Flyspray:: Flyspray::LOVD 2.0: Recently opened tasks http://www.lovd.nl/bugs/ 2013-02-21T15:26:52Z FS#57: Unescaped ampersands in XML output 2013-02-21T15:26:52Z 2012-07-03T17:43:24Z
XML feeds can produce invalid output, notably by including unescaped ampersands (&).

Example gene feed:
<?xml version="1.0" encoding="ISO-8859-1"?>
<entry xmlns="http://www.w3.org/2005/Atom">
<title>TSC2</title>
<link rel="alternate" type="text/html" href="http://chromium.liacs.nl/LOVD2/TSC/home.php?select_db=TSC2"/>
<id>tag:chromium.liacs.nl,2005-01-24:TSC2</id>
<author>
<name>Dr. Johan T. den Dunnen</name>
</author>
<contributor>
<name>Sue Povey & Rosemary Ekong</name>
</contributor>
<published>2005-01-24T00:00:00+01:00</published>
<updated>2012-07-02T16:34:29+02:00</updated>
<content type="text">
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
</content>
</entry>

The ampersand in root>entry>contributor>name should be escaped. Unescaped ampersands can defeat XML parsers :(
Adam Webb http://www.lovd.nl/bugs/:57
FS#56: ability to import multi-gene variants for high throughput tests 2012-05-16T22:38:06Z 2012-05-16T20:48:40Z
Title: feature request to import variants reports often generated by high throughput technology such as next generation sequencing etc
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
Ammar Husami http://www.lovd.nl/bugs/:56
FS#55: Variants reported as uncurated 2012-07-26T16:39:38Z 2012-04-20T15:09:03Z
On the Configuration tab near the top right there is a 'Quicklink' to uncurated variants for the selected gene. More correctly, this seems to link instead to any variant that is Submitted, Non-public or Marked. I have instances of the latter two in my databases where the entries are curated, but not yet made public, or are marked to remind me to go back to them later.

I suggest that the Uncurated Quicklink be replaced by Quicklinks for 'Submitted', 'Non-public' and 'Marked'. This would improve the usability of LOVD.
Raymond Dalgleish http://www.lovd.nl/bugs/:55
FS#54: NoCurrDB at HCI-LOVD 2012-04-18T13:05:47Z 2012-03-31T03:34:20Z
We've set up LOVD at our institution using the network security mandated version 5.5 of PHP
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
Russell Bell http://www.lovd.nl/bugs/:54
FS#53: Editing the list of available detection techniques 2012-03-15T15:37:32Z 2012-02-24T14:56:48Z
In build 26, changes were made to LOVD 2.0 with regard to the "Detection" columns:

'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.
Raymond Dalgleish http://www.lovd.nl/bugs/:53
FS#52: Support for Google Analytics 2011-10-18T15:14:01Z 2011-10-06T16:07:21Z
I use Google Analytics to track hits to my two LOVD installations. I do this by embedding the tracking code into the bottom of the file inc-bot.php. It's not an ideal solution because any change to inc-bot.php in future builds will mean having to edit the tracking code back into the file again. Indeed, there might be a better file into which to paste the code, but the present solution does work. In addition, my solution is feasible only because I host the two installations on my own server and can edit the inc-bot.php file. Curators whose sites are hosted at LUMC do not (presumably) have this luxury.

Would it be possible to provide direct support for Google Analytics by providing a box into which the tracking code could be pasted by the database curator. Some thought might need to be given for the situation where a single shared-installation hosts genes which need to be tracked individually because these genes belong to different curators. A single-installation wide solution is not the answer, but neither is one which does it gene by gene.
Raymond Dalgleish http://www.lovd.nl/bugs/:52
FS#51: Link to exon table during variant submission 2011-09-30T13:28:49Z 2011-08-31T15:09:02Z
LOVD creates tables (text and HTML) of exon coordinates which are stored in the /refseq sub-directory. It would be useful to provide a link to the HTML version of the table (to open in a new tab) on the variant submission form. At present, there is a link adjacent to the DNA change box (just below the "Check variant with Mutalyzer 2.0" button) that allows access to the HTML view of the cDNA and intron sequence. A link to the exon table would be useful too because most of the time I just want to work out (or confirm) the exon in which the variant lies. The data displayed in the table are a more convenient source of information for this task.
Raymond Dalgleish http://www.lovd.nl/bugs/:51
FS#50: Display patient number on Status page 2011-09-30T13:29:06Z 2011-08-23T10:10:30Z
The "LOVD - Current system status" page displays the total "Total variants" and "Unique variants" for each gene. It would be useful to add an additional column to display the "Number of patients" for each gene.
Raymond Dalgleish http://www.lovd.nl/bugs/:50
FS#49: Locking out new submitters temporarily 2011-07-07T14:22:34Z 2011-07-07T14:22:34Z
I sometimes have a problem whereby a person registers as a submitter and goes ahead and submits data without understanding what they doing. I recently had such a submitter who entered a single patient with six dominant disease-causing variants, any one of which would have been sufficient to cause the disease in question. The problem is that there is no mechanism, at present, to prevent this.

Ideally, I would like the submitter to be automatically presented with the "How to" document which I send out manually to new submitters. Submitters would hopefully read these guidance notes and would have to tick a check-box to indicate that they'd done so before being allowed to submit data. This type of solution probably needs to wait for version 3.

In the meantime, version 2 could be modified so that new submitters are temporarily locked out from submitting data until approved by the database manager. That would give me time to intervene and send guidance notes to potential submitters.
Raymond Dalgleish http://www.lovd.nl/bugs/:49
FS#48: Reply-To header for submitter registrations 2011-07-29T16:25:41Z 2011-07-07T14:07:01Z
LOVD was modified in build 30 so that the Reply-To header in emails sent out by LOVD now points to the data submitter. Could this also be fixed for submitter registrations?
Raymond Dalgleish http://www.lovd.nl/bugs/:48