Page History

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• • Logic

    • The field values are generated from quickLoadUrl + "/" + genome_name + "/annots.xml".
    • Consider only <file> tags where reference="none".
    • This URL returns the following fields: track, bigDataUrl, shortLabel, longLabel, type, and visibility.

1. 1. 1. 1. track – The first Track should be unique single word in the title attribute.uscs. It is title with spaces replaced with "_"
         2. bigDataUrl – The name field of the <file> tag if it is already a URL. Otherwise, it is constructed as quickLoadUrl + "/" + genome_name + "/" + name.
         3. shortLabel – The last word of the title attribute.
         4. longLabel – The description field of the <file> tag.
         5. type – Determined based on the file extension of bigDataUrl.
            1. genomic_extensions = {
                           'bigWig': ['bw', 'bigwig'],
                           'bigBed 12': ['bb', 'bigbed'],
                           'bigGenePred': ['bb'],
                           'bigChain': ['bigchain'],
                           'bigNarrowPeak': ['bb'],
                           'bigBarChart': ['bb'],
                           'bigInteract': ['bb'],
                           'bigPsl': ['bb'],
                           'bigMaf': ['bb'],
                           'hic': ['hic'],
                           'bam': ['bam', 'cram'],
                           'HAL': ['hal'],
                           'vcfTabix': ['vcf', 'vcf.gz']
                       }
            2. Get the extension of bigDataUrl.
            3. If the extension is present in genomic_extensions and equals "bb", check whether the word before .bb matches a key in genomic_extensions. If yes, return that key (e.g., bigGenePred).
            4. Example: GSE63189_Catalog_of_lncRNAs_in_MCF-7cells.bigGenePred.bb → bigGenePred
            5. Otherwise, if the extension matches a value in genomic_extensions, return the corresponding key.
            6. If the extension is just .bb, return bigBed 12.
         6. visibility – Always set to "dense".

• • • SuperTrack
      • If a title has "/" in it, it means it has subfolders. Creating subfolders is not possible in ucsc but we can create top level folder. To do that we need to use superTrack. 
        1. track – It is first word before "/" in title with " " replaced with "_"
        2. superTrack on show
        3. shortLabel – It is first word before "/" in title.
        4. longLabel – The description field of the <file> tag.
           1. In side this superTrack we create subtracks.
              1. track – It is similar to normal track name.
              2. bigDataUrl – It is similar to normal track bigDataUrl.
                 
              3. shortLabel – It is the title name excluding the first word.
              4. longLabel – It is similar to normal track longLabel.
              5. type – It is similar to normal track type.
              6. visibility – Always set to "hide".
              7. parent – It is the superTrack track name.

Head Request

• • Logic

    • Returns headers and status_code. The status_code is determined by verifying all GET calls.

  • Purpose

    • UCSC makes a HEAD request to validate the URL when it is added to Connected Hubs.
      • To test:
        1. Go to UCSC Track Data Hubs → Connected Hubs tab.
        2. When the URL is pasted, UCSC sends a HEAD request to verify the status code.

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