Registry:Bug reports

Revision as of 23:44, 9 August 2011 by J3harvey (Talk | contribs) (→‎API problem: some XML files are not well-formed)

BARCODES NOT BEING REPRESENTED!!

The coding sequences for many of the original BioBrick parts had a ~23bp "barcode" sequence following the TAATAA stop codons. The Registry database is no longer showing these barcade sequences. As a result, folks are now finding these sequences for the first time when they locally sequence the parts, and then reporting their "discoveries" on the part experience pages as random sequences. Please see part E1010 for one example. IIRC there are a few dozen early CDSs that have these barcodes postpended, including many of the core (i.e., highly used CDSs). Drew 14:39, 1 November 2010 (UTC)

OTHER

Construction intermediate parts not updated when intermediate parts change

I created a construction intermediate part BBa_S03941. Then I went back to edit an intermediate part BBa_J70010 because there was an extra "t" at the end. When I went back to the construction intermediate part, it didn't update to include the change to BBa_J70010 and I don't know how to update BBa_S03941 to include this change.

Adding local locations

I don't see a way to add locations in the physical DNA page. Is there a way to do this?

The documentation says to enter a part to search for in the box in the upper left but the box is in the upper RIGHT. Once I find a part, I don't get the tools across the top which link to the Physical DNA, etc. Basically, the system is not working at all as documented or I am missing something. I'm using WinXP with IE7. We just tested the page using Safari on a Mac and it looks fine. It would be nice if IE7 was also supported.

Deleting Parts

Deleting parts doesn't seem to work. I've tried from the Hard Information page, setting the Status to Deleted, but there is no effect. In fact, all Status changes seem to be ignored. I've also tried by editing the Team Parts table, eg at https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2007&group=iGEM2007_Alberta, same behavior. --Dridgway 22:12, 1 March 2009 (UTC)


The part we are using, BBa_E2050, seems to have had its page deleted! Now when I search for it I can't find it. Have some parts been deleted? -- A few parts have been deleted because they were just iGEM Workshop parts. None of them would have been E2050. -- - Randy

API problem: some XML files are not well-formed

A number of [http://www.gibthon.org/ software tools] now access the registry by grabbing BioBrick data in XML format using an URL such as https://parts.igem.org/xml/part.BBa_B0034. Certain characters cannot be included in a legal XML file as detailed [http://www.w3.org/TR/2004/REC-xml-20040204/#charsets here]. Certain parts in the registry unfortunately contain illegal characters in their description or other data and so the XML files are unavailable. For example this part was designed by "Andr� Green II" (containing an illegal character) and this is the result of trying to obtain the XML data for the part.

Possible solutions include:

  • Remove all offending characters from the data in the registry
  • Remove offending characters as XML data is generated

-- j3harvey, 10th August 2011