WIP: Fix files verification with spaces

Author: kks32

dapi/files.py

@@ -316,13 +316,15 @@ def get_ds_path_uri(t: Tapis, path: str, verify_exists: bool = False) -> str:
         print(f"Verifying existence of translated path: {input_uri}")
         try:
             system_id, remote_path = _parse_tapis_uri(input_uri)
+            # The Tapis API expects URL-encoded paths when they contain spaces or special characters
+            encoded_remote_path = urllib.parse.quote(remote_path)
             print(f"Checking system '{system_id}' for path '{remote_path}'...")
             # Use limit=1 for efficiency, we only care if it *exists*
             # Note: listFiles might return successfully for the *parent* directory
             # if the final component doesn't exist. A more robust check might
             # involve checking the result count or specific item name, but this
             # basic check catches non-existent parent directories.
-            t.files.listFiles(systemId=system_id, path=remote_path, limit=1)
+            t.files.listFiles(systemId=system_id, path=encoded_remote_path, limit=1)
             print(f"Verification successful: Path exists.")
         except BaseTapyException as e:
             # Specifically check for 404 on the listFiles call

examples/mpm/uniaxial_stress/test_benchmark.py

@@ -1,11 +1,11 @@
 import unittest
 from unittest.mock import patch, MagicMock
-from dapi.auth.auth import init
+from dapi.auth import init
 
 
 class TestAuthInit(unittest.TestCase):
-    @patch("dapi.auth.auth.Tapis")
-    @patch("dapi.auth.auth.os.environ")
+    @patch("dapi.auth.Tapis")
+    @patch("dapi.auth.os.environ")
     def test_init_with_env_variables(self, mock_environ, mock_tapis):
         # Setup
         mock_environ.get.side_effect = {
@@ -27,10 +27,10 @@ def test_init_with_env_variables(self, mock_environ, mock_tapis):
         mock_tapis_obj.get_tokens.assert_called_once()
         self.assertEqual(result, mock_tapis_obj)
 
-    @patch("dapi.auth.auth.Tapis")
-    @patch("dapi.auth.auth.os.environ")
-    @patch("dapi.auth.auth.input")
-    @patch("dapi.auth.auth.getpass")
+    @patch("dapi.auth.Tapis")
+    @patch("dapi.auth.os.environ")
+    @patch("dapi.auth.input")
+    @patch("dapi.auth.getpass")
     def test_init_with_user_input(
         self, mock_getpass, mock_input, mock_environ, mock_tapis
     ):
@@ -53,8 +53,8 @@ def test_init_with_user_input(
         mock_tapis_obj.get_tokens.assert_called_once()
         self.assertEqual(result, mock_tapis_obj)
 
-    @patch("dapi.auth.auth.Tapis")
-    @patch("dapi.auth.auth.os.environ")
+    @patch("dapi.auth.Tapis")
+    @patch("dapi.auth.os.environ")
     def test_init_authentication_failure(self, mock_environ, mock_tapis):
         # Setup
         mock_environ.get.side_effect = {

tests/auth/test_auth.py

@@ -61,6 +61,27 @@ def test_empty_path(self):
         result = tapis_uri_to_local_path(input_uri)
         self.assertEqual(result, expected)
 
+    def test_path_with_spaces(self):
+        """Test handling of paths with spaces (URL encoded)"""
+        input_uri = "tapis://designsafe.storage.default/kks32/DS%20input/file.txt"
+        expected = "/home/jupyter/MyData/DS input/file.txt"
+        result = tapis_uri_to_local_path(input_uri)
+        self.assertEqual(result, expected)
+
+    def test_community_path_with_spaces(self):
+        """Test handling of community paths with spaces"""
+        input_uri = "tapis://designsafe.storage.community/My%20Dataset/data.csv"
+        expected = "/home/jupyter/CommunityData/My Dataset/data.csv"
+        result = tapis_uri_to_local_path(input_uri)
+        self.assertEqual(result, expected)
+
+    def test_project_path_with_spaces(self):
+        """Test handling of project paths with spaces"""
+        input_uri = "tapis://project-1234-abcd/simulation%20results/output.txt"
+        expected = "/home/jupyter/MyProjects/simulation results/output.txt"
+        result = tapis_uri_to_local_path(input_uri)
+        self.assertEqual(result, expected)
+
 
 # This allows running the test from the command line
 if __name__ == "__main__":

tests/files/test_uri_translation.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock, patch
-from dapi.jobs import get_ds_path_uri
+from dapi.files import get_ds_path_uri
 from tapipy.tapis import Tapis
 
 

tests/jobs/test_dir_uri.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import Mock, patch
-from dapi.jobs import jobs
+from dapi.jobs import generate_job_request
 from datetime import datetime
 
 
@@ -20,10 +20,10 @@ def setUp(self):
         self.app_info_mock.jobAttributes.execSystemLogicalQueue = "normal"
         self.t_mock.apps.getAppLatestVersion.return_value = self.app_info_mock
 
-    @patch("dapi.jobs.jobs.datetime")
+    @patch("dapi.jobs.datetime")
     def test_generate_job_info_default(self, mock_datetime):
         mock_datetime.now.return_value = datetime(2023, 5, 1, 12, 0, 0)
-        result = jobs.generate_job_info(
+        result = generate_job_request(
             self.t_mock, self.app_name, self.input_uri, self.input_file
         )
         self.assertEqual(result["name"], f"{self.app_name}_20230501_120000")
@@ -52,11 +52,10 @@ def test_generate_job_info_custom(self):
         custom_cores_per_node = 4
         custom_queue = "high-priority"
         custom_allocation = "project123"
-        result = jobs.generate_job_info(
+        result = generate_job_request(
             self.t_mock,
             self.app_name,
             self.input_uri,
-            self.input_file,
             job_name=custom_job_name,
             max_minutes=custom_max_minutes,
             node_count=custom_node_count,
@@ -77,15 +76,11 @@ def test_generate_job_info_custom(self):
     def test_generate_job_info_invalid_app(self):
         self.t_mock.apps.getAppLatestVersion.side_effect = Exception("Invalid app")
         with self.assertRaises(Exception):
-            jobs.generate_job_info(
-                self.t_mock, "invalid-app", self.input_uri, self.input_file
-            )
+            generate_job_request(self.t_mock, "invalid-app", self.input_uri)
 
     def test_generate_job_info_opensees(self):
         opensees_app_name = "opensees-express"
-        result = jobs.generate_job_info(
-            self.t_mock, opensees_app_name, self.input_uri, self.input_file
-        )
+        result = generate_job_request(self.t_mock, opensees_app_name, self.input_uri)
         self.assertIn("parameterSet", result)
         self.assertIn("envVariables", result["parameterSet"])
         self.assertEqual(