Consolidate usage of 'valid_chars' in the application.

lib/galaxy/datatypes/binary.py

@@ -17,7 +17,7 @@
 
 from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListParameter, DictParameter
 from galaxy.datatypes import metadata
-from galaxy.util import nice_size, sqlite, which
+from galaxy.util import nice_size, sqlite, which, FILENAME_VALID_CHARS
 from . import data, dataproviders
 
 
@@ -78,8 +78,7 @@ def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None
         trans.log_event( "Display dataset id: %s" % str( dataset.id ) )
         trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size )
         to_ext = dataset.extension
-        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-        fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150]
+        fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in dataset.name)[0:150]
         trans.response.set_content_type( "application/octet-stream" )  # force octet-stream so Safari doesn't append mime extensions to filename
         trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
         return open( dataset.file_name )

lib/galaxy/datatypes/data.py

@@ -15,6 +15,7 @@
 
 from galaxy import util
 from galaxy.datatypes.metadata import MetadataElement  # import directly to maintain ease of use in Datatype class definitions
+from galaxy.util import FILENAME_VALID_CHARS
 from galaxy.util import inflector
 from galaxy.util import unicodify
 from galaxy.util.bunch import Bunch
@@ -236,9 +237,8 @@ def _archive_main_file(self, archive, display_name, data_filename):
     def _archive_composite_dataset( self, trans, data=None, **kwd ):
         # save a composite object into a compressed archive for downloading
         params = util.Params( kwd )
-        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
         outfname = data.name[0:150]
-        outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
+        outfname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in outfname)
         if params.do_action is None:
             params.do_action = 'zip'  # default
         msg = util.restore_text( params.get( 'msg', ''  ) )
@@ -308,8 +308,7 @@ def _archive_composite_dataset( self, trans, data=None, **kwd ):
 
     def _serve_raw(self, trans, dataset, to_ext):
         trans.response.headers['Content-Length'] = int( os.stat( dataset.file_name ).st_size )
-        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-        fname = ''.join(c in valid_chars and c or '_' for c in dataset.name)[0:150]
+        fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in dataset.name)[0:150]
         trans.response.set_content_type( "application/octet-stream" )  # force octet-stream so Safari doesn't append mime extensions to filename
         trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (dataset.hid, fname, to_ext)
         return open( dataset.file_name )
@@ -358,8 +357,7 @@ def display_data(self, trans, data, preview=False, filename=None, to_ext=None, *
                 trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size )
                 if not to_ext:
                     to_ext = data.extension
-                valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-                fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
+                fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
                 trans.response.set_content_type( "application/octet-stream" )  # force octet-stream so Safari doesn't append mime extensions to filename
                 trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (data.hid, fname, to_ext)
                 return open( data.file_name )

lib/galaxy/datatypes/neo4j.py

@@ -5,8 +5,10 @@
 import sys
 import shutil
 import os
-from galaxy.datatypes.images import Html
+
 from galaxy.datatypes.data import Data
+from galaxy.datatypes.images import Html
+from galaxy.util import FILENAME_VALID_CHARS
 
 gal_Log = logging.getLogger(__name__)
 verbose = True
@@ -69,8 +71,7 @@ def display_data(self, trans, data, preview=False, filename=None,
             dir_name = str(os.path.dirname(trans.app.object_store.get_filename(data.dataset))) + neo4j_dir_name
 
             # generate unique filename for this dataset
-            valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-            fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
+            fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
 
             # zip the target directory (dir_name) using the fname
             shutil.make_archive(fname, 'zip', dir_name)

lib/galaxy/tools/imp_exp/export_history.py

@@ -12,13 +12,14 @@
 import tarfile
 from json import dumps, loads
 
+from galaxy.util import FILENAME_VALID_CHARS
+
 
 def get_dataset_filename( name, ext, hid ):
     """
     Builds a filename for a dataset using its name an extension.
     """
-    valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-    base = ''.join( c in valid_chars and c or '_' for c in name )
+    base = ''.join( c in FILENAME_VALID_CHARS and c or '_' for c in name )
     return base + "_%s.%s" % (hid, ext)
 
 
@@ -67,7 +68,7 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
                         dataset_extra_files_path = 'datasets/extra_files_path_%s' % dataset_hid
                         for fname in file_list:
                             history_archive.add( os.path.join( extra_files_path, fname ),
-                                                arcname=( os.path.join( dataset_extra_files_path, fname ) ) )
+                                                 arcname=( os.path.join( dataset_extra_files_path, fname ) ) )
                         dataset_attrs[ 'extra_files_path' ] = dataset_extra_files_path
                     else:
                         dataset_attrs[ 'extra_files_path' ] = ''

lib/galaxy/util/__init__.py

@@ -62,6 +62,7 @@ def list_map(f, input):
 DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8')
 NULL_CHAR = '\000'
 BINARY_CHARS = [ NULL_CHAR ]
+FILENAME_VALID_CHARS = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
 
 
 def remove_protocol_from_url( url ):

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -324,8 +324,7 @@ def get_metadata_file( self, trans, history_content_id, history_id, metadata_fil
         try:
             hda = self.hda_manager.get_accessible( decoded_content_id, trans.user )
             file_ext = hda.metadata.spec.get(metadata_file).get("file_ext", metadata_file)
-            valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-            fname = ''.join(c in valid_chars and c or '_' for c in hda.name)[0:150]
+            fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in hda.name)[0:150]
             trans.response.headers["Content-Type"] = "application/octet-stream"
             trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (hda.hid, fname, file_ext)
             return open(hda.metadata.get(metadata_file).file_name)

lib/galaxy/webapps/galaxy/api/lda_datasets.py

@@ -709,9 +709,8 @@ def traverse( folder ):
                 fStat = os.stat( dataset.file_name )
                 trans.response.set_content_type( ldda.get_mime() )
                 trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
-                valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
                 fname = ldda.name
-                fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
+                fname = ''.join( c in util.FILENAME_VALID_CHARS and c or '_' for c in fname )[ 0:150 ]
                 trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname
                 try:
                     return open( dataset.file_name )

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -181,8 +181,7 @@ def get_metadata_file(self, trans, hda_id, metadata_name):
         if not data or not self._can_access_dataset( trans, data ):
             return trans.show_error_message( "You are not allowed to access this dataset" )
 
-        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
-        fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150]
+        fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in data.name)[0:150]
 
         file_ext = data.metadata.spec.get(metadata_name).get("file_ext", metadata_name)
         trans.response.headers["Content-Type"] = "application/octet-stream"

lib/galaxy/webapps/galaxy/controllers/library_common.py

@@ -19,7 +19,7 @@
 from galaxy import util, web
 from galaxy.security import Action
 from galaxy.tools.actions import upload_common
-from galaxy.util import inflector, unicodify
+from galaxy.util import inflector, unicodify, FILENAME_VALID_CHARS
 from galaxy.util.streamball import StreamBall
 from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
 from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field
@@ -1519,9 +1519,8 @@ def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **
             trans.response.set_content_type( ldda.get_mime() )
             fStat = os.stat( ldda.file_name )
             trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
-            valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
             fname = ldda.name
-            fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
+            fname = ''.join( c in FILENAME_VALID_CHARS and c or '_' for c in fname )[ 0:150 ]
             trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname
             try:
                 return open( ldda.file_name )

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -9,7 +9,7 @@
 
 from galaxy import web
 from galaxy import util
-from galaxy.util import listify, Params, string_as_bool
+from galaxy.util import listify, Params, string_as_bool, FILENAME_VALID_CHARS
 
 from galaxy.web.base import controller
 from galaxy.model.item_attrs import UsesAnnotations
@@ -217,9 +217,8 @@ def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", encoded_
                     trans.response.headers['Content-Length'] = int(fStat.st_size)
                     if toext[0:1] != ".":
                         toext = "." + toext
-                    valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
                     fname = data.name
-                    fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150]
+                    fname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in fname)[0:150]
                     trans.response.headers["Content-Disposition"] = 'attachment; filename="GalaxyHistoryItem-%s-[%s]%s"' % (data.hid, fname, toext)
                 trans.log_event( "Display dataset id: %s" % str(id) )
                 try:

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -18,7 +18,7 @@
 from galaxy.managers import workflows
 from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.model.mapping import desc
-from galaxy.util import unicodify
+from galaxy.util import unicodify, FILENAME_VALID_CHARS
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import error, url_for
 from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
@@ -815,9 +815,8 @@ def export_to_file( self, trans, id ):
             # This workflow has a tool that's missing from the distribution
             trans.response.status = 400
             return "Workflow cannot be exported due to missing tools."
-        valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
         sname = stored.name
-        sname = ''.join(c in valid_chars and c or '_' for c in sname)[0:150]
+        sname = ''.join(c in FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150]
         trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy-Workflow-%s.ga"' % ( sname )
         trans.response.set_content_type( 'application/galaxy-archive' )
         return stored_dict

tools/genomespace/genomespace_file_browser.py

@@ -7,6 +7,7 @@
 import urllib2
 import urlparse
 
+from galaxy.util import FILENAME_VALID_CHARS
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
 
@@ -46,8 +47,6 @@
 GENOMESPACE_UNKNOWN_FORMAT_KEY = 'unknown'
 GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = None
 
-VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
-
 
 def chunk_write( source_stream, target_stream, source_method="read", target_method="write" ):
     source_method = getattr( source_stream, source_method )
@@ -166,7 +165,7 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
         metadata_dict = None
         original_filename = filename
         if output_filename is None:
-            filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
+            filename = ''.join( c in FILENAME_VALID_CHARS and c or '-' for c in filename )
             while filename in used_filenames:
                 filename = "-%s" % filename
             used_filenames.append( filename )

tools/genomespace/genomespace_importer.py

@@ -12,6 +12,7 @@
 
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
+from galaxy.util import FILENAME_VALID_CHARS
 
 GENOMESPACE_API_VERSION_STRING = "v1.0"
 GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING )
@@ -45,8 +46,6 @@
                                  'gmt': 'gmt',
                                  'gct': 'gct'}
 
-VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
-
 
 def chunk_write( source_stream, target_stream, source_method="read", target_method="write" ):
     source_method = getattr( source_stream, source_method )
@@ -192,7 +191,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
         # if using tmp file, move the file to the new file path dir to get scooped up later
         if using_temp_file:
             original_filename = filename
-            filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
+            filename = ''.join( c in FILENAME_VALID_CHARS and c or '-' for c in filename )
             while filename in used_filenames:
                 filename = "-%s" % filename
             used_filenames.append( filename )