clintrials_gov_convert {eudract}

applies a conversion using xslt from a simple xml file to a ClinicalTrials.gov compatible file, and checks against the schema

Description

applies a conversion using xslt from a simple xml file to a ClinicalTrials.gov compatible file, and checks against the schema

Usage

clintrials_gov_convert(
  input,
  original,
  output,
  xslt = system.file("extdata", "simpleToCtGov.xslt", package = "eudract"),
  schema_input = system.file("extdata", "simple.xsd", package = "eudract"),
  schema_results = system.file("extdata", "RRSUploadSchema.xsd", package = "eudract"),
  schema_output = system.file("extdata", "ProtocolRecordSchema.xsd", package = "eudract"),
  soc = system.file("extdata", "soc.xml", package = "eudract")
)

Arguments

input

a character string giving the file path to the simple xml file

original

a character string giving the file path to the study file downloaded from ClinicalTrials.gov

output

a character string naming the output file

xslt

a character string giving the file path to the xslt script. Defaults to the script provided in this package

schema_input

a character string giving the file path to the schema for the simple xml file. Defaults to the schema provided in this package

schema_results

a character string giving the file path to the schema for the results section of the output. A copy was downloaded and is provided in this package as the default.

schema_output

a character string giving the file path to the schema for the overall output. A copy was downloaded and is provided in this package as the default.

soc

a character string giving an xml file that contains the System Organ Class look-up table going from EudraCT numbers to ClinicalTrials words.

Value

the output from the validation against the schema. A new file is created as a side-effect, which is suitable to upload into ClinicalTrials.gov. This over-writes the file given in original with the additional safety events.

See Also

safety_summary simple_safety_xml

Examples

safety_statistics <- safety_summary(safety,
                                    exposed=c("Experimental"=60,"Control"=67))
simple <- tempfile(fileext = ".xml")
eudract <- tempfile(fileext = ".xml")
ct <- tempfile(fileext = ".xml")
simple_safety_xml(safety_statistics, simple)
eudract_convert(input=simple,
                output=eudract)
clintrials_gov_convert(input=simple,
                       original=system.file("extdata", "1234.xml", package ="eudract"),
                output=ct)
## Not run: 
  # This needs a real user account to work
  clintrials_gov_upload(
    input=simple,
    orgname="CTU",
    username="Student",
    password="Guinness",
    studyid="1234"
    )


## End(Not run)