dxpy 0.393.0__tar.gz → 0.395.0__tar.gz

{dxpy-0.393.0 → dxpy-0.395.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.393.0
+Version: 0.395.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/__init__.py

@@ -136,9 +136,11 @@ import socket
 import threading
 import certifi
 from collections import namedtuple
+from http.client import BadStatusLine
+from io import StringIO
+from reprlib import Repr
 
 from . import exceptions
-from .compat import BadStatusLine, StringIO, bytes, Repr
 from .utils.printing import BOLD, BLUE, YELLOW, GREEN, RED, WHITE
 
 from random import randint
@@ -351,9 +353,16 @@ def _calculate_retry_delay(response, num_attempts):
         resource, including the most recent failed one
     :type num_attempts: int
     '''
-    if response is not None and response.status == 503 and 'retry-after' in response.headers:
+    if response is not None and response.status in (503, 429) and 'retry-after' in response.headers:
         try:
-            return int(response.headers['retry-after'])
+            suggested_delay = int(response.headers['retry-after'])
+
+            # By default, apiserver doesn't track attempts and doesn't provide increased timeout over attempts.
+            # So, increasing backoff for throttled requests up to x5 times from the original one.
+            # The current implementation of apiserver returns a retry-after header ranging from 20 to 30 seconds.
+            # Thus, after the 20th attempt the delay will always be between 100 and 150 seconds.
+            return suggested_delay if suggested_delay >= 60 \
+                else suggested_delay + int(0.25 * min(num_attempts - 1, 20) * suggested_delay)
         except ValueError:
             # In RFC 2616, retry-after can be formatted as absolute time
             # instead of seconds to wait. We don't bother to parse that,
@@ -361,7 +370,8 @@ def _calculate_retry_delay(response, num_attempts):
             pass
     if num_attempts <= 1:
         return 1
-    num_attempts = min(num_attempts, 7)
+    num_attempts = min(num_attempts, 8)
+    # After the 8th attempt the delay will always be between 64 and 128 seconds
     return randint(2 ** (num_attempts - 2), 2 ** (num_attempts - 1))
 
 
@@ -553,10 +563,10 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
 
     # Maintain two separate counters for the number of tries...
 
-    try_index = 0  # excluding 503 errors. The number of tries as given here
+    try_index = 0  # excluding 503/429 errors. The number of tries as given here
                    # cannot exceed (max_retries + 1).
-    try_index_including_503 = 0  # including 503 errors. This number is used to
-                                 # do exponential backoff.
+    try_index_including_throttled = 0  # including 503/429 errors. This number is used to
+                                       # do exponential backoff.
 
     retried_responses = []
     _url = None
@@ -730,7 +740,7 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
                        or isinstance(e, _RETRYABLE_WITH_RESPONSE)):
                         ok_to_retry = is_retryable
                     else:
-                        ok_to_retry = 500 <= response.status < 600
+                        ok_to_retry = response.status == 429 or 500 <= response.status < 600
 
                     # The server has closed the connection prematurely
                     if (response is not None
@@ -753,10 +763,10 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
                     if rewind_input_buffer_offset is not None:
                         data.seek(rewind_input_buffer_offset)
 
-                    delay = _calculate_retry_delay(response, try_index_including_503 + 1)
+                    delay = _calculate_retry_delay(response, try_index_including_throttled + 1)
 
                     range_str = (' (range=%s)' % (headers['Range'],)) if 'Range' in headers else ''
-                    if response is not None and response.status == 503:
+                    if response is not None and response.status in (503, 429):
                         waiting_msg = 'Waiting %d seconds before retry...' % (delay,)
                     else:
                         waiting_msg = 'Waiting %d seconds before retry %d of %d...' % (
@@ -768,8 +778,8 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
 
                     logger.warning(log_msg)
                     time.sleep(delay)
-                    try_index_including_503 += 1
-                    if response is None or response.status != 503:
+                    try_index_including_throttled += 1
+                    if response is None or response.status not in (503, 429):
                         try_index += 1
                     continue
 

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/app_builder.py

@@ -49,7 +49,6 @@ import dxpy.executable_builder
 from . import logger
 from .utils import merge
 from .utils.printing import fill
-from .compat import input
 from .cli import INTERACTIVE_CLI
 
 NUM_CORES = multiprocessing.cpu_count()

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/asset_builder.py

@@ -23,7 +23,6 @@ import tempfile
 import shutil
 import json
 
-from .compat import open
 from .exceptions import err_exit
 from .utils import json_load_raise_on_duplicates
 from .utils.resolver import is_container_id, resolve_path

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/bindings/dxdatabase.py

@@ -23,19 +23,16 @@ This remote database handler is a Python database-like object.
 
 from __future__ import print_function, unicode_literals, division, absolute_import
 
-import os, sys, logging, traceback, hashlib, copy, time
-import math
-import mmap
+import os, copy, time
+from io import BytesIO
 from threading import Lock
 from multiprocessing import cpu_count
 
 import dxpy
 from . import DXDataObject
-from ..exceptions import DXFileError, DXIncompleteReadsError
-from ..utils import warn
 from ..utils.resolver import object_exists_in_project
-from ..compat import BytesIO, basestring, USING_PYTHON2
 from .. import logger
+from ..compat import basestring
 
 
 DXFILE_HTTP_THREADS = min(cpu_count(), 8)

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/bindings/dxdatabase_functions.py

@@ -36,7 +36,7 @@ from .. import logger
 from . import dxfile, DXFile
 from . import dxdatabase, DXDatabase
 from .dxfile import FILE_REQUEST_TIMEOUT
-from ..compat import open, USING_PYTHON2, md5_hasher
+from ..compat import md5_hasher
 from ..exceptions import DXFileError, DXChecksumMismatchError, DXIncompleteReadsError, err_exit
 from ..utils import response_iterator
 import subprocess

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/bindings/dxfile.py

@@ -23,7 +23,8 @@ This remote file handler is a Python file-like object.
 
 from __future__ import print_function, unicode_literals, division, absolute_import
 
-import os, sys, logging, traceback, hashlib, copy, time
+import os, sys, traceback, copy, time
+from io import BytesIO
 import math
 import mmap
 from threading import Lock
@@ -34,7 +35,7 @@ from . import DXDataObject
 from ..exceptions import DXFileError, DXIncompleteReadsError
 from ..utils import warn
 from ..utils.resolver import object_exists_in_project
-from ..compat import BytesIO, basestring, USING_PYTHON2, md5_hasher
+from ..compat import md5_hasher, basestring
 
 
 DXFILE_HTTP_THREADS = min(cpu_count(), 8)
@@ -253,6 +254,8 @@ class DXFile(DXDataObject):
         self._file_length = None
         self._cur_part = 1
         self._num_uploaded_parts = 0
+        # Cache for object existence in project
+        self._exists_in_proj = None  
 
     def _new(self, dx_hash, media_type=None, **kwargs):
         """
@@ -486,8 +489,7 @@ class DXFile(DXDataObject):
             does not affect where the next :meth:`write` will occur.
 
         '''
-        if not USING_PYTHON2:
-            assert(isinstance(data, bytes))
+        assert(isinstance(data, bytes))
 
         self._ensure_write_bufsize(**kwargs)
 
@@ -544,31 +546,28 @@ class DXFile(DXDataObject):
             does not affect where the next :meth:`write` will occur.
 
         '''
-        if USING_PYTHON2:
-            self._write2(data, multithread=multithread, **kwargs)
+        # In python3, the underlying system methods use the 'bytes' type, not 'string'
+        #
+        # This is, hopefully, a temporary hack. It is not a good idea for two reasons:
+        # 1) Performance, we need to make a pass on the data, and need to allocate
+        #    another buffer of similar size
+        # 2) The types are wrong. The "bytes" type should be visible to the caller
+        #    of the write method, instead of being hidden.
+
+        # Should we throw an exception if the file is opened in binary mode,
+        # and the data is unicode/text?
+        if isinstance(data, str):
+            bt = data.encode("utf-8")
+        elif isinstance(data, bytearray):
+            bt = bytes(data)
+        elif isinstance(data, bytes):
+            bt = data
+        elif isinstance(data, mmap.mmap):
+            bt = bytes(data)
         else:
-            # In python3, the underlying system methods use the 'bytes' type, not 'string'
-            #
-            # This is, hopefully, a temporary hack. It is not a good idea for two reasons:
-            # 1) Performance, we need to make a pass on the data, and need to allocate
-            #    another buffer of similar size
-            # 2) The types are wrong. The "bytes" type should be visible to the caller
-            #    of the write method, instead of being hidden.
-
-            # Should we throw an exception if the file is opened in binary mode,
-            # and the data is unicode/text?
-            if isinstance(data, str):
-                bt = data.encode("utf-8")
-            elif isinstance(data, bytearray):
-                bt = bytes(data)
-            elif isinstance(data, bytes):
-                bt = data
-            elif isinstance(data, mmap.mmap):
-                bt = bytes(data)
-            else:
-                raise DXFileError("Invalid type {} for write data argument".format(type(data)))
-            assert(isinstance(bt, bytes))
-            self._write2(bt, multithread=multithread, **kwargs)
+            raise DXFileError("Invalid type {} for write data argument".format(type(data)))
+        assert(isinstance(bt, bytes))
+        self._write2(bt, multithread=multithread, **kwargs)
 
     def closed(self, **kwargs):
         '''
@@ -604,10 +603,7 @@ class DXFile(DXDataObject):
             # settings allow last empty part upload, try to upload
             # an empty part (otherwise files with 0 parts cannot be closed).
             try:
-                if USING_PYTHON2:
-                    self.upload_part('', 1, **kwargs)
-                else:
-                    self.upload_part(b'', 1, **kwargs)
+                self.upload_part(b'', 1, **kwargs)
             except dxpy.exceptions.InvalidState:
                 pass
 
@@ -646,9 +642,7 @@ class DXFile(DXDataObject):
         defaults to 1. This probably only makes sense if this is the
         only part to be uploaded.
         """
-        if not USING_PYTHON2:
-            # In python3, the underlying system methods use the 'bytes' type, not 'string'
-            assert(isinstance(data, bytes))
+        assert(isinstance(data, bytes))
 
         req_input = {}
         if index is not None:
@@ -934,18 +928,14 @@ class DXFile(DXDataObject):
             buf.seek(orig_buf_pos)
             return buf.read()
 
-        # Debug fallback
-        # import urllib2
-        # req = urllib2.Request(url, headers=headers)
-        # response = urllib2.urlopen(req)
-        # return response.read()
-
     def read(self, length=None, use_compression=None, project=None, **kwargs):
-        if project is None and object_exists_in_project(self.get_id(), self.get_proj_id()):
+        # Check if the file is present in dxfile project attribute if the project arg not specified 
+        if project is None and self._exists_in_proj is None and self.get_proj_id() is not None:
+            self._exists_in_proj = object_exists_in_project(self.get_id(), self.get_proj_id())
+        # Use the DXFile attribute if the project arg is not provided
+        if project is None and self._exists_in_proj:
             project = self.get_proj_id()
         data = self._read2(length=length, use_compression=use_compression, project=project, **kwargs)
-        if USING_PYTHON2:
-            return data
         # In python3, the underlying system methods use the 'bytes' type, not 'string'
         if self._binary_mode is True:
             return data

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/bindings/dxfile_functions.py

@@ -30,8 +30,6 @@ import traceback
 import warnings
 from collections import defaultdict
 import multiprocessing
-from random import randint
-from time import sleep
 import crc32c
 import zlib
 import base64
@@ -41,7 +39,7 @@ from .. import logger
 from . import dxfile, DXFile
 from .dxfile import FILE_REQUEST_TIMEOUT
 from ..exceptions import DXError, DXFileError, DXPartLengthMismatchError, DXChecksumMismatchError, DXIncompleteReadsError, err_exit
-from ..compat import open, md5_hasher, USING_PYTHON2
+from ..compat import md5_hasher
 from ..utils import response_iterator
 import subprocess
 import concurrent.futures

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/cli/__init__.py

@@ -26,7 +26,6 @@ import sys
 INTERACTIVE_CLI = sys.stdin and sys.stdin.isatty() and sys.stdout and sys.stdout.isatty()
 
 from ..exceptions import err_exit, default_expected_exceptions, DXError
-from ..compat import input
 
 def try_call_err_exit():
     err_exit(expected_exceptions=default_expected_exceptions + (DXError,))

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/cli/dataset_utilities.py

@@ -36,13 +36,11 @@ from ..bindings.dxfile import DXFile
 from ..utils.resolver import resolve_existing_path, is_hashid, ResolutionError, resolve_path, check_folder_exists
 from ..utils.file_handle import as_handle
 from ..utils.describe import print_desc
-from ..compat import USING_PYTHON2
 from ..exceptions import (
     err_exit,
     PermissionDenied,
     InvalidInput,
     InvalidState,
-    ResourceNotFound,
     default_expected_exceptions,
 )
 
@@ -1633,10 +1631,7 @@ def validate_cohort_ids(descriptor, project, resp, ids):
     gpk_type = descriptor.model["entities"][entity_name]["fields"][field_name]["mapping"]["column_sql_type"]
     # Prepare a payload to find entries matching the input ids in the dataset
     if gpk_type in ["integer", "bigint"]:
-        if USING_PYTHON2:
-            lambda_for_list_conv = lambda a, b: a+[long(b)]
-        else:
-            lambda_for_list_conv = lambda a, b: a+[int(b)]
+        lambda_for_list_conv = lambda a, b: a+[int(b)]
     elif gpk_type in ["float", "double"]:
         lambda_for_list_conv = lambda a, b: a+[float(b)]
     elif gpk_type in ["string"]:

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/cli/exec_io.py

@@ -33,7 +33,7 @@ from ..utils.describe import (get_find_executions_string, get_ls_l_desc, get_ls_
 from ..utils.resolver import (parse_input_keyval, is_hashid, is_job_id, is_localjob_id, paginate_and_pick, pick,
                               resolve_existing_path, resolve_multiple_existing_paths, split_unescaped, is_analysis_id)
 from ..utils import OrderedDefaultdict
-from ..compat import input, str, shlex, basestring, USING_PYTHON2
+from ..compat import basestring
 try:
     # Import gnureadline if installed for macOS
     import gnureadline as readline
@@ -604,8 +604,6 @@ class ExecutableInputs(object):
                 try:
                     parsed_input_value = json.loads(input_value, object_pairs_hook=collections.OrderedDict)
                     immediate_types = {collections.OrderedDict, list, int, float}
-                    if USING_PYTHON2:
-                        immediate_types.add(long) # noqa
                     if type(parsed_input_value) not in immediate_types:
                         raise Exception()
                 except:

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/cli/org.py

@@ -20,7 +20,6 @@ the org-based commands of the dx command-line client.
 '''
 from __future__ import print_function, unicode_literals, division, absolute_import
 
-from ..compat import input
 import dxpy
 from . import try_call, prompt_for_yn, INTERACTIVE_CLI
 from .parsers import process_find_by_property_args, process_phi_param

dxpy-0.395.0/dxpy/compat.py

@@ -0,0 +1,38 @@
+# Copyright (C) 2013-2016 DNAnexus, Inc.
+#
+# This file is part of dx-toolkit (DNAnexus platform client libraries).
+#
+#   Licensed under the Apache License, Version 2.0 (the "License"); you may not
+#   use this file except in compliance with the License. You may obtain a copy
+#   of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+#   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+#   License for the specific language governing permissions and limitations
+#   under the License.
+
+from __future__ import print_function, unicode_literals, division, absolute_import
+
+import sys, locale, threading, hashlib
+
+try:
+    sys_encoding = locale.getdefaultlocale()[1] or "UTF-8"
+except Exception:
+    sys_encoding = "UTF-8"
+
+USING_PYTHON2 = True if sys.version_info < (3, 0) else False
+
+basestring = (str, bytes)
+
+THREAD_TIMEOUT_MAX = threading.TIMEOUT_MAX
+
+# Support FIPS enabled Python
+def md5_hasher():
+    try:
+        md5_hasher = hashlib.new('md5', usedforsecurity=False)
+    except:
+        md5_hasher = hashlib.new('md5')
+    return md5_hasher

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/dxlog.py

@@ -21,7 +21,6 @@ import socket, json, time, os, logging
 from logging.handlers import SysLogHandler
 
 from dxpy.exceptions import DXError
-from dxpy.compat import USING_PYTHON2
 
 class DXLogHandler(SysLogHandler):
     '''
@@ -70,7 +69,7 @@ class DXLogHandler(SysLogHandler):
         return self.priority_names[self.priority_map.get(record.levelname, "warning")]
 
     def truncate_message(self, message):
-        msg_bytes = message if USING_PYTHON2 else message.encode('utf-8')
+        msg_bytes = message.encode('utf-8')
 
         if len(json.dumps(message)) <= 8015:
             return message
@@ -80,12 +79,9 @@ class DXLogHandler(SysLogHandler):
             msg_bytes = msg_bytes[:-1]
 
         message = _bytes2utf8(msg_bytes)
-        message = message.encode('utf-8') if USING_PYTHON2 else message
         return message + "... [truncated]"
 
     def is_resource_log(self, message):
-        if USING_PYTHON2:
-            return message.startswith(b"CPU: ")
         return message.startswith("CPU: ")
 
     def emit(self, record):
@@ -95,9 +91,6 @@ class DXLogHandler(SysLogHandler):
         # with the extra padding introduced by the log function, the
         # incoming message needs to be smaller - we truncate it to
         # at most 8015 bytes here.
-        # Note: we use Python 2 semantics here (byte strings). This
-        # script is not Python 3 ready. If *line* was a unicode string
-        # with wide chars, its byte length would exceed the limit.
         message = self.truncate_message(message)
 
         data = json.dumps({"source": self.source, "timestamp": int(round(time.time() * 1000)),

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/exceptions.py

@@ -28,7 +28,6 @@ import socket
 from urllib3.exceptions import HTTPError
 
 import dxpy
-from .compat import USING_PYTHON2
 import urllib3
 import ssl
 
@@ -246,10 +245,8 @@ network_exceptions = (urllib3.exceptions.ProtocolError,
                       urllib3.exceptions.SSLError,
                       ssl.SSLError,
                       HTTPError,
-                      socket.error)
-if not USING_PYTHON2:
-    network_exceptions += (ConnectionResetError,)
-
+                      socket.error,
+                      ConnectionResetError,)
 
 try:
     json_exceptions = (json.decoder.JSONDecodeError,)

dxpy-0.395.0/dxpy/nextflow/nextaur_assets.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzKXzG85y5b99vKK95b4vpKy",
+    "aws:eu-central-1": "record-GzKY0y04V0179X5Bz9K355k3",
+    "aws:eu-west-2-g": "record-GzKY3jBKXjZ413XPP0yv4fgy",
+    "aws:me-south-1": "record-GzKY5G132j8qz8yk710gjKJk",
+    "aws:us-east-1": "record-GzKXx300FZzQ73Q0ykjvQ1GV",
+    "azure:westeurope": "record-GzKY8zjB5PzvxVg2Gy3g77QK",
+    "azure:westus": "record-GzKYJf099Z602KYFxJzvJQj1"
+}

dxpy-0.395.0/dxpy/nextflow/nextaur_assets.staging.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzKXFyj51PXF1f67BYjP54Px",
+    "aws:eu-central-1": "record-GzKXJgj4bPkjfBg634qfx8pF",
+    "aws:eu-west-2-g": "record-GzKXPJ2K5b2xPyZbyx3pZg7Y",
+    "aws:me-south-1": "record-GzKXQv93j7qB0fVgGXVf71Z9",
+    "aws:us-east-1": "record-GzKX8p00kP5q1f67BYjP54PZ",
+    "azure:westeurope": "record-GzKXZGjB6fJ6vb04b7VBV2Kx",
+    "azure:westus": "record-GzKXgVj9YqqxPyZbyx3pZg8G"
+}

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/nextflow/nextflow_builder.py

@@ -182,7 +182,8 @@ def prepare_custom_inputs(schema_file="./nextflow_schema.json"):
 
     with open(schema_file, "r") as fh:
         schema = json.load(fh)
-    for d_key, d_schema in schema.get("definitions", {}).items():
+    defs_key = "definitions" if "definitions" in schema else "$defs" if "$defs" in schema else {}
+    for d_key, d_schema in schema.get(defs_key).items():
         required_inputs = d_schema.get("required", [])
         for property_key, property in d_schema.get("properties", {}).items():
             dx_input = {}

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/nextflow/nextflow_templates.py

@@ -5,7 +5,6 @@ from .nextflow_utils import (get_template_dir, get_source_file_name, get_resourc
 import json
 import os
 from dxpy import TOOLKIT_VERSION
-from dxpy.compat import USING_PYTHON2, sys_encoding
 
 
 def get_nextflow_dxapp(
@@ -94,11 +93,7 @@ def get_nextflow_src(custom_inputs=None, profile=None, resources_dir=None):
     src = src.replace("@@PROFILE_ARG@@", profile_arg)
     src = src.replace("@@EXCLUDE_INPUT_DOWNLOAD@@", exclude_input_download)
     src = src.replace("@@DXPY_BUILD_VERSION@@", TOOLKIT_VERSION)
-    if USING_PYTHON2:
-        src = src.replace("@@RESOURCES_SUBPATH@@",
-                          get_resources_subpath(resources_dir).encode(sys_encoding))
-    else:
-        src = src.replace("@@RESOURCES_SUBPATH@@",
+    src = src.replace("@@RESOURCES_SUBPATH@@",
                           get_resources_subpath(resources_dir))
 
     return src

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/scripts/dx.py

@@ -25,11 +25,7 @@ import csv
 
 logging.basicConfig(level=logging.INFO)
 
-from ..compat import (USING_PYTHON2, basestring, str, input, wrap_stdio_in_codecs, decode_command_line_args,
-                      unwrap_stream, sys_encoding)
-
-wrap_stdio_in_codecs()
-decode_command_line_args()
+from ..compat import sys_encoding, basestring
 
 import dxpy
 from dxpy.scripts import dx_build_app
@@ -311,8 +307,7 @@ def login(args):
                     else:
                         username = input('Username: ')
                 dxpy.config.write("DX_USERNAME", username)
-                with unwrap_stream('stdin'):
-                    password = getpass.getpass()
+                password = getpass.getpass()
 
             otp = input('Verification code: ') if get_otp else None
             return dict(username=username, password=password, otp=otp)
@@ -416,9 +411,8 @@ def logout(args):
         print("Deleting credentials from {}...".format(authserver))
         token = dxpy.AUTH_HELPER.security_context["auth_token"]
         try:
-            if not USING_PYTHON2:
-                # python 3 requires conversion to bytes before hashing
-                token = token.encode(sys_encoding)
+            # python 3 requires conversion to bytes before hashing
+            token = token.encode(sys_encoding)
             token_sig = hashlib.sha256(token).hexdigest()
             response = dxpy.DXHTTPRequest(authserver + "/system/destroyAuthToken",
                                           dict(tokenSignature=token_sig),
@@ -2782,8 +2776,6 @@ def build(args):
         src_dir = args.src_dir
         if src_dir is None:
             src_dir = os.getcwd()
-            if USING_PYTHON2:
-                src_dir = src_dir.decode(sys.getfilesystemencoding())
         return src_dir
 
     def handle_arg_conflicts(args):
@@ -4170,12 +4162,8 @@ def generate_batch_inputs(args):
         batch_fname = "{}.{:04d}.tsv".format(args.output_prefix, i)
 
         # In python-3 we need to open the file in textual mode.
-        if USING_PYTHON2:
-            write_mode = 'wb'
-            delimiter = '\t'.encode('ascii')
-        else:
-            write_mode = 'w'
-            delimiter = '\t'
+        write_mode = 'w'
+        delimiter = '\t'
 
         with open(batch_fname, write_mode) as csvfile:
             batchwriter = csv.writer(csvfile, delimiter=delimiter)
@@ -4523,10 +4511,6 @@ class DXArgumentParser(argparse.ArgumentParser):
                     msg += "\n\nDid you mean: " + BOLD("dx " + suggestion)
 
             err = argparse.ArgumentError(action, msg)
-            if USING_PYTHON2:
-                err.message = err.message.encode(sys_encoding)
-                if err.argument_name is not None:
-                    err.argument_name = err.argument_name.encode(sys_encoding)
             raise err
 
     def exit(self, status=0, message=None):
@@ -4538,8 +4522,6 @@ class DXArgumentParser(argparse.ArgumentParser):
         sys.exit(status)
 
     def error(self, message):
-        if USING_PYTHON2:
-            message = message.decode(sys_encoding)
         self.exit(2, '{help}\n{prog}: error: {msg}\n'.format(help=self.format_help(),
                                                              prog=self.prog,
                                                              msg=message))
@@ -6837,10 +6819,7 @@ def main():
         import argcomplete
 
         # In python-3 we need to use a binary output stream
-        if USING_PYTHON2:
-            output_stream = sys.stdout
-        else:
-            output_stream = sys.stdout.buffer
+        output_stream = sys.stdout.buffer
         argcomplete.autocomplete(parser,
                                  always_complete_options=False,
                                  exclude=['gtable', 'export'],

{dxpy-0.393.0 → dxpy-0.395.0}/dxpy/scripts/dx_app_wizard.py

@@ -31,8 +31,6 @@ from dxpy.utils.printing import fill, BOLD, UNDERLINE, DNANEXUS_LOGO, ENDC
 from dxpy.app_categories import APP_CATEGORIES
 from dxpy.utils.completer import InstanceTypesCompleter
 from dxpy.utils.pretty_print import format_table
-from dxpy.compat import wrap_stdio_in_codecs
-wrap_stdio_in_codecs()
 
 try:
     import colorama