--- 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 <b>Copy data into Galaxy?</b> selection to be ' + \
-                '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> 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 <root> <datatypes_conf> <json paramfile> <output spec> ...'
-        sys.exit( 1 )
-
-    output_paths = parse_outputs( sys.argv[4:] )
-    json_file = open( 'galaxy.json', 'w' )
-
-    registry = Registry()
-    registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] )
-
-    for line in open( sys.argv[3], 'r' ):
-        dataset = from_json_string( line )
-        dataset = util.bunch.Bunch( **safe_dict( dataset ) )
-        try:
-            output_path = output_paths[int( dataset.dataset_id )][0]
-        except:
-            print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id
-            sys.exit( 1 )
-        if dataset.type == 'composite':
-            files_path = output_paths[int( dataset.dataset_id )][1]
-            add_composite_file( dataset, registry, json_file, output_path, files_path )
-        else:
-            add_file( dataset, registry, json_file, output_path )
-
-    # clean up paramfile
-    # TODO: this will not work when running as the actual user unless the
-    # parent directory is writable by the user.
-    try:
-        os.remove( sys.argv[3] )
-    except:
-        pass
-
-if __name__ == '__main__':
-    __main__()