Data Provider

General Function Checklist

•  All Default DataProviders appear in the DataProviderManagementGui table

• • Observation:  The table lists several Quickload sites. (They may be different from those shown below.) If any are shown with a red background, that means that there is a problem with the site - IGB can't reach it. This is a bug and should be reported.

• Confirm that clicking in a ? icon in the rightmost 'information' column of the Data Sources window above opens a window with fields and values similar to the example below:
  

• Confirm the following species / genome versions are available 
  • Arabidopsis thaliana / A_thaliana_Jun2009
    • Observation: Available Data Tree appears with several sites. (They may be different from those shown below.)
      • 
  • Homo Sapiens/ H_sapiens_Dec_2013
    • Available data should list some data sets. (They may vary from those shown below.)
      
      • 
    • Important: Confirm that for the human genome assembly, 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. Important: Load these by selecting the checkboxes in the Data Access folder hierarchy, not from URLs displayed in a Web browser. To get examples of each file type, go the the Arabidopsis thaliana June 2009 genome.  Under RNA-Seq there are several folders labeled by experiment code and with a human-friendly name. Within those folders, there are folders labeled Reads, Graph, and Junctions. 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 click Load Data button at the top right of the IGB window. Click 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. Note: The UCSC DAS data source is not activated by default - you need to activate it in the Data Sources tab of the Preference window. Once this data source is active, it 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
      • http://igbquickload.org/secureQuickloadTestSites/secureSiteTest
        • username/password 
          • guest/guest
      • http://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 prompted for your password again on restarting IGB