code smells removed

rigdenlab · Apr 15, 2017 · f7d1a7e · f7d1a7e
1 parent 015aa15
commit f7d1a7e
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/simbad/lattice/search.py b/simbad/lattice/search.py
@@ -216,7 +216,7 @@ def copy_results(self, pdb_db, dir=os.getcwd()):
 
         for count, result in enumerate(search_results):
             if count <= self.max_to_keep:
-                f_name = os.path.join(pdb_db, '{0}', 'pdb{1}.ent.gz'.format(result.pdb_code[1:3], result.pdb_code))
+                f_name = os.path.join(pdb_db, '{0}', 'pdb{1}.ent.gz').format(result.pdb_code[1:3], result.pdb_code)
                 with gzip.open(f_name, 'rb') as f_in:
                     f_name_out = os.path.join(out_dir, '{0}.pdb'.format(result.pdb_code))
                     with open(f_name_out, 'w') as f_out:

diff --git a/simbad/main.py b/simbad/main.py
@@ -54,7 +54,7 @@ def __init__(self):
     def setup(self, optd):
 
         if optd['work_dir']:
-            logger.info('Making a named work directory: {0}', optd['work_dir'])
+            logger.info('Making a named work directory: %s', optd['work_dir'])
             if os.path.isdir(optd['work_dir']):
                 msg = "Cannot create work_dir {0}".format(optd['work_dir'])
                 exit_util.exit_error(msg, sys.exc_info()[2])

diff --git a/simbad/util/clusterize.py b/simbad/util/clusterize.py
@@ -257,7 +257,7 @@ def submitJob(self, subScript=None, jobDir=None):
             command_line='bsub'
             stdin = open( subScript, "r")
         else:
-            msg = "Unrecognised QTYPE: ".format(self.QTYPE)
+            msg = "Unrecognised QTYPE: {0}".format(self.QTYPE)
             raise RuntimeError(msg)            
 
         logger.debug("Submitting job with command: %s", command_line)

diff --git a/simbad/util/logging_util.py b/simbad/util/logging_util.py
@@ -22,7 +22,7 @@ def setup_console_logging(level=logging.INFO,
     try:
         cl = logging.StreamHandler(stream=sys.stdout)
     except TypeError:
-        cl = logging.StreamHandler(strm=sys.stdout)
+        cl = logging.StreamHandler(stream=sys.stdout)
     cl.setLevel(level)
     formatter = logging.Formatter(formatstr)
     cl.setFormatter(formatter)
@@ -48,4 +48,4 @@ def setup_file_logging(logfile,
     fl.setFormatter(formatter)
     logger.addHandler(fl)
 
-    return logger
+    return logger
diff --git a/simbad/util/options_processor.py b/simbad/util/options_processor.py
@@ -33,7 +33,7 @@ def _exit(msg):
 
     if (optd['mtz'] and optd['sf_cif']):
         msg = "Please supply a single crystallographic data file."
-        _exit(msg, optd['work_dir'])
+        _exit(msg)
 
     ####################################################################################################################
     # NEED TO ADD A SECTION HERE TO CHECK THAT DATABASES ARE INSTALLED