Fix build

README.md

@@ -363,14 +363,13 @@ Building the release packages from a fresh clone is a simple way of ensuring tha
 Create a Python venv to use for build and deploy:
 
 * The package `setup.py` scripts will run in this venv.
-* The venv can be reused indefinitly.
+* The venv can be reused indefinitely.
 
     $ pyenv virtualenv "x.y.z" venv_build
 
 * Where "x.y.z" is one of the versions listed in `pyenv versions`.
 * Pick a version that is close or the same as the version of Python used for testing on Travis.
 
-
 Build and publish the packages:
 
 * Download current master from GitHub, create binary wheel packages and push the packages to PyPI.

client_cli/src/d1_cli/version.py

@@ -16,4 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version__ = "3.4.6"
+__version__ = '3.4.7'

client_cli/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.cli",
-        version="3.4.6",
+        version='3.4.7',
         description="Command-Line Interface (CLI) for DataONE",
         author="DataONE Project",
         author_email="developers@dataone.org",
@@ -35,8 +35,8 @@ def main():
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.common >= 3.4.6",
-            "dataone.libclient >= 3.4.6",
+            "dataone.common >= 3.4.7",
+            "dataone.libclient >= 3.4.7",
             #
             "requests >= 2.22.0",
         ],

client_onedrive/src/setup.py

@@ -27,7 +27,7 @@
 def main():
     setuptools.setup(
         name="dataone.onedrive",
-        version="3.4.6",
+        version='3.4.7',
         description="Filesystem access to the DataONE Workspace",
         author="DataONE Project",
         author_email="developers@dataone.org",
@@ -36,8 +36,8 @@ def main():
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.common >= 3.4.6",
-            "dataone.libclient >= 3.4.6",
+            "dataone.common >= 3.4.7",
+            "dataone.libclient >= 3.4.7",
             #
             "fusepy >= 3.0.1",
             "pyxb >= 1.2.6",

dev_tools/src/d1_dev/setup-all.py

@@ -29,8 +29,6 @@
 import subprocess
 import sys
 
-import d1_common.utils.ulog
-
 try:
     import d1_dev.util
 except ImportError:
@@ -52,10 +50,8 @@
     # 'csw',
 ]
 
-
 log = logging.getLogger(__name__)
-d1_common.utils.ulog.setup(is_debug=True)
-
+logging.basicConfig(level=logging.DEBUG)
 
 def main():
     if sys.version_info[0] != 3:

dev_tools/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.dev",
-        version="3.4.6",
+        version='3.4.7',
         description="DataONE developer tools",
         author="DataONE Project",
         author_email="developers@dataone.org",

gmn/src/d1_gmn/version.py

@@ -16,4 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version__ = "3.4.6"
+__version__ = '3.4.7'

gmn/src/setup.py

@@ -28,7 +28,7 @@ def main():
     # noinspection PyUnresolvedReferences
     setuptools.setup(
         name="dataone.gmn",
-        version="3.4.6",
+        version='3.4.7',
         description="DataONE Generic Member Node (GMN)",
         author="DataONE Project",
         author_email="developers@dataone.org",
@@ -37,10 +37,10 @@ def main():
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.cli >= 3.4.6",
-            "dataone.common >= 3.4.6",
-            "dataone.libclient >= 3.4.6",
-            "dataone.scimeta >= 3.4.6",
+            "dataone.cli >= 3.4.7",
+            "dataone.common >= 3.4.7",
+            "dataone.libclient >= 3.4.7",
+            "dataone.scimeta >= 3.4.7",
             #
             "django >= 2.2.3",
             "iso8601 >= 0.1.12",

lib_client/src/d1_client/baseclient_1_1.py

@@ -101,19 +101,10 @@ def query(
         response = self.queryResponse(
             queryEngine, query_str, vendorSpecific, do_post, **kwargs
         )
-        try:
+        if self._content_type_is_json(response):
             return self._read_json_response(response)
-        except d1_common.types.exceptions.DataONEException:
-            pass
-        try:
-            return response.json()
-        except Exception:
-            pass
-        try:
-            return json.loads(response.text)
-        except Exception:
-            pass
-        return self._read_stream_response(response)
+        else:
+            return self._read_stream_response(response)
 
     def getQueryEngineDescriptionResponse(
         self, queryEngine, vendorSpecific=None, **kwargs

lib_client/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.libclient",
-        version="3.4.6",
+        version='3.4.7',
         description="A DataONE client library for Python",
         author="DataONE Project",
         author_email="developers@dataone.org",
@@ -35,7 +35,7 @@ def main():
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.common >= 3.4.6",
+            "dataone.common >= 3.4.7",
             #
             "pyxb >= 1.2.6",
             "requests-toolbelt >= 0.9.1",

lib_common/src/d1_common/const.py

@@ -36,7 +36,7 @@
 URL_DATAONE_SEARCH = "https://search.dataone.org"
 
 # Version of the DataONE Python stack
-VERSION = "3.4.6"
+VERSION = '3.4.7'
 
 # Default number of items in a single page of a multi-page result set
 DEFAULT_SLICE_SIZE = 100

lib_common/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.common",
-        version="3.4.6",
+        version='3.4.7',
         description=(
             "Contains functionality common to projects that interact with "
             "the DataONE infrastructure via Python"

lib_csw/src/setup.py

@@ -26,34 +26,33 @@
 def main():
     # noinspection PyUnresolvedReferences
     setuptools.setup(
-        name='dataone.csw',
-        version='3.4.6',
-        description='DataONE OpenGIS Catalogue Service for the Web (CSW) Harvester',
-        author='DataONE Project',
-        author_email='developers@dataone.org',
-        url='https://github.com/DataONEorg/d1_python',
-        license='Apache License, Version 2.0',
+        name="dataone.csw",
+        version='3.4.7',
+        description="DataONE OpenGIS Catalogue Service for the Web (CSW) Harvester",
+        author="DataONE Project",
+        author_email="developers@dataone.org",
+        url="https://github.com/DataONEorg/d1_python",
+        license="Apache License, Version 2.0",
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.common >= 3.4.6",
-            "dataone.libclient >= 3.4.6",
-            "dataone.scimeta >= 3.4.6",
+            "dataone.common >= 3.4.7",
+            "dataone.libclient >= 3.4.7",
+            "dataone.scimeta >= 3.4.7",
             #
-
         ],
-        setup_requires=['setuptools_git >= 1.1'],
+        setup_requires=["setuptools_git >= 1.1"],
         classifiers=[
-            'Development Status :: 5 - Production/Stable',
-            'Intended Audience :: Developers',
-            'Topic :: Scientific/Engineering',
-            'License :: OSI Approved :: Apache Software License',
-            'Programming Language :: Python :: 3',
-            'Programming Language :: Python :: 3.7',
+            "Development Status :: 5 - Production/Stable",
+            "Intended Audience :: Developers",
+            "Topic :: Scientific/Engineering",
+            "License :: OSI Approved :: Apache Software License",
+            "Programming Language :: Python :: 3",
+            "Programming Language :: Python :: 3.7",
         ],
-        keywords='DataONE client member-node coordinating-node',
+        keywords="DataONE client member-node coordinating-node",
     )
 
 
-if __name__ >= '__main__':
+if __name__ >= "__main__":
     sys.exit(main())

lib_scimeta/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.scimeta",
-        version="3.4.6",
+        version='3.4.7',
         description="Utilities for processing Science Metadata",
         author="DataONE Project",
         author_email="developers@dataone.org",

requirements.txt

@@ -8,6 +8,7 @@ MarkupSafe==1.1.1
 PyJWT==1.7.1
 PyXB==1.2.6
 Pygments==2.4.2
+Pyment==0.3.3
 Pyzotero==1.4.4
 Sphinx==2.1.2
 Werkzeug==0.15.4
@@ -31,6 +32,7 @@ coverage==4.5.3
 coveralls==1.8.1
 cryptography==2.7
 decorator==4.4.0
+doc8==0.8.0
 docopt==0.6.2
 docutils==0.14
 elementpath==1.1.8
@@ -56,8 +58,10 @@ multidict==4.5.2
 packaging==19.0
 path-and-address==2.0.1
 pathlib==1.0.1
+pbr==5.4.1
 pip==19.1.1
 pluggy==0.12.0
+pockets==0.7.2
 posix-ipc==1.0.4
 psutil==5.6.3
 psycopg2-binary==2.8.3
@@ -80,12 +84,14 @@ rdflib==4.2.2
 requests-toolbelt==0.9.1
 requests==2.22.0
 responses==0.10.6
+restructuredtext-lint==1.3.0
 rply==0.7.7
 setuptools==40.6.2
 six==1.12.0
 smmap2==2.0.5
 snowballstemmer==1.9.0
 soupsieve==1.9.2
+sphinx-argparse==0.2.5
 sphinx-better-theme==0.1.5
 sphinxcontrib-applehelp==1.0.1
 sphinxcontrib-devhelp==1.0.1
@@ -94,6 +100,7 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.2
 sphinxcontrib-serializinghtml==1.1.3
 sqlparse==0.3.0
+stevedore==1.30.1
 toml==0.10.0
 urllib3==1.24.3
 wcwidth==0.1.7

test_utilities/src/d1_test/test_docs/sample/test_baseclient_1_1_query_cn_v1.echo

@@ -1,18 +1,18 @@
 {
-  "body_base64": null,
-  "endpoint_str": "query",
-  "header_dict": {
-    "Accept": "*/*",
-    "Accept-Encoding": "gzip, deflate",
-    "Charset": "utf-8",
-    "Connection": "keep-alive",
-    "User-Agent": "DataONE-Python/[VERSION] +http://dataone.org/"
+  "request": {
+    "endpoint_str": "query",
+    "param_list": [
+      "Test Query Engine. Tricky Chars: \u0e44\u0e14:@$-_.!*()&=/?",
+      "Test Query String. Tricky Chars: \u0e44\u0e14:@$-_.!*()&="
+    ],
+    "pyxb_namespace": "http://ns.dataone.org/service/types/v1.1",
+    "query_dict": {},
+    "version_tag": "v1"
   },
-  "param_list": [
-    "Test Query Engine. Tricky Chars: \u0e44\u0e14:@$-_.!*()&=/?",
-    "Test Query String. Tricky Chars: \u0e44\u0e14:@$-_.!*()&="
-  ],
-  "pyxb_namespace": "http://ns.dataone.org/service/types/v1.1",
-  "query_dict": {},
-  "version_tag": "v1"
+  "wrapper": {
+    "class_name": "CoordinatingNodeClient_1_2",
+    "expected_type": null,
+    "received_303_redirect": false,
+    "vendor_specific_dict": null
+  }
 }

test_utilities/src/d1_test/test_docs/sample/test_baseclient_1_1_query_mn_v1.echo

@@ -1,18 +1,18 @@
 {
-  "body_base64": null,
-  "endpoint_str": "query",
-  "header_dict": {
-    "Accept": "*/*",
-    "Accept-Encoding": "gzip, deflate",
-    "Charset": "utf-8",
-    "Connection": "keep-alive",
-    "User-Agent": "DataONE-Python/[VERSION] +http://dataone.org/"
+  "request": {
+    "endpoint_str": "query",
+    "param_list": [
+      "Test Query Engine. Tricky Chars: \u0e44\u0e14:@$-_.!*()&=/?",
+      "Test Query String. Tricky Chars: \u0e44\u0e14:@$-_.!*()&="
+    ],
+    "pyxb_namespace": "http://ns.dataone.org/service/types/v1.1",
+    "query_dict": {},
+    "version_tag": "v1"
   },
-  "param_list": [
-    "Test Query Engine. Tricky Chars: \u0e44\u0e14:@$-_.!*()&=/?",
-    "Test Query String. Tricky Chars: \u0e44\u0e14:@$-_.!*()&="
-  ],
-  "pyxb_namespace": "http://ns.dataone.org/service/types/v1.1",
-  "query_dict": {},
-  "version_tag": "v1"
+  "wrapper": {
+    "class_name": "MemberNodeClient_1_2",
+    "expected_type": null,
+    "received_303_redirect": false,
+    "vendor_specific_dict": null
+  }
 }

test_utilities/src/setup.py

@@ -26,7 +26,7 @@
 def main():
     setuptools.setup(
         name="dataone.test_utilities",
-        version="3.4.6",
+        version='3.4.7',
         description="Utilities for testing DataONE infrastructure components",
         author="DataONE Project",
         author_email="developers@dataone.org",
@@ -35,7 +35,7 @@ def main():
         packages=setuptools.find_packages(),
         include_package_data=True,
         install_requires=[
-            "dataone.libclient >= 3.4.6",
+            "dataone.libclient >= 3.4.7",
             #
             "coverage >= 4.5.3",
             "coveralls >= 1.8.1",