Code for checking if a sample is external or not is incorrect

[Nicklas Nordborg]

There are various places in the codebase of Reggie that checks if an item is a SCAN-B item or an external item. However, it seems that in some of the places this check is not correct. For example, in reggie-2.js the isExternal() method requries that names start with External.r for all external items. It seems like this check is mostly used to enable/disable flagging of RNA/DNA items.

[Nicklas Nordborg]

In 5552:

References #1165: Code for checking if a sample is external or not is incorrect

Fixed the check in reggie-2.js. Some wizards needed an update to handle external samples in a backwards compatible way. For example, starting the next step in secondary analysis should be enabled, but flagging items should not.

[Nicklas Nordborg]

In 5553:

Fixes #1165: Code for checking if a sample is external or not is incorrect

The Rna.isSpecialRna() method has been replaced with Reggie.isExternalItem() (which is just a new names for Reggie.useExternalProjectArchive()). The major change is that the old method only checked for item names starting with External or Stratagene while the new method check for names starting with digits. Servlets and other code has been updated and the only real change should be that external RNA/DNA are not flagged.