merge

fgcz · Jan 25, 2018 · 457ba2a · 457ba2a
2 parents 2351904 + 743c9f3
commit 457ba2a
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Showing 5 changed files with 21 additions and 6 deletions.
diff --git a/fgcz/__init__.pyc b/fgcz/__init__.pyc
diff --git a/fgcz/biobeamer.pyc b/fgcz/biobeamer.pyc
diff --git a/fgcz/fcc.py b/fgcz/fcc.py
@@ -1,13 +1,13 @@
 #!/usr/bin/python
 # -*- coding: latin1 -*-
 
-# $HeadURL: http://fgcz-svn.uzh.ch/repos/fgcz/stable/proteomics/fcc/fcc.py $
+# $HeadURL: https://github.com/fgcz/PyFGCZ/fcc.py $
 # $Id: fcc.py 7518 2015-05-27 15:20:12Z cpanse $
 # $Date: 2015-05-27 17:20:12 +0200 (Wed, 27 May 2015) $
 # $Author: cpanse $
 
 
-# Copyright 2008-2015
+# Copyright 2008-2017
 # Christian Panse <[email protected]>
 # Simon Barkow-Oesterreicher 
 # Witold Eryk Wolski <[email protected]>
@@ -80,7 +80,7 @@
     2012-12-04 handles dirs as files, e.g. conversion of waters.com instruments raw folders (SB,CP)
     2015-07-07 on github.com
 """
-__version__ = "https://github.com/fgcz/fcc"
+__version__ = "https://github.com/fgcz/PyFGCZ"
 
 import os
 import urllib
@@ -98,6 +98,7 @@
 import logging
 import logging.handlers
 import hashlib
+import yaml
 
 
 def create_logger(name="fcc", address=("fgcz-ms.uzh.ch", 514)):
@@ -340,7 +341,7 @@ def matchFileToRules(fileDetails, rulesList, myHostname = None):
                         rule["converterDir"]) + " is already in the path.")
                     continue
                 matchedRules.append(rule)
-		print rule
+		# print rule
         except:
             pass
     return matchedRules
@@ -421,6 +422,19 @@ def read_config(self, url=''):
             logger.error("could not parse xml configuration")
             return None
 
+    """
+    write all considered cmds  into a file
+    """
+    def update_processed_cmd(self, filename = r'C:\FGCZ\fcc\cmds_conducted.yaml'):
+        if self.parameters['exec']:
+            try:
+                os.rename(filename, "{}.bak".format(filename))
+            except:
+                pass
+            with open(filename, "w") as f:
+                yaml.dump(self.processedCmdMD5Dict, f, default_flow_style=False)
+
+
     def process(self, file):
         """
         computes a match and executes cmd (add to spool dir)
@@ -502,6 +516,7 @@ def process(self, file):
                     if not candCmdLineMD5 in self.processedCmdMD5Dict:
 
                         self.processedCmdMD5Dict[candCmdLineMD5] = candCmdLine
+                        self.update_processed_cmd()
                         if self.parameters['exec']:
                             self.pool.map_async(myExecWorker0, [ candCmdLine ],
                                 callback=lambda i: logger.info("callback {0}".format(i)))

diff --git a/fgcz/fcc.pyc b/fgcz/fcc.pyc
diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@ def readme():
 
 
 setup(name='PyFGCZ',
-      version='0.5.8',
+      version='0.5.18',
       description="PyFGCZ contains BioBeamer and FCC python code.",
       long_description=readme(),
       classifiers=[
@@ -34,7 +34,7 @@ def readme():
       packages=['fgcz'],
       install_requires=[
         'PyYAML>=3',
-        'lxml==3.6.0' ],
+        'lxml>=3.4.2' ],
       scripts=[
         'fgcz/scripts/fgcz_biobeamer.py',
         'fgcz/scripts/fgcz_fcc_run_linux.py',