--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uploadzip.py	Mon Mar 30 07:58:17 2015 -0400
@@ -0,0 +1,391 @@
+#!/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__()