Fix the remaining 1334 flake8 errors in scripts/ . Close #391.

scripts/data_libraries/build_lucene_index.py

@@ -10,19 +10,21 @@ Run from the ~/scripts/data_libraries directory:
 %sh build_lucene_index.sh
 """
 
-import sys
-import os
-import csv
-import urllib, urllib2
 import ConfigParser
+import csv
+import os
+import sys
+import urllib
+import urllib2
 
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+new_path.extend( sys.path[1:] )  # remove scripts/ from the path
 sys.path = new_path
 
 import galaxy.model.mapping
 from galaxy import config, model
 
+
 def main( ini_file ):
     sa_session, gconfig = get_sa_session( ini_file )
     max_size = float( gconfig.get( "fulltext_max_size", 100 ) ) * 1048576
@@ -37,11 +39,13 @@ def main( ini_file ):
         if os.path.exists( dataset_file ):
             os.remove( dataset_file )
 
+
 def build_index( search_url, dataset_file ):
     url = "%s/index?%s" % ( search_url, urllib.urlencode( { "docfile" : dataset_file } ) )
     request = urllib2.Request( url )
     request.get_method = lambda: "PUT"
-    response = urllib2.urlopen( request )
+    urllib2.urlopen( request )
+
 
 def create_dataset_file( dataset_iter ):
     dataset_file = os.path.join( os.getcwd(), "full-text-search-files.csv" )
@@ -52,6 +56,7 @@ def create_dataset_file( dataset_iter ):
     out_handle.close()
     return dataset_file
 
+
 def get_lddas( sa_session, max_size, ignore_exts ):
     for ldda in sa_session.query( model.LibraryDatasetDatasetAssociation ).filter_by( deleted=False ):
         if ( float( ldda.dataset.get_size() ) > max_size or ldda.extension in ignore_exts ):
@@ -60,6 +65,7 @@ def get_lddas( sa_session, max_size, ignore_exts ):
             fname = ldda.dataset.get_file_name()
         yield ldda.id, fname, _get_dataset_metadata(ldda).replace("\n", " ")
 
+
 def _get_dataset_metadata(ldda):
     """Retrieve descriptions and information associated with a dataset.
     """
@@ -73,6 +79,7 @@ def _get_dataset_metadata(ldda):
     return "%s %s %s %s %s" % (lds.name or "", lds_info, ldda.metadata.dbkey,
                                ldda.message, folder_info)
 
+
 def _get_folder_info(folder):
     """Get names and descriptions for all parent folders except top level.
     """
@@ -81,11 +88,12 @@ def _get_folder_info(folder):
         folder_info = _get_folder_info(folder.parent)
         folder_info += " %s %s" % (
             folder.name.replace("Unnamed folder", ""),
-                folder.description or "")
+            folder.description or "")
     return folder_info
 
+
 def get_sa_session( ini_file ):
-    conf_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } )
+    conf_parser = ConfigParser.ConfigParser( { 'here': os.getcwd() } )
     conf_parser.read( ini_file )
     kwds = dict()
     for key, value in conf_parser.items( "app:main" ):

scripts/data_libraries/build_whoosh_index.py

@@ -8,32 +8,33 @@ data library search section for more details.
 Run from the ~/scripts/data_libraries directory:
 %sh build_whoosh_index.sh
 """
-import sys, os, csv, urllib, urllib2, ConfigParser
-    
+import ConfigParser
+import os
+import sys
+
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
-new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+new_path.extend( sys.path[1:] )  # remove scripts/ from the path
 sys.path = new_path
 
 
 # Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether search is enabled.
 try:
     from whoosh.filedb.filestore import FileStorage
-    from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT
-    from whoosh.index import Index
+    from whoosh.fields import Schema, STORED, TEXT
     whoosh_search_enabled = True
     schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT )
     import galaxy.model.mapping
     from galaxy import config, model
-    import pkg_resources
-    pkg_resources.require( "SQLAlchemy >= 0.4" )
 except ImportError, e:
     whoosh_search_enabled = False
     schema = None
 
+
 def build_index( sa_session, whoosh_index_dir ):
     storage = FileStorage( whoosh_index_dir )
     index = storage.create_index( schema )
     writer = index.writer()
+
     def to_unicode( a_basestr ):
         if type( a_basestr ) is str:
             return unicode( a_basestr, 'utf-8' )
@@ -50,6 +51,7 @@ def build_index( sa_session, whoosh_index_dir ):
     writer.commit()
     print "Number of active library datasets indexed: ", lddas_indexed
 
+
 def get_lddas( sa_session ):
     for ldda in sa_session.query( model.LibraryDatasetDatasetAssociation ).filter_by( deleted=False ):
         id = ldda.id
@@ -66,6 +68,7 @@ def get_lddas( sa_session ):
             message = ''
         yield id, name, info, dbkey, message
 
+
 def get_sa_session_and_needed_config_settings( ini_file ):
     conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } )
     conf_parser.read( ini_file )