Hello Jesse, Maybe you could add an xml validation step after every time that you generate a file (via search, validation, etc) -- and then choose to skip those files that do not pass. You can use any standard xml parser (such as xmllint) or co-opt the PepXMLViewer by creating an index on the command-line (with the -I option) -- if the file is not proper pepXML, this step will fail.
Of course a more pressing issue might be tracking down the source of incomplete/broken files! Hope this helps, --Luis On Tue, Feb 14, 2017 at 1:46 PM, Jesse <[email protected]> wrote: > Hello TPP team. > > I realize this may be a little out of your purview. I'm automating > xinteract and iProphet for out common pipeline using windows batch scripts > mostly, but when xinteract fails and creates a broken output, > interProphetParser throws an error that causes a windows pop-up. I check > the usage and I can't find anything explicitly that will prevent creation > of the output from xinteract, or that will ignore broken inputs for > interprophetparser. > > Can anyone think of an easy way to handle this within windows batch > scripts, or maybe some additional program I can run in between xinteract > and interprophetparser that could check the structure of the .pep.xml > allowing me to exclude the broken files? > > As of now, I'm manually removing the files that gave xinteract errors and > then repeating the batch script. > > Your thoughts would be appreciated. > > Best regards, > Jesse > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
