Difference between revisions of "Registry:Bug reports"

(→‎BARCODES NOT BEING REPRESENTED!!)
 
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===Wiki Errors===
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One this page http://partsregistry.org/Add_a_Part_to_the_Registry and this page http://partsregistry.org/Main_Page the menu bar does not appear. Therefore, we cannot log on using the pages. We have to go to another page and then back to Add a Part page.
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Malcolm Campbell, Davidson College, Sept., 2017
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===Slight problems with the new Parts Registry ===
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(1) For our BioBricks (for example https://parts.igem.org/Part:BBa_K1159014) the automatically generated group is  GEM08_TUDelft which is definitely not correct. We would be glad if this could be changed to iGEM13_TU-Munich.<br>
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(2) When we tried to edit the sequence "edit sequence and features" of this BioBrick, the edit button for the sequence was not a link and made impossible to enter sequence information. This problem only occured when using Firefox but not when using Opera.<br>
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(3) We could not find a edit button on the main page that would allow us to edit the text on the main page of this BioBrick.<br>
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[[User:TU_Munich|TU_Munich]] 13:58, 26 June 2013
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(A)We have the same problem with our BioBricks, which are put into the group "Group: iGEM08_Newcastle_University" (see BBa_K1045000 as an example), although it should be Göttingen.
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(B)As you can see, I can only edit this post, and not the page in order to add a new bug report.
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- Team Göttingen 11:11, 25 June 2013
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===XML Data incorrect===
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The XML data that can be retrieved from the front page does not show consistency. For example the sub parts, 940992 with part_id 4901 and subpart 2006301 with part_id 14010 do not have a parent in the parts table. When working with foreign keys ±6000 entry's cannot be inserted as the parent part_id is not present. Are there other sources available for consistent retrieval?
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[[User:JJkoehorst|JJkoehorst]] 15:32, 5 May 2012
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===BARCODES NOT BEING REPRESENTED!!===
 
===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).  [[User:Drew|Drew]] 14:39, 1 November 2010 (UTC)
 
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).  [[User:Drew|Drew]] 14:39, 1 November 2010 (UTC)
  
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===OTHER===
 
===OTHER===
 
Construction intermediate parts not updated when intermediate parts change  
 
Construction intermediate parts not updated when intermediate parts change  
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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.
 
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.
  
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Adding local locations
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Also I noticed if features are added they are totally misplaced if font size has been changed. I have to change font size of the whole page so I can click the save button on the sequence window. Please trouble shoot the registry its super hard to use...
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===Adding local locations===
  
 
I don't see a way to add locations in the physical DNA page.  Is there a way to do this?
 
I don't see a way to add locations in the physical DNA page.  Is there a way to do this?
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===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. --[[User:Dridgway|Dridgway]] 22:12, 1 March 2009 (UTC)
 
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. --[[User:Dridgway|Dridgway]] 22:12, 1 March 2009 (UTC)
  
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-- A few parts have been deleted because they were just iGEM Workshop parts. None of them would have been E2050.
 
-- A few parts have been deleted because they were just iGEM Workshop parts. None of them would have been E2050.
 
-- - Randy
 
-- - Randy
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Deleting parts don't seem to work yet . I tried to delete parts BBa_K1230005 and BBa_K1230006 (which I submitted) from the Hard Information Page and no there seems to be no effect.
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16 August 2013.
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CAHM
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Deleting parts stil seems to not be working. I've tried deleting part BBa_K1560000 a few times now and still has not gone through.
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29 September 2014.
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Chris Lee, UCSC
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===API problem: some XML files are not well-formed===
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A number of [http://django.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 https://parts.igem.org/xml/part.BBa_B0034]. A valid XML file should not include certain characters as detailed [http://www.w3.org/TR/2004/REC-xml-20040204/#charsets here]. The descriptions or authors of certain parts in the registry contain some of these characters, e.g. [https://parts.igem.org/Part:BBa_J45002 BBa_J45002] was designed by "Andr� Green II". A relatively forgiving XML parser will accept this, but trying to view the data in a browser usually results in some [https://parts.igem.org/cgi/xml/part.cgi?part=BBa_J45002 error message].
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-- j3harvey, 10th August 2011
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===Image display/ memory problem===
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I've been having trouble displaying images on my parts pages. For instance... https://parts.igem.org/Part:BBa_J176028<br>
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''' "Error creating thumbnail: <br>
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libgomp: Thread creation failed: Cannot allocate memory'''<br>
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Are we no longer allowed to upload and display images on the Registry pages? Is there not enough memory?<br>
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[[User:Kahaynes|Karmella]]

Latest revision as of 11:45, 7 September 2017

Wiki Errors

One this page http://partsregistry.org/Add_a_Part_to_the_Registry and this page http://partsregistry.org/Main_Page the menu bar does not appear. Therefore, we cannot log on using the pages. We have to go to another page and then back to Add a Part page. Malcolm Campbell, Davidson College, Sept., 2017

Slight problems with the new Parts Registry

(1) For our BioBricks (for example https://parts.igem.org/Part:BBa_K1159014) the automatically generated group is GEM08_TUDelft which is definitely not correct. We would be glad if this could be changed to iGEM13_TU-Munich.
(2) When we tried to edit the sequence "edit sequence and features" of this BioBrick, the edit button for the sequence was not a link and made impossible to enter sequence information. This problem only occured when using Firefox but not when using Opera.
(3) We could not find a edit button on the main page that would allow us to edit the text on the main page of this BioBrick.
TU_Munich 13:58, 26 June 2013

(A)We have the same problem with our BioBricks, which are put into the group "Group: iGEM08_Newcastle_University" (see BBa_K1045000 as an example), although it should be Göttingen. (B)As you can see, I can only edit this post, and not the page in order to add a new bug report. - Team Göttingen 11:11, 25 June 2013

XML Data incorrect

The XML data that can be retrieved from the front page does not show consistency. For example the sub parts, 940992 with part_id 4901 and subpart 2006301 with part_id 14010 do not have a parent in the parts table. When working with foreign keys ±6000 entry's cannot be inserted as the parent part_id is not present. Are there other sources available for consistent retrieval? JJkoehorst 15:32, 5 May 2012

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.

Also I noticed if features are added they are totally misplaced if font size has been changed. I have to change font size of the whole page so I can click the save button on the sequence window. Please trouble shoot the registry its super hard to use...

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


Deleting parts don't seem to work yet . I tried to delete parts BBa_K1230005 and BBa_K1230006 (which I submitted) from the Hard Information Page and no there seems to be no effect. 16 August 2013. CAHM


Deleting parts stil seems to not be working. I've tried deleting part BBa_K1560000 a few times now and still has not gone through. 29 September 2014. Chris Lee, UCSC

API problem: some XML files are not well-formed

A number of [http://django.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. A valid XML file should not include certain characters as detailed [http://www.w3.org/TR/2004/REC-xml-20040204/#charsets here]. The descriptions or authors of certain parts in the registry contain some of these characters, e.g. BBa_J45002 was designed by "Andr� Green II". A relatively forgiving XML parser will accept this, but trying to view the data in a browser usually results in some error message.

-- j3harvey, 10th August 2011

Image display/ memory problem

I've been having trouble displaying images on my parts pages. For instance... https://parts.igem.org/Part:BBa_J176028
"Error creating thumbnail:
libgomp: Thread creation failed: Cannot allocate memory
 Are we no longer allowed to upload and display images on the Registry pages? Is there not enough memory?
Karmella