Mercurial > repos > davidvanzessen > upload_zip_file
changeset 0:4f3d79062c18 draft
Uploaded
author | davidvanzessen |
---|---|
date | Wed, 13 Nov 2013 10:48:56 -0500 |
parents | |
children | fb547483e7bd |
files | uploadzip.py |
diffstat | 1 files changed, 234 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uploadzip.py Wed Nov 13 10:48:56 2013 -0500 @@ -0,0 +1,234 @@ +#!/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] + if not data_type: + shutil.move( dataset.path, output_path ) + #data_type = "data" + # 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': + if os.path.exists(dataset.path): + 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__()