Syed Haider wrote:
Hi Allan
On Wed, 2007-09-26 at 12:44 +0200, allank wrote:
Hi Syed,
As requested, attached please find the configuration files. The filter I
am trying to configure has the following characteristics: has an
internal name of 'gene_region' and is contained in FilterGroup
internalName="hiv_sequence", FilterCollection internalName="hiv_sequence".
Looking at the saved xml files, the mid_template.template.xml seems to
contain the above data, but the accompanying mid.xml seems to have even
a single entry for 'gene_region' filter.
correct, thats one of the known problems, that changes dont propagate
from template to individual xml. You need to redeclare your filter
manually as proposed in the last email.
Finally, a completely unrelated question, is there a way to load xml
documents into marteditor, I remember the older martj did have this option.
If you want to add biomart configuration xmls, yes!, its possible. All
you need to do is dump the xmls (both .xml and template), followed by
Upload option of marteditor, then select all the files in one go.
Thanks Syed, am now interested in manually editing the .xml file for the
shy filters, how do I actually get to upload the xml documents into
marteditor.
For export I would use the File->Export main menu option, what option
(within the file menu? perhaps) may I use for the importation of the same.
Allan.
Syed Haider wrote:
Hi Allan
could you please save your xmls and send them to me, with the name of
the filter causing this trouble. In addition, could you please try
deleting the filter, export. Then, recreate it manually rather copying
from another filter, export, check if its displayed. then populate its
option menu, export and see if its displayed. Each time you export, you
need to do perl bin/configure.pl -r conf/your_registry.xml --clean,
kill/restart the server to see the changes on martView.
hope this helps.
cheers
syed
On Wed, 2007-09-26 at 11:39 +0200, allank wrote:
Hi all,
I have been having a problem having filters created as lists created in
marteditor not been displayed in Biomart 0.6.
Am using Biomart 0.6 and Martj-0.6 (latest release obtained directly
from CVS each day I've attempted to solve this puzzle) and PostgreSQL 8.1.4.
This is how I am creating the filters in a rather conservative way, let
me explain. In marteditor, I copy a list filter that works (gets
displayed just fine in Biomart) whose field in the DB is of the same
type as that of the field on which I am creating the new list based
filter on, I modify the name and the field name of the copied and now
pasted control, next I select 'clear option' in it's context menu, then
after I select 'make drop down' from the context menu. The control get's
correctly populated with options which are based on unique data values
of the underlying field and all seems well. I then export the entire
configuration. I kill biomart process the recommended way, I 'cd' into
the Biomart perl directory and run 'perl bin/configure.pl --clean -r
conf/biomart3___postgresql.xml;' command, then I start biomart. Going to
my webbrower, I click on new on the main menu, I select the dataset and
so on till I get to select the 'filters' the new filter does not appear.
What should I do?
Please advise.
Allan.
