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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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Unable to parse any XML input #46

Closed abbatidanilo closed 5 years ago

abbatidanilo commented 5 years ago

I used the following command CytoML::GatingSet2flowJo(manual_gs, outFile = "./manual_gs.xml") to generate an .xml file for a gatingset. The error in the uploaded file seems to be on line 20: The prefix "transforms" for element "transforms:spilloverMatrix" is not bound. The attached file is with the txt extension (actually is the xml file I'm trying to parse) manual_gs-sublime2.txt I am currently using ‘CytoML’ version 1.7.9 within R-3.5.1

gfinak commented 5 years ago

What exactly is the problem you are having? I'm able to read the xml file you uploaded in FlowJo. image

Are you trying to read in an xml file created by GatingSetflowJo using flowWorkspace ? If so, why?

abbatidanilo commented 5 years ago

Thank you Greg for getting back to me. You are right: flowJo can read that, but Excel reports a parsing issue in line 16 column 218: the "transforms" prexif seems does not have any reference in the xml namespace. But actually is not the only one. Also other online xml reader tool (e.g: https://jsonformatter.org/xml-viewer) clearly shows that just a small portion of the whole xml tree is correctly parsed. I discovered this by using the flowSOM package, and in particular the ProcessGatingML function which is intended for labelling the clustered population using the the gatingSet imported as .xml file. I was tempted to report this issue to that package, but first I wanted to have some feedback from your relevant experience in this parsing subject. Frankly speaking, with your important feedback I am even more confused now... but that's life. Thank you anyway for your valuable contribution Danilo

gfinak commented 5 years ago

FlowJo xml is not GatingML. The only thing that we strive to guarantee is that GatingSet2FlowJo will create an xml file that can be read by FlowJo.