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Topic/change analysis upload requirements #5318

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Topic/change analysis upload requirements #5318

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23fbe3e
Add stored analyses link in toolbar like musabase and cassavabase
ryan-preble Feb 11, 2025
f61fe13
Add correlation analysis to toolbar. Remove requirements for files an…
ryan-preble Feb 11, 2025
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105 changes: 56 additions & 49 deletions lib/SGN/Controller/AJAX/Analysis.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -436,55 +436,62 @@ sub store_data {
my $dir = $c->tempfiles_subdir('/delete_nd_experiment_ids');
my $temp_file_nd_experiment_id = $c->config->{basepath}."/".$c->tempfile( TEMPLATE => 'delete_nd_experiment_ids/fileXXXX');

my $m = CXGN::Analysis::AnalysisCreate->new({
bcs_schema=>$bcs_schema,
people_schema=>$people_schema,
metadata_schema=>$metadata_schema,
phenome_schema=>$phenome_schema,
archive_path=>$c->config->{archive_path},
tempfile_for_deleting_nd_experiment_ids=>$temp_file_nd_experiment_id,
base_path=>$c->config->{basepath},
dbhost=>$c->config->{dbhost},
dbname=>$c->config->{dbname},
dbuser=>$c->config->{dbuser},
dbpass=>$c->config->{dbpass},
analysis_to_save_boolean=>$analysis_to_save_boolean,
analysis_name=>$analysis_name,
analysis_description=>$analysis_description,
analysis_year=>$analysis_year,
analysis_breeding_program_id=>$analysis_breeding_program_id,
analysis_protocol=>$analysis_protocol,
analysis_dataset_id=>$analysis_dataset_id,
analysis_accession_names=>$analysis_accession_names,
analysis_trait_names=>$analysis_trait_names,
analysis_statistical_ontology_term=>$analysis_statistical_ontology_term,
analysis_precomputed_design_optional=>$analysis_precomputed_design_optional,
analysis_result_values=>$analysis_result_values,
analysis_result_values_type=>$analysis_result_values_type,
analysis_result_summary=>$analysis_result_summary,
analysis_result_trait_compose_info_time=>$analysis_result_trait_compose_info,
analysis_model_id=>$analysis_model_id,
analysis_model_name=>$analysis_model_name,
analysis_model_description=>$analysis_model_description,
analysis_model_is_public=>$analysis_model_is_public,
analysis_model_language=>$analysis_model_language,
analysis_model_type=>$analysis_model_type,
analysis_model_properties=>$analysis_model_properties,
analysis_model_application_name=>$analysis_model_application_name,
analysis_model_application_version=>$analysis_model_application_version,
analysis_model_file=>$analysis_model_file,
analysis_model_file_type=>$analysis_model_file_type,
analysis_model_training_data_file=>$analysis_model_training_data_file,
analysis_model_training_data_file_type=>$analysis_model_training_data_file_type,
analysis_model_auxiliary_files=>$analysis_model_auxiliary_files,
allowed_composed_cvs=>\@allowed_composed_cvs,
composable_cvterm_delimiter=>$composable_cvterm_delimiter,
composable_cvterm_format=>$composable_cvterm_format,
user_id=>$user_id,
user_name=>$user_name,
user_role=>$user_role
});
my $saved_analysis_object = $m->store();
my $saved_analysis_object;

eval {
my $m = CXGN::Analysis::AnalysisCreate->new({
bcs_schema=>$bcs_schema,
people_schema=>$people_schema,
metadata_schema=>$metadata_schema,
phenome_schema=>$phenome_schema,
archive_path=>$c->config->{archive_path},
tempfile_for_deleting_nd_experiment_ids=>$temp_file_nd_experiment_id,
base_path=>$c->config->{basepath},
dbhost=>$c->config->{dbhost},
dbname=>$c->config->{dbname},
dbuser=>$c->config->{dbuser},
dbpass=>$c->config->{dbpass},
analysis_to_save_boolean=>$analysis_to_save_boolean,
analysis_name=>$analysis_name,
analysis_description=>$analysis_description,
analysis_year=>$analysis_year,
analysis_breeding_program_id=>$analysis_breeding_program_id,
analysis_protocol=>$analysis_protocol,
analysis_dataset_id=>$analysis_dataset_id,
analysis_accession_names=>$analysis_accession_names,
analysis_trait_names=>$analysis_trait_names,
analysis_statistical_ontology_term=>$analysis_statistical_ontology_term,
analysis_precomputed_design_optional=>$analysis_precomputed_design_optional,
analysis_result_values=>$analysis_result_values,
analysis_result_values_type=>$analysis_result_values_type,
analysis_result_summary=>$analysis_result_summary,
analysis_result_trait_compose_info_time=>$analysis_result_trait_compose_info,
analysis_model_id=>$analysis_model_id,
analysis_model_name=>$analysis_model_name,
analysis_model_description=>$analysis_model_description,
analysis_model_is_public=>$analysis_model_is_public,
analysis_model_language=>$analysis_model_language,
analysis_model_type=>$analysis_model_type,
analysis_model_properties=>$analysis_model_properties,
analysis_model_application_name=>$analysis_model_application_name,
analysis_model_application_version=>$analysis_model_application_version,
analysis_model_file=>$analysis_model_file,
analysis_model_file_type=>$analysis_model_file_type,
analysis_model_training_data_file=>$analysis_model_training_data_file,
analysis_model_training_data_file_type=>$analysis_model_training_data_file_type,
analysis_model_auxiliary_files=>$analysis_model_auxiliary_files,
allowed_composed_cvs=>\@allowed_composed_cvs,
composable_cvterm_delimiter=>$composable_cvterm_delimiter,
composable_cvterm_format=>$composable_cvterm_format,
user_id=>$user_id,
user_name=>$user_name,
user_role=>$user_role
});
$saved_analysis_object = $m->store();
};
if ($@) {
die "An error occurred storing analysis! $@";
}

$c->stash->{rest} = $saved_analysis_object;
}
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46 changes: 23 additions & 23 deletions mason/analyses/upload_analysis_dialogs.mas
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Original file line number Diff line number Diff line change
Expand Up @@ -374,46 +374,46 @@ jQuery(document).ready(function () {
var upload_new_analysis_model_auxiliary_file_3 = jQuery('#upload_new_analysis_model_auxiliary_file_3').val();
var upload_new_analysis_model_auxiliary_file_type_3 = jQuery('#upload_new_analysis_model_auxiliary_file_type_3').val();

if (upload_new_analysis_model_id != '' && upload_new_analysis_model_name != '') {
alert('Please select a model or create a new model, not both!');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name == '') {
alert('Please select a saved model or give a new model name');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_description == '') {
// if (upload_new_analysis_model_id != '' && upload_new_analysis_model_name != '') {
// alert('Please select a model or create a new model, not both!');
// return false;
// }
// if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name == '') {
// alert('Please select a saved model or give a new model name');
// return false;
// }
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_description == '') {
alert('Please give a new model description');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_is_public == '') {
alert('Please give a new model is public');
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_is_public == '') {
alert('Please specify if the new model is public');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_language == '') {
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_language == '') {
alert('Please give a new model language');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_properties_string == '') {
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_properties_string == '') {
alert('Please give a new model properties. At least one key:value!');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_application_name == '') {
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_application_name == '') {
alert('Please give a new model application name');
return false;
}
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_application_version == '') {
if (upload_new_analysis_model_id == '' && upload_new_analysis_model_name !== '' && upload_new_analysis_model_application_version == '') {
alert('Please give a new model application version');
return false;
}
if (upload_new_analysis_model_training_data_file === '') {
alert('Please give a new model training data file (or the main phenotype file you used to do the analysis)');
return false;
}
if (upload_new_analysis_model_training_data_file_type == '') {
alert('Please give a new model training data file type (or the main phenotype file you used to do the analysis)');
return false;
}
// if (upload_new_analysis_model_training_data_file === '') {
// alert('Please give a new model training data file (or the main phenotype file you used to do the analysis)');
// return false;
// }
// if (upload_new_analysis_model_training_data_file_type == '') {
// alert('Please give a new model training data file type (or the main phenotype file you used to do the analysis)');
// return false;
// }
if ( (upload_new_analysis_model_file == '' && upload_new_analysis_model_file_type != '') || (upload_new_analysis_model_file != '' && upload_new_analysis_model_file_type == '') ) {
alert('If you give a new model file, please give a new model file type also');
return false;
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2 changes: 2 additions & 0 deletions mason/site/toolbar/analyze.mas
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@@ -1,13 +1,15 @@
<li class="dropdown"><a class="menu_click_dropdown dropdown-toggle" data-toggle="dropdown">Analyze</a>
<!-- <li class="dropdown"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Genomes<span class="caret"></span></a> -->
<ul class="dropdown-menu">
<li><a href="/analyses">Stored Analyses</a></li>
<li class="dropdown-header">Breeder Tools</li>
<li><a href="/selection/index">Selection Index</a></li>
<!-- li><a href="/analyze/phenotypes">Analyze Phenotypes</a><li -->
<!-- li><a href="/barcode">Barcode Tools</a></li -->
<!--li><a href="/solgs/search">Genomic Selection</a></li -->
<li><a href="/pca/analysis">Population Structure</a></li>
<li><a href="/cluster/analysis">Clustering</a></li>
<li><a href="/correlation/analysis">Correlation</a></li>
<li><a href="/kinship/analysis">Kinship & Inbreeding</a></li>
<li><a href="/tools/stability">Stability AMMI/GGE</a></li>
<li><a href="/tools/heritability">Heritability</a></li>
Expand Down