Windows path handling

.gitignore

@@ -22,3 +22,4 @@ AllItems.xls
 Custom_scripts/
 Data_Files/MicroscopyCalibration/Files/
 .pytest_cache/
+.python-version

CHANGELOG.rst

@@ -7,14 +7,19 @@ Change Log
 ----------
 
 
+3.0.1
+=====
+
+* Bug fix: Windows paths were not handled properly for File upload.
+
 3.0.0
 =======
 
 `PR 159: Remove Python3.6 support <https://github.com/4dn-dcic/Submit4DN/pull/159>`_
 
 * Drop support for Python3.6
 
-* Add this CHANGELOG and test warning if it's not updated 
+* Add this CHANGELOG and test warning if it's not updated
 
 * Update dependency to use dcicutils >=4.0
 
@@ -212,4 +217,3 @@ Change Log
 
 0.2.2
 =====
-

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "Submit4DN"
-version = "3.0.0"
+version = "3.0.1"
 description = "Utility package for submitting data to the 4DN Data Portal"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

tests/test_import_data.py

@@ -1,5 +1,6 @@
 import wranglertools.import_data as imp
 import pytest
+import pathlib as pp
 # test data is in conftest.py
 
 
@@ -1556,3 +1557,15 @@ def test_get_collections(mock_profiles):
     colls = imp.get_collections(mock_profiles)
     for c in mock_profiles.keys():
         assert c.lower() in colls
+
+
+def test_get_just_filename_posix():
+    test_path = pp.PurePosixPath('Users', 'username', 'test_dir', 'test_file.fastq.gz')
+    filename = imp.get_just_filename(test_path)
+    assert filename == 'test_file.fastq.gz'
+
+
+def test_get_just_filename_windows():
+    test_path = pp.PureWindowsPath('c:/', 'Users', 'username', 'test_dir', 'test_file.fastq.gz')
+    filename = imp.get_just_filename(test_path)
+    assert filename == 'test_file.fastq.gz'

wranglertools/get_field_info.py

@@ -61,8 +61,8 @@ def create_common_arg_parser():
                         help="The keypair identifier from the keyfile.  \
                         Default is --key=default")
     parser.add_argument('--keyfile',
-                        default=f"{home}/keypairs.json",
-                        help=f"The keypair file.  Default is --keyfile={home}/keypairs.json")
+                        default=home / 'keypairs.json',
+                        help=f"The keypair file.  Default is --keyfile={home / 'keypairs.json'}")
     parser.add_argument('--debug',
                         default=False,
                         action='store_true',

wranglertools/import_data.py

@@ -590,7 +590,7 @@ def build_patch_json(fields, fields2types):
 
 
 def get_just_filename(path):
-    return path.split('/')[-1]
+    return pp.Path(path).name
 
 
 def check_extra_file_meta(ef_info, seen_formats, existing_formats):
@@ -1452,15 +1452,25 @@ def upload_file(creds, path):  # pragma: no cover
     print("Uploading file.")
     start = time.time()
     try:
-        subprocess.check_call(['aws', 's3', 'cp', '--only-show-errors', path, creds['upload_url']], env=env)
+        source = path
+        target = creds['upload_url']
+        print("Going to upload {} to {}.".format(source, target))
+        command = ['aws', 's3', 'cp']
+        command = command + ['--only-show-errors', source, target]
+        options = {}
+        if running_on_windows_native():
+            options = {"shell": True}
+        subprocess.check_call(command, env=env, **options)
     except subprocess.CalledProcessError as e:
-        # The aws command returns a non-zero exit code on error.
-        print("Upload failed with exit code %d" % e.returncode)
-        sys.exit(e.returncode)
+        raise RuntimeError("Upload failed with exit code %d" % e.returncode)
     else:
         end = time.time()
         duration = end - start
-        print("Uploaded in %.2f seconds" % duration)
+        show("Uploaded in %.2f seconds" % duration)
+
+
+def running_on_windows_native():
+    return os.name == 'nt'
 
 
 # the order to try to upload / update the items