implemented further tests

fs_irods/iRODSFS.py

@@ -2,10 +2,11 @@
 import os
 
 from multiprocessing import RLock
+from typing import Text
 from fs.base import FS
 from fs.info import Info
 from fs.permissions import Permissions
-from fs.errors import DirectoryExists, ResourceNotFound, RemoveRootError, DirectoryExpected, FileExpected, FileExists
+from fs.errors import DirectoryExists, ResourceNotFound, RemoveRootError, DirectoryExpected, FileExpected, FileExists, DirectoryNotEmpty
 
 from irods.session import iRODSSession
 from irods.collection import iRODSCollection
@@ -28,6 +29,8 @@ def __init__(self, host: str, port:int, user:str, password: str, zone: str) -> N
         self._zone = zone
 
     def _wrap(self, path: str) -> str:
+        if path.startswith(f"/{self._zone}"):
+            return path
         return str(iRODSPath(self._zone, path))
 
 
@@ -51,7 +54,7 @@ def getinfo(self, path: str, namespaces: list|None = None) -> Info:
         Raises:
             ResourceNotFound: If the path does not exist.
         """
-        self._assert_exists(path)
+        self._check_exists(path)
 
         with self._session() as session:
             raw_info = {"basic": {"name": path}}
@@ -74,7 +77,7 @@ def listdir(self, path: str) -> list:
             ResourceNotFound: If the path does not exist.
             DirectoryExpected: If the path is not a directory.
         """
-        self._assert_exists(path)
+        self._check_exists(path)
         with self._session() as session:
             coll: iRODSCollection = session.collections.get(self._wrap(path))
             return [item.path for item in coll.data_objects + coll.subcollections]
@@ -121,8 +124,8 @@ def openbin(self, path: str, mode:str = "r", buffering: int = -1, **options) ->
             FileExpected: If the path is not a file.
             FileExists: If the path exists, and exclusive mode is specified (x in the mode).
         """
-        if self.isdir(path):
-            raise FileExpected(path)
+        self._check_isfile(path)
+
         with self._session() as session:
             if not session.data_objects.exists(self._wrap(path)):
                 if not can_create(mode):
@@ -140,12 +143,22 @@ def remove(self, path: str):
             ResourceNotFound: If the path does not exist.
             FileExpected: If the path is not a file.
         """
-        self._assert_exists(path)
-        with self._session() as session:
-            if not self.isfile(path):
-                raise FileExpected(path)
-
+        self._check_exists(path)
+        self._check_isfile(path)
+
+        with self._session() as session:            
             session.data_objects.unlink(self._wrap(path))
+
+    def _check_isfile(self, path: str):
+        """Check if a path points to a file and raise an FileExpected error if not.
+        Args:
+            path (str): A path to a file on the filesystem.
+        Raises:
+            ResourceNotFound: If the path does not exist.
+            FileExpected: If the path is not a file.
+        """
+        if not self.isfile(path):
+            raise FileExpected(path)
 
     def removedir(self, path: str):
         """Remove a directory from the filesystem.
@@ -155,16 +168,62 @@ def removedir(self, path: str):
             ResourceNotFound: If the path does not exist.
             DirectoryExpected: If the path is not a directory.
             RemoveRootError: If the path is the root directory.
+            DirectoryNotEmpty: If the directory is not empty.
         """
+        self._check_exists(path)
+        self._check_isdir(path)
+
+        if self._is_root(path):
+            raise RemoveRootError()
+        if not self.isempty(path):
+            raise DirectoryNotEmpty(path)
+
         with self._session() as session:
-            if not session.collections.exists(self._wrap(path)):
-                raise ResourceNotFound(path)
-            if not self.isdir(path):
-                raise DirectoryExpected(path)
-            if path == "/":
-                raise RemoveRootError()
-
             session.collections.remove(self._wrap(path), recurse=False)
+
+    def _is_root(self, path: str) -> bool:
+        """Check if path points to root of the filesystem.
+
+        Args:
+            path (str): Path to a directory.
+
+        Returns:
+            bool: True if path points to root.
+        """
+        return path in ["/", "", self._zone]
+
+    def removetree(self, path: str):
+        """Recursively remove a directory and all its contents. 
+        This method is similar to removedir, but will remove the contents of the directory if it is not empty.
+
+        Args:
+            path (str):  A path to a directory on the filesystem.
+        Raises:
+            ResourceNotFound: If the path does not exist.
+            DirectoryExpected: If the path is not a directory.
+        """
+        self._check_exists(path)
+        self._check_isdir(path)
+
+        with self._session() as session:
+            if self._is_root(path):
+                root: iRODSCollection = session.collections.get(self._wrap(path))
+                for item in root.data_objects:
+                    item.unlink()
+                for item in root.subcollections:
+                    item.remove()
+            else:
+                session.collections.remove(self._wrap(path), recurse=True)
+
+    def _check_isdir(self, path: str):
+        """Check if a path is a directory.
+        Args:
+            path (str): A path to a resource on the filesystem.
+        Raises:
+            DirectoryExpected: If the path is not a directory.
+        """
+        if not self.isdir(path):
+            raise DirectoryExpected(path)
 
     def setinfo(self, path: str, info: dict) -> None:
         """Set information about a resource on the filesystem.
@@ -174,11 +233,10 @@ def setinfo(self, path: str, info: dict) -> None:
         Raises:
             ResourceNotFound: If the path does not exist.
         """
-        path = self._wrap(path)
-        self.exists(path)           
+        self._check_exists(path)           
         raise NotImplementedError()
 
-    def _assert_exists(self, path:str):
+    def _check_exists(self, path:str):
         """Check if a resource exists.
         Args:
             path (str): A path to a resource on the filesystem.
@@ -237,10 +295,3 @@ def exists(self, path: str) -> bool:
         with self._session() as session:
             path = self._wrap(path)
             return session.data_objects.exists(path) or session.collections.exists(path)
-
-    def clean(self):
-        """Clean up the filesystem.
-        """
-        with self._session() as session:
-            root_collection = session.collections.get(self._wrap(""))
-

tests/irods_session_testing.ipynb

@@ -119,7 +119,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.collections.remove(\"/tempZone/foo/bar\")\n",
+    "session.collections.remove(\"/tempZone/foo\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -129,16 +139,24 @@
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mCAT_NO_ROWS_FOUND\u001b[0m                         Traceback (most recent call last)",
-      "\u001b[1;32m/home/hechth/git/hechth/fs-irods/tests/irods_session_testing.ipynb Cell 7\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell://ssh-remote%2Babiff.ics.muni.cz/home/hechth/git/hechth/fs-irods/tests/irods_session_testing.ipynb#W6sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m session\u001b[39m.\u001b[39;49mcollections\u001b[39m.\u001b[39;49mremove(\u001b[39m\"\u001b[39;49m\u001b[39m/tempZone/foo/bar\u001b[39;49m\u001b[39m\"\u001b[39;49m)\n\u001b[1;32m      <a href='vscode-notebook-cell://ssh-remote%2Babiff.ics.muni.cz/home/hechth/git/hechth/fs-irods/tests/irods_session_testing.ipynb#W6sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1'>2</a>\u001b[0m session\u001b[39m.\u001b[39mcollections\u001b[39m.\u001b[39mremove(\u001b[39m\"\u001b[39m\u001b[39m/tempZone/foo\u001b[39m\u001b[39m\"\u001b[39m)\n",
+      "\u001b[1;32m/home/hechth/git/hechth/fs-irods/tests/irods_session_testing.ipynb Cell 10\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell://ssh-remote%2Babiff.ics.muni.cz/home/hechth/git/hechth/fs-irods/tests/irods_session_testing.ipynb#X15sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m session\u001b[39m.\u001b[39;49mcollections\u001b[39m.\u001b[39;49mremove(\u001b[39m\"\u001b[39;49m\u001b[39m/tempZone/test\u001b[39;49m\u001b[39m\"\u001b[39;49m)\n",
       "File \u001b[0;32m/m2b/home/hechth/micromamba/envs/fs-irods/lib/python3.12/site-packages/irods/manager/collection_manager.py:70\u001b[0m, in \u001b[0;36mCollectionManager.remove\u001b[0;34m(self, path, recurse, force, **options)\u001b[0m\n\u001b[1;32m     68\u001b[0m \u001b[39mwith\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39msess\u001b[39m.\u001b[39mpool\u001b[39m.\u001b[39mget_connection() \u001b[39mas\u001b[39;00m conn:\n\u001b[1;32m     69\u001b[0m     conn\u001b[39m.\u001b[39msend(message)\n\u001b[0;32m---> 70\u001b[0m     response \u001b[39m=\u001b[39m conn\u001b[39m.\u001b[39;49mrecv()\n\u001b[1;32m     72\u001b[0m     \u001b[39mwhile\u001b[39;00m response\u001b[39m.\u001b[39mint_info \u001b[39m==\u001b[39m SYS_SVR_TO_CLI_COLL_STAT:\n\u001b[1;32m     73\u001b[0m         conn\u001b[39m.\u001b[39mreply(SYS_CLI_TO_SVR_COLL_STAT_REPLY)\n",
       "File \u001b[0;32m/m2b/home/hechth/micromamba/envs/fs-irods/lib/python3.12/site-packages/irods/connection.py:132\u001b[0m, in \u001b[0;36mConnection.recv\u001b[0;34m(self, into_buffer, return_message, acceptable_errors)\u001b[0m\n\u001b[1;32m    130\u001b[0m         err_msg \u001b[39m=\u001b[39m \u001b[39mNone\u001b[39;00m\n\u001b[1;32m    131\u001b[0m     \u001b[39mif\u001b[39;00m nominal_code(msg\u001b[39m.\u001b[39mint_info) \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m acceptable_codes:\n\u001b[0;32m--> 132\u001b[0m         \u001b[39mraise\u001b[39;00m get_exception_by_code(msg\u001b[39m.\u001b[39mint_info, err_msg)\n\u001b[1;32m    133\u001b[0m \u001b[39mreturn\u001b[39;00m msg\n",
       "\u001b[0;31mCAT_NO_ROWS_FOUND\u001b[0m: None"
      ]
     }
    ],
    "source": [
-    "session.collections.remove(\"/tempZone/foo/bar\")\n",
-    "session.collections.remove(\"/tempZone/foo\")"
+    "session.collections.remove(\"/tempZone/test\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "session.collections.remove(\"/tempZone/home/subcollection\")"
    ]
   },
   {

tests/test_fs_extension.py

@@ -9,11 +9,6 @@
 
 class TestMyFS(FSTestCases, unittest.TestCase):
 
-    @patch("fs_irods.iRODSFS.iRODSSession", new=DelayedSession)
     def make_fs(self):
         sut = iRODSFSBuilder().build()
         return sut
-
-    def destroy_fs(self, fs):
-        fs.clean()
-        self.fs.clean()

tests/test_iRODSFS.py

@@ -1,12 +1,13 @@
 import time
 import pytest
+import os
 
 from fs_irods import iRODSFS
 from unittest.mock import patch
 from tests.DelayedSession import DelayedSession
 from tests.builder_iRODSFS import iRODSFSBuilder
 
-from fs.errors import DirectoryExists, ResourceNotFound, RemoveRootError, DirectoryExpected, FileExpected, FileExists
+from fs.errors import *
 
 
 @patch("fs_irods.iRODSFS.iRODSSession")
@@ -62,7 +63,7 @@ def test_makedir_exceptions(fs:iRODSFS, path: str, exception: type):
 @pytest.mark.parametrize("path", [
     "test.txt", "home/rods/test.txt"
 ])
-def test_create(fs: iRODSFS, path):
+def test_create_remove(fs: iRODSFS, path):
     fs.create(path)
     assert fs.isfile(path) == True
     fs.remove(path)
@@ -111,7 +112,7 @@ def test_exists(fs: iRODSFS, path: str, expected: bool):
 
 
 @pytest.mark.parametrize("path", [
-    "foo", "foo/bar"
+    "foo", "home/rods/test"
 ])
 def test_removedir(fs: iRODSFS, path: str):
     fs.makedir(path)
@@ -120,6 +121,27 @@ def test_removedir(fs: iRODSFS, path: str):
     assert fs.isdir(path) == False
 
 
+@pytest.mark.parametrize("path, exception", [
+    ["", RemoveRootError],
+    ["/", RemoveRootError],
+    ["existing_file.txt", DirectoryExpected],
+    ["home/something", ResourceNotFound],
+    ["existing_collection", DirectoryNotEmpty]
+])
+def test_removedir_exceptions(fs: iRODSFS, path: str, exception: type):
+    with pytest.raises(exception):
+        fs.removedir(path)
+
+
+@pytest.mark.parametrize("path, exception", [
+    ["home", FileExpected],
+    ["some_file.txt", ResourceNotFound]
+])
+def test_remove_exceptions(fs: iRODSFS, path: str, exception: type):
+    with pytest.raises(exception):
+        fs.remove(path)
+
+
 @pytest.mark.parametrize("path, expected", [
     ["/", ["/tempZone/existing_file.txt",  "/tempZone/existing_collection", "/tempZone/home", "/tempZone/trash", ]],
     ["", ["/tempZone/existing_file.txt",  "/tempZone/existing_collection", "/tempZone/home", "/tempZone/trash"]],
@@ -128,3 +150,32 @@ def test_removedir(fs: iRODSFS, path: str):
 def test_listdir(fs: iRODSFS, path: str, expected: list[str]):
     actual = fs.listdir(path)
     assert actual == expected
+
+@pytest.mark.parametrize("path, expected", [
+    ["home", False],
+    ["home/rods", True]
+])
+def test_isempty(fs: iRODSFS, path: str, expected: bool):
+    assert fs.isempty(path) == expected
+
+@pytest.mark.parametrize("path", [
+    "test/subdir"
+])
+def test_makedirs(fs:iRODSFS, path: str):
+    fs.makedirs(path)
+    assert fs.isdir(path)
+    fs.removedir(path)
+    fs.removedir(os.path.dirname(path))
+    assert fs.isdir(path) == False
+    assert fs.isdir(os.path.dirname(path)) == False
+
+
+def test_removetree(fs: iRODSFS):
+    fs.makedirs("test/subdir")
+    fs.create("test/subdir/file.txt")
+    assert fs.isfile("test/subdir/file.txt")
+
+    fs.removetree("test")
+    assert fs.exists("test/subdir/file.txt") == False
+    assert fs.exists("test/subdir") == False
+    assert fs.exists("test") == False

tests/test_utils.py

@@ -16,5 +16,5 @@
     ["w+b", True],
     ["a+b", True]
 ])
-def test_can_create(mode, expected):
+def test_can_create(mode: str, expected: bool):
     assert can_create(mode) == expected