store pca scores results

db/00187/AddPrcompCvterm.pm

@@ -0,0 +1,84 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+ AddPHGGenotypingCvterms
+
+=head1 SYNOPSIS
+
+mx-run AddPHGGenotypingCvterms [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 pcr_marker_details, pcr_marker_genotyping and pcr_marker_protocol cvterms
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Isaak Y Tecle <iyt2@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 AddPrcompCvterm;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch adds the 'prcomp' protocol_type cvterm.
+
+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 = {
+        'protocol_type' => [
+            'prcomp',
+        ]
+    };
+
+	foreach my $t (keys %$terms){
+		foreach (@{$terms->{$t}}){
+			$schema->resultset("Cv::Cvterm")->create_with({
+				name => $_,
+				cv => $t
+			});
+		}
+	}
+
+    print "You're done!\n";
+}
+
+
+####
+1; #
+####

js/source/legacy/solGS/analysisSave.js

@@ -1,39 +1,49 @@
 /*
- *Saves solgs modeling output
+ *Saves solGS modeling and other analysis output
  * Isaak Y Tecle <iyt2@cornell.edu>
  *
  */
 
 var solGS = solGS || function solGS() {};
 
 solGS.save = {
-  checkStoredAnalysis: function () {
-    var args = this.saveGebvsArgs();
-    var checkArgs = JSON.stringify(args);
+  checkStoredAnalysis: function (analysisArgs) {
+    analysisArgs = JSON.stringify(analysisArgs);
     var stored = jQuery.ajax({
       dataType: "json",
       type: "POST",
-      data: {'arguments': checkArgs},
+      data: {'arguments': analysisArgs},
       url: "/solgs/check/stored/analysis/",
     });
 
     return stored;
   },
 
-  getResultDetails: function () {
-    var args = this.saveGebvsArgs();
-    var resultArgs = JSON.stringify(args);
+  getGebvsResultDetails: function (analysisArgs) {
+    analysisArgs = JSON.stringify(analysisArgs);
     var details = jQuery.ajax({
       dataType: "json",
       type: "POST",
-      data: {'arguments': resultArgs},
-      url: "/solgs/analysis/result/details",
+      data: {'arguments': analysisArgs},
+      url: "/solgs/gebvs/result/details",
     });
 
     return details;
   },
 
-  saveGebvs: function (args) {
+  getPcaResultDetails: function (analysisArgs) {
+    analysisArgs = JSON.stringify(analysisArgs);
+    var details = jQuery.ajax({
+      dataType: "json",
+      type: "POST",
+      data: {'arguments': analysisArgs},
+      url: "/solgs/pca/result/details",
+    });
+
+    return details;
+  },
+
+  storeAnalysisResults: function (args) {
     var save = jQuery.ajax({
       dataType: "json",
       type: "POST",
@@ -44,6 +54,14 @@ solGS.save = {
     return save;
   },
 
+  checkUserStatus: function () {
+    return jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      url: "/solgs/check/user/login/",
+    });
+  },
+
   saveGebvsArgs: function () {
 
     var analysisArgs = solGS.getSelectionPopArgs();
@@ -52,80 +70,13 @@ solGS.save = {
 
     return analysisArgs;
   },
-
+  
   analysisResultType: function () {
     return jQuery('#analysis_type').val();
   },
-
-  checkUserStatus: function () {
-    return jQuery.ajax({
-      type: "POST",
-      dataType: "json",
-      url: "/solgs/check/user/login/",
-    });
-  },
+
 };
 
-jQuery(document).ready(function () {
-  solGS.save.checkStoredAnalysis().done(function (res) {
-    if (res.analysis_id) {
-      jQuery("#save_gebvs").hide();
-      var link = '<a href="/analyses/' + res.analysis_id + '">View stored GEBVs</a>';
-      jQuery("#gebvs_output").append(link);
-      }
-  });
-
-  jQuery("#save_gebvs").click(function () {
-    jQuery("#gebvs_output .multi-spinner-container").show();
-    jQuery("#gebvs_save_message")
-      .html("Please wait...saving the GEBVs may take a few minutes.")
-      .show();
-    jQuery("#save_gebvs").hide();
 
-    solGS.save.checkUserStatus().done(function (res) {
-      if (!res.loggedin) {
-        solGS.submitJob.loginAlert();
-      } else {
-      }
-    });
-
-    solGS.save.checkUserStatus().fail(function () {
-      solGS.alertMessage("Error occured checking for user status");
-    });
-
-    solGS.save.getResultDetails().done(function (res) {
-
-      if (res.error) {
-        jQuery("#gebvs_output .multi-spinner-container").hide();
-        jQuery("#gebvs_save_message")
-          .html(res.error + ". The logged info may not exist for the result.")
-          .show()
-          .fadeOut(50000);
 
-        jQuery("#save_gebvs").show();
-      } else {
-        var save = solGS.save.saveGebvs(res.analysis_details);
 
-        save.done(function (res) {
-          jQuery("#gebvs_output .multi-spinner-container").hide();
-          if (res.error) {
-            jQuery("#gebvs_save_message").html(res.error).show().fadeOut(50000);
-
-            jQuery("#save_gebvs").show();
-          } else {
-            jQuery("#gebvs_save_message").hide();
-
-            var link = '<a href="/analyses/' + res.analysis_id + '">View stored GEBVs</a>';
-            jQuery("#gebvs_output").append(link);
-          }
-        });
-
-        save.fail(function (res) {
-          jQuery("#gebvs_output .multi-spinner-container").hide();
-          jQuery("#save_gebvs").show();
-          jQuery("#gebvs_save_message").html(res.error).show().fadeOut(50000);
-        });
-      }
-    });
-  });
-});

js/source/legacy/solGS/anova.js

@@ -176,7 +176,7 @@ jQuery(document).ready(function () {
     var traitId = jQuery("#anova_selected_trait_id").val();
     if (traitId) {
       jQuery(runDiv).hide();
-      solGS.anova.showMessage("Please wait...Querying the database for trait data...");
+      solGS.anova.showMessage("Please wait...querying the database for the trait data...");
       jQuery(`${canvas} .multi-spinner-container`).show();
 
       solGS.anova.queryPhenoData(traitId).done(function (queryRes) {
@@ -187,7 +187,7 @@ jQuery(document).ready(function () {
         } else {
           var traitsAbbrs = queryRes.traits_abbrs;
           traitsAbbrs = JSON.parse(traitsAbbrs);
-          solGS.anova.showMessage("Validated trait data...Now running ANOVA...");
+          solGS.anova.showMessage("Validated trait data...now running ANOVA...");
 
           solGS.anova
             .runAnovaAnalysis(traitsAbbrs)

js/source/legacy/solGS/cluster.js

@@ -1378,7 +1378,7 @@ jQuery(document).ready(function () {
 
     solGS.cluster.displayClusterPopsTable(tableId, clusterPopsRows)
 
-    jQuery("#add_new_pops").show();
+    jQuery("#create_new_list_dataset").show();
 
   }
 });

js/source/legacy/solGS/correlation.js

@@ -530,7 +530,7 @@ jQuery(document).ready(function () {
 
     solGS.correlation.displayCorrPopsTable(tableId, corrPopsRows);
 
-    jQuery("#add_new_pops").show();
+    jQuery("#create_new_list_dataset").show();
 
   }
 });

js/source/legacy/solGS/gebvsSave.js

@@ -0,0 +1,65 @@
+jQuery(document).ready(function () {
+    var analysisArgs = solGS.save.saveGebvsArgs();
+      solGS.save.checkStoredAnalysis(analysisArgs).done(function (res) {
+      if (res.analysis_id) {
+        jQuery("#save_gebvs").hide();
+        var link = '<a href="/analyses/' + res.analysis_id + '">View stored GEBVs</a>';
+        jQuery("#gebvs_output").append(link);
+        }
+    });
+
+    jQuery("#save_gebvs").click(function () {
+      jQuery("#gebvs_output .multi-spinner-container").show();
+      jQuery("#gebvs_save_message")
+        .html("Please wait...saving the GEBVs may take a few minutes.")
+        .show();
+      jQuery("#save_gebvs").hide();
+
+      solGS.save.checkUserStatus().done(function (res) {
+        if (!res.loggedin) {
+          solGS.submitJob.loginAlert();
+        } else {
+        }
+      });
+
+      solGS.save.checkUserStatus().fail(function () {
+        solGS.alertMessage("Error occured checking for user status");
+      });
+
+      solGS.save.getGebvsResultDetails(analysisArgs).done(function (res) {
+
+        if (res.error) {
+          jQuery("#gebvs_output .multi-spinner-container").hide();
+          jQuery("#gebvs_save_message")
+            .html(res.error + ". The logged info may not exist for the result.")
+            .show()
+            .fadeOut(50000);
+
+          jQuery("#save_gebvs").show();
+        } else {
+          var save = solGS.save.storeAnalysisResults(res.analysis_details);
+
+          save.done(function (res) {
+            jQuery("#gebvs_output .multi-spinner-container").hide();
+            if (res.error) {
+              jQuery("#gebvs_save_message").html(res.error).show().fadeOut(50000);
+
+              jQuery("#save_gebvs").show();
+            } else {
+              jQuery("#gebvs_save_message").hide();
+
+              var link = '<a href="/analyses/' + res.analysis_id + '">View stored GEBVs</a>';
+              jQuery("#gebvs_output").append(link);
+            }
+          });
+
+          save.fail(function (res) {
+            jQuery("#gebvs_output .multi-spinner-container").hide();
+            jQuery("#save_gebvs").show();
+            jQuery("#gebvs_save_message").html(res.error).show().fadeOut(50000);
+          });
+        }
+      });
+    });
+  });
+

js/source/legacy/solGS/kinship.js

@@ -574,6 +574,6 @@ jQuery(document).ready(function () {
     var kinshipPopsRows = solGS.kinship.getKinshipPopsRows(kinshipPops);
 
     solGS.kinship.displayKinshipPopsTable(tableId, kinshipPopsRows);
-    jQuery("#add_new_pops").show();
+    jQuery("#create_new_list_dataset").show();
   }
 });

js/source/legacy/solGS/listTypeSelectionPopulation.js

@@ -358,6 +358,6 @@ jQuery(document).ready(function () {
 
   jQuery("#lists_datasets_message").hide();
   jQuery("#lists_datasets_progress .multi-spinner-container").hide();
-  jQuery("#add_new_pops").show();
+  jQuery("#create_new_list_dataset").show();
 
 });

js/source/legacy/solGS/listTypeTrainingPopulation.js

@@ -287,6 +287,6 @@ jQuery(document).ready(function () {
 
   jQuery("#lists_datasets_message").hide();
   jQuery("#lists_datasets_progress .multi-spinner-container").hide();
-  jQuery("#add_new_pops").show();
+  jQuery("#create_new_list_dataset").show();
 
 });