Fixes #4 issue with tapis filenames have spaces

README.md

@@ -148,11 +148,4 @@ poetry install
 poetry run mkdocs serve
 ```
 
-This will start a local server at `http://127.0.0.1:8000/dapi/` where you can view the documentation.
-
-### API docs
-To generate API docs:
-
-```
-pdoc --html --output-dir api-docs dapi --force
-```
+This will start a local server at `http://127.0.0.1:8000/dapi/` where you can view the documentation.

dapi/files.py

@@ -19,7 +19,7 @@ def _parse_tapis_uri(tapis_uri: str) -> (str, str):
         tapis_uri (str): URI in the format 'tapis://system_id/path'.
 
     Returns:
-        tuple: A tuple containing (system_id, path) where path is URL-decoded.
+        tuple: A tuple containing (system_id, path).
 
     Raises:
         ValueError: If the URI format is invalid or missing required components.
@@ -190,8 +190,7 @@ def get_ds_path_uri(t: Tapis, path: str, verify_exists: bool = False) -> str:
                 )
             else:
                 tapis_path = path_remainder
-            encoded_path = urllib.parse.quote(tapis_path)
-            input_uri = f"tapis://{storage_system_id}/{encoded_path}"
+            input_uri = f"tapis://{storage_system_id}/{tapis_path}"
             print(f"Translated '{path}' to '{input_uri}' using t.username")
             break  # Found match, exit loop
 
@@ -206,8 +205,7 @@ def get_ds_path_uri(t: Tapis, path: str, verify_exists: bool = False) -> str:
             if pattern in path:
                 path_remainder = path.split(pattern, 1)[1].lstrip("/")
                 tapis_path = path_remainder
-                encoded_path = urllib.parse.quote(tapis_path)
-                input_uri = f"tapis://{storage_system_id}/{encoded_path}"
+                input_uri = f"tapis://{storage_system_id}/{tapis_path}"
                 print(f"Translated '{path}' to '{input_uri}'")
                 break  # Found match, exit loop
 
@@ -295,8 +293,7 @@ def get_ds_path_uri(t: Tapis, path: str, verify_exists: bool = False) -> str:
                         f"Could not resolve project ID '{project_id_part}' to a Tapis system ID."
                     )
 
-                encoded_path_within_project = urllib.parse.quote(path_within_project)
-                input_uri = f"tapis://{found_system_id}/{encoded_path_within_project}"
+                input_uri = f"tapis://{found_system_id}/{path_within_project}"
                 print(f"Translated '{path}' to '{input_uri}' using Tapis v3 lookup")
                 break  # Found match, exit loop
 
@@ -316,26 +313,26 @@ 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)
-            # Decode the path part for the listFiles call, as it expects unencoded paths
-            decoded_remote_path = urllib.parse.unquote(remote_path)
-            print(f"Checking system '{system_id}' for path '{decoded_remote_path}'...")
+            # 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=decoded_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
             if hasattr(e, "response") and e.response and e.response.status_code == 404:
                 raise FileOperationError(
-                    f"Verification failed: Path '{decoded_remote_path}' does not exist on system '{system_id}'. Translated URI: {input_uri}"
+                    f"Verification failed: Path '{remote_path}' does not exist on system '{system_id}'. Translated URI: {input_uri}"
                 ) from e
             else:
                 # Re-raise other Tapis errors encountered during verification
                 raise FileOperationError(
-                    f"Verification error for path '{decoded_remote_path}' on system '{system_id}': {e}"
+                    f"Verification error for path '{remote_path}' on system '{system_id}': {e}"
                 ) from e
         except (
             ValueError

dapi/jobs.py

@@ -1007,9 +1007,7 @@ def archive_uri(self) -> Optional[str]:
         details = self._get_details()
         if details.archiveSystemId and details.archiveSystemDir:
             archive_path = details.archiveSystemDir.lstrip("/")
-            return (
-                f"tapis://{details.archiveSystemId}/{urllib.parse.quote(archive_path)}"
-            )
+            return f"tapis://{details.archiveSystemId}/{archive_path}"
         return None
 
     def list_outputs(
@@ -1048,7 +1046,7 @@ def list_outputs(
         full_archive_path = os.path.join(details.archiveSystemDir, path.lstrip("/"))
         full_archive_path = os.path.normpath(full_archive_path).lstrip("/")
         try:
-            archive_base_uri = f"tapis://{details.archiveSystemId}/{urllib.parse.quote(full_archive_path)}"
+            archive_base_uri = f"tapis://{details.archiveSystemId}/{full_archive_path}"
             from .files import list_files
 
             return list_files(self._tapis, archive_base_uri, limit=limit, offset=offset)
@@ -1084,9 +1082,7 @@ def download_output(self, remote_path: str, local_target: str):
             details.archiveSystemDir, remote_path.lstrip("/")
         )
         full_archive_path = os.path.normpath(full_archive_path).lstrip("/")
-        remote_uri = (
-            f"tapis://{details.archiveSystemId}/{urllib.parse.quote(full_archive_path)}"
-        )
+        remote_uri = f"tapis://{details.archiveSystemId}/{full_archive_path}"
         try:
             from .files import download_file