2012-04-13 00:48:34 +02:00
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#!/usr/bin/env python
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# encoding: utf-8
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# Hans-Martin von Gaudecker, 2012
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"""
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Run a R script in the directory specified by **ctx.bldnode**.
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For error-catching purposes, keep an own log-file that is destroyed if the
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task finished without error. If not, it will show up as rscript_[index].log
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in the bldnode directory.
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2012-04-13 08:36:02 +02:00
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Usage::
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2012-04-13 00:48:34 +02:00
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ctx(features='run_r_script',
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source='some_script.r',
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target=['some_table.tex', 'some_figure.eps'],
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deps='some_data.csv')
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"""
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2012-04-13 08:37:48 +02:00
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import os, sys
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2012-04-13 00:48:34 +02:00
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from waflib import Task, TaskGen, Logs
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R_COMMANDS = ['RTerm', 'R', 'r']
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def configure(ctx):
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ctx.find_program(R_COMMANDS, var='RCMD', errmsg = """\n
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No R executable found!\n\n
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If R is needed:\n
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1) Check the settings of your system path.
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2) Note we are looking for R executables called: %s
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If yours has a different name, please report to hmgaudecker [at] gmail\n
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Else:\n
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Do not load the 'run_r_script' tool in the main wscript.\n\n""" % R_COMMANDS)
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ctx.env.RFLAGS = 'CMD BATCH --slave'
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@Task.update_outputs
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class run_r_script_base(Task.Task):
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"""Run a R script."""
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run_str = '"${RCMD}" ${RFLAGS} "${SRC[0].abspath()}" "${LOGFILEPATH}"'
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shell = True
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class run_r_script(run_r_script_base):
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"""Erase the R overall log file if everything went okay, else raise an
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error and print its 10 last lines.
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"""
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def run(self):
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ret = run_r_script_base.run(self)
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logfile = self.env.LOGFILEPATH
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if ret:
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mode = 'r'
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if sys.version_info.major >= 3:
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mode = 'rb'
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with open(logfile, mode=mode) as f:
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tail = f.readlines()[-10:]
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Logs.error("""Running R on %s returned the error %r\n\nCheck the log file %s, last 10 lines\n\n%s\n\n\n""" % (
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self.inputs[0].nice_path(), ret, logfile, '\n'.join(tail)))
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else:
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os.remove(logfile)
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return ret
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@TaskGen.feature('run_r_script')
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@TaskGen.before_method('process_source')
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def apply_run_r_script(tg):
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"""Task generator customising the options etc. to call R in batch
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mode for running a R script.
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"""
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# Convert sources and targets to nodes
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src_node = tg.path.find_resource(tg.source)
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tgt_nodes = [tg.path.find_or_declare(t) for t in tg.to_list(tg.target)]
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tsk = tg.create_task('run_r_script', src=src_node, tgt=tgt_nodes)
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tsk.env.LOGFILEPATH = os.path.join(tg.bld.bldnode.abspath(), '%s_%d.log' % (os.path.splitext(src_node.name)[0], tg.idx))
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# dependencies (if the attribute 'deps' changes, trigger a recompilation)
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for x in tg.to_list(getattr(tg, 'deps', [])):
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node = tg.path.find_resource(x)
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if not node:
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tg.bld.fatal('Could not find dependency %r for running %r' % (x, src_node.nice_path()))
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tsk.dep_nodes.append(node)
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Logs.debug('deps: found dependencies %r for running %r' % (tsk.dep_nodes, src_node.nice_path()))
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# Bypass the execution of process_source by setting the source to an empty list
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tg.source = []
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