How do I call external files in Python Geoprocessing Service?

Question

I have created a Python script which calls an R script and then reads the output back into Python. I can run this tool in ArcGIS Desktop (10.2.1) and it works fine. When I publish as a geoprocessing service it fails once it reaches the R script. I have checked the file paths and they are fine. Is it even possible to call external scripts from a geoprocessing service? Here is my code.

import sys, os, arcpy
arcpy.AddMessage("Loaded Python Imports...")

try:
#User Input
lat = arcpy.GetParameterAsText(0)
long = arcpy.GetParameterAsText(1)

arcpy.AddMessage("LAT: " + "".join(lat))
arcpy.AddMessage("LONG: " + "".join(long))

#Create R Command
rScript = "test.R"
args = " ".join([lat, long])
RCMD = "R --slave --vanilla --args "
cmd = RCMD + args + " < " + rScript

#Execute
os.system(cmd)

#Render the Results
output = open("FILE PATH")
finalNumber = output.read()
print("The output is: " + " ".join(finalNumber))
arcpy.AddMessage("The output is: " + " ".join(finalNumber))
output.close()

#Delete Text File
os.remove("FILE PATH")

except Exception as e:
    print e.message
    arcpy.AddError(e.message)

Answer 1

I found this article: Integrating external programs within ModelBuilder, it is older and initially looks like it is off topic, but if you look at this: , you can see that it explicitly sets the path to the R script.

When your geoprocessing script runs on the server, it runs in a scratch folder within the jobs directory. Depending on the publishing process, your R script may not be there. Whenever I refer to external script within my geoprocessing services, I always explicitly refer to them from a folder that has been registered as a datasource.

Answer 2

You will need to use the ESRI tool structure and include the files in your script folder if you would like to reference them directly by name like you are doing in your code. http://resources.esri.com/help/9.3/ArcGISDesktop/com/Gp_ToolRef/sharing_tools_and_toolboxes/a_structure_for_sharing_tools.htm

Otherwise, you will need to append the location of the script in your sys.path. The example below references file "\myFolder\myModules\myExtFile.py". After you have a valid reference to your file you can use your custom functions in the GP service as long as where you are publishing to has access to the folder path.

import sys, arcpy
sys.path.append(r'\\myFolder\myModules')

import myExtFile as extFile

if __name__ == '__main__':
    # Get values from ESRI
    param1 = arcpy.GetParameterAsText(0)

    # Use custom python library
    myVal = extFile.someFunc(param1)