Merge branch '14885-ciso-and-conda-packaging-pr'

refs #14885

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 5fe29bc8f225a8f56da72dee262279a4e9357e74..9f93f0a6a6895780b2aca6e5ed235aca64d6aac9 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -342,7 +342,7 @@ class ArvadosContainer(JobBase):
             if record["output_uuid"]:
                 if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
                     # Compute the trash time to avoid requesting the collection record.
-                    trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+                    trash_at = ciso8601.parse_datetime(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
                     aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
                     orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
                     oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index a815dedaf3a30924145939598b476c1302915bcb..d97e7428da0488e04009d4a0baeca01bbb18aa8b 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -39,10 +39,11 @@ setup(name='arvados-cwl-runner',
           'ruamel.yaml >=0.15.54, <=0.15.77',
           'arvados-python-client>=1.3.0.20190205182514',
           'setuptools',
-          'ciso8601 >=1.0.6, <2.0.0',
+          'ciso8601 >= 2.0.0',
       ],
       extras_require={
           ':os.name=="posix" and python_version<"3"': ['subprocess32 >= 3.5.1'],
+          ':python_version<"3"': ['pytz'],
       },
       data_files=[
           ('share/doc/arvados-cwl-runner', ['LICENSE-2.0.txt', 'README.rst']),

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 667315d4f3d57d206fc0ff621aacb4548d7e414f..cf1a36f9fdfbbfdf739fe75027d00eaa782df4f2 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -1347,7 +1347,10 @@ class Collection(RichCollectionBase):
 
     def get_trash_at(self):
         if self._api_response and self._api_response["trash_at"]:
-            return ciso8601.parse_datetime(self._api_response["trash_at"])
+            try:
+                return ciso8601.parse_datetime(self._api_response["trash_at"])
+            except ValueError:
+                return None
         else:
             return None
 

diff --git a/sdk/python/arvados/commands/keepdocker.py b/sdk/python/arvados/commands/keepdocker.py
index ac387a6f6c7a29ea56e143279f20aca5c166947f..e596e669156f9014ce5b9ad66d05fc2ba561bb3a 100644 (file)
--- a/sdk/python/arvados/commands/keepdocker.py
+++ b/sdk/python/arvados/commands/keepdocker.py
@@ -230,12 +230,15 @@ def docker_link_sort_key(link):
     Docker metadata links to sort them from least to most preferred.
     """
     try:
-        image_timestamp = ciso8601.parse_datetime_unaware(
+        image_timestamp = ciso8601.parse_datetime(
             link['properties']['image_timestamp'])
     except (KeyError, ValueError):
         image_timestamp = EARLIEST_DATETIME
-    return (image_timestamp,
-            ciso8601.parse_datetime_unaware(link['created_at']))
+    try:
+        created_timestamp = ciso8601.parse_datetime(link['created_at'])
+    except ValueError:
+        created_timestamp = None
+    return (image_timestamp, created_timestamp)
 
 def _get_docker_links(api_client, num_retries, **kwargs):
     links = arvados.util.list_all(api_client.links().list,

diff --git a/sdk/python/setup.py b/sdk/python/setup.py
index aaa07103381ccb8dd78d321cb90907bec727ec75..ffca23495c475828184b31e355cfdaa42b6e0bdc 100644 (file)
--- a/sdk/python/setup.py
+++ b/sdk/python/setup.py
@@ -46,7 +46,7 @@ setup(name='arvados-python-client',
           ('share/doc/arvados-python-client', ['LICENSE-2.0.txt', 'README.rst']),
       ],
       install_requires=[
-          'ciso8601 >=1.0.6, <2.0.0',
+          'ciso8601 >=2.0.0',
           'future',
           'google-api-python-client >=1.6.2, <1.7',
           'httplib2 >=0.9.2',
@@ -57,6 +57,7 @@ setup(name='arvados-python-client',
       ],
       extras_require={
           ':os.name=="posix" and python_version<"3"': ['subprocess32 >= 3.5.1'],
+          ':python_version<"3"': ['pytz'],
       },
       classifiers=[
           'Programming Language :: Python :: 2',

diff --git a/services/fuse/arvados_fuse/fresh.py b/services/fuse/arvados_fuse/fresh.py
index 2a3a19c54c66005a6f96cd8d1dbd6de3c6345aad..acebe2b1b7eaaffdc642a93849be9d3ab03b2e02 100644 (file)
--- a/services/fuse/arvados_fuse/fresh.py
+++ b/services/fuse/arvados_fuse/fresh.py
@@ -12,7 +12,7 @@ def convertTime(t):
     if not t:
         return 0
     try:
-        return calendar.timegm(ciso8601.parse_datetime_unaware(t).timetuple())
+        return calendar.timegm(ciso8601.parse_datetime(t).timetuple())
     except (TypeError, ValueError):
         return 0
 

diff --git a/services/fuse/setup.py b/services/fuse/setup.py
index 5a1aa809146db0f4b5a89e32390877963302e9e6..9b4b997cdc68dd14353e4621a77da7f30f7146a1 100644 (file)
--- a/services/fuse/setup.py
+++ b/services/fuse/setup.py
@@ -42,9 +42,12 @@ setup(name='arvados_fuse',
         # llfuse 1.3.4 fails to install via pip
         'llfuse >=1.2, <1.3.4',
         'python-daemon',
-        'ciso8601 >=1.0.6, <2.0.0',
+        'ciso8601 >= 2.0.0',
         'setuptools'
         ],
+      extras_require={
+          ':python_version<"3"': ['pytz'],
+      },
       test_suite='tests',
       tests_require=['pbr<1.7.0', 'mock>=1.0', 'PyYAML'],
       zip_safe=False