Data Provider

General Function Checklist

•  All Default DataProviders appear in the DataProviderManagementGui table

• • Observation:  The table matches the image below
    • 

• Confirm the following species / genome versions are available 
  • Arabidopsis thaliana / A_thaliana_Jun2009
    • Observation: Available Data Tree appears with the following sites (IgbQuickload, Pollen, and Cytokinin)
      • 
  • Homo Sapiens/ H_sapiens_Dec_2013
    • Available data sites include UCSC and IgbQuickload
      
      • 
    • Confirm the Cytobands track is visible
      • 

•  Load a bed file, a bam file, a bedgraph file, and some sequence data to ensure basic file parsing from the data providers is working as expected. (Load these directly from the Data Access Tree, not from the urls). For an example of each file type, go the the Arabidopsis thaliana genome.  Under RNA-Seq / Pollen there are three folders.  The Reads folder has bam files.  The Graph folder has bedgraph files.  The Junctions folder has bed files.  Select one file from each folder, zoom in to show only several thousand bases, and Load Data.  Most RNA-Seq experiments have a similar structure, are several examples in RNA-Seq and IGB-Quickload.  Use the "Load Sequence" button to load sequence and zoom in to make sure you can see individual letter (A, C, T, G) under the coordinate axis. 
  • Bed File
  • Bam File
  • Bedgraph File
  • Load Sequence

• Load a few tracks from the UCSC DAS data source (should be visible on Human/Mouse species)

• Adding/Removing DataProviders
  • Add a quickload data provider and confirm it is working as expected
    • Go to the Arabidopsis thaliana/A_thaliana_Jun_2009 genome version
    • Navigate to the File->Preferences->Data Sources tab
    • Click the "Add..." button
    • Enter in a valid quickload url (e.g. http://www.igbquickload.org/abiotic)
    • Enter a name for this quickload site and click the "Submit" button
    • Observations:
      • The quickload site shows up in the "Available Data" tree
      • The data sets listed in the tree can be loaded 
    • Confirm restarting IGB does not cause the newly added site to be forgotten
  • Add a few "Secured" quickload sites and confirm they are working as expected
    • Following the same steps listed above in the previous step, add the following two sites
      • igbquickload.org/secureQuickloadTestSites/secureSiteTest
        • username/password 
          • guest/guest
      • igbquickload.org/secureQuickloadTestSites/secureSiteTest2
        • username/password
          • guest2/guest2
    • Navigate to the Arabidopsis thaliana Jun_2009 genome version
      • Confirm the two sites are listed the "Available Data" tree and data can be loaded from each site
    • Confirm you were not prompted for a password for any site more than a single time per session
    • Confirm restarting IGB does not cause the newly added sites to be forgotten
    • Confirm that if you checked the "Save Password" option you are not promted for your password again on restarting IGB