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Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

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This commit is contained in:
Dannon Baker
2014-01-10 07:29:05 -05:00
parent 5ad08852a9
commit 559ecb4ec8
44 changed files with 279 additions and 279 deletions
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eggs.ini
-1
View File
@@ -26,7 +26,6 @@ pycrypto = 2.5
pysam = 0.4.2
pysqlite = 2.5.6
python_lzo = 1.08_2.03_static
simplejson = 2.1.1
threadframe = 0.2
guppy = 0.1.8
SQLAlchemy = 0.7.9
lib/galaxy/datatypes/metadata.py
+9 -11
View File
@@ -2,15 +2,13 @@
Galaxy Metadata
"""
from galaxy import eggs
eggs.require("simplejson")
import copy
import cPickle
import json
import logging
import os
import shutil
import simplejson
import sys
import tempfile
import weakref
@@ -130,7 +128,7 @@ class MetadataCollection( object ):
def from_JSON_dict( self, filename ):
dataset = self.parent
log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
JSONified_dict = simplejson.load( open( filename ) )
JSONified_dict = json.load( open( filename ) )
for name, spec in self.spec.items():
if name in JSONified_dict:
dataset._metadata[ name ] = spec.param.from_external_value( JSONified_dict[ name ], dataset )
@@ -146,7 +144,7 @@ class MetadataCollection( object ):
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
simplejson.dump( meta_dict, open( filename, 'wb+' ) )
json.dump( meta_dict, open( filename, 'wb+' ) )
def __getstate__( self ):
return None #cannot pickle a weakref item (self._parent), when data._metadata_collection is None, it will be recreated on demand
@@ -456,7 +454,7 @@ class ListParameter( MetadataParameter ):
class DictParameter( MetadataParameter ):
def to_string( self, value ):
return simplejson.dumps( value )
return json.dumps( value )
class PythonObjectParameter( MetadataParameter ):
@@ -594,7 +592,7 @@ class MetadataTempFile( object ):
@classmethod
def cleanup_from_JSON_dict_filename( cls, filename ):
try:
for key, value in simplejson.load( open( filename ) ).items():
for key, value in json.load( open( filename ) ).items():
if cls.is_JSONified_value( value ):
value = cls.from_JSON( value )
if isinstance( value, cls ) and os.path.exists( value.file_name ):
@@ -686,10 +684,10 @@ class JobExternalOutputMetadataWrapper( object ):
#file to store a 'return code' indicating the results of the set_meta() call
#results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure )
metadata_files.filename_results_code = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name )
simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
json.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
#file to store kwds passed to set_meta()
metadata_files.filename_kwds = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name )
simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
json.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
#existing metadata file parameters need to be overridden with cluster-writable file locations
metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name )
open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
@@ -699,7 +697,7 @@ class JobExternalOutputMetadataWrapper( object ):
metadata_temp = MetadataTempFile()
shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name )
override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) )
simplejson.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
json.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
#add to session and flush
sa_session.add( metadata_files )
sa_session.flush()
@@ -711,7 +709,7 @@ class JobExternalOutputMetadataWrapper( object ):
metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
if not metadata_files:
return False # this file doesn't exist
rval, rstring = simplejson.load( open( metadata_files.filename_results_code ) )
rval, rstring = json.load( open( metadata_files.filename_results_code ) )
if not rval:
log.debug( 'setting metadata externally failed for %s %s: %s' % ( dataset.__class__.__name__, dataset.id, rstring ) )
return rval
lib/galaxy/datatypes/sequence.py
+9 -9
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@@ -2,12 +2,14 @@
Sequence classes
"""
import data
from . import data
import gzip
import json
import logging
import os
import re
import string
from cgi import escape
from galaxy import eggs, util
@@ -16,8 +18,6 @@ from galaxy.datatypes.checkers import is_gzip
from galaxy.datatypes.sniff import get_test_fname, get_headers
from galaxy.datatypes.metadata import MetadataElement
eggs.require("simplejson")
import simplejson
try:
eggs.require( "bx-python" )
@@ -44,8 +44,8 @@ class SequenceSplitLocations( data.Text ):
def set_peek( self, dataset, is_multi_byte=False ):
if not dataset.dataset.purged:
try:
parsed_data = simplejson.load(open(dataset.file_name))
# dataset.peek = simplejson.dumps(data, sort_keys=True, indent=4)
parsed_data = json.load(open(dataset.file_name))
# dataset.peek = json.dumps(data, sort_keys=True, indent=4)
dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
dataset.blurb = '%d sections' % len(parsed_data['sections'])
except Exception, e:
@@ -60,7 +60,7 @@ class SequenceSplitLocations( data.Text ):
def sniff( self, filename ):
if os.path.getsize(filename) < 50000:
try:
data = simplejson.load(open(filename))
data = json.load(open(filename))
sections = data['sections']
for section in sections:
if 'start' not in section or 'end' not in section or 'sequences' not in section:
@@ -155,7 +155,7 @@ class Sequence( data.Text ):
do_slow_split = classmethod(do_slow_split)
def do_fast_split( cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
data = simplejson.load(open(toc_file_datasets[0].file_name))
data = json.load(open(toc_file_datasets[0].file_name))
sections = data['sections']
total_sequences = long(0)
for section in sections:
@@ -191,7 +191,7 @@ class Sequence( data.Text ):
toc = toc_file_datasets[ds_no]
split_data['args']['toc_file'] = toc.file_name
f = open(os.path.join(dir, 'split_info_%s.json' % base_name), 'w')
simplejson.dump(split_data, f)
json.dump(split_data, f)
f.close()
start_sequence += sequences_per_file[part_no]
return directories
@@ -557,7 +557,7 @@ class Fastq ( Sequence ):
sequence_count = long(args['num_sequences'])
if 'toc_file' in args:
toc_file = simplejson.load(open(args['toc_file'], 'r'))
toc_file = json.load(open(args['toc_file'], 'r'))
commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)
else:
commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
lib/galaxy/jobs/runners/drmaa.py
+4 -4
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@@ -2,13 +2,13 @@
Job control via the DRMAA API.
"""
import json
import logging
import os
import string
import subprocess
import sys
import time
import string
import logging
import subprocess
import simplejson as json
from galaxy import eggs
from galaxy import model
lib/galaxy/jobs/runners/lwr_client/action_mapper.py
+1 -1
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@@ -1,4 +1,4 @@
from simplejson import load
from json import load
from os.path import abspath
from os.path import dirname
from os.path import join
lib/galaxy/jobs/runners/lwr_client/client.py
+2 -3
View File
@@ -1,7 +1,6 @@
import os
import shutil
import simplejson
from simplejson import dumps
from json import dumps, loads
from time import sleep
from .destination import submit_params
@@ -16,7 +15,7 @@ class parseJson(object):
def __call__(self, func):
def replacement(*args, **kwargs):
response = func(*args, **kwargs)
return simplejson.loads(response)
return loads(response)
return replacement
lib/galaxy/model/__init__.py
+2 -3
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@@ -6,7 +6,6 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
"""
from galaxy import eggs
eggs.require("simplejson")
eggs.require("pexpect")
import codecs
@@ -15,7 +14,7 @@ import logging
import operator
import os
import pexpect
import simplejson
import json
import socket
import time
from string import Template
@@ -2250,7 +2249,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
template_data[template.name] = tmp_dict
return template_data
def templates_json( self, use_name=False ):
return simplejson.dumps( self.templates_dict( use_name=use_name ) )
return json.dumps( self.templates_dict( use_name=use_name ) )
def get_display_name( self ):
"""
lib/galaxy/model/custom_types.py
+3 -5
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@@ -1,8 +1,6 @@
from sqlalchemy.types import *
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
import json
import pickle
import copy
import uuid
@@ -19,8 +17,8 @@ import logging
log = logging.getLogger( __name__ )
# Default JSON encoder and decoder
json_encoder = simplejson.JSONEncoder( sort_keys=True )
json_decoder = simplejson.JSONDecoder( )
json_encoder = json.JSONEncoder( sort_keys=True )
json_decoder = json.JSONDecoder( )
def _sniffnfix_pg9_hex(value):
"""
lib/galaxy/tools/__init__.py
+6 -7
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@@ -4,6 +4,7 @@ Classes encapsulating galaxy tools and tool configuration.
import binascii
import glob
import json
import logging
import os
import pipes
@@ -19,14 +20,12 @@ import urllib
from math import isinf
from galaxy import eggs
eggs.require( "simplejson" )
eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako
eggs.require( "Mako" )
eggs.require( "elementtree" )
eggs.require( "Paste" )
eggs.require( "SQLAlchemy >= 0.4" )
import simplejson
from cgi import FieldStorage
from elementtree import ElementTree
from mako.template import Template
@@ -869,7 +868,7 @@ class DefaultToolState( object ):
value = params_to_strings( tool.inputs, self.inputs, app )
value["__page__"] = self.page
value["__rerun_remap_job_id__"] = self.rerun_remap_job_id
value = simplejson.dumps( value )
value = json.dumps( value )
# Make it secure
if secure:
a = hmac_new( app.config.tool_secret, value )
@@ -888,7 +887,7 @@ class DefaultToolState( object ):
test = hmac_new( app.config.tool_secret, value )
assert a == test
# Restore from string
values = json_fix( simplejson.loads( value ) )
values = json_fix( json.loads( value ) )
self.page = values.pop( "__page__" )
if '__rerun_remap_job_id__' in values:
self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" )
@@ -2921,7 +2920,7 @@ class Tool( object, Dictifiable ):
try:
json_file = open( os.path.join( job_working_directory, jobs.TOOL_PROVIDED_JOB_METADATA_FILE ), 'r' )
for line in json_file:
line = simplejson.loads( line )
line = json.loads( line )
if line.get( 'type' ) == 'new_primary_dataset':
new_primary_datasets[ os.path.split( line.get( 'filename' ) )[-1] ] = line
except Exception:
@@ -3085,7 +3084,7 @@ class OutputParameterJSONTool( Tool ):
if json_filename is None:
json_filename = file_name
out = open( json_filename, 'w' )
out.write( simplejson.dumps( json_params ) )
out.write( json.dumps( json_params ) )
out.close()
class DataSourceTool( OutputParameterJSONTool ):
@@ -3145,7 +3144,7 @@ class DataSourceTool( OutputParameterJSONTool ):
if json_filename is None:
json_filename = file_name
out = open( json_filename, 'w' )
out.write( simplejson.dumps( json_params ) )
out.write( json.dumps( json_params ) )
out.close()
class AsyncDataSourceTool( DataSourceTool ):
lib/galaxy/tools/data_manager/manager.py
+4 -7
View File
@@ -1,9 +1,6 @@
import pkg_resources
pkg_resources.require( "simplejson" )
import os, errno
import simplejson
import errno
import json
import os
from galaxy import util
from galaxy.util.odict import odict
@@ -226,7 +223,7 @@ class DataManager( object ):
#TODO: fix this merging below
for output_name, output_dataset in out_data.iteritems():
try:
output_dict = simplejson.loads( open( output_dataset.file_name ).read() )
output_dict = json.loads( open( output_dataset.file_name ).read() )
except Exception, e:
log.warning( 'Error reading DataManagerTool json for "%s": %s' % ( output_name, e ) )
continue
lib/galaxy/tools/genome_index/__init__.py
+7 -5
View File
@@ -1,6 +1,11 @@
from __future__ import with_statement
import os, shutil, logging, tempfile, tarfile
import json
import logging
import os
import shutil
import tarfile
import tempfile
from galaxy import model, util
from galaxy.web.framework.helpers import to_unicode
@@ -9,9 +14,6 @@ from galaxy.util.json import *
from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.tools.data import ToolDataTableManager
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
log = logging.getLogger(__name__)
@@ -74,7 +76,7 @@ class GenomeIndexToolWrapper( object ):
fp = open( gitd.dataset.get_file_name(), 'r' )
deferred = sa_session.query( model.DeferredJob ).filter_by( id=gitd.deferred_job_id ).first()
try:
logloc = simplejson.load( fp )
logloc = json.load( fp )
except ValueError:
deferred.state = app.model.DeferredJob.states.ERROR
sa_session.add( deferred )
lib/galaxy/tools/genome_index/index_genome.py
+12 -6
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@@ -7,11 +7,17 @@ usage: %prog history_attrs dataset_attrs job_attrs out_file
"""
from __future__ import with_statement
import optparse, sys, os, tempfile, time, subprocess, shlex, tarfile, shutil
import json
import optparse
import os
import shlex
import shutil
import subprocess
import sys
import tarfile
import tempfile
import time
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
class ManagedIndexer():
def __init__( self, output_file, infile, workingdir, rsync_url, tooldata ):
@@ -76,7 +82,7 @@ class ManagedIndexer():
return result
def _flush_files( self ):
simplejson.dump( self.locations, self.outfile )
json.dump( self.locations, self.outfile )
self.outfile.close()
self.logfile.close()
@@ -318,4 +324,4 @@ if __name__ == "__main__":
returncode = idxobj.run_indexer( indexer )
if not returncode:
exit(1)
exit(0)
exit(0)
lib/galaxy/tools/imp_exp/__init__.py
+5 -5
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@@ -1,4 +1,4 @@
import os, shutil, logging, tempfile, simplejson
import os, shutil, logging, tempfile, json
from galaxy import model
from galaxy.tools.parameters.basic import UnvalidatedValue
from galaxy.web.framework.helpers import to_unicode
@@ -226,13 +226,13 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
self.sa_session.add( imported_job )
self.sa_session.flush()
class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ):
class HistoryDatasetAssociationIDEncoder( json.JSONEncoder ):
""" Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """
def default( self, obj ):
""" Encode an HDA, default encoding for everything else. """
if isinstance( obj, model.HistoryDatasetAssociation ):
return obj.id
return simplejson.JSONEncoder.default( self, obj )
return json.JSONEncoder.default( self, obj )
# Set parameters. May be useful to look at metadata.py for creating parameters.
# TODO: there may be a better way to set parameters, e.g.:
@@ -311,7 +311,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
del metadata[ name ]
return metadata
class HistoryDatasetAssociationEncoder( simplejson.JSONEncoder ):
class HistoryDatasetAssociationEncoder( json.JSONEncoder ):
""" Custom JSONEncoder for a HistoryDatasetAssociation. """
def default( self, obj ):
""" Encode an HDA, default encoding for everything else. """
@@ -337,7 +337,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
}
if isinstance( obj, UnvalidatedValue ):
return obj.__str__()
return simplejson.JSONEncoder.default( self, obj )
return json.JSONEncoder.default( self, obj )
#
# Create attributes/metadata files for export.
lib/galaxy/util/__init__.py
+23 -7
View File
@@ -2,7 +2,26 @@
Utility functions used systemwide.
"""
import binascii, errno, grp, logging, os, pickle, random, re, shutil, smtplib, stat, string, sys, tempfile, threading
from __future__ import absolute_import
import binascii
import errno
import grp
import json
import logging
import os
import pickle
import random
import re
import shutil
import smtplib
import stat
import string
import sys
import tempfile
import threading
from email.MIMEText import MIMEText
from os.path import relpath
@@ -21,12 +40,9 @@ from elementtree import ElementTree, ElementInclude
eggs.require( "wchartype" )
import wchartype
from inflection import Inflector, English
from .inflection import Inflector, English
inflector = Inflector(English)
eggs.require( "simplejson" )
import simplejson
log = logging.getLogger(__name__)
_lock = threading.RLock()
@@ -292,8 +308,8 @@ def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginnin
def pretty_print_json(json_data, is_json_string=False):
if is_json_string:
json_data = simplejson.loads(json_data)
return simplejson.dumps(json_data, sort_keys=True, indent=4 * ' ')
json_data = json.loads(json_data)
return json.dumps(json_data, sort_keys=True, indent=4 * ' ')
# characters that are valid
valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
lib/galaxy/util/json.py
+7 -8
View File
@@ -1,16 +1,15 @@
from __future__ import absolute_import
__all__ = [ "to_json_string", "from_json_string", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
import random, string, logging
import json
import logging
import random
import socket
import string
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
to_json_string = simplejson.dumps
from_json_string = simplejson.loads
to_json_string = json.dumps
from_json_string = json.loads
log = logging.getLogger( __name__ )
lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
+2 -4
View File
@@ -1,6 +1,4 @@
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
import json
class Node(object):
"""Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree"""
@@ -118,7 +116,7 @@ class Base_Parser(object):
def toJson(self, jsonDict):
"""Convenience method to get a json string from a python json dict"""
return simplejson.dumps(jsonDict)
return json.dumps(jsonDict)
def _writeJsonToFile(self, filepath, json):
"""Writes the file out to the system"""
lib/galaxy/web/framework/__init__.py
+17 -19
View File
@@ -2,6 +2,7 @@
Galaxy web application framework
"""
import hashlib
import inspect
import os
import pkg_resources
@@ -9,27 +10,24 @@ import random
import socket
import string
import time
import hashlib
from Cookie import CookieError
from functools import wraps
from Cookie import CookieError
pkg_resources.require( "Cheetah" )
from Cheetah.Template import Template
#TODO: Relative imports to be removed
import base
from functools import wraps
from galaxy import util
from galaxy.exceptions import MessageException
from galaxy.util.json import to_json_string, from_json_string
from galaxy.util.backports.importlib import import_module
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util import safe_str_cmp
pkg_resources.require( "simplejson" )
import simplejson
import helpers
from galaxy import util
from galaxy.exceptions import MessageException
from galaxy.util import asbool
from galaxy.util import safe_str_cmp
from galaxy.util.backports.importlib import import_module
from galaxy.util.json import from_json_string, to_json_string
from galaxy.util.sanitize_html import sanitize_html
import paste.httpexceptions
@@ -76,7 +74,7 @@ def json( func ):
@wraps(func)
def decorator( self, trans, *args, **kwargs ):
trans.response.set_content_type( "text/javascript" )
return simplejson.dumps( func( self, trans, *args, **kwargs ) )
return to_json_string( func( self, trans, *args, **kwargs ) )
if not hasattr(func, '_orig'):
decorator._orig = func
decorator.exposed = True
@@ -86,7 +84,7 @@ def json_pretty( func ):
@wraps(func)
def decorator( self, trans, *args, **kwargs ):
trans.response.set_content_type( "text/javascript" )
return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
return to_json_string( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
if not hasattr(func, '_orig'):
decorator._orig = func
decorator.exposed = True
@@ -158,7 +156,7 @@ def expose_api( func, to_json=True, user_required=True ):
for k, v in payload.iteritems():
if isinstance(v, (str, unicode)):
try:
payload[k] = simplejson.loads(v)
payload[k] = from_json_string(v)
except:
# may not actually be json, just continue
pass
@@ -167,7 +165,7 @@ def expose_api( func, to_json=True, user_required=True ):
# Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check
# should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding
# such as multipart/form-data. Leaving it as is for backward compatibility, just in case.
payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) )
payload = util.recursively_stringify_dictionary_keys( from_json_string( trans.request.body ) )
return payload
try:
kwargs['payload'] = extract_payload_from_request(trans, func, kwargs)
@@ -198,9 +196,9 @@ def expose_api( func, to_json=True, user_required=True ):
try:
rval = func( self, trans, *args, **kwargs)
if to_json and trans.debug:
rval = simplejson.dumps( rval, indent=4, sort_keys=True )
rval = to_json_string( rval, indent=4, sort_keys=True )
elif to_json:
rval = simplejson.dumps( rval )
rval = to_json_string( rval )
return rval
except paste.httpexceptions.HTTPException:
raise # handled
lib/galaxy/webapps/demo_sequencer/framework/__init__.py
+7 -4
View File
@@ -2,9 +2,15 @@
Demo sequencer web application framework
"""
import json
import os
import pkg_resources
import random
import socket
import string
import sys
import time
import os, sys, time, socket, random, string
pkg_resources.require( "Cheetah" )
from Cheetah.Template import Template
@@ -19,9 +25,6 @@ import galaxy.web.framework.base
from galaxy.util import asbool
pkg_resources.require( "simplejson" )
import simplejson
pkg_resources.require( "Mako" )
import mako.template
import mako.lookup
lib/galaxy/webapps/galaxy/controllers/data_admin.py
+8 -9
View File
@@ -1,14 +1,13 @@
import sys, ftplib
import ftplib
import json
import sys
from galaxy import model, util
from galaxy.jobs import transfer_manager
from galaxy.web.base.controller import *
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import *
from galaxy.web.base.controller import *
from galaxy.web.framework.helpers import grids, iff, time_ago
from library_common import get_comptypes, lucene_search, whoosh_search
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
# Older py compatibility
try:
@@ -161,7 +160,7 @@ class DataAdmin( BaseUIController ):
gname = deferred.params[ 'intname' ]
indexers = ', '.join( deferred.params[ 'indexes' ] )
jobs = self._get_jobs( deferred, trans )
jsonjobs = simplejson.dumps( jobs )
jsonjobs = json.dumps( jobs )
return trans.fill_template( '/admin/data_admin/download_status.mako', name=gname, indexers=indexers, mainjob=jobid, jobs=jobs, jsonjobs=jsonjobs )
@web.expose
@@ -173,7 +172,7 @@ class DataAdmin( BaseUIController ):
jobid = params.get( 'jobid', '' )
job = sa_session.query( model.DeferredJob ).filter_by( id=jobid ).first()
jobs = self._get_jobs( job, trans )
return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=simplejson.dumps( jobs ) )
return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=json.dumps( jobs ) )
def _get_job( self, jobid, jobtype, trans ):
sa = trans.app.model.context.current
@@ -297,4 +296,4 @@ def build_param_dict( params, trans ):
params = dict( status='ok', dbkey=dbkey, datatype='fasta', url=url, user=trans.user.id, liftover=newlift, longname=longname, indexers=indexers )
return params
return params
lib/galaxy/webapps/galaxy/controllers/root.py
+1 -1
View File
@@ -508,7 +508,7 @@ class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAsso
Attempts to parse values passed as boolean, float, then int. Defaults
to string. Non-recursive (will not parse lists).
"""
#TODO: use simplejson or json
#TODO: use json
rval = {}
for k in kwd:
rval[ k ] = kwd[k]
lib/galaxy/webapps/galaxy/controllers/workflow.py
+7 -8
View File
@@ -1,13 +1,12 @@
import pkg_resources
pkg_resources.require( "simplejson" )
pkg_resources.require( "SVGFig" )
import base64
import httplib
import json
import math
import os
import sgmllib
import simplejson
import svgfig
import urllib2
@@ -20,17 +19,17 @@ from galaxy import util
from galaxy import web
from galaxy.datatypes.data import Data
from galaxy.jobs.actions.post import ActionBox
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.model.mapping import desc
from galaxy.tools.parameters import RuntimeValue, visit_input_values
from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
from galaxy.tools.parameters.grouping import Conditional, Repeat
from galaxy.util.odict import odict
from galaxy.util.json import to_json_string
from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.topsort import CycleError, topsort, topsort_levels
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.web.framework import form
from galaxy.web.framework.helpers import grids, time_ago
from galaxy.web.framework.helpers import to_unicode
@@ -812,7 +811,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
# Put parameters in workflow mode
trans.workflow_building_mode = True
# Convert incoming workflow data from json
data = simplejson.loads( workflow_data )
data = json.loads( workflow_data )
# Create new workflow from incoming data
workflow = model.Workflow()
# Just keep the last name (user can rename later)
@@ -920,7 +919,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
#
# Create workflow content JSON.
workflow_content = simplejson.dumps( workflow_dict, indent=4, sort_keys=True )
workflow_content = json.dumps( workflow_dict, indent=4, sort_keys=True )
# Create myExperiment request.
request_raw = trans.fill_template( "workflow/myexp_export.mako", \
@@ -1073,7 +1072,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
if workflow_data:
# Convert incoming workflow data from json
try:
data = simplejson.loads( workflow_data )
data = json.loads( workflow_data )
except Exception, e:
data = None
message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e )
@@ -1294,7 +1293,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
# It is possible for a workflow to have 0 steps
if len( workflow.steps ) == 0:
error( "Workflow cannot be run because it does not have any steps" )
#workflow = Workflow.from_simple( simplejson.loads( stored.encoded_value ), trans.app )
#workflow = Workflow.from_simple( json.loads( stored.encoded_value ), trans.app )
if workflow.has_cycles:
error( "Workflow cannot be run because it contains cycles" )
if workflow.has_errors:
lib/tool_shed/scripts/api/common.py
+13 -12
View File
@@ -1,4 +1,8 @@
import os, sys, urllib, urllib2
import json
import os
import sys
import urllib
import urllib2
new_path = [ os.path.join( os.path.dirname( __file__ ), '..', '..', '..', '..', 'lib' ) ]
new_path.extend( sys.path[ 1: ] )
@@ -7,9 +11,6 @@ sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
pkg_resources.require( "pycrypto" )
from Crypto.Cipher import Blowfish
from Crypto.Util.randpool import RandomPool
@@ -29,9 +30,9 @@ def delete( api_key, url, data, return_formatted=True ):
# Sends an API DELETE request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
try:
url = make_url( api_key, url )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'DELETE'
r = simplejson.loads( urllib2.urlopen( req ).read() )
r = json.loads( urllib2.urlopen( req ).read() )
except urllib2.HTTPError, e:
if return_formatted:
print e
@@ -86,8 +87,8 @@ def get( url, api_key=None ):
# Do the actual GET.
url = make_url( url, api_key=api_key )
try:
return simplejson.loads( urllib2.urlopen( url ).read() )
except simplejson.decoder.JSONDecodeError, e:
return json.loads( urllib2.urlopen( url ).read() )
except ValueError, e:
print "URL did not return JSON data"
sys.exit(1)
@@ -106,15 +107,15 @@ def make_url( url, api_key=None, args=None ):
def post( url, data, api_key=None ):
# Do the actual POST.
url = make_url( url, api_key=api_key )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
return simplejson.loads( urllib2.urlopen( req ).read() )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
return json.loads( urllib2.urlopen( req ).read() )
def put( url, data, api_key=None ):
# Do the actual PUT.
url = make_url( url, api_key=api_key )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'PUT'
return simplejson.loads( urllib2.urlopen( req ).read() )
return json.loads( urllib2.urlopen( req ).read() )
def submit( url, data, api_key=None, return_formatted=True ):
# Sends an API POST request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
+6 -7
View File
@@ -5,17 +5,16 @@ PUT/update script to update appropriate values in a repository_metadata table re
usage: tool_shed_repository_revision_update.py key url key1=value1 key2=value2 ...
"""
import os, sys
import json
import os
import sys
sys.path.insert( 0, os.path.dirname( __file__ ) )
from common import update
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
to_json_string = simplejson.dumps
from_json_string = simplejson.loads
to_json_string = json.dumps
from_json_string = json.loads
data = {}
for key, value in [ kwarg.split( '=', 1 ) for kwarg in sys.argv[ 3: ] ]:
lib/tool_shed/util/encoding_util.py
+3 -7
View File
@@ -1,14 +1,10 @@
import binascii
import json
import logging
from galaxy import eggs
from galaxy.util.hash_util import hmac_new
from galaxy.util.json import json_fix
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
log = logging.getLogger( __name__ )
encoding_sep = '__esep__'
@@ -23,7 +19,7 @@ def tool_shed_decode( value ):
# Restore from string
values = None
try:
values = simplejson.loads( value )
values = json.loads( value )
except Exception, e:
#log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) )
pass
@@ -39,7 +35,7 @@ def tool_shed_decode( value ):
def tool_shed_encode( val ):
if isinstance( val, dict ):
value = simplejson.dumps( val )
value = json.dumps( val )
else:
value = val
a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
scripts/api/common.py
+9 -11
View File
@@ -1,3 +1,4 @@
import json
import logging
import os
import sys
@@ -10,9 +11,6 @@ sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
pkg_resources.require( "pycrypto" )
from Crypto.Cipher import Blowfish
from Crypto.Util.randpool import RandomPool
@@ -35,30 +33,30 @@ def get( api_key, url ):
# Do the actual GET.
url = make_url( api_key, url )
try:
return simplejson.loads( urllib2.urlopen( url ).read() )
except simplejson.decoder.JSONDecodeError, e:
return json.loads( urllib2.urlopen( url ).read() )
except json.decoder.JSONDecodeError, e:
print "URL did not return JSON data"
sys.exit(1)
def post( api_key, url, data ):
# Do the actual POST.
url = make_url( api_key, url )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
return simplejson.loads( urllib2.urlopen( req ).read() )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
return json.loads( urllib2.urlopen( req ).read() )
def put( api_key, url, data ):
# Do the actual PUT
url = make_url( api_key, url )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'PUT'
return simplejson.loads( urllib2.urlopen( req ).read() )
return json.loads( urllib2.urlopen( req ).read() )
def __del( api_key, url, data ):
# Do the actual DELETE
url = make_url( api_key, url )
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
req.get_method = lambda: 'DELETE'
return simplejson.loads( urllib2.urlopen( req ).read() )
return json.loads( urllib2.urlopen( req ).read() )
def display( api_key, url, return_formatted=True ):
scripts/api/workflow_import_from_file_rpark.py
+2 -2
View File
@@ -11,11 +11,11 @@ sys.path.insert( 0, os.path.dirname( __file__ ) )
from common import submit
### Rpark edit ###
import simplejson
import json
def openWorkflow(in_file):
with open(in_file) as f:
temp_data = simplejson.load(f)
temp_data = json.load(f)
return temp_data;
scripts/drmaa_external_killer.py
+3 -4
View File
@@ -4,10 +4,11 @@
Terminates a DRMAA job if given a job id and (appropriate) user id.
"""
import os
import sys
import errno
import json
import os
import pwd
import sys
#import drmaa
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
@@ -15,8 +16,6 @@ sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require("simplejson")
import simplejson as json
pkg_resources.require("drmaa")
import drmaa
scripts/drmaa_external_runner.py
+1 -3
View File
@@ -10,8 +10,8 @@ import os
import sys
import errno
import pwd
import json
#import simplejson as json
#import drmaa
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
@@ -19,8 +19,6 @@ sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require("simplejson")
import simplejson as json
pkg_resources.require("drmaa")
import drmaa
scripts/external_chown_script.py
+4 -4
View File
@@ -1,17 +1,17 @@
#!/usr/bin/env python
import os
import sys
import errno
import json
import os
import pwd
import sys
#import drmaa
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require("simplejson")
import simplejson as json
pkg_resources.require("drmaa")
import drmaa
scripts/extract_dataset_part.py
+3 -7
View File
@@ -6,9 +6,10 @@ Used by jobs that split large files into pieces to be processed concurrently
on a gid in a scatter-gather mode. This does part of the scatter.
"""
import json
import logging
import os
import sys
import logging
logging.basicConfig()
log = logging.getLogger( __name__ )
@@ -16,11 +17,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
# This junk is here to prevent loading errors
import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
@@ -33,7 +29,7 @@ def __main__():
if not os.path.isfile(file_path):
#Nothing to do - some splitters don't write a JSON file
sys.exit(0)
data = simplejson.load(open(file_path, 'r'))
data = json.load(open(file_path, 'r'))
try:
class_name_parts = data['class_name'].split('.')
module_name = '.'.join(class_name_parts[:-1])
scripts/galaxy_messaging/server/data_transfer.py
+12 -6
View File
@@ -13,12 +13,21 @@ python data_transfer.py <config_file>
"""
import ConfigParser
import sys, os, time, traceback
import cookielib
import datetime
import logging
import optparse
import urllib,urllib2, cookielib, shutil
import logging, time, datetime
import os
import shutil
import sys
import time
import time
import traceback
import urllib
import urllib2
import xml.dom.minidom
from xml_helper import get_value, get_value_index
log = logging.getLogger( "datatx_" + str( os.getpid() ) )
@@ -39,14 +48,11 @@ new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
from galaxy.util.json import from_json_string, to_json_string
from galaxy.model import SampleDataset
from galaxy.web.api.samples import SamplesAPIController
import pkg_resources
pkg_resources.require( "pexpect" )
import pexpect
pkg_resources.require( "simplejson" )
import simplejson
log.debug(str(dir(api)))
scripts/set_metadata.py
+7 -7
View File
@@ -10,9 +10,11 @@ import logging
logging.basicConfig()
log = logging.getLogger( __name__ )
import cPickle
import json
import os
import sys
import cPickle
# ensure supported version
from check_python import check_python
try:
@@ -26,8 +28,6 @@ sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
galaxy.model.Job() # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
from galaxy.util import stringify_dictionary_keys
@@ -107,17 +107,17 @@ def __main__():
dataset.extension = ext_override[ dataset.dataset.id ]
# Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
if override_metadata:
override_metadata = simplejson.load( open( override_metadata ) )
override_metadata = json.load( open( override_metadata ) )
for metadata_name, metadata_file_override in override_metadata:
if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
setattr( dataset.metadata, metadata_name, metadata_file_override )
kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) ) # load kwds; need to ensure our keywords are not unicode
kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) ) # load kwds; need to ensure our keywords are not unicode
dataset.datatype.set_meta( dataset, **kwds )
dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta
simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) # setting metadata has succeeded
json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) # setting metadata has succeeded
except Exception, e:
simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow
json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow
clear_mappers()
# Shut down any additional threads that might have been created via the ObjectStore
object_store.shutdown()
test/base/interactor.py
+1 -1
View File
@@ -5,7 +5,7 @@ from galaxy.util.odict import odict
import galaxy.model
from galaxy.model.orm import and_, desc
from base.test_db_util import sa_session
from simplejson import dumps, loads
from json import dumps, loads
from logging import getLogger
log = getLogger( __name__ )
test/functional/test_workflow.py
+1 -1
View File
@@ -5,7 +5,7 @@ from base.interactor import GalaxyInteractorApi, stage_data_in_history
from galaxy.util import parse_xml
from galaxy.tools.test import parse_param_elem, require_file, test_data_iter, parse_output_elems
from simplejson import load, dumps
from json import load, dumps
from logging import getLogger
log = getLogger( __name__ )
test/tool_shed/base/twilltestcase.py
-1
View File
@@ -3,7 +3,6 @@ import string
import os
import re
import test_db_util
import simplejson
import shutil
import logging
import time
tools/filters/join.py
+10 -17
View File
@@ -8,20 +8,15 @@ User can also opt to have have non-joining rows of file1 echoed.
"""
import optparse, os, sys, tempfile, struct
import json
import optparse
import os
import psyco_full
try:
simple_json_exception = None
from galaxy import eggs
from galaxy.util.bunch import Bunch
from galaxy.util import stringify_dictionary_keys
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
except Exception, e:
simplejson_exception = e
simplejson = None
import struct
import sys
import tempfile
from galaxy.util.bunch import Bunch
from galaxy.util import stringify_dictionary_keys
class OffsetList:
@@ -337,11 +332,9 @@ def main():
fill_options = None
if options.fill_options_file is not None:
try:
if simplejson is None:
raise simplejson_exception
fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) ) #simplejson.load( open( options.fill_options_file ) )
fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) ) #json.load( open( options.fill_options_file ) )
except Exception, e:
print "Warning: Ignoring fill options due to simplejson error (%s)." % e
print "Warning: Ignoring fill options due to json error (%s)." % e
if fill_options is None:
fill_options = Bunch()
if 'fill_unjoined_only' not in fill_options:
tools/filters/joiner.xml
+2 -2
View File
@@ -51,7 +51,7 @@
</inputs>
<configfiles>
<configfile name="fill_options_file">&lt;%
import simplejson
import json
%&gt;
#set $__fill_options = {}
#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
@@ -72,7 +72,7 @@ import simplejson
#end for
#end if
#end if
${simplejson.dumps( __fill_options )}
${json.dumps( __fill_options )}
</configfile>
</configfiles>
<outputs>
tools/genomespace/genomespace_exporter.py
+16 -12
View File
@@ -1,12 +1,16 @@
#Dan Blankenberg
import optparse, os, urllib2, urllib, cookielib, hashlib, base64, cgi, binascii, logging
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
import base64
import binascii
import cgi
import cookielib
import hashlib
import json
import logging
import optparse
import os
import urllib
import urllib2
log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ )
@@ -58,7 +62,7 @@ def get_directory( url_opener, dm_url, path ):
dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } )
dir_request.get_method = lambda: 'GET'
try:
dir_dict = simplejson.loads( url_opener.open( dir_request ).read() )
dir_dict = json.loads( url_opener.open( dir_request ).read() )
except urllib2.HTTPError, e:
#print "e", e, url #punting, assuming lack of permissions at this low of a level...
continue
@@ -81,16 +85,16 @@ def create_directory( url_opener, directory_dict, new_dir, dm_url ):
if dir_slice in ( '', '/', None ):
continue
url = '/'.join( ( directory_dict['url'], urllib.quote( dir_slice.replace( '/', '_' ), safe='' ) ) )
new_dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' }, data = simplejson.dumps( payload ) )
new_dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' }, data = json.dumps( payload ) )
new_dir_request.get_method = lambda: 'PUT'
directory_dict = simplejson.loads( url_opener.open( new_dir_request ).read() )
directory_dict = json.loads( url_opener.open( new_dir_request ).read() )
return directory_dict
def get_genome_space_launch_apps( atm_url, url_opener, file_url, file_type ):
gs_request = urllib2.Request( "%s/%s/webtool/descriptor" % ( atm_url, GENOMESPACE_API_VERSION_STRING ) )
gs_request.get_method = lambda: 'GET'
opened_gs_request = url_opener.open( gs_request )
webtool_descriptors = simplejson.loads( opened_gs_request.read() )
webtool_descriptors = json.loads( opened_gs_request.read() )
webtools = []
for webtool in webtool_descriptors:
webtool_name = webtool.get( 'name' )
@@ -125,7 +129,7 @@ def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, va
except urllib2.HTTPError, e:
log.debug( 'GenomeSpace export tool failed reading a directory "%s": %s' % ( url, e ) )
return #bad url, go to next
cur_directory = simplejson.loads( cur_directory )
cur_directory = json.loads( cur_directory )
directory = cur_directory.get( 'directory', {} )
contents = cur_directory.get( 'contents', [] )
if directory.get( 'isDirectory', False ):
tools/genomespace/genomespace_file_browser.py
+11 -10
View File
@@ -1,12 +1,13 @@
#Dan Blankenberg
import optparse, os, urllib, urllib2, urlparse, cookielib
import cookielib
import json
import optparse
import os
import urllib
import urllib2
import urlparse
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
GENOMESPACE_API_VERSION_STRING = "v1.0"
GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING )
@@ -87,12 +88,12 @@ def set_genomespace_format_identifiers( url_opener, dm_site ):
gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
gs_request.get_method = lambda: 'GET'
opened_gs_request = url_opener.open( gs_request )
genomespace_formats = simplejson.loads( opened_gs_request.read() )
genomespace_formats = json.loads( opened_gs_request.read() )
for format in genomespace_formats:
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
def download_from_genomespace_file_browser( json_parameter_file, genomespace_site ):
json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
json_params = json.loads( open( json_parameter_file, 'r' ).read() )
datasource_params = json_params.get( 'param_dict' )
username = datasource_params.get( "gs-username", None )
token = datasource_params.get( "gs-token", None )
@@ -150,14 +151,14 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
filename = "-%s" % filename
used_filenames.append( filename )
output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) )
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset',
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset',
base_dataset_id = dataset_id,
ext = galaxy_ext,
filename = output_filename,
name = "GenomeSpace import on %s" % ( original_filename ) ) ) )
else:
if dataset_id is not None:
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'dataset',
dataset_id = dataset_id,
ext = galaxy_ext,
name = "GenomeSpace import on %s" % ( filename ) ) ) )
tools/genomespace/genomespace_importer.py
+14 -12
View File
@@ -1,12 +1,14 @@
#Dan Blankenberg
import optparse, os, urllib2, urllib, cookielib, urlparse, tempfile, shutil
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
import cookielib
import json
import optparse
import os
import shutil
import tempfile
import urllib
import urllib2
import urlparse
import galaxy.model # need to import model before sniff to resolve a circular import dependency
from galaxy.datatypes import sniff
@@ -91,12 +93,12 @@ def set_genomespace_format_identifiers( url_opener, dm_site ):
gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
gs_request.get_method = lambda: 'GET'
opened_gs_request = url_opener.open( gs_request )
genomespace_formats = simplejson.loads( opened_gs_request.read() )
genomespace_formats = json.loads( opened_gs_request.read() )
for format in genomespace_formats:
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
def download_from_genomespace_importer( username, token, json_parameter_file, genomespace_site ):
json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
json_params = json.loads( open( json_parameter_file, 'r' ).read() )
datasource_params = json_params.get( 'param_dict' )
assert None not in [ username, token ], "Missing GenomeSpace username or token."
output_filename = datasource_params.get( "output_file1", None )
@@ -152,7 +154,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
metadata_request = urllib2.Request( "%s/%s/filemetadata/%s" % ( genomespace_site_dict['dmServer'], GENOMESPACE_API_VERSION_STRING, download_file_path ) )
metadata_request.get_method = lambda: 'GET'
metadata_url = url_opener.open( metadata_request )
file_metadata_dict = simplejson.loads( metadata_url.read() )
file_metadata_dict = json.loads( metadata_url.read() )
metadata_url.close()
file_type = file_metadata_dict.get( 'dataFormat', None )
if file_type and file_type.get( 'url' ):
@@ -176,7 +178,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
#save json info for single primary dataset
if dataset_id is not None:
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'dataset',
dataset_id = dataset_id,
ext = file_type,
name = "GenomeSpace importer on %s" % ( filename ) ) ) )
@@ -189,7 +191,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
used_filenames.append( filename )
target_output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) )
shutil.move( output_filename, target_output_filename )
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset',
metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset',
base_dataset_id = base_dataset_id,
ext = file_type,
filename = target_output_filename,
tools/new_operations/column_join.py
+11 -16
View File
@@ -13,19 +13,16 @@ usage: %prog -o output -1 input1 -2 input2 -c column1[,column2[,column3[,...]]]
other_inputs: the other input files to join
"""
import optparse, os, re, struct, sys, tempfile
import json
import optparse
import os
import re
import struct
import sys
import tempfile
try:
simple_json_exception = None
from galaxy import eggs
from galaxy.util.bunch import Bunch
from galaxy.util import stringify_dictionary_keys
import pkg_resources
pkg_resources.require("simplejson")
import simplejson
except Exception, e:
simplejson_exception = e
simplejson = None
from galaxy.util.bunch import Bunch
from galaxy.util import stringify_dictionary_keys
def stop_err( msg ):
sys.stderr.write( msg )
@@ -162,11 +159,9 @@ def __main__():
fill_options = None
if options.fill_options_file != 'None' and options.fill_options_file is not None:
try:
if simplejson is None:
raise simplejson_exception
fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) )
fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) )
except Exception, e:
print 'Warning: Ignoring fill options due to simplejson error (%s).' % e
print 'Warning: Ignoring fill options due to json error (%s).' % e
if fill_options is None:
fill_options = Bunch()
if 'file1_columns' not in fill_options:
tools/new_operations/column_join.xml
+2 -2
View File
@@ -49,7 +49,7 @@
</inputs>
<configfiles>
<configfile name="fill_options_file">&lt;%
import simplejson
import json
%&gt;
#set $__fill_options = {}
#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
@@ -65,7 +65,7 @@ import simplejson
#end for
#end if
#end if
${simplejson.dumps( __fill_options )}
${json.dumps( __fill_options )}
</configfile>
</configfiles>
<outputs>
tools/peak_calling/macs_wrapper.py
+10 -6
View File
@@ -1,8 +1,12 @@
import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
from galaxy import eggs
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
import glob
import gzip
import json
import os
import os.path
import shutil
import subprocess
import sys
import tempfile
CHUNK_SIZE = 1024
@@ -42,7 +46,7 @@ def xls_to_interval( xls_file, interval_file, header = None ):
out.close()
def main():
options = simplejson.load( open( sys.argv[1] ) )
options = json.load( open( sys.argv[1] ) )
output_bed = sys.argv[2]
output_extra_html = sys.argv[3]
output_extra_path = sys.argv[4]
tools/peak_calling/macs_wrapper.xml
+2 -2
View File
@@ -93,7 +93,7 @@
</outputs>
<configfiles>
<configfile name="options_file">&lt;%
import simplejson
import json
%&gt;
#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) }
#if str( $xls_to_interval ) == 'create':
@@ -135,7 +135,7 @@ import simplejson
#if $diag_type['diag_type_selector'] == 'diag':
#set $__options['diag'] = { 'fe-min':str( $diag_type['fe-min'] ), 'fe-max':str( $diag_type['fe-max'] ), 'fe-step':str( $diag_type['fe-step'] ) }
#end if
${ simplejson.dumps( __options ) }
${ json.dumps( __options ) }
</configfile>
</configfiles>
<tests>