old_contents: """
  this is the stuff specific to the plant studies that are loaded. It can include comments and all that. The studytreelist will be read from the load_synth_extract file. Other variables in the conf could be overridden here. 
  """
  import load_synth_extract
  from general_tm_utils import *
  from general_utils import *
  
  studytreelist=["pg_2539_6294", #Soltis et al. 2011
                 "pg_715_1289",  #Barnadesioideae
                 "pg_329_324",   #Hieracium
          #       "pg_9_1",       #Campanulidae
                 "pg_709_1276",  #Lobelioideae, very non monophyletic
                 "pg_41_1396",   #Feddea
                 "pg_82_5792",   #Campanula, very non monophyletic campanula
                 "pg_932_1831"   #Goodeniaceae, tons of non monophyly
                 ]
  
  studytreelistTF = [True] * len(studytreelist)
  
  if __name__ == "__main__":
      treemloc = "/home/josephwb/Work/OToL/treemachine/target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar" #treemachine location, machine-specific
      javapre = "java -Xmx8g -jar" #java running information
      dott = "example/asterales_taxonomy.db" #database location for taxonomy
      taxfile = "example/aster/taxonomy.tsv" #location of taxonomy loading file
      synfile = "example/aster/synonyms.tsv" #location of synonyms file
      dload = "example/asterales_loading.db" #database location for loading studies
      dsynth = "example/asterales_synth.db" #databsae location for synthesis
      synthottolid = "1042120" #ott id for starting synthesis
      treefn = "example/asterales_synth.tre" #filename for tree
      generallogfileloc = "example/logfile" #log file for spitting out lots of information
      studyloc = "example/nexsons/" #location for the nexsons
      ottv = "ottv2.6" #version of taxonomy to build DB
  
      delete_database(dott)
      print "loading taxonomy"
      load_taxonomy(treemloc,javapre,dott,taxfile,synfile,ottv)
  
      print "loading synthottolid:",synthottolid
      print "loading studytreelist:",studytreelist
      
      download = True
      if download:
          get_all_studies_opentreeapi(studytreelist,studyloc)
  
      load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,
                   treemloc,generallogfileloc,dsynth,synthottolid,treefn,studytreelistTF)
  
new_contents: """
  this is the stuff specific to the plant studies that are loaded. It can include comments and all that. The studytreelist will be read from the load_synth_extract file. Other variables in the conf could be overridden here. 
  """
  import load_synth_extract
  from general_tm_utils import *
  from general_utils import *
  
  studytreelist=["pg_2539_6294", #Soltis et al. 2011
                 "pg_715_1289",  #Barnadesioideae
                 "pg_329_324",   #Hieracium
                 "9_1",       #Campanulidae
                 "pg_709_1276",  #Lobelioideae, very non monophyletic
                 "pg_41_1396",   #Feddea
                 "pg_82_5792",   #Campanula, very non monophyletic campanula
                 "pg_932_1831"   #Goodeniaceae, tons of non monophyly
                 ]
  
  studytreelistTF = [True] * len(studytreelist)
  
  if __name__ == "__main__":
      treemloc = "/home/josephwb/Work/OToL/treemachine/target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar" #treemachine location, machine-specific
      javapre = "java -Xmx8g -jar" #java running information
      dott = "example/asterales_taxonomy.db" #database location for taxonomy
      taxfile = "example/aster/taxonomy.tsv" #location of taxonomy loading file
      synfile = "example/aster/synonyms.tsv" #location of synonyms file
      dload = "example/asterales_loading.db" #database location for loading studies
      dsynth = "example/asterales_synth.db" #databsae location for synthesis
      synthottolid = "1042120" #ott id for starting synthesis
      treefn = "example/asterales_synth.tre" #filename for tree
      generallogfileloc = "example/logfile" #log file for spitting out lots of information
      studyloc = "example/nexsons/" #location for the nexsons
      ottv = "ottv2.6" #version of taxonomy to build DB
  
      delete_database(dott)
      print "loading taxonomy"
      load_taxonomy(treemloc,javapre,dott,taxfile,synfile,ottv)
  
      print "loading synthottolid:",synthottolid
      print "loading studytreelist:",studytreelist
      
      download = True
      if download:
          get_all_studies_opentreeapi(studytreelist,studyloc)
  
      load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,
                   treemloc,generallogfileloc,dsynth,synthottolid,treefn,studytreelistTF)
  
subject: fix study 9