dxpy 0.391.0__tar.gz → 0.393.0__tar.gz

{dxpy-0.391.0 → dxpy-0.393.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.391.0
+Version: 0.393.0
 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-0.391.0 → dxpy-0.393.0}/dxpy/bindings/dxfile.py

@@ -314,39 +314,19 @@ class DXFile(DXDataObject):
             raise
 
     def __iter__(self):
-        _buffer = self.read(self._read_bufsize)
-        done = False
-        if USING_PYTHON2:
-            while not done:
-                if b"\n" in _buffer:
-                    lines = _buffer.splitlines()
-                    for i in range(len(lines) - 1):
-                        yield lines[i]
-                    _buffer = lines[len(lines) - 1]
-                else:
-                    more = self.read(self._read_bufsize)
-                    if more == b"":
-                        done = True
-                    else:
-                        _buffer = _buffer + more
-        else:
-            if self._binary_mode:
-                raise DXFileError("Cannot read lines when file opened in binary mode")
-            # python3 is much stricter about distinguishing
-            # 'bytes' from 'str'.
-            while not done:
-                if "\n" in _buffer:
-                    lines = _buffer.splitlines()
-                    for i in range(len(lines) - 1):
-                        yield lines[i]
-                    _buffer = lines[len(lines) - 1]
-                else:
-                    more = self.read(self._read_bufsize)
-                    if more == "":
-                        done = True
-                    else:
-                        _buffer = _buffer + more
-
+        _buffer = ""
+        if self._binary_mode:
+            raise DXFileError("Cannot read lines when file opened in binary mode")
+        while True:
+            more = self.read(self._read_bufsize)
+            if not more:
+                break
+            _buffer += more
+            parts = _buffer.split("\n")
+            for i in range(len(parts) - 1):
+                yield parts[i]
+            # The final piece may be incomplete, so keep it in the buffer
+            _buffer = parts[-1]
         if _buffer:
             yield _buffer
 
@@ -961,6 +941,8 @@ class DXFile(DXDataObject):
         # 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()):
+            project = self.get_proj_id()
         data = self._read2(length=length, use_compression=use_compression, project=project, **kwargs)
         if USING_PYTHON2:
             return data

{dxpy-0.391.0 → dxpy-0.393.0}/dxpy/scripts/dx_app_wizard.py

@@ -395,7 +395,7 @@ array:boolean  array:int      boolean        hash           string''')
     ######################
 
     app_json['runSpec']['distribution'] = 'Ubuntu'
-    app_json['runSpec']['release'] = '20.04'
+    app_json['runSpec']['release'] = '24.04'
     app_json['runSpec']['version'] = "0"
 
     #################

dxpy-0.393.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.393.0'

{dxpy-0.391.0 → dxpy-0.393.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.391.0
+Version: 0.393.0
 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-0.391.0 → dxpy-0.393.0}/test/test_dx_app_wizard.py

@@ -153,7 +153,7 @@ class TestDXAppWizard(DXTestCase):
         self.assertEqual(dxapp_json['regionalOptions']['aws:us-east-1']['systemRequirements']['*']['instanceType'],
                          InstanceTypesCompleter.default_instance_type.Name)
         self.assertEqual(dxapp_json['runSpec']['distribution'], 'Ubuntu')
-        self.assertEqual(dxapp_json['runSpec']['release'], '20.04')
+        self.assertEqual(dxapp_json['runSpec']['release'], '24.04')
         self.assertEqual(dxapp_json['runSpec']['version'], '0')
         self.assertEqual(dxapp_json['runSpec']['interpreter'], 'python3')
         self.assertEqual(dxapp_json['runSpec']['timeoutPolicy']['*']['hours'], 24)

{dxpy-0.391.0 → dxpy-0.393.0}/test/test_dxpy.py

@@ -2551,26 +2551,6 @@ class TestHTTPResponses(testutil.DXTestCaseCompat):
             with self.assertRaisesRegex((SSLError, IOError, OpenSSL.SSL.Error), "file"):
                 dxpy.DXHTTPRequest("/system/whoami", {}, cert_file="nonexistent")
 
-    def test_fake_errors(self):
-        dxpy.DXHTTPRequest('/system/fakeError', {'errorType': 'Valid JSON'}, always_retry=True)
-
-        # Minimal latency with retries, in seconds. This makes sure we actually did a retry.
-        min_sec_with_retries = 1
-        max_num_retries = 2
-        start_time = time.time()
-        with self.assertRaises(ValueError):
-            dxpy.DXHTTPRequest('/system/fakeError', {'errorType': 'Invalid JSON'},
-                               max_retries=max_num_retries, always_retry=True)
-        end_time = time.time()
-        self.assertGreater(end_time - start_time, min_sec_with_retries)
-
-        start_time = time.time()
-        with self.assertRaises(ValueError):
-            dxpy.DXHTTPRequest('/system/fakeError', {'errorType': 'Error not decodeable'},
-                               max_retries=max_num_retries, always_retry=True)
-        end_time = time.time()
-        self.assertGreater(end_time - start_time, min_sec_with_retries)
-
     def test_system_headers_user_agent(self):
         headers = dxpy.api.system_headers()
         self.assertTrue('user-agent' in headers)

dxpy-0.391.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.391.0'