tweak_xml.py

#!/usr/bin/env python

# T. Carman, Spring 2019

# A quick 'n dirty helper script for adjusting the pecan.xml file
# when doing several similar pecan runs.


import os
import sys
import datetime
from lxml import etree

ERRORS = 0

def usage():
  print '''
     $ ./tweak_xml.py [-h | --help] path/to/pecan.xml
  
  '''

def verify_single_tag(tree, tag):
  global ERRORS
  if len(tree.findall(tag)) == 0:
    print "ERROR! Can't find {}".format(tag)
    ERRORS += 1
  elif len(tree.findall(tag)) > 1:
    print "ERROR! found more than one entry for tag: {}".format(tag)
    ERRORS += 1
  elif len(tree.findall(tag)) == 1:
    pass # Nothing to do, all ok


def get_element(tree, tag):
  global ERRORS
  if len(tree.findall(tag)) != 1:
    ERRORS += 1
    return None
  else:
    return tree.findall(tag)[0]




if __name__ == '__main__':

  if len(sys.argv) != 2:
    usage()
    sys.exit()

  if '-h' in sys.argv or '--help' in sys.argv:
    usage()
    sys.exit()

  OK_TO_WRITE = False
 
  in_pecan_xml = sys.argv[1] 

  tree = etree.parse(in_pecan_xml)
 
  verify_single_tag(tree, 'outdir')
  verify_single_tag(tree, 'info')
  verify_single_tag(tree, 'info/notes')
 
  get_element(tree, 'info/notes').text = "This file adjusted by the tweak_xml.py script"
  print "Set info/notes..."


  print "Checking output directory setting..." 
  od_setting = tree.find('outdir').text
  should_be = os.path.dirname(os.path.abspath(in_pecan_xml))
  if od_setting.rstrip('/') != should_be:
    print "outdir setting: {}".format(od_setting.rstrip('/'))
    print "should be path: {}".format(should_be) 
    print "ERROR! Looks like the outdir setting does not agree with the pecan.xml file you are editing!!!"
    ERRORS += 1 


  if len(tree.findall('info/date')) == 0:
    for e in tree.findall('info'): # Should only be one item
      e.append(etree.Element('date'))
      print "Added info/date..."

  verify_single_tag(tree, 'info/date')

  # Now that we are sure the tag exists, modify it. 
  get_element(tree, 'info/date').text = datetime.datetime.now().isoformat()
  print "Set info/date..."

  get_element(tree, 'ensemble/size').text = '300'
  print "Set ensemble/size..."
  
  get_element(tree, 'ensemble/samplingspace/parameters/method').text = 'sobol'
  print "Set ensemble/samplingspace/parameters/method..."

  # deprecated
  #get_element(tree, 'model/dvmdostem_output_spec').text = '/data/tcarman/ngee_dhs_runs/custom_output_spec.csv' 
  #print "Set model/dvmdostem_output_spec..."

  etree.strip_elements(tree, 'dvmdostem_output_spec')
  print "Removing deprecated output spec tag..."

  if len(tree.findall('model/dvmdostem_pecan_outputs')) == 0:
    for e in tree.findall('model'):
      e.append(etree.Element('dvmdostem_pecan_outputs'))
      print "Added model/dvmdostem_pecan_outputs tag..."

  get_element(tree, 'model/dvmdostem_pecan_outputs').text = "AvailN,GPP,LAI,NPP,NUptakeLab,NUptakeSt,OrgN,HeteroResp,AutoResp,SoilOrgC,VegC,VegN"
  print "Adding new output variable specification tag..."

  print "Set model binary and type..."
  if len(tree.findall('model/type')) == 0:
    for e in tree.findall('model'):
      e.append(etree.Element('type'))
      print "Added model/type tag..."
  if len(tree.findall('model/binary')) == 0:
    for e in tree.findall('model'):
      e.append(etree.Element('binary'))
      print "Added model/binary tag..."
    
  get_element(tree, 'model/binary').text = "/home/tcarman/dvm-dos-tem/dvmdostem"
  get_element(tree, 'model/type').text = "dvmdostem"

  print "Set model run years, various options, prerun environmental setup and module loading..."
  get_element(tree, 'model/dvmdostem_prerun').text = '100'
  get_element(tree, 'model/dvmdostem_equil').text = '1000'
  get_element(tree, 'model/dvmdostem_spinup').text = '250'
  get_element(tree, 'model/dvmdostem_transient').text = '115'
  get_element(tree, 'model/dvmdostem_scenerio').text = '10'
  get_element(tree, 'model/dvmdostem_loglevel').text = 'fatal'
  get_element(tree, 'model/dvmdostem_forcecmtnum').text = 'yes'
  get_element(tree, 'model/dvmdostem_dynamic_modeled_lai').text = '1'
  get_element(tree, 'model/prerun').text = 'module purge; module load python/2.7.14 gcc/5.4.0 boost/1.67.0 netcdf/4.3.3.1 jsoncpp/jsoncpp-1.8.4; module list; export LD_LIBRARY_PATH="/data/software/src/openblas/OpenBLAS-0.3.7/:$LD_LIBRARY_PATH"'


  if len(tree.findall('database/dbfiles')) == 0:
    for e in tree.findall('database'):
      e.append(etree.Element('dbfiles'))
      print "Added database/dbfiles tag..."

  get_element(tree, 'database/dbfiles').text = '/data/pecan_dbfiles/'
  print "Making sure dbfiles is set correctly..."


  if len(tree.findall('host/modellauncher')) == 0:
    print "Adding modellauncher tag and sub tags <binary> and <qsub.extra>'..."
    for e in tree.findall('host'):
      e.append(etree.Element('modellauncher'))

    for ee in tree.findall('host/modellauncher'):
      ee.append(etree.Element('binary'))
      ee.append(etree.Element('qsub.extra'))

  get_element(tree, 'host/modellauncher/binary').text = '/data/software/modellauncher'
  get_element(tree, 'host/modellauncher/qsub.extra').text='-l nodes=2:ppn=18'
  print "Setting model launcher sub-tags."

  if ERRORS == 0:
    OK_TO_WRITE = True

  if OK_TO_WRITE:
    tree.write(in_pecan_xml, pretty_print=True, xml_declaration=True,   encoding="utf-8")
  else:
    print etree.tostring(tree, pretty_print=True, xml_declaration=True,   encoding="utf-8")
    print ""
    print "Something is eff'd up with the xml..."



  #from IPython import embed; embed()