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update biodb-to-json test for test data changes, make it a little les…
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…s brittle
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@rbuels
rbuels committed Aug 1, 2012
1 parent 1ce7297 commit bd0296f
Showing 1 changed file with 2 additions and 229 deletions.
231 changes: 2 additions & 229 deletions tests/perl_tests/biodb-to-json.pl.t
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Expand Up @@ -48,235 +48,8 @@ use FileSlurping 'slurp';
) or diag explain $genes_trackdata->{intervals}{nclist}[0];

my $tracklist = $read_json->('trackList.json');
is_deeply( $tracklist,
{
'formatVersion' => 1,
'tracks' => [
{
'chunkSize' => 20000,
'urlTemplate' => 'seq/{refseq}/',
'key' => 'DNA',
'label' => 'DNA',
'type' => 'SequenceTrack'
},
{
'autocomplete' => 'all',
style => { 'className' => 'feature2' },
'compress' => 0,
'feature' => [
'remark'
],
'track' => 'ExampleFeatures',
'urlTemplate' => 'tracks/ExampleFeatures/{refseq}/trackData.json',
'key' => 'Example Features',
'label' => 'ExampleFeatures',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
style => { 'className' => 'feature2' },
'compress' => 0,
'feature' => [
'protein_coding_primary_transcript',
'polypeptide'
],
'track' => 'NameTest',
'urlTemplate' => 'tracks/NameTest/{refseq}/trackData.json',
'key' => 'Name test track',
'label' => 'NameTest',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
'compress' => 0,
'feature' => [
'SNP'
],
'style' => {
'className' => 'triangle hgred'
},
'track' => 'snps',
'urlTemplate' => 'tracks/snps/{refseq}/trackData.json',
'key' => 'Test SNPs',
'label' => 'snps',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
style => {'className' => 'feature3'},
'compress' => 0,
'description' => 1,
'feature' => [
'polypeptide_domain'
],
'key' => 'Example motifs',
'track' => 'Motifs',
'urlTemplate' => 'tracks/Motifs/{refseq}/trackData.json',
'key' => 'Example motifs',
'label' => 'Motifs',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
'category' => 'Alignments',
style => {
'className' => 'feature4',
},
'compress' => 0,
'feature' => [
'match'
],
'track' => 'Alignments',
'urlTemplate' => 'tracks/Alignments/{refseq}/trackData.json',
'key' => 'Example alignments',
'label' => 'Alignments',
'type' => 'FeatureTrack',

'menuTemplate' => [
{
'children' => [
{
'children' => [
{
'iconClass' => 'dijitIconBookmark',
'label' => 'Query trin for {name}',
'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}'
},
{
'iconClass' => 'dijitIconSearch',
'label' => 'Query example.com for {name}',
'url' => 'http://example.com/{name}-{start}-{end}'
}
],
'label' => 'Check gene on databases'
},
{
'label' => '2nd child of demo'
},
{
'label' => '3rd child: this is a track'
}
],
'label' => 'Item with submenu'
},
{
'dialog' => 'true',
'dialogTitle' => 'The magnificent example.com',
'iconClass' => 'dijitIconDatabase',
'label' => 'Open example.com in an iframe popup',
'url' => 'http://www.example.com?featurename={name}'
},
{
'dialog' => 'snippet',
'iconClass' => 'dijitIconDatabase',
'label' => 'Open a popup with a snippet of HTML',
'url' => 'sample_data/test_snippet.html'
}
],

},
{
'autocomplete' => 'all',
style => {'className' => 'feature5'},
'compress' => 0,
'feature' => [
'gene'
],
'track' => 'Genes',
'urlTemplate' => 'tracks/Genes/{refseq}/trackData.json',
'key' => 'Protein-coding genes',
'label' => 'Genes',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
'category' => 'Genes',
style => { 'className' => 'dblhelix' },
'compress' => 0,
'feature' => [
'mRNA'
],
'track' => 'ReadingFrame',
'urlTemplate' => 'tracks/ReadingFrame/{refseq}/trackData.json',
'key' => 'Frame usage',
'label' => 'ReadingFrame',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
'category' => 'Genes',
style => {
'className' => 'cds',
'linkTemplate' => 'http://example.com/{name}-{start}-{end}'
},
'compress' => 0,
'feature' => [
'CDS:predicted',
'mRNA:exonerate',
'mRNA:predicted',
],
'phase' => 1,
'track' => 'CDS',
'urlTemplate' => 'tracks/CDS/{refseq}/trackData.json',
'key' => 'Predicted genes',
'label' => 'CDS',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
'category' => 'Genes',
'compress' => 0,
'description' => 1,
'feature' => [
'mRNA:exonerate'
],
'key' => 'Exonerate predictions',
'style' => {
'className' => 'transcript',
'arrowheadClass' => 'transcript-arrowhead',
'subfeatureClasses' => {
'CDS' => 'transcript-CDS',
'UTR' => 'transcript-UTR'
},
},
'subfeatures' => 'true',
'track' => 'Transcript',
'urlTemplate' => 'tracks/Transcript/{refseq}/trackData.json',
'key' => 'Exonerate predictions',
'label' => 'Transcript',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
style => {'className' => 'exon'},
'compress' => 0,
'description' => 1,
'feature' => [
'BAC'
],
'track' => 'Clones',
'urlTemplate' => 'tracks/Clones/{refseq}/trackData.json',
'key' => 'Fingerprinted BACs',
'label' => 'Clones',
'type' => 'FeatureTrack'
},
{
'autocomplete' => 'all',
style => {'className' => 'est'},
'compress' => 0,
'feature' => [
'EST_match:est'
],
'track' => 'EST',
'urlTemplate' => 'tracks/EST/{refseq}/trackData.json',
'key' => 'ESTs',
'label' => 'EST',
'type' => 'FeatureTrack'
}
]
},
'made right trackList.json',
) or diag explain $tracklist;
is( scalar( @{$tracklist->{tracks}} ), 12 );
is( $tracklist->{tracks}[8]{style}{linkTemplate}, 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}' );

my $names_output = $read_json->(qw( tracks Transcript ctgA names.json ));
is_deeply( $names_output,
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