# HG changeset patch
# User davidvanzessen
# Date 1427716716 14400
# Node ID 9dd557f1715307c163f3df372193623868d3d993
# Parent 072167754619f8569fdea078ac1ac8c94dc85fde
Deleted selected files
diff -r 072167754619 -r 9dd557f17153 uploadzip.py
--- a/uploadzip.py Mon Mar 30 07:58:17 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,391 +0,0 @@
-#!/usr/bin/env python
-#Processes uploads from the user.
-
-# WARNING: Changes in this tool (particularly as related to parsing) may need
-# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
-
-import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii
-from galaxy import eggs
-# need to import model before sniff to resolve a circular import dependency
-import galaxy.model
-from galaxy.datatypes.checkers import *
-from galaxy.datatypes import sniff
-from galaxy.datatypes.binary import *
-from galaxy.datatypes.images import Pdf
-from galaxy.datatypes.registry import Registry
-from galaxy import util
-from galaxy.datatypes.util.image_util import *
-from galaxy.util.json import *
-
-try:
- import Image as PIL
-except ImportError:
- try:
- from PIL import Image as PIL
- except:
- PIL = None
-
-try:
- import bz2
-except:
- bz2 = None
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def stop_err( msg, ret=1 ):
- sys.stderr.write( msg )
- sys.exit( ret )
-def file_err( msg, dataset, json_file ):
- json_file.write( to_json_string( dict( type = 'dataset',
- ext = 'data',
- dataset_id = dataset.dataset_id,
- stderr = msg ) ) + "\n" )
- # never remove a server-side upload
- if dataset.type in ( 'server_dir', 'path_paste' ):
- return
- try:
- os.remove( dataset.path )
- except:
- pass
-def safe_dict(d):
- """
- Recursively clone json structure with UTF-8 dictionary keys
- http://mellowmachines.com/blog/2009/06/exploding-dictionary-with-unicode-keys-as-python-arguments/
- """
- if isinstance(d, dict):
- return dict([(k.encode('utf-8'), safe_dict(v)) for k,v in d.iteritems()])
- elif isinstance(d, list):
- return [safe_dict(x) for x in d]
- else:
- return d
-def parse_outputs( args ):
- rval = {}
- for arg in args:
- id, files_path, path = arg.split( ':', 2 )
- rval[int( id )] = ( path, files_path )
- return rval
-def add_file( dataset, registry, json_file, output_path ):
- data_type = None
- line_count = None
- converted_path = None
- stdout = None
- link_data_only = dataset.get( 'link_data_only', 'copy_files' )
- in_place = dataset.get( 'in_place', True )
-
- try:
- ext = dataset.file_type
- except AttributeError:
- file_err( 'Unable to process uploaded file, missing file_type parameter.', dataset, json_file )
- return
-
- if dataset.type == 'url':
- try:
- page = urllib.urlopen( dataset.path ) #page will be .close()ed by sniff methods
- temp_name, dataset.is_multi_byte = sniff.stream_to_file( page, prefix='url_paste', source_encoding=util.get_charset_from_http_headers( page.headers ) )
- except Exception, e:
- file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file )
- return
- dataset.path = temp_name
- # See if we have an empty file
- if not os.path.exists( dataset.path ):
- file_err( 'Uploaded temporary file (%s) does not exist.' % dataset.path, dataset, json_file )
- return
- if not os.path.getsize( dataset.path ) > 0:
- file_err( 'The uploaded file is empty', dataset, json_file )
- return
- if not dataset.type == 'url':
- # Already set is_multi_byte above if type == 'url'
- try:
- dataset.is_multi_byte = util.is_multi_byte( codecs.open( dataset.path, 'r', 'utf-8' ).read( 100 ) )
- except UnicodeDecodeError, e:
- dataset.is_multi_byte = False
- # Is dataset an image?
- image = check_image( dataset.path )
- if image:
- if not PIL:
- image = None
- # get_image_ext() returns None if nor a supported Image type
- ext = get_image_ext( dataset.path, image )
- data_type = ext
- # Is dataset content multi-byte?
- elif dataset.is_multi_byte:
- data_type = 'multi-byte char'
- ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
- # Is dataset content supported sniffable binary?
- else:
- type_info = Binary.is_sniffable_binary( dataset.path )
- if type_info:
- data_type = type_info[0]
- ext = type_info[1]
- data_type="binary"
- if not data_type:
- # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
- is_gzipped, is_valid = check_gzip( dataset.path )
- if is_gzipped and not is_valid:
- file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file )
- return
- elif is_gzipped and is_valid:
- if link_data_only == 'copy_files':
- # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
- CHUNK_SIZE = 2**20 # 1Mb
- fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
- gzipped_file = gzip.GzipFile( dataset.path, 'rb' )
- while 1:
- try:
- chunk = gzipped_file.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- os.remove( uncompressed )
- file_err( 'Problem decompressing gzipped data', dataset, json_file )
- return
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- gzipped_file.close()
- # Replace the gzipped file with the decompressed file if it's safe to do so
- if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place:
- dataset.path = uncompressed
- else:
- shutil.move( uncompressed, dataset.path )
- os.chmod(dataset.path, 0644)
- dataset.name = dataset.name.rstrip( '.gz' )
- data_type = 'gzip'
- if not data_type and bz2 is not None:
- # See if we have a bz2 file, much like gzip
- is_bzipped, is_valid = check_bz2( dataset.path )
- if is_bzipped and not is_valid:
- file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file )
- return
- elif is_bzipped and is_valid:
- if link_data_only == 'copy_files':
- # We need to uncompress the temp_name file
- CHUNK_SIZE = 2**20 # 1Mb
- fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
- bzipped_file = bz2.BZ2File( dataset.path, 'rb' )
- while 1:
- try:
- chunk = bzipped_file.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- os.remove( uncompressed )
- file_err( 'Problem decompressing bz2 compressed data', dataset, json_file )
- return
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- bzipped_file.close()
- # Replace the bzipped file with the decompressed file if it's safe to do so
- if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place:
- dataset.path = uncompressed
- else:
- shutil.move( uncompressed, dataset.path )
- os.chmod(dataset.path, 0644)
- dataset.name = dataset.name.rstrip( '.bz2' )
- data_type = 'bz2'
- if not data_type:
- # See if we have a zip archive
- is_zipped = check_zip( dataset.path )
- if is_zipped:
- if link_data_only == 'copy_files':
- CHUNK_SIZE = 2**20 # 1Mb
- uncompressed = None
- uncompressed_name = None
- unzipped = False
- z = zipfile.ZipFile( dataset.path )
- for name in z.namelist():
- if name.endswith('/'):
- continue
- if unzipped:
- stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.'
- break
- fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
- if sys.version_info[:2] >= ( 2, 6 ):
- zipped_file = z.open( name )
- while 1:
- try:
- chunk = zipped_file.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- os.remove( uncompressed )
- file_err( 'Problem decompressing zipped data', dataset, json_file )
- return
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- zipped_file.close()
- uncompressed_name = name
- unzipped = True
- else:
- # python < 2.5 doesn't have a way to read members in chunks(!)
- try:
- outfile = open( uncompressed, 'wb' )
- outfile.write( z.read( name ) )
- outfile.close()
- uncompressed_name = name
- unzipped = True
- except IOError:
- os.close( fd )
- os.remove( uncompressed )
- file_err( 'Problem decompressing zipped data', dataset, json_file )
- return
- z.close()
- # Replace the zipped file with the decompressed file if it's safe to do so
- if uncompressed is not None:
- if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place:
- dataset.path = uncompressed
- else:
- shutil.move( uncompressed, dataset.path )
- os.chmod(dataset.path, 0644)
- dataset.name = uncompressed_name
- data_type = 'zip'
- if not data_type:
- if check_binary( dataset.path ):
- # We have a binary dataset, but it is not Bam, Sff or Pdf
- data_type = 'binary'
- #binary_ok = False
- parts = dataset.name.split( "." )
- if len( parts ) > 1:
- ext = parts[-1].strip().lower()
- if not Binary.is_ext_unsniffable(ext):
- file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file )
- return
- elif Binary.is_ext_unsniffable(ext) and dataset.file_type != ext:
- err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext )
- file_err( err_msg, dataset, json_file )
- return
- if not data_type:
- # We must have a text file
- if check_html( dataset.path ):
- file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file )
- return
- if data_type != 'binary':
- if link_data_only == 'copy_files':
- if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]:
- in_place = False
- # Convert universal line endings to Posix line endings, but allow the user to turn it off,
- # so that is becomes possible to upload gzip, bz2 or zip files with binary data without
- # corrupting the content of those files.
- if dataset.to_posix_lines:
- if dataset.space_to_tab:
- line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place )
- else:
- line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )
- if dataset.file_type == 'auto':
- ext = sniff.guess_ext( dataset.path, registry.sniff_order )
- else:
- ext = dataset.file_type
- data_type = ext
- # Save job info for the framework
- if ext == 'auto' and dataset.ext:
- ext = dataset.ext
- if ext == 'auto':
- ext = 'data'
- datatype = registry.get_datatype_by_extension( ext )
- if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files':
- # Never alter a file that will not be copied to Galaxy's local file store.
- if datatype.dataset_content_needs_grooming( dataset.path ):
- err_msg = 'The uploaded files need grooming, so change your Copy data into Galaxy? selection to be ' + \
- 'Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed.'
- file_err( err_msg, dataset, json_file )
- return
- if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]:
- # Move the dataset to its "real" path
- if converted_path is not None:
- shutil.copy( converted_path, output_path )
- try:
- os.remove( converted_path )
- except:
- pass
- else:
- # This should not happen, but it's here just in case
- shutil.copy( dataset.path, output_path )
- elif link_data_only == 'copy_files':
- shutil.move( dataset.path, output_path )
- # Write the job info
- stdout = stdout or 'uploaded %s file' % data_type
- info = dict( type = 'dataset',
- dataset_id = dataset.dataset_id,
- ext = ext,
- stdout = stdout,
- name = dataset.name,
- line_count = line_count )
- if dataset.get('uuid', None) is not None:
- info['uuid'] = dataset.get('uuid')
- json_file.write( to_json_string( info ) + "\n" )
-
- if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
- # Groom the dataset content if necessary
- datatype.groom_dataset_content( output_path )
-
-def add_composite_file( dataset, registry, json_file, output_path, files_path ):
- if dataset.composite_files:
- os.mkdir( files_path )
- for name, value in dataset.composite_files.iteritems():
- value = util.bunch.Bunch( **value )
- if dataset.composite_file_paths[ value.name ] is None and not value.optional:
- file_err( 'A required composite data file was not provided (%s)' % name, dataset, json_file )
- break
- elif dataset.composite_file_paths[value.name] is not None:
- dp = dataset.composite_file_paths[value.name][ 'path' ]
- isurl = dp.find('://') <> -1 # todo fixme
- if isurl:
- try:
- temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dp ), prefix='url_paste' )
- except Exception, e:
- file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file )
- return
- dataset.path = temp_name
- dp = temp_name
- if not value.is_binary:
- if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ):
- sniff.convert_newlines_sep2tabs( dp )
- else:
- sniff.convert_newlines( dp )
- shutil.move( dp, os.path.join( files_path, name ) )
- # Move the dataset to its "real" path
- shutil.move( dataset.primary_file, output_path )
- # Write the job info
- info = dict( type = 'dataset',
- dataset_id = dataset.dataset_id,
- stdout = 'uploaded %s file' % dataset.file_type )
- json_file.write( to_json_string( info ) + "\n" )
-
-def __main__():
-
- if len( sys.argv ) < 4:
- print >>sys.stderr, 'usage: upload.py