[Git][debian-gis-team/pywps][upstream] New upstream version 4.5.2
Bas Couwenberg (@sebastic)
gitlab at salsa.debian.org
Thu Apr 14 04:32:48 BST 2022
Bas Couwenberg pushed to branch upstream at Debian GIS Project / pywps
Commits:
65a5131e by Bas Couwenberg at 2022-04-14T05:22:54+02:00
New upstream version 4.5.2
- - - - -
18 changed files:
- .github/workflows/main.yml
- LICENSE.txt
- README.md
- VERSION.txt
- debian/changelog
- pywps/__init__.py
- pywps/app/WPSRequest.py
- pywps/inout/basic.py
- pywps/inout/inputs.py
- requirements-dev.txt
- setup.cfg
- setup.py
- tests/processes/__init__.py
- tests/test_exceptions.py
- tests/test_inout.py
- tests/test_processing.py
- tests/test_wpsrequest.py
- tox.ini
Changes:
=====================================
.github/workflows/main.yml
=====================================
@@ -1,41 +1,55 @@
name: build ⚙️
-on: [ push, pull_request ]
+on:
+ push:
+ branches:
+ - main
+ pull_request:
jobs:
- main:
+ test:
runs-on: ubuntu-latest
strategy:
matrix:
- python-version: [3.7, 3.8, 3.9]
- env:
- GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- COVERALLS_SERVICE_NAME: github
+ include:
+ - tox-env: py37-extra
+ python-version: 3.7
+ - tox-env: py38-extra
+ python-version: 3.8
+ - tox-env: py39-extra
+ python-version: 3.9
steps:
- uses: actions/checkout at v2
- - name: Install packages
+ - name: Install packages 📦
run: |
- sudo apt-get update && sudo apt-get -y install libnetcdf-dev libhdf5-dev
+ sudo apt-get update
+ sudo apt-get -y install libnetcdf-dev libhdf5-dev
- uses: actions/setup-python at v2
name: Setup Python ${{ matrix.python-version }}
with:
python-version: ${{ matrix.python-version }}
- - name: Install requirements 📦
+ - name: Run flake8 ⚙️
run: |
- pip3 install pip --upgrade
- pip3 install -r requirements.txt
- pip3 install -r requirements-dev.txt
- pip3 install -r requirements-extra.txt
- - name: run tests ⚙️
- run: pytest -v tests
- - name: run coveralls ⚙️
- run: coveralls
+ pip install flake8
+ flake8 pywps
if: matrix.python-version == 3.7
- - name: build docs 🏗️
- run: |
- pip3 install -e .
- cd docs && make html
- if: matrix.python-version == 3.7
- - name: run flake8 ⚙️
- run: flake8 pywps
+ - name: Install tox 📦
+ run: pip install tox
+ - name: Run tests with tox ⚙️
+ run: tox -e ${{ matrix.tox-env }}
+ - name: Run coveralls ⚙️
if: matrix.python-version == 3.7
+ uses: AndreMiras/coveralls-python-action at develop
+
+ docs:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout at v2
+ - uses: actions/setup-python at v2
+ name: Setup Python 3.7
+ with:
+ python-version: 3.7
+ - name: Build docs 🏗️
+ run: |
+ pip install -e .[dev]
+ cd docs && make html
=====================================
LICENSE.txt
=====================================
@@ -1,4 +1,4 @@
-Copyright (C) 2014-2016 PyWPS Development Team, represented by Jachym Cepicky
+Copyright (C) 2014-2021 PyWPS Development Team, represented by Jachym Cepicky
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to
=====================================
README.md
=====================================
@@ -5,7 +5,7 @@ the Open Geospatial Consortium. PyWPS is written in Python.
[](https://pywps.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/geopython/pywps/actions/workflows/main.yml)
-[](https://coveralls.io/github/geopython/pywps?branch=master)
+[](https://coveralls.io/github/geopython/pywps?branch=main)
[](https://pypi.org/project/pywps/)
[]()
@@ -26,7 +26,7 @@ See [requirements.txt](requirements.txt) file
```bash
pip install -r requirements-dev.txt
# run unit tests
-python -m unittest tests
+python -m pytest tests
# run code coverage
python -m coverage run --source=pywps -m unittest tests
python -m coverage report -m
=====================================
VERSION.txt
=====================================
@@ -1 +1 @@
-4.5.1
+4.5.2
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pywps (4.5.2) trusty; urgency=medium
+
+ * Fix test section in README.md about pytest (#653)
+ * Fix ComplexInput.from_json to handle data_format.encoding="base64" (#652)
+ * Fix invalide use of encode on bytes object (#651)
+ * Fix JSON encoding of CRS type in BoundingBox (#610)
+ * Modernize CI using Tox, add a "[dev]" recipe, re-enable coveralls (#643)
+ * Fix deprecated logging.warn() call (#642)
+
+ -- Carsten Ehbrecht <ehbrecht at dkrz.de> Wed, 13 Apr 2022 18:00:00 +0000
+
pywps (4.5.1) trusty; urgency=medium
* Fix app/Process.py to cope with None mimetype (#620)
=====================================
pywps/__init__.py
=====================================
@@ -9,7 +9,7 @@ import os
from lxml.builder import ElementMaker
-__version__ = "4.5.1"
+__version__ = "4.5.2"
LOGGER = logging.getLogger('PYWPS')
LOGGER.debug('setting core variables')
=====================================
pywps/app/WPSRequest.py
=====================================
@@ -575,7 +575,7 @@ def get_inputs_from_xml(doc):
inpt = {}
inpt['identifier'] = identifier_el.text
inpt['data'] = [bbox.minx, bbox.miny, bbox.maxx, bbox.maxy]
- inpt['crs'] = bbox.crs
+ inpt['crs'] = bbox.crs.getcodeurn() if bbox.crs else None
inpt['dimensions'] = bbox.dimensions
the_inputs[identifier].append(inpt)
return the_inputs
=====================================
pywps/inout/basic.py
=====================================
@@ -1010,7 +1010,7 @@ class ComplexInput(BasicIO, BasicComplex, IOHandler):
except Exception:
# TODO: handle os.symlink on windows
# raise NoApplicableCode("Could not link file reference: {}".format(e))
- LOGGER.warn("Could not link file reference")
+ LOGGER.warning("Could not link file reference")
shutil.copy2(inpt_file, tmp_file)
return tmp_file
=====================================
pywps/inout/inputs.py
=====================================
@@ -2,7 +2,7 @@
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
-
+import base64
import re
from pywps import xml_util as etree
@@ -220,12 +220,15 @@ class ComplexInput(basic.ComplexInput):
instance.url = json_input['href']
elif json_input.get('data'):
data = json_input['data']
- # remove cdata tag if it exists (issue #553)
- if isinstance(data, str):
- match = CDATA_PATTERN.match(data)
- if match:
- data = match.group(1)
- instance.data = data
+ if data_format.encoding == 'base64':
+ instance.data = base64.b64decode(data)
+ else:
+ # remove cdata tag if it exists (issue #553)
+ if isinstance(data, str):
+ match = CDATA_PATTERN.match(data)
+ if match:
+ data = match.group(1)
+ instance.data = data
return instance
@@ -247,7 +250,7 @@ class ComplexInput(basic.ComplexInput):
else:
# Otherwise we assume all other formats are unsafe and need to be enclosed in a CDATA tag.
if isinstance(self.data, bytes):
- out = self.data.encode(self.data_format.encoding or 'utf-8')
+ out = self.data.decode(self.data_format.encoding or 'utf-8')
else:
out = self.data
=====================================
requirements-dev.txt
=====================================
@@ -1,6 +1,7 @@
coverage
coveralls
pytest
+pytest-cov
flake8
pylint
Sphinx
=====================================
setup.cfg
=====================================
@@ -1,16 +1,11 @@
[bumpversion]
-current_version = 4.5.1
+current_version = 4.5.2
commit = False
tag = False
parse = (?P<major>\d+)\.(?P<minor>\d+).(?P<patch>\d+)
serialize =
{major}.{minor}.{patch}
-[flake8]
-ignore = F401,E402,W606
-max-line-length = 120
-exclude = tests
-
[bumpversion:file:pywps/__init__.py]
search = __version__ = "{current_version}"
replace = __version__ = "{new_version}"
@@ -18,3 +13,14 @@ replace = __version__ = "{new_version}"
[bumpversion:file:VERSION.txt]
search = {current_version}
replace = {new_version}
+
+[coverage:run]
+relative_files = True
+
+[flake8]
+ignore =
+ F401
+ E402
+ W606
+max-line-length = 120
+exclude = tests
=====================================
setup.py
=====================================
@@ -12,57 +12,68 @@ except ImportError:
from setuptools import find_packages
-with open('VERSION.txt') as ff:
+with open("VERSION.txt") as ff:
VERSION = ff.read().strip()
-DESCRIPTION = ('PyWPS is an implementation of the Web Processing Service '
- 'standard from the Open Geospatial Consortium. PyWPS is '
- 'written in Python.')
+DESCRIPTION = (
+ "PyWPS is an implementation of the Web Processing Service "
+ "standard from the Open Geospatial Consortium. PyWPS is "
+ "written in Python."
+)
-with open('README.md') as ff:
+with open("README.md") as ff:
LONG_DESCRIPTION = ff.read()
-KEYWORDS = 'PyWPS WPS OGC processing'
+KEYWORDS = "PyWPS WPS OGC processing"
-with open('requirements.txt') as f:
- INSTALL_REQUIRES = f.read().splitlines()
+with open("requirements.txt") as fr:
+ INSTALL_REQUIRES = fr.read().splitlines()
+
+with open("requirements-dev.txt") as frd:
+ DEV_REQUIRES = frd.read().splitlines()
CONFIG = {
- 'name': 'pywps',
- 'version': VERSION,
- 'description': DESCRIPTION,
- 'long_description': LONG_DESCRIPTION,
- 'long_description_content_type': 'text/markdown',
- 'keywords': KEYWORDS,
- 'license': 'MIT',
- 'platforms': 'all',
- 'author': 'Jachym Cepicky',
- 'author_email': 'jachym.cepicky at gmail.com',
- 'maintainer': 'Jachym Cepicky',
- 'maintainer_email': 'jachym.cepicky at gmail.com',
- 'url': 'https://pywps.org',
- 'download_url': 'https://github.com/geopython/pywps',
- 'classifiers': [
- 'Development Status :: 5 - Production/Stable',
- 'Environment :: Web Environment',
- 'Intended Audience :: Developers',
- 'Intended Audience :: Science/Research',
- 'License :: OSI Approved :: MIT License',
- 'Operating System :: OS Independent',
- 'Programming Language :: Python',
+ "name": "pywps",
+ "version": VERSION,
+ "description": DESCRIPTION,
+ "long_description": LONG_DESCRIPTION,
+ "long_description_content_type": "text/markdown",
+ "keywords": KEYWORDS,
+ "license": "MIT",
+ "platforms": "all",
+ "author": "Jachym Cepicky",
+ "author_email": "jachym.cepicky at gmail.com",
+ "maintainer": "Jachym Cepicky",
+ "maintainer_email": "jachym.cepicky at gmail.com",
+ "url": "https://pywps.org",
+ "download_url": "https://github.com/geopython/pywps",
+ "classifiers": [
+ "Development Status :: 5 - Production/Stable",
+ "Environment :: Web Environment",
+ "Intended Audience :: Developers",
+ "Intended Audience :: Science/Research",
+ "License :: OSI Approved :: MIT License",
+ "Operating System :: OS Independent",
+ "Programming Language :: Python",
"Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
- 'Topic :: Scientific/Engineering :: GIS'
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
+ "Topic :: Scientific/Engineering :: GIS",
],
- 'install_requires': INSTALL_REQUIRES,
- 'python_requires': '>=3.6, <4',
- 'packages': find_packages(exclude=["docs", "tests.*", "tests"]),
- 'include_package_data': True,
- 'scripts': [],
- 'entry_points': {
- 'console_scripts': [
- 'joblauncher=pywps.processing.job:launcher', ]},
+ "install_requires": INSTALL_REQUIRES,
+ "extras_require": dict(
+ dev=DEV_REQUIRES,
+ ),
+ "python_requires": ">=3.7,<4",
+ "packages": find_packages(exclude=["docs", "tests.*", "tests"]),
+ "include_package_data": True,
+ "scripts": [],
+ "entry_points": {
+ "console_scripts": [
+ "joblauncher=pywps.processing.job:launcher",
+ ]
+ },
}
setup(**CONFIG)
=====================================
tests/processes/__init__.py
=====================================
@@ -4,7 +4,7 @@
##################################################################
from pywps import Process
-from pywps.inout import LiteralInput, LiteralOutput
+from pywps.inout import LiteralInput, LiteralOutput, BoundingBoxInput, BoundingBoxOutput
from pywps.inout.literaltypes import ValuesReference
@@ -71,3 +71,31 @@ class InOut(Process):
a_string = request.inputs['string'][0].data
response.outputs['string'].data = "".format(a_string)
return response
+
+
+class BBox(Process):
+ def __init__(self):
+ super(BBox, self).__init__(
+ self.bbox,
+ identifier='bbox_test',
+ title='BBox Test',
+ inputs=[
+ BoundingBoxInput(
+ 'area',
+ 'An area',
+ abstract='Define the area of interest',
+ crss=['epsg:4326', 'epsg:3857'],
+ min_occurs=1,
+ max_occurs=1
+ ),
+ ],
+ outputs=[
+ BoundingBoxOutput('extent', 'Extent', crss=['epsg:4326', 'epsg:3857'])
+ ]
+ )
+
+ @staticmethod
+ def bbox(request, response):
+ area = request.inputs['area'][0].data
+ response.outputs['extent'].data = area
+ return response
=====================================
tests/test_exceptions.py
=====================================
@@ -10,10 +10,11 @@ from pywps.tests import assert_pywps_version, client_for
import re
-VERSION="1.0.0"
+VERSION = "1.0.0"
WPS, OWS = get_ElementMakerForVersion(VERSION)
xpath_ns = get_xpath_ns(VERSION)
+
class ExceptionsTest(unittest.TestCase):
def setUp(self):
@@ -24,7 +25,7 @@ class ExceptionsTest(unittest.TestCase):
exception_el = resp.xpath('/ows:ExceptionReport/ows:Exception')[0]
assert exception_el.attrib['exceptionCode'] == 'InvalidParameterValue'
assert resp.status_code == 400
- assert re.match('text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
+ assert re.match(r'text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
assert_pywps_version(resp)
def test_missing_parameter_value(self):
@@ -32,20 +33,21 @@ class ExceptionsTest(unittest.TestCase):
exception_el = resp.xpath('/ows:ExceptionReport/ows:Exception')[0]
assert exception_el.attrib['exceptionCode'] == 'MissingParameterValue'
assert resp.status_code == 400
- assert re.match('text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
+ assert re.match(r'text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
def test_missing_request(self):
resp = self.client.get("?service=wps")
exception_el = resp.xpath('/ows:ExceptionReport/ows:Exception/ows:ExceptionText')[0]
# should mention something about a request
assert 'request' in exception_el.text
- assert re.match('text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
+ assert re.match(r'text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
def test_bad_request(self):
resp = self.client.get("?service=wps&request=xyz")
exception_el = resp.xpath('/ows:ExceptionReport/ows:Exception')[0]
assert exception_el.attrib['exceptionCode'] == 'OperationNotSupported'
- assert re.match('text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
+ assert re.match(r'text/xml(;\s*charset=.*)?', resp.headers['Content-Type'])
+
def load_tests(loader=None, tests=None, pattern=None):
if not loader:
=====================================
tests/test_inout.py
=====================================
@@ -284,6 +284,41 @@ class SerializationComplexInputTest(unittest.TestCase):
self.assertEqual(complex2.prop, 'data')
self.assertEqual(complex.data, complex2.data)
+ def test_complex_input_binary_data(self):
+ complex = self.make_complex_input()
+ complex.data = b"some data"
+ # the data is enclosed by a CDATA tag in json
+ assert complex.json['data'] == '<![CDATA[some data]]>'
+ self.assertEqual(complex.prop, 'data')
+
+ def test_complex_input_data_with_binary_data_format(self):
+ complex = inout.inputs.ComplexInput(
+ identifier="complexinput",
+ title='MyComplex',
+ abstract='My complex input',
+ keywords=['kw1', 'kw2'],
+ workdir=self.tmp_dir,
+ supported_formats=[FORMATS.ZIP],
+ metadata=[Metadata("special data")],
+ default="/some/file/path",
+ default_type=SOURCE_TYPE.FILE,
+ translations={"fr-CA": {"title": "Mon input", "abstract": "Une description"}},
+ data_format=FORMATS.ZIP
+ )
+ complex.as_reference = False
+ complex.method = "GET"
+ complex.max_size = 1000
+ complex.data = b"some data"
+ # the data is enclosed by a CDATA tag in json
+ assert complex.json['data'] == 'c29tZSBkYXRh'
+ # dump to json and load it again
+ complex2 = inout.inputs.ComplexInput.from_json(complex.json)
+
+ self.assert_complex_equals(complex, complex2)
+ self.assertEqual(complex.prop, 'data')
+ self.assertEqual(complex2.prop, 'data')
+ self.assertEqual(complex.data, complex2.data)
+
def test_complex_input_stream(self):
complex = self.make_complex_input()
complex.stream = StringIO("{'name': 'test', 'input1': ']]'}")
=====================================
tests/test_processing.py
=====================================
@@ -18,7 +18,7 @@ from pywps.processing.basic import MultiProcessing
from pywps.app import WPSRequest
from pywps.response.execute import ExecuteResponse
-from .processes import Greeter, InOut
+from .processes import Greeter, InOut, BBox
class GreeterProcessingTest(unittest.TestCase):
@@ -97,6 +97,39 @@ class InOutProcessingTest(unittest.TestCase):
self.assertEqual(new_job.json, self.job.json) # idempotent test
+class BBoxProcessingTest(unittest.TestCase):
+ """Processing test case with BBox input and output process"""
+
+ def setUp(self):
+ self.uuid = uuid.uuid1()
+ self.dummy_process = BBox()
+ self.dummy_process._set_uuid(self.uuid)
+ self.dummy_process.set_workdir('/tmp')
+ self.wps_request = WPSRequest()
+ self.wps_response = ExecuteResponse(self.wps_request, self.uuid,
+ process=self.dummy_process)
+ self.job = Job(
+ process=self.dummy_process,
+ wps_request=self.wps_request,
+ wps_response=self.wps_response)
+
+ def test_job_json(self):
+ new_job = Job.from_json(json.loads(self.job.json))
+ self.assertEqual(new_job.name, 'bbox_test')
+ self.assertEqual(new_job.uuid, str(self.uuid))
+ self.assertEqual(new_job.workdir, '/tmp')
+ self.assertEqual(len(new_job.process.inputs), 1)
+ self.assertEqual(new_job.json, self.job.json) # idempotent test
+
+ def test_job_dump(self):
+ new_job = Job.load(self.job.dump())
+ self.assertEqual(new_job.name, 'bbox_test')
+ self.assertEqual(new_job.uuid, str(self.uuid))
+ self.assertEqual(new_job.workdir, '/tmp')
+ self.assertEqual(len(new_job.process.inputs), 1)
+ self.assertEqual(new_job.json, self.job.json) # idempotent test
+
+
def load_tests(loader=None, tests=None, pattern=None):
"""Load local tests
"""
@@ -104,6 +137,7 @@ def load_tests(loader=None, tests=None, pattern=None):
loader = unittest.TestLoader()
suite_list = [
loader.loadTestsFromTestCase(GreeterProcessingTest),
- loader.loadTestsFromTestCase(InOutProcessingTest)
+ loader.loadTestsFromTestCase(InOutProcessingTest),
+ loader.loadTestsFromTestCase(BBoxProcessingTest)
]
return unittest.TestSuite(suite_list)
=====================================
tests/test_wpsrequest.py
=====================================
@@ -8,6 +8,7 @@ from pywps.app import WPSRequest
import tempfile
import datetime
import json
+from owslib.crs import Crs
from pywps.inout.literaltypes import AnyValue
@@ -116,6 +117,46 @@ class WPSRequestTest(unittest.TestCase):
self.assertEqual(self.request.inputs['date'][0].data, datetime.date(2017, 4, 20), 'Data set')
self.assertEqual(self.request.inputs['time'][0].data, datetime.time(9, 0, 0), 'Time set')
+ def test_json_inout_bbox(self):
+ obj = {
+ 'operation': 'getcapabilities',
+ 'version': '1.0.0',
+ 'language': 'eng',
+ 'identifier': 'arghhhh',
+ 'identifiers': 'arghhhh', # TODO: why identifierS?
+ 'store_execute': True,
+ 'status': True,
+ 'lineage': True,
+ 'inputs': {
+ 'bbox': [{
+ 'identifier': 'bbox',
+ 'type': 'bbox',
+ 'bbox': '6.117602,46.176194,6.22283,46.275832',
+ 'crs': 'urn:ogc:def:crs:EPSG::4326',
+ 'crss': ['epsg:4326'],
+ 'dimensions': 2,
+ 'translations': None
+ }],
+ },
+ 'outputs': {},
+ 'raw': False
+ }
+
+ self.request = WPSRequest()
+ self.request.json = obj
+
+ self.assertEqual(self.request.inputs['bbox'][0].data, [6.117602, 46.176194, 6.22283, 46.275832], 'BBox data set')
+ self.assertTrue(isinstance(self.request.inputs['bbox'][0].crs, str), 'CRS is a string')
+ self.assertEqual(self.request.inputs['bbox'][0].crs, 'epsg:4326', 'CRS data correctly parsed')
+
+ # dump to json and reload
+ dump = self.request.json
+ self.request.json = json.loads(dump)
+
+ self.assertEqual(self.request.inputs['bbox'][0].data, [6.117602, 46.176194, 6.22283, 46.275832], 'BBox data set')
+ self.assertTrue(isinstance(self.request.inputs['bbox'][0].crs, str), 'CRS is a string')
+ self.assertEqual(self.request.inputs['bbox'][0].crs, 'epsg:4326', 'CRS data correctly parsed')
+
def load_tests(loader=None, tests=None, pattern=None):
if not loader:
=====================================
tox.ini
=====================================
@@ -1,23 +1,21 @@
[tox]
-envlist=py36
+envlist = py{37,38,39}{-extra,}
+requires = pip >= 20.0
+opts = --verbose
[testenv]
-
-pip_pre=True
-deps=
- lxml
- flask
- owslib
- simplejson
- jsonschema
- geojson
- shapely
- unipath
- werkzeug
- SQLAlchemy
- jinja2
-
-commands=
- # check first which version is installed "gdal-config --version"
- pip install GDAL==2.1.0 --global-option=build_ext --global-option="-I/usr/include/gdal"
- python -m unittest tests
+setenv =
+ PYTEST_ADDOPTS = "--color=yes"
+ PYTHONPATH = {toxinidir}
+ COV_CORE_SOURCE =
+passenv = CI GITHUB_* LD_LIBRARY_PATH
+download = True
+install_command =
+ python -m pip install --no-user {opts} {packages}
+extras = dev
+deps =
+ extra: -rrequirements-extra.txt
+commands =
+; # magic for gathering the GDAL version within tox
+; sh -c 'pip install GDAL=="$(gdal-config --version)" --global-option=build_ext --global-option="-I/usr/include/gdal"'
+ pytest --cov
View it on GitLab: https://salsa.debian.org/debian-gis-team/pywps/-/commit/65a5131e569338743146f24cedcbb55993111b8e
--
View it on GitLab: https://salsa.debian.org/debian-gis-team/pywps/-/commit/65a5131e569338743146f24cedcbb55993111b8e
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