From: Brandon King <kingb@caltech.edu>
Date: Wed, 14 Nov 2007 03:33:04 +0000 (+0000)
Subject: [project @ First attempt at script for configuring pipeline automatically.]
X-Git-Tag: 0.1.0~72
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=3708c0a4a5037527553de3090535a541740315d0

[project @ First attempt at script for configuring pipeline automatically.]
 * More of prof of concept.
 * FIXME: hardcoded config script path.
 * Uses logging module
   * Info for everything going fine.
   * Error when it breaks in a bad way.
---

diff --git a/bin/config_pipeline.py b/bin/config_pipeline.py
new file mode 100644
index 0000000..c559ebe
--- /dev/null
+++ b/bin/config_pipeline.py
@@ -0,0 +1,67 @@
+#!/usr/bin/python
+import subprocess
+import re
+import logging
+
+logging.basicConfig(level=logging.DEBUG,
+                    format='%(asctime)s %(levelname)-8s %(message)s',
+                    datefmt='%a, %d %b %Y %H:%M:%S',
+                    filename='config_pipeline.log',
+                    filemode='w')
+
+#Info
+s_start = re.compile('Starting Genome Analyzer Pipeline')
+s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
+s_generating = re.compile('Generating journals, Makefiles and parameter files')
+
+#Errors
+s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
+
+#Ignore
+s_skip = re.compile('s_[0-8]_[0-9]+')
+
+def handler(line):
+
+  # Irrelevant line
+  if s_skip.search(line):
+    pass
+  elif s_invalid_cmdline.search(line):
+    logging.error("Invalid commandline options!")
+  elif s_start.search(line):
+    logging.info('START: Configuring pipeline')
+  elif s_gerald.search(line):
+    logging.info('Running make now')
+  elif s_generating.search(line):
+    logging.info('Make files generted')
+  else:
+    logging.warning('How to handle: %s' % (line))
+  
+
+def configure():
+  #ERROR Test:
+  #pipe = subprocess.Popen(['goat_pipeline.py',
+  #                         '--GERALD=config32bk.txt',
+  #                         '--make .',],
+  #                         #'.'],
+  #                        stdout=subprocess.PIPE,
+  #                        stderr=subprocess.PIPE)
+
+  #Not a test; actual run attempt.
+  pipe = subprocess.Popen(['goat_pipeline.py',
+                           '--GERALD=config32bk.txt',
+                           '--make',
+                           '.'],
+                          stdout=subprocess.PIPE,
+                          stderr=subprocess.PIPE)
+  
+  line = pipe.stdout.readline()
+
+  while line != '':
+    handler(line)
+    line = pipe.stdout.readline()
+
+  #print pipe.poll()
+
+
+if __name__ == '__main__':
+  configure()