From 5ac4cb45a73bf42bae88cfc87988f80c261b56fa Mon Sep 17 00:00:00 2001
From: Christian Panse <cpanse@users.noreply.github.com>
Date: Thu, 2 Feb 2017 10:06:13 +0100
Subject: [PATCH 1/8] Update fcc.py

cosmetics on initial configuration host
---
 fgcz/fcc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fgcz/fcc.py b/fgcz/fcc.py
index 4d5e972..260f184 100644
--- a/fgcz/fcc.py
+++ b/fgcz/fcc.py
@@ -358,7 +358,7 @@ def usage():
 class Fcc:
     """
     """
-    parameters = {'config_url': "http://fgcz-s-021.uzh.ch/config/fcc_config.xml", 'readme_url': "http://fgcz-s-021.uzh.ch/config/fcc_readme.txt",
+    parameters = {'config_url': "http://fgcz-data.uzh.ch/config/fcc_config.xml", 'readme_url': "http://fgcz-s-021.uzh.ch/config/fcc_readme.txt",
                  'crawl_pattern': ['/srv/www/htdocs/Data2San/',
                         'p[0-9]{2,4}', 'Metabolomics',
                         '(GCT)_[0-9]',

From 1872626d82ba46da4e0f0716f8b18dd6bf57be7a Mon Sep 17 00:00:00 2001
From: Christian Panse <cpanse@users.noreply.github.com>
Date: Thu, 2 Feb 2017 10:09:05 +0100
Subject: [PATCH 2/8] Update fcc.py

---
 fgcz/fcc.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fgcz/fcc.py b/fgcz/fcc.py
index 260f184..8e774a2 100644
--- 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 <cp@fgcz.ethz.ch>
 # Simon Barkow-Oesterreicher 
 # Witold Eryk Wolski <wew@fgcz.ethz.ch>
@@ -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

From 975bd321881fc212025347113c93906a7f6dd982 Mon Sep 17 00:00:00 2001
From: Christian Panse <cpanse@users.noreply.github.com>
Date: Wed, 8 Mar 2017 09:02:21 +0100
Subject: [PATCH 3/8] Delete fcc.pyc

---
 fgcz/fcc.pyc | Bin 16991 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 fgcz/fcc.pyc

diff --git a/fgcz/fcc.pyc b/fgcz/fcc.pyc
deleted file mode 100644
index 5f7e0e555f0b700467bb2dde1c58d64b73040f18..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 2ca9ed080e425acc1f2e9e694b98314afc78a8dd Mon Sep 17 00:00:00 2001
From: Christian Panse <cpanse@users.noreply.github.com>
Date: Wed, 8 Mar 2017 09:02:29 +0100
Subject: [PATCH 4/8] Delete biobeamer.pyc

---
 fgcz/biobeamer.pyc | Bin 15477 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 fgcz/biobeamer.pyc

diff --git a/fgcz/biobeamer.pyc b/fgcz/biobeamer.pyc
deleted file mode 100644
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literal 0
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From 805f0f084d9365bdf62a966270976125d84302b2 Mon Sep 17 00:00:00 2001
From: Christian Panse <cpanse@users.noreply.github.com>
Date: Wed, 8 Mar 2017 09:02:38 +0100
Subject: [PATCH 5/8] Delete __init__.pyc

---
 fgcz/__init__.pyc | Bin 222 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 fgcz/__init__.pyc

diff --git a/fgcz/__init__.pyc b/fgcz/__init__.pyc
deleted file mode 100644
index adcdf471bc1c6672e44a3bf23d46a0c31eba7d86..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 222
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zDAomX^+StOi;DG=3-sgTlQUA2v-3+!iuD63-Q1m{^g-Hz;+c7wCGqik1(hWnKpi%@
S`6;D2sdgX}i$UHHU<3dL)h#9f


From d0cd25c3900050c5bc51c984e9ded35747e60594 Mon Sep 17 00:00:00 2001
From: Christian Panse <cp@fgcz.ethz.ch>
Date: Wed, 8 Mar 2017 09:25:53 +0100
Subject: [PATCH 6/8] added cmd file

---
 fgcz/fcc.py | 6 ++++++
 setup.py    | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/fgcz/fcc.py b/fgcz/fcc.py
index 8e774a2..97bfb5e 100644
--- a/fgcz/fcc.py
+++ b/fgcz/fcc.py
@@ -480,11 +480,17 @@ def process(self, file):
 
                     if not candCmdLineMD5 in self.processedCmdMD5Dict:
                         self.processedCmdMD5Dict[candCmdLineMD5] = candCmdLine
+                        update_processedCmdMD5Dict()
                         if self.parameters['exec']:
                             self.pool.map_async(myExecWorker0, [ candCmdLine ],
                                 callback=lambda i: logger.info("callback {0}".format(i)))
                             logger.info("added|cmd='{}' to pool".format(candCmdLine))
 
+    def update_processedCmdMD5Dict(self, filename = r'C:\FGCZ\fcc\processedCmd.txt'):
+        os.rename(filename, "{}.bak".format(filename))
+        with open(filename,"w") as f:
+            for cl in processedCmdMD5Dict.keys:
+                f.write("{}\n".format(cl))
 
     def run(self):
         """
diff --git a/setup.py b/setup.py
index f244624..6574927 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@ def readme():
 
 
 setup(name='PyFGCZ',
-      version='0.5.8',
+      version='0.5.9',
       description="PyFGCZ contains BioBeamer and FCC python code.",
       long_description=readme(),
       classifiers=[

From bd09cb525ef1562ab7d1afa428ffaceb747b188d Mon Sep 17 00:00:00 2001
From: cpanse <cp@fgcz.ethz.ch>
Date: Wed, 8 Mar 2017 12:22:02 +0100
Subject: [PATCH 7/8] try except

---
 fgcz/fcc.py | 24 ++++++++++++++++--------
 setup.py    |  4 ++--
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/fgcz/fcc.py b/fgcz/fcc.py
index 97bfb5e..ed5d119 100644
--- a/fgcz/fcc.py
+++ b/fgcz/fcc.py
@@ -340,7 +340,7 @@ 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 +421,20 @@ 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\processedCmd.txt'):
+        if self.parameters['exec']:
+            try:
+                os.rename(filename, "{}.bak".format(filename))
+            except:
+                pass
+            with open(filename,"w") as f:
+                for cl in processedCmdMD5Dict.keys:
+                    f.write("{}\n".format(cl))
+
+
     def process(self, file):
         """
         computes a match and executes cmd (add to spool dir)
@@ -480,18 +494,12 @@ def process(self, file):
 
                     if not candCmdLineMD5 in self.processedCmdMD5Dict:
                         self.processedCmdMD5Dict[candCmdLineMD5] = candCmdLine
-                        update_processedCmdMD5Dict()
+                        self.update_processed_cmd()
                         if self.parameters['exec']:
                             self.pool.map_async(myExecWorker0, [ candCmdLine ],
                                 callback=lambda i: logger.info("callback {0}".format(i)))
                             logger.info("added|cmd='{}' to pool".format(candCmdLine))
 
-    def update_processedCmdMD5Dict(self, filename = r'C:\FGCZ\fcc\processedCmd.txt'):
-        os.rename(filename, "{}.bak".format(filename))
-        with open(filename,"w") as f:
-            for cl in processedCmdMD5Dict.keys:
-                f.write("{}\n".format(cl))
-
     def run(self):
         """
 
diff --git a/setup.py b/setup.py
index 6574927..8be52a6 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@ def readme():
 
 
 setup(name='PyFGCZ',
-      version='0.5.9',
+      version='0.5.14',
       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',

From 743c9f3806ea77898d50f197c57c2ce4d20c9a23 Mon Sep 17 00:00:00 2001
From: cpanse <cp@fgcz.ethz.ch>
Date: Wed, 8 Mar 2017 12:44:44 +0100
Subject: [PATCH 8/8] 0.5.18

---
 fgcz/fcc.py | 8 ++++----
 setup.py    | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/fgcz/fcc.py b/fgcz/fcc.py
index ed5d119..b21b825 100644
--- a/fgcz/fcc.py
+++ b/fgcz/fcc.py
@@ -98,6 +98,7 @@
 import logging
 import logging.handlers
 import hashlib
+import yaml
 
 
 def create_logger(name="fcc", address=("130.60.81.148", 514)):
@@ -424,15 +425,14 @@ def read_config(self, url=''):
     """
     write all considered cmds  into a file
     """
-    def update_processed_cmd(self, filename = r'C:\FGCZ\fcc\processedCmd.txt'):
+    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:
-                for cl in processedCmdMD5Dict.keys:
-                    f.write("{}\n".format(cl))
+            with open(filename, "w") as f:
+                yaml.dump(self.processedCmdMD5Dict, f, default_flow_style=False)
 
 
     def process(self, file):
diff --git a/setup.py b/setup.py
index 8be52a6..74d8119 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@ def readme():
 
 
 setup(name='PyFGCZ',
-      version='0.5.14',
+      version='0.5.18',
       description="PyFGCZ contains BioBeamer and FCC python code.",
       long_description=readme(),
       classifiers=[