new (smaller) sam files are available here:
http://igbquickload.org/smokeTestingQuickload/H_sapiens_Dec_2013/Sam
Quickload site address is:
http://igbquickload.org/smokeTestingQuickload

Note:

Error may be due to SAM files not using the correct genome assembly version.
Nowlan noticed it.

I am able to get the SAM files with header load successfully from Local copy and Quickload.
The issue might be with no header files, will talk to Nowlan about this.

Need a first level review for the following branch

https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1425-stream#diff

Some requests:

• Please handle FTP protocol in addition to HTTPS, HTTP and local file.
• Check this line: "String reachable_url = LocalUrlCacher.getReachableUrl(uri.toASCIIString());" If the LocalUrlCacher fails and has to return a null value, does it already open an error dialog? What sort of logging is done when that happens? We need to check that if there is an error, it will be easy to diagnose the problem. We will be asking users to tell us what they see in the Console, so we need to make sure something informative is printed.
• If there is an error, use the logger to report useful diagnostic information to the Console. For example, the log message should report the URI that could not be reached.
• Please change the error message to make it more user-friendly. Proposed new user-friendly text: "The data set you requested could not be loaded. Select Help > Show Console for more information." If possible, "Help > Show Console" should be rendered in bold font.

• Please handle FTP protocol in addition to HTTPS, HTTP and local file.
  • Done
• Check this line: "String reachable_url = LocalUrlCacher.getReachableUrl(uri.toASCIIString());" If the LocalUrlCacher fails and has to return a null value, does it already open an error dialog? What sort of logging is done when that happens? We need to check that if there is an error, it will be easy to diagnose the problem. We will be asking users to tell us what they see in the Console, so we need to make sure something informative is printed.
  • No the method does not have any error dialog, but there is error logger (console) if there is any exception in the method.
  • Added a error logger showing URL and HTTP Status when the URL is not reachable.
• If there is an error, use the logger to report useful diagnostic information to the Console. For example, the log message should report the URI that could not be reached.
  • Done.
• Please change the error message to make it more user-friendly. Proposed new user-friendly text: "The data set you requested could not be loaded. Select Help > Show Console for more information." If possible, "Help > Show Console" should be rendered in bold font.
  • Done.

The following Scenarios needs to be tested for this issue:
(Scenario --> expected behavior)

Reachable valid URL --> Sam File should be loaded.

Reachable valid URL but unauthorized --> Exception in the log saying URL not reachable and HTTP_status code (404)

Invalid / Unreachable URL --> Exception in the log saying URL not reachable and HTTP_status code ( 401 0r 403)

Reachable URL but invalid File --> Exception in the log saying invalid file format.

For the positive scenario, with a valid reachable URL on the quickload it works. On the console it prints:
org.lorainelab.igb.bam.SAM initTheSeqs
SEVERE: Sam file must be sorted by coordinate.

For a reachable but invalid File, it does not load anything. On the console it prints:
org.lorainelab.igb.bam.XAM initTheSeqs
WARNING: Couldn't find sequences in file

For a reachable valid URL but unauthorized this error message is shown:
Format not recognized for file: https://drive.google.com/open?id=14KYlPVkMnvUuSnSAwDbwe400hqC3bKFf

Please have a look.

Srishti Tiwari

I think that is the expected behavior.
Because when you go to the URL google redirects you to a login page which is an unrecognized format for IGB.

Thank you for confirming this. Marking this as ready for pull request

Merged to master branch.
Tagged for release with 9.1.0