Flyspray:: Thu, 21 Feb 2013 15:26:52 +0100 Flyspray::LOVD 2.0: Recently closed tasks http://www.lovd.nl/bugs/ FS#57: Unescaped ampersands in XML output Adam Webb Tue, 03 Jul 2012 17:43:24 +0200
Example gene feed:


TSC2

tag:chromium.liacs.nl,2005-01-24:TSC2

Dr. Johan T. den Dunnen


Sue Povey & Rosemary Ekong

2005-01-24T00:00:00+01:00
2012-07-02T16:34:29+02:00

id:TSC2
entrez_id:7249
symbol:TSC2
name:Tuberous sclerosis 2
chromosome_location:16p13.3
position_start:chr16:2097990
position_end:chr16:2138712
refseq_genomic:NG_005895.1
refseq_mrna:NM_000548.3
refseq_build:hg19



The ampersand in root>entry>contributor>name should be escaped. Unescaped ampersands can defeat XML parsers :(]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=57 http://www.lovd.nl/bugs/index.php?do=details&task_id=57
FS#41: Variant colums for dbSNP amd OMIM Raymond Dalgleish Fri, 17 Apr 2009 16:12:36 +0200
It would be useful to have decicated dbSNP and OMIM columns associated with Variants. The input fields would only require appropriate DBSNP or OMIM numbers to be inserted; nothing else.

I guess that I could create custom Variant columns myself and then make the dbSNP and OMIM links active in these columns. However, that\'s an untidy solution that perhaps might have unwanted consequences for data exchange. A field containg only a dbSNP rs number is easier to exchange that one that contains code for a link.]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=41 http://www.lovd.nl/bugs/index.php?do=details&task_id=41
FS#55: Variants reported as uncurated Raymond Dalgleish Fri, 20 Apr 2012 15:09:03 +0200
I suggest that the Uncurated Quicklink be replaced by Quicklinks for 'Submitted', 'Non-public' and 'Marked'. This would improve the usability of LOVD.]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=55 http://www.lovd.nl/bugs/index.php?do=details&task_id=55
FS#56: ability to import multi-gene variants for high throughput tests Ammar Husami Wed, 16 May 2012 20:48:40 +0200 Description of the problem: the current filed of genetic testing is moving from single gene testing to multi gene testing where handful of gene variants are reported at once. The current LOVD submission scheme is limited to uploading single gene variants. Thus if I have variants for 50 samples for 24 genes, the most efficient way is to create variant import file for each gene adding considerable time to the submission process while it is technically possible to do in one step
solution: add subsection to /config_import.php to identify gene and separate variant tables based on gene symbol allowing import of multiple genes from one file
]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=56 http://www.lovd.nl/bugs/index.php?do=details&task_id=56
FS#54: NoCurrDB at HCI-LOVD Russell Bell Sat, 31 Mar 2012 03:34:20 +0200 and are having the following trouble with the installation:

when Im on a the gene home page,
http://hci-lovd.hci.utah.edu/home.php?select_db=MSH2
,and select type, or simple or advanced
the next page is the select gene database
which will send me back to a gene home page depending on which I select

another behavior:
If I go to a gene page and select Unique sequence variants it will take me to
http://hci-lovd.hci.utah.edu/variants.php?select_db=MSH2&action=view_unique


but if I click on Hide Specific Columns I get this error:
Error: NoCurrDB (Logged)
Currently, no gene was selected or sent, but the currdb class has been initiated. This is a in LOVD or in one of it's modules.
Debug: /views_columns.php?action=view_all&hide=true

any ideas would be greatly appreciated
]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=54 http://www.lovd.nl/bugs/index.php?do=details&task_id=54
FS#53: Editing the list of available detection techniques Raymond Dalgleish Fri, 24 Feb 2012 14:56:48 +0100
'In new LOVD installations, the following columns are now on the variant side: "Detection/Template", "Detection/Technique", "Detection/Tissue".'

I have just created a new installation of LOVD 2.0 and find that I cannot edit the contents of the "Detection/Technique" column now that it's "Variant/Detection/Technique" using the box at the bottom of 'LOVD Setup - Systems settings' page. Of course, the list of techniques can still be edited using the column data type wizard, but the box which was formerly used for editing the list now seems to be non-functional and redundant.
]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=53 http://www.lovd.nl/bugs/index.php?do=details&task_id=53
FS#50: Display patient number on Status page Raymond Dalgleish Tue, 23 Aug 2011 10:10:30 +0200 http://www.lovd.nl/bugs/index.php?do=details&task_id=50 http://www.lovd.nl/bugs/index.php?do=details&task_id=50 FS#51: Link to exon table during variant submission Raymond Dalgleish Wed, 31 Aug 2011 15:09:02 +0200 http://www.lovd.nl/bugs/index.php?do=details&task_id=51 http://www.lovd.nl/bugs/index.php?do=details&task_id=51 FS#40: Adding variants in different genes to a patient Raymond Dalgleish Fri, 13 Feb 2009 15:08:42 +0100
The ideal solution would be the ability to change gene, as necessary, for each additional variant to be recorded for a patient. Alternatively, there should be the ability to look-up the patient.]]>
http://www.lovd.nl/bugs/index.php?do=details&task_id=40 http://www.lovd.nl/bugs/index.php?do=details&task_id=40
FS#48: Reply-To header for submitter registrations Raymond Dalgleish Thu, 07 Jul 2011 14:07:01 +0200 http://www.lovd.nl/bugs/index.php?do=details&task_id=48 http://www.lovd.nl/bugs/index.php?do=details&task_id=48