Typo fixes and small cleanups

lib/galaxy/datatypes/proteomics.py

@@ -62,7 +62,7 @@ class PepXmlReport(Tabular):
 
     def __init__(self, **kwd):
         super(PepXmlReport, self).__init__(**kwd)
-        self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probabaility']
+        self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probability']
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""

lib/galaxy/jobs/runners/__init__.py

@@ -367,7 +367,7 @@ def _handle_runner_state(self, runner_state, job_state):
                 if job_state.runner_state_handled:
                     break
         except:
-            log.exception('Caught exception in runner state handler:')
+            log.exception('Caught exception in runner state handler')
 
     def fail_job(self, job_state, exception=False):
         if getattr(job_state, 'stop_job', True):
@@ -593,11 +593,11 @@ def finish_job(self, job_state):
 
         # wait for the files to appear
         which_try = 0
-        while which_try < (self.app.config.retry_job_output_collection + 1):
+        while which_try < self.app.config.retry_job_output_collection + 1:
             try:
                 stdout = shrink_stream_by_size(open(job_state.output_file, "r"), DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
                 stderr = shrink_stream_by_size(open(job_state.error_file, "r"), DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
-                which_try = (self.app.config.retry_job_output_collection + 1)
+                break
             except Exception as e:
                 if which_try == self.app.config.retry_job_output_collection:
                     stdout = ''

lib/galaxy/managers/collections.py

@@ -23,7 +23,7 @@
 
 class DatasetCollectionManager(object):
     """
-    Abstraction for interfacing with dataset collections instance - ideally abstarcts
+    Abstraction for interfacing with dataset collections instance - ideally abstracts
     out model and plugin details.
     """
     ELEMENTS_UNINITIALIZED = object()

lib/galaxy/tools/loader.py

@@ -1,13 +1,13 @@
 from galaxy.util.xml_macros import (
     imported_macro_paths,
     load,
-    load_with_refereces,
+    load_with_references,
     raw_xml_tree,
     template_macro_params,
 )
 
 load_tool = load
-load_tool_with_refereces = load_with_refereces
+load_tool_with_refereces = load_with_references
 raw_tool_xml_tree = raw_xml_tree
 
 __all__ = (

lib/galaxy/tools/xsd/galaxy.xsd

@@ -1299,7 +1299,7 @@ provides a demonstration of using this tag.
     </xs:annotation>
     <xs:attribute name="name" type="xs:string" use="required">
       <xs:annotation>
-        <xs:documentation xml:lang="en">Name of the metdata element to check.</xs:documentation>
+        <xs:documentation xml:lang="en">Name of the metadata element to check.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="value" type="xs:string" use="required">
@@ -2770,7 +2770,7 @@ dataset for the contained input of the type specified using the ``type`` tag.
     </xs:annotation>
     <xs:attribute name="name" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">Name of cheetah variable to create for converted dataset.</xs:documentation>
+        <xs:documentation xml:lang="en">Name of Cheetah variable to create for converted dataset.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="type" type="xs:string">

lib/galaxy/util/__init__.py

@@ -785,9 +785,9 @@ def write(self, str):
                                   # number of sections in help content.
     }
 
-    return unicodify(docutils_core.publish_string(s,
-                      writer=docutils_html4css1.Writer(),
-                      settings_overrides=settings_overrides))
+    return unicodify(docutils_core.publish_string(
+        s, writer=docutils_html4css1.Writer(),
+        settings_overrides=settings_overrides))
 
 
 def xml_text(root, name=None):

lib/galaxy/util/xml_macros.py

@@ -7,7 +7,7 @@
 REQUIRED_PARAMETER = object()
 
 
-def load_with_refereces(path):
+def load_with_references(path):
     """Load XML documentation from file system and preprocesses XML macros.
 
     Return the XML representation of the expanded tree and paths to
@@ -29,7 +29,7 @@ def load_with_refereces(path):
 
 
 def load(path):
-    tree, _ = load_with_refereces(path)
+    tree, _ = load_with_references(path)
     return tree
 
 
@@ -307,7 +307,7 @@ def _parse_xml(fname):
 __all__ = (
     "imported_macro_paths",
     "load",
-    "load_with_refereces",
+    "load_with_references",
     "raw_xml_tree",
     "template_macro_params",
 )