See the last example in ?xml2::xml_find_all or use xml2::xml2::xml_ns_strip()
Hadley On Tue, Jan 31, 2017 at 9:43 AM, Mark Sharp <msh...@txbiomed.org> wrote: > I am trying to read a series of XML files that use a namespace and I have > failed, thus far, to discover the proper syntax. I have a reproducible > example below. I have two XML character strings defined: one without a > namespace and one with. I show that I can successfully extract the node using > the XML string without the namespace and fail when using the XML string with > the namespace. > > Mark > PS I am having the same problem with the xml2 package and am hoping > understanding one with help with the other. > > ## > library(XML) > ## The first XML text (no_ns_xml) does not have a namespace defined > no_ns_xml <- c("<?xml version=\"1.0\" ?>", "<WorkSet>", > "<Description>MFIA 9-Plex (CharlesRiver)</Description>", > "</WorkSet>") > l_no_ns_xml <-xmlTreeParse(no_ns_xml, asText = TRUE, getDTD = FALSE, > useInternalNodes = TRUE) > ## The node is found > getNodeSet(l_no_ns_xml, "/WorkSet//Description") > > ## The second XML text (with_ns_xml) has a namespace defined > with_ns_xml <- c("<?xml version=\"1.0\" ?>", > "<WorkSet xmlns=\"http://labkey.org/etl/xml\">", > "<Description>MFIA 9-Plex (CharlesRiver)</Description>", > "</WorkSet>") > > l_with_ns_xml <-xmlTreeParse(with_ns_xml, asText = TRUE, getDTD = FALSE, > useInternalNodes = TRUE) > ## The node is not found > getNodeSet(l_with_ns_xml, "/WorkSet//Description") > ## I attempt to provide the namespace, but fail. > ns <- "http://labkey.org/etl/xml" > names(ns)[1] <- "xmlns" > getNodeSet(l_with_ns_xml, "/WorkSet//Description", namespaces = ns) > > R. Mark Sharp, Ph.D. > Director of Data Science Core > Southwest National Primate Research Center > Texas Biomedical Research Institute > P.O. Box 760549 > San Antonio, TX 78245-0549 > Telephone: (210)258-9476 > e-mail: msh...@txbiomed.org > > > > > > > > > > CONFIDENTIALITY NOTICE: This e-mail and any files and/or...{{dropped:10}} > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- http://hadley.nz ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.