remove validated field from crispr_es_qc_wells tables

htgt · Dec 3, 2014 · 4da287d · 4da287d
1 parent 0aa4789
commit 4da287d
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Showing 8 changed files with 4 additions and 34 deletions.
diff --git a/ddl/versions/78/audit-up.sql b/ddl/versions/78/audit-up.sql
@@ -1,3 +1,2 @@
-ALTER TABLE audit.crispr_es_qc_wells ADD COLUMN validated BOOLEAN;
 ALTER TABLE audit.crispr_es_qc_wells ADD COLUMN variant_size INT;
 ALTER TABLE audit.crispr_es_qc_runs ADD COLUMN validated BOOLEAN;
diff --git a/ddl/versions/78/up.sql b/ddl/versions/78/up.sql
@@ -1,3 +1,2 @@
-ALTER TABLE crispr_es_qc_wells ADD COLUMN validated BOOLEAN DEFAULT FALSE;
 ALTER TABLE crispr_es_qc_wells ADD COLUMN variant_size INT;
 ALTER TABLE crispr_es_qc_runs ADD COLUMN validated BOOLEAN DEFAULT FALSE;
diff --git a/lib/LIMS2/Model/Plugin/CrisprEsQc.pm b/lib/LIMS2/Model/Plugin/CrisprEsQc.pm
@@ -182,11 +182,7 @@ sub validate_crispr_es_qc_run {
     my $crispr_es_qc_run = $self->retrieve_crispr_es_qc_run( $params );
     $crispr_es_qc_run->update( { validated => 1 } );
 
-    for my $well ( $crispr_es_qc_run->crispr_es_qc_wells->all ) {
-        $well->update( { validated => 1 } );
-    }
-    $self->log->info(
-        'Updated crispr es qc run and all its wells to validated ' . $crispr_es_qc_run->id );
+    $self->log->info( 'Validated crispr es qc run ' . $crispr_es_qc_run->id );
 
     return;
 }
@@ -200,7 +196,6 @@ sub pspec_update_crispr_es_qc_well {
             rename   => 'crispr_damage_type_id'
             },
         variant_size => { validate => 'integer', optional => 1 },
-        validated    => { validate => 'boolean_string', optional => 1 },
         accepted     => { validate => 'boolean_string', optional => 1 },
         MISSING_OPTIONAL_VALID => 1,
     };

diff --git a/lib/LIMS2/Model/Schema/Result/CrisprEsQcWell.pm b/lib/LIMS2/Model/Schema/Result/CrisprEsQcWell.pm
@@ -111,12 +111,6 @@ __PACKAGE__->table("crispr_es_qc_wells");
   is_foreign_key: 1
   is_nullable: 1
 
-=head2 validated
-
-  data_type: 'boolean'
-  default_value: false
-  is_nullable: 1
-
 =head2 variant_size
 
   data_type: 'integer'
@@ -156,8 +150,6 @@ __PACKAGE__->add_columns(
   { data_type => "text", is_nullable => 1 },
   "crispr_damage_type_id",
   { data_type => "text", is_foreign_key => 1, is_nullable => 1 },
-  "validated",
-  { data_type => "boolean", default_value => \"false", is_nullable => 1 },
   "variant_size",
   { data_type => "integer", is_nullable => 1 },
 );
@@ -247,8 +239,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-11-27 08:52:51
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rL/y7FDvyVvB/xU1ZFBn7g
+# Created by DBIx::Class::Schema::Loader v0.07022 @ 2014-12-03 11:52:40
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HLxWkhqfpzrHco4xOT7tdQ
 
 use JSON;
 use List::Util qw ( min max );
@@ -383,7 +375,6 @@ sub format_well_data {
         damage_type             => $self->crispr_damage_type_id,
         vep_output              => $json->{vep_output},
         variant_size            => $self->variant_size,
-        validated               => $self->validated,
     };
 }
 

diff --git a/root/lib/crispr_qc_view.tt b/root/lib/crispr_qc_view.tt
@@ -68,15 +68,6 @@
    </div>
 </td>
 
-
-<td>
-  <div class="control-group">
-    <div class="controls">
-     <input type="checkbox" name="validated_[% row.well_id %]" class="update_crispr_es_qc_well validate_well" data-crispr_well_id="[% row.es_qc_well_id %]" data-crispr_data_type="validated" [% row.validated ? "checked='checked'" : "" %] />
-    </div>
-  </div>
-</td>
-
 <td>
   [% IF row.has_vcf_file %]
     <a href="[% c.uri_for( '/user/crispr_qc_well', row.es_qc_well_id, 'vcf_file' ) %]" target="_blank" >vcf_file</a>

diff --git a/root/site/user/crisprqc/crispr_es_qc_run.tt b/root/site/user/crisprqc/crispr_es_qc_run.tt
@@ -31,7 +31,6 @@ $(document).ready(function() {
         var element = $(this);
         element.removeClass('btn-primary').addClass('btn-warning');
         element.text('... validating');
-        var success = 0;
 
         $.ajax({
             type: "POST",
@@ -44,9 +43,6 @@ $(document).ready(function() {
                 element.delay(500).queue(function(){
                     $(this).removeClass('btn-warning').addClass('btn-success').addClass('disabled').dequeue();
                     element.text('Validated');
-                    $(".validate_well").each( function() {
-                        this.checked = true;
-                    });
                 });
             },
             error: function(data) {
@@ -118,7 +114,6 @@ $(document).ready(function() {
             <th>Accept</th>
             <th>Damage Type</th>
             <th>Variant Size</th>
-            <th>Validated</th>
             <th>Variant Files</th>
             <th>Protein Sequences</th>
             <th>Reads</th>

diff --git a/root/site/user/crisprqc/gene_crispr_es_qc.tt b/root/site/user/crisprqc/gene_crispr_es_qc.tt
@@ -46,7 +46,6 @@ $(document).ready(function() {
             <th>Alignment</th>
             <th>Damage Type</th>
             <th>Variant Size</th>
-            <th>Validated</th>
             <th>Variant Files</th>
             <th>Protein Sequences</th>
             <th>Reads</th>

diff --git a/root/static/test/fixtures/reference_data/CrisprDamageType.csv b/root/static/test/fixtures/reference_data/CrisprDamageType.csv
@@ -3,3 +3,4 @@
 "frameshift","Damage that causes a frameshift mutation"
 "in-frame","Damage that does not cause a frameshift mutation"
 "mosaic","Multiple types of damage"
+"no-call","No automatic damage type call"