Merge pull request #537 from nsoranzo/dev

Standardize nice_size() import.

lib/galaxy/datatypes/binary.py

@@ -1,7 +1,6 @@
 """Binary classes"""
 
 import binascii
-import data
 import gzip
 import logging
 import os
@@ -14,13 +13,12 @@
 
 from galaxy import eggs
 eggs.require( "bx-python" )
-
 from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE
 
-from galaxy.util import sqlite
 from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListParameter, DictParameter
 from galaxy.datatypes import metadata
-import dataproviders
+from galaxy.util import nice_size, sqlite
+from . import data, dataproviders
 
 with warnings.catch_warnings():
     warnings.simplefilter( "ignore" )
@@ -71,7 +69,7 @@ def set_peek( self, dataset, is_multi_byte=False ):
         """Set the peek and blurb text"""
         if not dataset.dataset.purged:
             dataset.peek = 'binary data'
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -99,7 +97,7 @@ class Ab1( Binary ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary ab1 sequence file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -108,7 +106,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary ab1 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Binary ab1 sequence file (%s)" % ( nice_size( dataset.get_size() ) )
 
 Binary.register_unsniffable_binary_ext("ab1")
 
@@ -143,7 +141,7 @@ class CompressedArchive( Binary ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Compressed binary file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -152,7 +150,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Compressed binary file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Compressed binary file (%s)" % ( nice_size( dataset.get_size() ) )
 
 Binary.register_unsniffable_binary_ext("compressed_archive")
 
@@ -369,7 +367,7 @@ def sniff( self, filename ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary bam alignments file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -378,7 +376,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Binary bam alignments file (%s)" % ( nice_size( dataset.get_size() ) )
 
     # ------------- Dataproviders
     # pipe through samtools view
@@ -524,7 +522,7 @@ class H5( Binary ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary h5 file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -533,7 +531,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary h5 sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Binary h5 sequence file (%s)" % ( nice_size( dataset.get_size() ) )
 
 Binary.register_unsniffable_binary_ext("h5")
 
@@ -546,7 +544,7 @@ class Scf( Binary ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary scf sequence file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -555,7 +553,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary scf sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Binary scf sequence file (%s)" % ( nice_size( dataset.get_size() ) )
 
 Binary.register_unsniffable_binary_ext("scf")
 
@@ -582,7 +580,7 @@ def sniff( self, filename ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary sff file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -591,7 +589,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary sff file (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "Binary sff file (%s)" % ( nice_size( dataset.get_size() ) )
 
 Binary.register_sniffable_binary_format("sff", "sff", Sff)
 
@@ -624,7 +622,7 @@ def sniff( self, filename ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary UCSC %s file" % self._name
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -633,7 +631,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "Binary UCSC %s file (%s)" % ( self._name, data.nice_size( dataset.get_size() ) )
+            return "Binary UCSC %s file (%s)" % ( self._name, nice_size( dataset.get_size() ) )
 
 Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig)
 
@@ -671,15 +669,15 @@ def sniff(self, filename):
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
             dataset.peek = "Binary TwoBit format nucleotide file"
-            dataset.blurb = data.nice_size(dataset.get_size())
+            dataset.blurb = nice_size(dataset.get_size())
         else:
             return super(TwoBit, self).set_peek(dataset, is_multi_byte)
 
     def display_peek(self, dataset):
         try:
             return dataset.peek
         except:
-            return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size()))
+            return "Binary TwoBit format nucleotide file (%s)" % (nice_size(dataset.get_size()))
 
 Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit)
 
@@ -747,7 +745,7 @@ def set_peek( self, dataset, is_multi_byte=False ):
                     except:
                         continue
             dataset.peek = '\n'.join(lines)
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -756,7 +754,7 @@ def display_peek( self, dataset ):
         try:
             return dataset.peek
         except:
-            return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) )
+            return "SQLite Database (%s)" % ( nice_size( dataset.get_size() ) )
 
     @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings )
     def sqlite_dataprovider( self, dataset, **settings ):
@@ -817,7 +815,7 @@ def sniff( self, filename ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "Gemini SQLite Database, version %s" % ( dataset.metadata.gemini_version or 'unknown' )
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -875,7 +873,7 @@ def sniff( self, filename ):
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
             dataset.peek = 'Binary sra file'
-            dataset.blurb = data.nice_size(dataset.get_size())
+            dataset.blurb = nice_size(dataset.get_size())
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -884,7 +882,7 @@ def display_peek(self, dataset):
         try:
             return dataset.peek
         except:
-            return 'Binary sra file (%s)' % (data.nice_size(dataset.get_size()))
+            return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
 
 Binary.register_sniffable_binary_format('sra', 'sra', Sra)
 

lib/galaxy/datatypes/genetics.py

@@ -22,8 +22,8 @@
 from galaxy.datatypes.images import Html
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.tabular import Tabular
+from galaxy.util import nice_size
 from galaxy.web import url_for
-from . import data
 
 gal_Log = logging.getLogger(__name__)
 verbose = False
@@ -341,7 +341,7 @@ class SNPMatrix(Rgenetics):
     def set_peek( self, dataset, **kwd ):
         if not dataset.dataset.purged:
             dataset.peek = "Binary RGenetics file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'

lib/galaxy/datatypes/images.py

@@ -2,14 +2,16 @@
 Image classes
 """
 
-import data
+import imghdr
 import logging
+import zipfile
+from urllib import quote_plus
+
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.util.image_util import check_image_type
-from urllib import quote_plus
-import zipfile
-import imghdr
+from galaxy.util import nice_size
+from . import data
 
 try:
     import Image as PIL
@@ -39,7 +41,7 @@ class Image( data.Data ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = 'Image in %s format' % dataset.extension
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -303,7 +305,7 @@ class Html( data.Text ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = "HTML file"
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'

lib/galaxy/datatypes/msa.py

@@ -1,12 +1,12 @@
-from galaxy.datatypes.data import Text
+import logging
+import os
+
 from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.data import get_file_peek
-from galaxy.datatypes.data import nice_size
+from galaxy.datatypes.data import get_file_peek, Text
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.util import generic_util
-import os
+from galaxy.util import nice_size
 
-import logging
 log = logging.getLogger(__name__)
 
 

lib/galaxy/datatypes/proteomics.py

@@ -1,17 +1,16 @@
 """
 Proteomics Datatypes
 """
+import binascii
 import logging
 import re
-import binascii
 
 from galaxy.datatypes import data
+from galaxy.datatypes.binary import Binary, SQlite
 from galaxy.datatypes.data import Text
-from galaxy.datatypes.xml import GenericXml
-from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.binary import SQlite
 from galaxy.datatypes.tabular import Tabular
-from galaxy.util import sqlite
+from galaxy.datatypes.xml import GenericXml
+from galaxy.util import nice_size, sqlite
 
 
 log = logging.getLogger(__name__)
@@ -268,7 +267,7 @@ def sniff(self, filename):
     def set_peek(self, dataset, is_multi_byte=False):
         if not dataset.dataset.purged:
             dataset.peek = "Thermo Finnigan RAW file"
-            dataset.blurb = data.nice_size(dataset.get_size())
+            dataset.blurb = nice_size(dataset.get_size())
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -277,7 +276,7 @@ def display_peek(self, dataset):
         try:
             return dataset.peek
         except:
-            return "Thermo Finnigan RAW file (%s)" % (data.nice_size(dataset.get_size()))
+            return "Thermo Finnigan RAW file (%s)" % (nice_size(dataset.get_size()))
 
 Binary.register_sniffable_binary_format("thermo.raw", "raw", ThermoRAW )
 

lib/galaxy/datatypes/sequence.py

@@ -2,22 +2,22 @@
 Sequence classes
 """
 
-from . import data
 import gzip
 import json
 import logging
 import os
 import re
 import string
-
 from cgi import escape
 
 from galaxy import eggs, util
 from galaxy.datatypes import metadata
 from galaxy.datatypes.checkers import is_gzip
-from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.util.image_util import check_image_type
+from galaxy.util import nice_size
+from . import data
 
 try:
     eggs.require( "bx-python" )
@@ -103,7 +103,7 @@ def set_peek( self, dataset, is_multi_byte=False ):
             if dataset.metadata.sequences:
                 dataset.blurb = "%s sequences" % util.commaify( str( dataset.metadata.sequences ) )
             else:
-                dataset.blurb = data.nice_size( dataset.get_size() )
+                dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
@@ -940,7 +940,7 @@ class RNADotPlotMatrix( data.Data ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             dataset.peek = 'RNA Dot Plot format (Postscript derivative)'
-            dataset.blurb = data.nice_size( dataset.get_size() )
+            dataset.blurb = nice_size( dataset.get_size() )
         else:
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'