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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Reverted missing python version check for zipfile setup
Changed download archive names for both libraries and for history items so they're related to the content - uses data.name rather than one fixed string for all
This commit is contained in:
Ross Lazarus
@@ -1,4 +1,4 @@
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import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob
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import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob, sys
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from galaxy.web.base.controller import *
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from galaxy.web.framework.helpers import time_ago, iff, grids
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@@ -11,6 +11,11 @@ import pkg_resources;
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pkg_resources.require( "Paste" )
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import paste.httpexceptions
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if sys.version_info[:2] < ( 2, 6 ):
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zipfile.BadZipFile = zipfile.error
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if sys.version_info[:2] < ( 2, 5 ):
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zipfile.LargeZipFile = zipfile.error
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tmpd = tempfile.mkdtemp()
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comptypes=[]
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ziptype = '32'
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@@ -204,6 +209,9 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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def archive_composite_dataset( self, trans, data=None, **kwd ):
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# save a composite object into a compressed archive for downloading
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params = util.Params( kwd )
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valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
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outfname = data.name[0:150]
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outfname = ''.join(c in valid_chars and c or '_' for c in outfname)
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if (params.do_action == None):
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params.do_action = 'zip' # default
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msg = util.restore_text( params.get( 'msg', '' ) )
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@@ -230,7 +238,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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except (OSError, zipfile.BadZipFile):
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error = True
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log.exception( "Unable to create archive for download" )
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msg = "Unable to create archive for %s for download, please report this error" % data.name
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msg = "Unable to create archive for %s for download, please report this error" % outfname
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messagetype = 'error'
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if not error:
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current_user_roles = trans.get_current_user_roles()
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@@ -239,7 +247,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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fname = os.path.split(path)[-1]
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basename = data.metadata.base_name
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efp = data.extra_files_path
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htmlname = os.path.splitext(data.name)[0]
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htmlname = os.path.splitext(outfname)[0]
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if not htmlname.endswith(ext):
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htmlname = '%s_%s' % (htmlname,ext)
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archname = '%s.html' % htmlname # fake the real nature of the html file
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@@ -276,14 +284,14 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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messagetype = 'error'
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if not error:
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trans.response.set_content_type( "application/x-zip-compressed" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyCompositeObject.zip"
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.zip" % outfname
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return tmpfh
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else:
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trans.response.set_content_type( "application/x-tar" )
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outext = 'tgz'
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if params.do_action == 'tbz':
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outext = 'tbz'
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % outext
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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return archive.stream
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@@ -294,7 +302,8 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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@web.expose
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def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd):
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"""Catches the dataset id and displays file contents as directed"""
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composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
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composite_extensions.append('html') # for archiving composite datatypes
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# DEPRECATION: We still support unencoded ids for backward compatibility
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try:
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dataset_id = int( dataset_id )
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@@ -329,8 +338,6 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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trans.log_event( "Display dataset id: %s" % str( dataset_id ) )
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if to_ext: # Saving the file
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composite_extensions = trans.app.datatypes_registry.get_composite_extensions( )
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composite_extensions.append('html')
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if data.ext in composite_extensions:
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return self.archive_composite_dataset( trans, data, **kwd )
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else:
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@@ -340,7 +347,7 @@ class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssoc
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valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
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fname = data.name
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fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150]
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trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext)
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trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s]%s" % (data.hid, fname, to_ext)
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return open( data.file_name )
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if os.path.exists( data.file_name ):
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max_peek_size = 1000000 # 1 MB
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@@ -1312,6 +1312,7 @@ class LibraryCommon( BaseController ):
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else:
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error = False
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try:
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outext = 'zip'
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if action == 'zip':
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# Can't use mkstemp - the file must not exist first
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tmpd = tempfile.mkdtemp()
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@@ -1323,8 +1324,10 @@ class LibraryCommon( BaseController ):
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archive.add = lambda x, y: archive.write( x, y.encode('CP437') )
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elif action == 'tgz':
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archive = util.streamball.StreamBall( 'w|gz' )
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outext = 'gz'
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elif action == 'tbz':
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archive = util.streamball.StreamBall( 'w|bz2' )
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outext = 'bz2'
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except (OSError, zipfile.BadZipFile):
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error = True
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log.exception( "Unable to create archive for download" )
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@@ -1357,11 +1360,11 @@ class LibraryCommon( BaseController ):
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seen.append( path )
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if is_composite: # need to add all the components from the extra_files_path to the zip
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zpath = os.path.split(path)[-1] # comes as base_name/fname
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zpathext = os.path.splitext(zpath)[-1]
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outfname,zpathext = os.path.splitext(zpath)
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if zpathext == '':
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zpath = '%s.html' % zpath # fake the real nature of the html file
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try:
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archive.add(ldda.dataset.file_name,zpath)
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archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set
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except IOError:
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error = True
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log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
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@@ -1375,7 +1378,7 @@ class LibraryCommon( BaseController ):
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archive.add( fpath,fname )
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except IOError:
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error = True
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log.exception( "Unable to add %s to temporary library download archive" % fname)
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log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
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msg = "Unable to create archive for download, please report this error"
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messagetype = 'error'
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continue
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@@ -1402,11 +1405,11 @@ class LibraryCommon( BaseController ):
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messagetype = 'error'
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if not error:
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trans.response.set_content_type( "application/x-zip-compressed" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext)
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return tmpfh
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else:
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trans.response.set_content_type( "application/x-tar" )
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action
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trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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return archive.stream
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