Hi,
I am trying to write a plugin to automatically make objects from sample
-> rawbioassay.
however, after you call dc.commit() it closes the connection. what is
the normal way to
re-establish a connection? dc.reconnect() does not seem to work.
getting a new dc via
dc = sc.newDbControl(); does not seem to work either.
i need to commit the created objects between steps because subsequent
objects do database
lookups of previous objects to create themselves.
here is my general outline.
ArraySlide slide;
for (Sample sourceObj : sources)
{
dc.reattachItem(sourceObj);
/**
* 1. get the slide
*/
slideName = sourceObj.getName().split(" ")[0];
slide = getSlideByName(dc, slideName);
/**
* 2. make chromatin input sample from pooled sample
*/
Sample chromatinSample = getChromatinSample(dc, sourceObj);
Extract chromatinExtract = addExtract(dc, chromatinSample);
/**
* 3. make the extract from the pooled sample
*/
Extract pooledExtract = addExtract(dc, sourceObj);
dc.commit();
dc = sc.newDbControl();
/**
* 4. make the labelled extracts from extracts
*/
LabeledExtract chromatinLabeledExtract =
addLabeledExtract(dc, inputLabel, chromatinExtract);
LabeledExtract pooledLabeledExtract =
addLabeledExtract(dc, poolLabel, pooledExtract);
dc.commit();
dc = sc.newDbControl();
/**
* 5. make the hybridization from the matched pairs, add
the slide
*/
Hybridization hyb = addHybridization(dc,
chromatinLabeledExtract, pooledLabeledExtract, slide);
dc.commit();
dc = sc.newDbControl();
/**
* 6. make the scan
*/
Scan scan = addScan(dc, hyb);
dc.commit();
dc = sc.newDbControl();
/**
* 7. make the rawbioassay
*/
String datatype = "GenePix";
RawBioAssay myRawBioAssay = addRawBioAssay(dc, scan,
RawDataTypes.getRawDataType(datatype) );
dc.commit();
dc = sc.newDbControl();
// group into experiment ?
fileNames = fileNames + " " +
myRawBioAssay.getName();
}
--
Keith Ching, Ph.D.
Bioinformatics, Laboratory of Gene Regulation
Ludwig Institute for Cancer Research
9500 Gilman Drive, #0653
CMM East, Room 3020
La Jolla, CA 92093-0653
[EMAIL PROTECTED]
858-822-5767
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