return $json->decode($contents || '[]'); | ||
| } | ||
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| sub _shell_quote { | ||
| my $value = shift; | ||
| my @parts = split(/'/, $value, -1); | ||
| return "'" . join("'\"'\"'", @parts) . "'"; | ||
| } | ||
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| sub _build_map_locations { | ||
| my $schema = shift; | ||
| my $group_membership = shift || []; | ||
| my $ungrouped = shift || []; | ||
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| my @rows; | ||
| my %location_names; | ||
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| foreach my $row (@$group_membership) { | ||
| next if !$row->{location}; | ||
| push @rows, { | ||
| environment => $row->{environment_label} || $row->{environment} || '', | ||
| location => $row->{location}, | ||
| trial => $row->{trial} || '', | ||
| year => $row->{year} || '', | ||
| group_id => $row->{group_id} || '', | ||
| group_label => $row->{group_id} || '', | ||
| }; | ||
| $location_names{$row->{location}} = 1; | ||
| } | ||
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| foreach my $row (@$ungrouped) { | ||
| next if !$row->{location}; | ||
| push @rows, { | ||
| environment => $row->{environment_label} || $row->{environment} || '', | ||
| location => $row->{location}, | ||
| trial => $row->{trial} || '', | ||
| year => $row->{year} || '', | ||
| group_id => 'Ungrouped', | ||
| group_label => 'Ungrouped', | ||
| }; | ||
| $location_names{$row->{location}} = 1; | ||
| } | ||
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| return [] if !@rows; | ||
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| my %coordinates; | ||
| my @locations = keys %location_names; | ||
| my $rs = $schema->resultset("NaturalDiversity::NdGeolocation")->search({ | ||
| description => { -in => \@locations }, | ||
| }); | ||
| while (my $loc = $rs->next()) { | ||
| $coordinates{$loc->description()} = { | ||
| latitude => $loc->latitude(), | ||
| longitude => $loc->longitude(), | ||
| }; | ||
| } | ||
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| foreach my $row (@rows) { | ||
| my $coords = $coordinates{$row->{location}} || {}; | ||
| $row->{latitude} = $coords->{latitude}; | ||
| $row->{longitude} = $coords->{longitude}; | ||
| $row->{has_coordinates} = defined($row->{latitude}) && length($row->{latitude}) && defined($row->{longitude}) && length($row->{longitude}) ? 1 : 0; | ||
| } | ||
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| return \@rows; | ||
| } | ||
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| 1; | ||
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This is different from how all the other tools determine compatibility. It seems like this only requires a dataset to have trials and traits, but does not impose any requirement on the number of observed phenotypes. The other tools have a "warn" condition that explains the dataset meets the minimum requirements but may have low N, making results unreliable. The "dataset requirements" key is not present in any other tool. It is also unclear to me what the "Dataset Analysis" tool is and why it has the same requirements as environment stratification.
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I think this part should be flexible for breeders to decide how they are mounting the dataset to construct zones. They just need trials and at least a trait. Make it too restrict I think can cause more complains.