third_party/waf/waflib/extras/run_r_script.py

   1 #!/usr/bin/env python
   2 # encoding: utf-8
   3 # Hans-Martin von Gaudecker, 2012
   4
   5 """
   6 Run a R script in the directory specified by **ctx.bldnode**.
   7
   8 For error-catching purposes, keep an own log-file that is destroyed if the
   9 task finished without error. If not, it will show up as rscript_[index].log
  10 in the bldnode directory.
  11
  12 Usage::
  13
  14     ctx(features='run_r_script',
  15         source='some_script.r',
  16         target=['some_table.tex', 'some_figure.eps'],
  17         deps='some_data.csv')
  18 """
  19
  20
  21 import os, sys
  22 from waflib import Task, TaskGen, Logs
  23
  24 R_COMMANDS = ['RTerm', 'R', 'r']
  25
  26 def configure(ctx):
  27         ctx.find_program(R_COMMANDS, var='RCMD', errmsg = """\n
  28 No R executable found!\n\n
  29 If R is needed:\n
  30         1) Check the settings of your system path.
  31         2) Note we are looking for R executables called: %s
  32            If yours has a different name, please report to hmgaudecker [at] gmail\n
  33 Else:\n
  34         Do not load the 'run_r_script' tool in the main wscript.\n\n"""  % R_COMMANDS)
  35         ctx.env.RFLAGS = 'CMD BATCH --slave'
  36
  37 class run_r_script_base(Task.Task):
  38         """Run a R script."""
  39         run_str = '"${RCMD}" ${RFLAGS} "${SRC[0].abspath()}" "${LOGFILEPATH}"'
  40         shell = True
  41
  42 class run_r_script(run_r_script_base):
  43         """Erase the R overall log file if everything went okay, else raise an
  44         error and print its 10 last lines.
  45         """
  46         def run(self):
  47                 ret = run_r_script_base.run(self)
  48                 logfile = self.env.LOGFILEPATH
  49                 if ret:
  50                         mode = 'r'
  51                         if sys.version_info.major >= 3:
  52                                 mode = 'rb'
  53                         with open(logfile, mode=mode) as f:
  54                                 tail = f.readlines()[-10:]
  55                         Logs.error("""Running R on %r returned the error %r\n\nCheck the log file %s, last 10 lines\n\n%s\n\n\n""",
  56                                 self.inputs[0], ret, logfile, '\n'.join(tail))
  57                 else:
  58                         os.remove(logfile)
  59                 return ret
  60
  61
  62 @TaskGen.feature('run_r_script')
  63 @TaskGen.before_method('process_source')
  64 def apply_run_r_script(tg):
  65         """Task generator customising the options etc. to call R in batch
  66         mode for running a R script.
  67         """
  68
  69         # Convert sources and targets to nodes
  70         src_node = tg.path.find_resource(tg.source)
  71         tgt_nodes = [tg.path.find_or_declare(t) for t in tg.to_list(tg.target)]
  72
  73         tsk = tg.create_task('run_r_script', src=src_node, tgt=tgt_nodes)
  74         tsk.env.LOGFILEPATH = os.path.join(tg.bld.bldnode.abspath(), '%s_%d.log' % (os.path.splitext(src_node.name)[0], tg.idx))
  75
  76         # dependencies (if the attribute 'deps' changes, trigger a recompilation)
  77         for x in tg.to_list(getattr(tg, 'deps', [])):
  78                 node = tg.path.find_resource(x)
  79                 if not node:
  80                         tg.bld.fatal('Could not find dependency %r for running %r' % (x, src_node.abspath()))
  81                 tsk.dep_nodes.append(node)
  82         Logs.debug('deps: found dependencies %r for running %r', tsk.dep_nodes, src_node.abspath())
  83
  84         # Bypass the execution of process_source by setting the source to an empty list
  85         tg.source = []
  86