run_r_script.py (2766B)
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