categories?

[Emily Greenfest-Allen]

Hi all-

After switching to WDK 2.2 I am now getting a model parsing error in my
categories.xml --

/www/allenem.bc.genomics.upenn.edu/gus_home/lib/wdk/genomicsBCModel/questions/categories.xml:4:87:
error: unknown element "category"

How are category assignations now handled?

Thanks

Emily

[Cristina Aurrecoechea]

I do not recall any changes in categories this release.

cristina

[Emily Greenfest-Allen]

Any idea then why its not working -- yesterday morning when I was on the
2.1 branch ... it was fine. Now its not. Same file.

-Emily

[Emily Greenfest-Allen]

If it helps, this is what is in my categories.xml -- there is always a
chance I have a missing / or " that I don't see. But my text editor
does tell me that the xml is valid.

<wdkModel>
<category name="GeneRecordClasses.GeneRecordClass" displayName="Search
for Genes" />
<category name="GeneIdentifiers"
displayName="Name Keyword Search or Identifiers"
parentRef="GeneRecordClasses.GeneRecordClass">
<questionRef>GeneQuestions.GeneKeywordSearch</questionRef>
<questionRef>GeneQuestions.GeneFromIdentifierList</questionRef>
</category>

<category name="DynSpanRecordClasses.DynSpanRecordClass"
displayName="Genomic Segments (DNA Motif)" />

<category name="dynspan" displayName="Search for Genomic Segments (DNA
Motif)"
parentRef="DynSpanRecordClasses.DynSpanRecordClass">
<questionRef>SpanQuestions.DynSpansByMotifSearch</questionRef>
<questionRef>SpanQuestions.DynSpansBySourceId</questionRef>
<questionRef>SpanQuestions.DynSpansByLocation</questionRef>

</category>
</wdkModel>

[Jerric Gao]

The name of the tag is changed from "category" to "searchCategory", and we also
introduced attributeCategory for the tree structure of the column selection.

Jerric

[Emily Greenfest-Allen]

Ok. I had seen those in the WdkModel.rng -- now it makes more sense.

When you get a chance could you explain the attributeCategory in a bit
more detail -- what is the "tree structure of the column selection"? Is
this in reference to the organization of categories in the AddStep pop-up?

Thanks,

Emily

[Emily Greenfest-Allen]

Oh - one more question -- is this still specified in the separate
categories.xml file or do we specify in the question definition?

Thanks,

Emily

On 9/30/2011 3:18 PM, Jerric Gao wrote:

[Jerric Gao]

The categories are still in separate <category> tags. However, it's not
necessary to put it in separate files, and in fact, you can have every piece of
information in one big xml file, although it would be hard to read if the file
is too big.

jerric

[Jerric Gao]

The best way to explain this attributeCategory is to take a look at the
beta.plasmodb.org, run any gene searches, and in the result page, configure the
columns of the result. You should see the tree structure in the popup window.

The attributeCategory is defined in a different way than searchCategory. you can
define a nested <attributeCategory> tree structure, and then you use
attributeCategory as a property of any <attribute> tag in the record class to
reference the attributeCategories you definie.