How to...access assay information from AssayBridge.

[pconesa]

Hi! Eamon.

I am currently working on "extending" the index with metabolites from our metabolite assignment file. I have dome some tests and it looks fine so far but at this point I need you help.

INITIAL SITUATION: As you pointed out in a previous email, the easy way to index is to change, AssayBridge to have extra lucene index information. So I am doing some test locally.

QUESTIONS: 1st.: I assume we need to fork BioInvIndex to do this, right?

the AssayBridge.set method is receiving a collection of assays and 2 lucene objects. So I have the assay collection to do all my job.

2nd.: How can a know if the assay has a column named "metabolite assignment file". Shall I do it manually?, opening the assayfile (in this case, how can I get the file name?).

All the best, Pablo

[eamonnmag]

Hey Pablo,

So, yes for the first part, but such an extension would probably be useful inside the core codebase as well.

I'll have to check out where exactly the metabolite assignment file lives. I guess if you get the XREFs from the assay object assay.getXrefs() and iterate around those objects, you'll get it in there.

If it is not contained within the Xref, you'll find it in the annotations for the assay.

for(Annotation annotation : assay.getAnnotation("Metabolite Assignment File")) {
    // do stuff
}

^ You would obviously guard against assay.getAnnotation("Metabolite Assignment File") being null.

I've not really got access to my computer at present since I'm now flying to Perth :-o.

Let me know how you get on,

Eamonn