From ce624514eb04bb66440fdc8b65685a4c5093a9c2 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:27:33 +0100
Subject: [PATCH 01/17] Add iRODS file source integration with configuration
 and listing support

---
 lib/galaxy/files/sources/irods.py | 171 ++++++++++++++++++++++++++++++
 1 file changed, 171 insertions(+)
 create mode 100644 lib/galaxy/files/sources/irods.py

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
new file mode 100644
index 00000000000..4e36e0489b9
--- /dev/null
+++ b/lib/galaxy/files/sources/irods.py
@@ -0,0 +1,171 @@
+import ssl
+from fnmatch import fnmatch
+import os
+from typing import (
+    Optional,
+    Union,
+)
+
+import fs
+import fs.errors
+
+from galaxy.files.models import (
+    AnyRemoteEntry,
+    BaseFileSourceConfiguration,
+    BaseFileSourceTemplateConfiguration,
+    FilesSourceRuntimeContext,
+)
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
+from galaxy.util.config_templates import TemplateExpansion
+from ._pyfilesystem2 import PyFilesystem2FilesSource
+
+try:
+    from fs_irods import iRODSFS
+except ImportError:
+    iRODSFS = None
+
+try:
+    from irods.session import iRODSSession
+except ImportError:
+    iRODSSession = None
+
+
+class IrodsFileSourceTemplateConfiguration(BaseFileSourceTemplateConfiguration):
+    host: Union[str, TemplateExpansion]
+    port: Union[int, TemplateExpansion] = 1247
+    username: Union[str, TemplateExpansion]
+    password: Union[str, TemplateExpansion]
+    zone: Union[str, TemplateExpansion]
+    root: Optional[Union[str, TemplateExpansion]] = None
+    timeout: Union[int, TemplateExpansion] = 30
+    refresh_time: Union[int, TemplateExpansion] = 300
+    client_server_negotiation: Optional[Union[str, TemplateExpansion]] = None
+    client_server_policy: Optional[Union[str, TemplateExpansion]] = None
+    encryption_algorithm: Optional[Union[str, TemplateExpansion]] = None
+    encryption_key_size: Optional[Union[int, TemplateExpansion]] = None
+    encryption_num_hash_rounds: Optional[Union[int, TemplateExpansion]] = None
+    encryption_salt_size: Optional[Union[int, TemplateExpansion]] = None
+    ssl_verify_server: Optional[Union[str, TemplateExpansion]] = None
+    ssl_ca_certificate_file: Optional[Union[str, TemplateExpansion]] = None
+    resource: Optional[Union[str, TemplateExpansion]] = None
+
+
+class IrodsFileSourceConfiguration(BaseFileSourceConfiguration):
+    host: str
+    port: int = 1247
+    username: str
+    password: str
+    zone: str
+    root: Optional[str] = None
+    timeout: int = 30
+    refresh_time: int = 300
+    client_server_negotiation: Optional[str] = None
+    client_server_policy: Optional[str] = None
+    encryption_algorithm: Optional[str] = None
+    encryption_key_size: Optional[int] = None
+    encryption_num_hash_rounds: Optional[int] = None
+    encryption_salt_size: Optional[int] = None
+    ssl_verify_server: Optional[str] = None
+    ssl_ca_certificate_file: Optional[str] = None
+    resource: Optional[str] = None
+
+
+class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfiguration, IrodsFileSourceConfiguration]):
+    plugin_type = "irods"
+    required_module = iRODSFS
+    required_package = "fs-irods"
+
+    template_config_class = IrodsFileSourceTemplateConfiguration
+    resolved_config_class = IrodsFileSourceConfiguration
+
+    def _normalize_listdir_name(self, value: str) -> str:
+        # fs-irods currently returns absolute iRODS paths from listdir; convert to simple entry names.
+        return os.path.basename(str(value).rstrip("/"))
+
+    def _list(
+        self,
+        context: FilesSourceRuntimeContext[IrodsFileSourceConfiguration],
+        path="/",
+        recursive=False,
+        write_intent: bool = False,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
+        query: Optional[str] = None,
+        sort_by: Optional[str] = None,
+    ) -> tuple[list[AnyRemoteEntry], int]:
+        try:
+            with self._open_fs(context) as h:
+                if recursive:
+                    result: list[AnyRemoteEntry] = []
+                    pending = [path]
+                    while pending:
+                        current_path = pending.pop(0)
+                        for raw_name in h.listdir(current_path):
+                            name = self._normalize_listdir_name(raw_name)
+                            if not name:
+                                continue
+                            entry_path = fs.path.join(current_path, name)
+                            info = h.getinfo(entry_path, namespaces=["details"])
+                            result.append(self._resource_info_to_dict(current_path, info))
+                            if info.is_dir:
+                                pending.append(entry_path)
+                    return result, len(result)
+
+                normalized_query = query.lower() if query else None
+                entries = []
+                for raw_name in h.listdir(path):
+                    name = self._normalize_listdir_name(raw_name)
+                    if not name:
+                        continue
+                    if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
+                        continue
+                    entry_path = fs.path.join(path, name)
+                    info = h.getinfo(entry_path, namespaces=["details"])
+                    entries.append(self._resource_info_to_dict(path, info))
+
+                count = len(entries)
+                page = self._to_page(limit, offset)
+                if page is not None:
+                    entries = entries[page[0] : page[1]]
+                return entries, count
+        except fs.errors.PermissionDenied as e:
+            raise AuthenticationRequired(
+                f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
+            ) from e
+        except fs.errors.FSError as e:
+            raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
+
+    def _open_fs(self, context: FilesSourceRuntimeContext[IrodsFileSourceConfiguration]):
+        if iRODSFS is None or iRODSSession is None:
+            raise self.required_package_exception
+
+        config = context.config
+        session_kwargs = {
+            "host": config.host,
+            "port": config.port,
+            "user": config.username,
+            "password": config.password,
+            "zone": config.zone,
+            "refresh_time": config.refresh_time,
+            "client_server_negotiation": config.client_server_negotiation,
+            "client_server_policy": config.client_server_policy,
+            "encryption_algorithm": config.encryption_algorithm,
+            "encryption_key_size": config.encryption_key_size,
+            "encryption_num_hash_rounds": config.encryption_num_hash_rounds,
+            "encryption_salt_size": config.encryption_salt_size,
+            "ssl_verify_server": config.ssl_verify_server,
+            "ssl_ca_certificate_file": config.ssl_ca_certificate_file,
+            "ssl_context": ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH),
+        }
+        session = iRODSSession(**session_kwargs)
+        session.connection_timeout = config.timeout
+        if config.resource:
+            session.default_resource = config.resource
+
+        return iRODSFS(session=session, root=config.root)
+
+
+__all__ = ("IrodsFilesSource",)

From 995cd8cc1b757a967872f91bf92be4a6815ab648 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:32:10 +0100
Subject: [PATCH 02/17] Add iRODS file source configuration and template
 classes

---
 lib/galaxy/files/templates/models.py | 32 ++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py
index f3e51324ed5..e1e36e80a24 100644
--- a/lib/galaxy/files/templates/models.py
+++ b/lib/galaxy/files/templates/models.py
@@ -38,6 +38,7 @@ FileSourceTemplateType = Literal[
     "s3fs",
     "azure",
     "azureflat",
+    "irods",
     "onedata",
     "webdav",
     "dropbox",
@@ -248,6 +249,34 @@ class AzureFlatFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class IrodsFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["irods"]
+    host: Union[str, TemplateExpansion]
+    port: Union[int, TemplateExpansion] = 1247
+    username: Union[str, TemplateExpansion]
+    password: Union[str, TemplateExpansion]
+    zone: Union[str, TemplateExpansion]
+    root: Optional[Union[str, TemplateExpansion]] = None
+    timeout: Union[int, TemplateExpansion] = 30
+    refresh_time: Union[int, TemplateExpansion] = 300
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class IrodsFileSourceConfiguration(StrictModel):
+    type: Literal["irods"]
+    host: str
+    port: int = 1247
+    username: str
+    password: str
+    zone: str
+    root: Optional[str] = None
+    timeout: int = 30
+    refresh_time: int = 300
+    writable: bool = False
+
+
 class OnedataFileSourceTemplateConfiguration(StrictModel):
     type: Literal["onedata"]
     access_token: Union[str, TemplateExpansion]
@@ -438,6 +467,7 @@ FileSourceTemplateConfiguration = Annotated[
         FtpFileSourceTemplateConfiguration,
         AzureFileSourceTemplateConfiguration,
         AzureFlatFileSourceTemplateConfiguration,
+        IrodsFileSourceTemplateConfiguration,
         OnedataFileSourceTemplateConfiguration,
         WebdavFileSourceTemplateConfiguration,
         DropboxFileSourceTemplateConfiguration,
@@ -463,6 +493,7 @@ FileSourceConfiguration = Annotated[
         FtpFileSourceConfiguration,
         AzureFileSourceConfiguration,
         AzureFlatFileSourceConfiguration,
+        IrodsFileSourceConfiguration,
         OnedataFileSourceConfiguration,
         WebdavFileSourceConfiguration,
         DropboxFileSourceConfiguration,
@@ -546,6 +577,7 @@ TypesToConfigurationClasses: dict[FileSourceTemplateType, type[FileSourceConfigu
     "s3fs": S3FSFileSourceConfiguration,
     "azure": AzureFileSourceConfiguration,
     "azureflat": AzureFlatFileSourceConfiguration,
+    "irods": IrodsFileSourceConfiguration,
     "onedata": OnedataFileSourceConfiguration,
     "webdav": WebdavFileSourceConfiguration,
     "dropbox": DropboxFileSourceConfiguration,

From 24f4c07fe4e878e4eb3b1365b395d52cf67c378a Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:43:07 +0100
Subject: [PATCH 03/17] Add iRODS template for file source repository
 configuration

---
 lib/galaxy/files/templates/examples/irods.yml | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 lib/galaxy/files/templates/examples/irods.yml

diff --git a/lib/galaxy/files/templates/examples/irods.yml b/lib/galaxy/files/templates/examples/irods.yml
new file mode 100644
index 00000000000..22b168a32eb
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/irods.yml
@@ -0,0 +1,61 @@
+- id: irods
+  version: 0
+  name: iRODS
+  description: |
+    Use this template to connect an iRODS collection as a Galaxy file source for
+    importing and exporting datasets.
+
+    You need valid iRODS credentials and the target root collection path.
+  variables:
+    host:
+      label: iRODS host
+      type: string
+      help: Hostname of the iRODS server.
+    port:
+      label: iRODS port
+      type: integer
+      help: Port of the iRODS server.
+      default: 1247
+    username:
+      label: iRODS user
+      type: string
+      help: Username used to authenticate against iRODS.
+    zone:
+      label: iRODS zone
+      type: string
+      help: Zone used for authentication (for example tempZone).
+    root:
+      label: Root collection path
+      type: string
+      help: |
+        Collection path exposed in Galaxy, for example /tempZone/home/rods.
+    timeout:
+      label: Connection timeout (seconds)
+      type: integer
+      help: Timeout in seconds for iRODS connection attempts.
+      default: 30
+    refresh_time:
+      label: Session refresh time (seconds)
+      type: integer
+      help: Seconds between refresh checks for active iRODS sessions.
+      default: 300
+    writable:
+      label: Writable?
+      type: boolean
+      help: Allow writing datasets back to iRODS.
+      default: false
+  secrets:
+    password:
+      label: Password
+      help: Password used to authenticate against iRODS.
+  configuration:
+    type: irods
+    host: "{{ variables.host }}"
+    port: "{{ variables.port }}"
+    username: "{{ variables.username }}"
+    password: "{{ secrets.password }}"
+    zone: "{{ variables.zone }}"
+    root: "{{ variables.root }}"
+    timeout: "{{ variables.timeout }}"
+    refresh_time: "{{ variables.refresh_time }}"
+    writable: "{{ variables.writable }}"
\ No newline at end of file

From 8f2afdf8416a70d17d34d3f473f4131785e5d693 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 26 Mar 2026 17:27:36 +0100
Subject: [PATCH 04/17] Add unit tests for iRODS file source functionality

---
 test/unit/files/test_irods.py | 232 ++++++++++++++++++++++++++++++++++
 1 file changed, 232 insertions(+)
 create mode 100644 test/unit/files/test_irods.py

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
new file mode 100644
index 00000000000..b867088f6d1
--- /dev/null
+++ b/test/unit/files/test_irods.py
@@ -0,0 +1,232 @@
+import os
+import socket
+import pytest
+import yaml
+
+from galaxy.files.models import (
+    FileSourcePluginsConfig,
+    FilesSourceRuntimeContext,
+    UserData,
+)
+from galaxy.files.plugins import FileSourcePluginLoader
+from galaxy.files.sources.irods import IrodsFilesSource
+from ._util import (
+    assert_realizes_contains,
+    configured_file_sources,
+    write_from,
+)
+
+try:
+    from irods.session import iRODSSession
+except ImportError:
+    iRODSSession = None
+
+
+ROUNDTRIP_TEST_FILENAME = "numerical_sort_and_write_back_to_irods_v2.tab"
+
+
+class _FakeSession:
+    init_kwargs = None
+
+    def __init__(self, **kwargs):
+        type(self).init_kwargs = kwargs
+        self.connection_timeout = None
+        self.default_resource = None
+
+
+class _FakeIrodsFs:
+    def __init__(self, session, root=None):
+        self.session = session
+        self.root = root
+
+
+def _get_setting(irods_config: dict, env_name: str, key: str, cast=None):
+    raw = os.environ.get(env_name)
+    if raw is None:
+        raw = irods_config.get(key)
+    if raw is None:
+        pytest.skip(f"Missing iRODS setting '{key}' in file_sources_conf.yml or env {env_name}.")
+    return cast(raw) if cast else raw
+
+
+def _file_sources_config(irods_config: dict) -> dict:
+    return {
+        "host": _get_setting(irods_config, "GALAXY_TEST_IRODS_HOST", "host"),
+        "port": _get_setting(irods_config, "GALAXY_TEST_IRODS_PORT", "port", int),
+        "username": _get_setting(irods_config, "GALAXY_TEST_IRODS_USER", "username"),
+        "password": _get_setting(irods_config, "GALAXY_TEST_IRODS_PASSWORD", "password"),
+        "zone": _get_setting(irods_config, "GALAXY_TEST_IRODS_ZONE", "zone"),
+        "root": _get_setting(irods_config, "GALAXY_TEST_IRODS_ROOT", "root"),
+        "timeout": _get_setting(irods_config, "GALAXY_TEST_IRODS_TIMEOUT", "timeout", int),
+        "refresh_time": _get_setting(irods_config, "GALAXY_TEST_IRODS_REFRESH_TIME", "refresh_time", int),
+    }
+
+
+def _irods_live_settings() -> dict:
+    config_path = os.environ.get(
+        "GALAXY_TEST_FILE_SOURCES_CONFIG",
+        os.path.abspath(
+            os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "config", "file_sources_conf.yml")
+        ),
+    )
+    if not os.path.exists(config_path):
+        pytest.skip(f"No file sources config at {config_path}; set file_sources_conf.yml to enable iRODS live tests.")
+
+    with open(config_path, "rb") as handle:
+        configs = yaml.safe_load(handle) or []
+
+    irods_id = os.environ.get("GALAXY_TEST_IRODS_SOURCE_ID")
+    irods_configs = [c for c in configs if isinstance(c, dict) and c.get("type") == "irods"]
+    if irods_id:
+        irods_configs = [c for c in irods_configs if c.get("id") == irods_id]
+
+    if not irods_configs:
+        pytest.skip("No iRODS file source found in file_sources_conf.yml; configure one to enable live tests.")
+
+    irods_config = irods_configs[0]
+
+    return _file_sources_config(irods_config)
+
+
+def _skip_if_irods_unreachable(host: str, port: int):
+    try:
+        with socket.create_connection((host, port), timeout=1):
+            return
+    except OSError:
+        pytest.skip(
+            f"No reachable iRODS service at {host}:{port}. "
+            "Start your local iRODS Docker stack or override GALAXY_TEST_IRODS_* settings."
+        )
+
+
+def _live_file_source_config(settings: dict, writable: bool = False) -> list[dict]:
+    return [
+        {
+            "type": "irods",
+            "id": "test1",
+            "label": "iRODS Live Test",
+            "doc": "Live iRODS connectivity smoke test",
+            "host": settings["host"],
+            "port": settings["port"],
+            "username": settings["username"],
+            "password": settings["password"],
+            "zone": settings["zone"],
+            "root": settings["root"],
+            "timeout": settings["timeout"],
+            "refresh_time": settings["refresh_time"],
+            "writable": writable,
+        }
+    ]
+
+
+def _cleanup_live_test_artifacts(settings: dict):
+    root = settings["root"].rstrip("/")
+    logical_path = f"{root}/{ROUNDTRIP_TEST_FILENAME}"
+
+    session = iRODSSession(
+        host=settings["host"],
+        port=settings["port"],
+        user=settings["username"],
+        password=settings["password"],
+        zone=settings["zone"],
+        refresh_time=settings["refresh_time"],
+    )
+    session.connection_timeout = settings["timeout"]
+
+    try:
+        if session.data_objects.exists(logical_path):
+            session.data_objects.unlink(logical_path)
+    finally:
+        session.cleanup()
+
+
+def test_irods_plugin_registered():
+    plugin_loader = FileSourcePluginLoader()
+    plugin_class = plugin_loader.get_plugin_type_class("irods")
+    assert plugin_class is IrodsFilesSource
+
+
+def test_irods_open_fs_builds_session(monkeypatch):
+    monkeypatch.setattr("galaxy.files.sources.irods.iRODSSession", _FakeSession)
+    monkeypatch.setattr("galaxy.files.sources.irods.iRODSFS", _FakeIrodsFs)
+    monkeypatch.setattr(IrodsFilesSource, "required_module", _FakeIrodsFs)
+
+    file_source = IrodsFilesSource(
+        IrodsFilesSource.build_template_config(
+            type="irods",
+            id="test_irods",
+            file_sources_config=FileSourcePluginsConfig(),
+            host="irods.example.org",
+            port=1247,
+            username="rods",
+            password="secret",
+            zone="tempZone",
+            root="/tempZone/home/rods",
+            timeout=42,
+            refresh_time=120,
+            resource="demoResc",
+            writable=True,
+        )
+    )
+
+    resolved_config = file_source._evaluate_template_config(UserData())
+    context = FilesSourceRuntimeContext(user_data=UserData(), config=resolved_config)
+
+    fs = file_source._open_fs(context)
+    init_kwargs = _FakeSession.init_kwargs
+
+    assert isinstance(fs, _FakeIrodsFs)
+    assert fs.root == "/tempZone/home/rods"
+    assert init_kwargs is not None
+    assert init_kwargs["host"] == "irods.example.org"
+    assert init_kwargs["port"] == 1247
+    assert init_kwargs["user"] == "rods"
+    assert init_kwargs["password"] == "secret"
+    assert init_kwargs["zone"] == "tempZone"
+    assert init_kwargs["refresh_time"] == 120
+    assert fs.session.connection_timeout == 42
+    assert fs.session.default_resource == "demoResc"
+
+
+def test_irods_live_touch():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    assert file_source_pair.path == "/"
+    entries, count = file_source_pair.file_source.list("/", recursive=False)
+    assert isinstance(entries, list)
+    assert count >= 0
+    _cleanup_live_test_artifacts(settings)
+
+
+def test_irods_live_recursive_list():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    entries, count = file_source_pair.file_source.list("/", recursive=True)
+    assert isinstance(entries, list)
+    assert count >= 0
+    _cleanup_live_test_artifacts(settings)
+
+
+def test_irods_live_write_and_read_roundtrip():
+    settings = _irods_live_settings()
+    _skip_if_irods_unreachable(settings["host"], settings["port"])
+    _cleanup_live_test_artifacts(settings)
+
+    test_contents = "1\t2\t999\n666\t6\t555\n3\t4\t5\n"
+    target_uri = f"gxfiles://test1/{ROUNDTRIP_TEST_FILENAME}"
+
+    file_sources = configured_file_sources(_live_file_source_config(settings, writable=True))
+    _ = write_from(file_sources, target_uri, test_contents)
+    assert_realizes_contains(file_sources, target_uri, test_contents)
+
+    _cleanup_live_test_artifacts(settings)

From e2a03550dff0cae9fec46a555169c9f8348bb0b3 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 31 Mar 2026 14:52:43 +0200
Subject: [PATCH 05/17] Refactor iRODS file source listing methods for improved
 maintenance

---
 lib/galaxy/files/sources/irods.py | 78 +++++++++++++++++--------------
 1 file changed, 42 insertions(+), 36 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 4e36e0489b9..d1e2ed07f19 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -81,9 +81,45 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
     template_config_class = IrodsFileSourceTemplateConfiguration
     resolved_config_class = IrodsFileSourceConfiguration
 
-    def _normalize_listdir_name(self, value: str) -> str:
-        # fs-irods currently returns absolute iRODS paths from listdir; convert to simple entry names.
-        return os.path.basename(str(value).rstrip("/"))
+    def _iter_directory_entries(self, fs_handle, parent_path: str, normalized_query: Optional[str] = None):
+        for raw_name in fs_handle.listdir(parent_path):
+            name = os.path.basename(str(raw_name).rstrip("/"))
+            if not name:
+                continue
+            if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
+                continue
+            entry_path = fs.path.join(parent_path, name)
+            info = fs_handle.getinfo(entry_path, namespaces=["details"])
+            yield entry_path, info
+
+    def _list_recursive(self, fs_handle, path: str) -> tuple[list[AnyRemoteEntry], int]:
+        result: list[AnyRemoteEntry] = []
+        pending = [path]
+        while pending:
+            current_path = pending.pop(0)
+            for entry_path, info in self._iter_directory_entries(fs_handle, current_path):
+                result.append(self._resource_info_to_dict(current_path, info))
+                if info.is_dir:
+                    pending.append(entry_path)
+        return result, len(result)
+
+    def _list_non_recursive(
+        self,
+        fs_handle,
+        path: str,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
+        query: Optional[str] = None,
+    ) -> tuple[list[AnyRemoteEntry], int]:
+        normalized_query = query.lower() if query else None
+        entries = []
+        for _, info in self._iter_directory_entries(fs_handle, path, normalized_query):
+            entries.append(self._resource_info_to_dict(path, info))
+        count = len(entries)
+        page = self._to_page(limit, offset)
+        if page is not None:
+            entries = entries[page[0] : page[1]]
+        return entries, count
 
     def _list(
         self,
@@ -97,40 +133,10 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
         sort_by: Optional[str] = None,
     ) -> tuple[list[AnyRemoteEntry], int]:
         try:
-            with self._open_fs(context) as h:
+            with self._open_fs(context) as fs_handle:
                 if recursive:
-                    result: list[AnyRemoteEntry] = []
-                    pending = [path]
-                    while pending:
-                        current_path = pending.pop(0)
-                        for raw_name in h.listdir(current_path):
-                            name = self._normalize_listdir_name(raw_name)
-                            if not name:
-                                continue
-                            entry_path = fs.path.join(current_path, name)
-                            info = h.getinfo(entry_path, namespaces=["details"])
-                            result.append(self._resource_info_to_dict(current_path, info))
-                            if info.is_dir:
-                                pending.append(entry_path)
-                    return result, len(result)
-
-                normalized_query = query.lower() if query else None
-                entries = []
-                for raw_name in h.listdir(path):
-                    name = self._normalize_listdir_name(raw_name)
-                    if not name:
-                        continue
-                    if normalized_query and not fnmatch(name.lower(), f"*{normalized_query}*"):
-                        continue
-                    entry_path = fs.path.join(path, name)
-                    info = h.getinfo(entry_path, namespaces=["details"])
-                    entries.append(self._resource_info_to_dict(path, info))
-
-                count = len(entries)
-                page = self._to_page(limit, offset)
-                if page is not None:
-                    entries = entries[page[0] : page[1]]
-                return entries, count
+                    return self._list_recursive(fs_handle, path)
+                return self._list_non_recursive(fs_handle, path, limit, offset, query)
         except fs.errors.PermissionDenied as e:
             raise AuthenticationRequired(
                 f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."

From c907c33a919f814e12912693fc08f34dff57d131 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 18 May 2026 15:19:03 +0200
Subject: [PATCH 06/17] Format by isort and black

---
 lib/galaxy/files/sources/irods.py | 10 +++++-----
 test/unit/files/test_irods.py     |  1 +
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index d1e2ed07f19..86d28427fe0 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -1,6 +1,6 @@
+import os
 import ssl
 from fnmatch import fnmatch
-import os
 from typing import (
     Optional,
     Union,
@@ -9,16 +9,16 @@ from typing import (
 import fs
 import fs.errors
 
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
 from galaxy.files.models import (
     AnyRemoteEntry,
     BaseFileSourceConfiguration,
     BaseFileSourceTemplateConfiguration,
     FilesSourceRuntimeContext,
 )
-from galaxy.exceptions import (
-    AuthenticationRequired,
-    MessageException,
-)
 from galaxy.util.config_templates import TemplateExpansion
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index b867088f6d1..8a6eac4847a 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -1,5 +1,6 @@
 import os
 import socket
+
 import pytest
 import yaml
 

From 54c688fd8c2bb4b7a00558d1633c65a5b38cd529 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 19 May 2026 14:27:52 +0200
Subject: [PATCH 07/17] Add iRODS file source configuration to sample YAML

---
 .../config/sample/file_sources_conf.yml.sample   | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 5b46c69cb07..0cd93f07fef 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -1,3 +1,19 @@
+- type: irods
+  id: irods_local_instance
+  label: Local iRODS
+  doc: iRODS in local Docker stack
+  writable: true
+
+  host: 127.0.0.1
+  port: 1247
+  username: user
+  password: password
+  zone: exampleZone
+  root: /exampleZone/home/user
+
+  timeout: 30
+  refresh_time: 300
+
 - type: dropbox
   id: dropbox1
   label: Dropbox files (configure access in user preferences)

From fccf68f2e29366895eacf1adeb2e98c2e9d43b9a Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Fri, 22 May 2026 10:11:43 +0200
Subject: [PATCH 08/17] Remove the setting from the admin-defined file sources
 sample

---
 .../config/sample/file_sources_conf.yml.sample   | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 0cd93f07fef..5b46c69cb07 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -1,19 +1,3 @@
-- type: irods
-  id: irods_local_instance
-  label: Local iRODS
-  doc: iRODS in local Docker stack
-  writable: true
-
-  host: 127.0.0.1
-  port: 1247
-  username: user
-  password: password
-  zone: exampleZone
-  root: /exampleZone/home/user
-
-  timeout: 30
-  refresh_time: 300
-
 - type: dropbox
   id: dropbox1
   label: Dropbox files (configure access in user preferences)

From dc0e7b1b1f8f1d650a44d4a282385414c672edd3 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Sun, 24 May 2026 12:01:33 +0200
Subject: [PATCH 09/17] Update the way how conditional dependencies are handled

---
 lib/galaxy/files/sources/irods.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 86d28427fe0..8a28c530216 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -24,12 +24,9 @@ from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 try:
     from fs_irods import iRODSFS
-except ImportError:
-    iRODSFS = None
-
-try:
     from irods.session import iRODSSession
 except ImportError:
+    iRODSFS = None
     iRODSSession = None
 
 

From ddd7f8aa12efe0226fa37dbcd04723bde7c1d0b9 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Sun, 24 May 2026 12:04:23 +0200
Subject: [PATCH 10/17] Refactor the iRODS YAML configuration to improve
 optional path handling and remove the connection time setting for the user

---
 lib/galaxy/files/templates/examples/irods.yml | 33 +++++++------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/lib/galaxy/files/templates/examples/irods.yml b/lib/galaxy/files/templates/examples/irods.yml
index 22b168a32eb..de088c60dc1 100644
--- a/lib/galaxy/files/templates/examples/irods.yml
+++ b/lib/galaxy/files/templates/examples/irods.yml
@@ -16,32 +16,23 @@
       type: integer
       help: Port of the iRODS server.
       default: 1247
+    zone:
+      label: iRODS zone
+      type: string
+      help: Zone used for authentication (for example teamZone).
     username:
       label: iRODS user
       type: string
       help: Username used to authenticate against iRODS.
-    zone:
-      label: iRODS zone
+    subpath:
+      label: Subfolder path
       type: string
-      help: Zone used for authentication (for example tempZone).
-    root:
-      label: Root collection path
-      type: string
-      help: |
-        Collection path exposed in Galaxy, for example /tempZone/home/rods.
-    timeout:
-      label: Connection timeout (seconds)
-      type: integer
-      help: Timeout in seconds for iRODS connection attempts.
-      default: 30
-    refresh_time:
-      label: Session refresh time (seconds)
-      type: integer
-      help: Seconds between refresh checks for active iRODS sessions.
-      default: 300
+      optional: true
+      help: Optional subfolder under your personal directory (for example projectName).
     writable:
       label: Writable?
       type: boolean
+      optional: true
       help: Allow writing datasets back to iRODS.
       default: false
   secrets:
@@ -55,7 +46,7 @@
     username: "{{ variables.username }}"
     password: "{{ secrets.password }}"
     zone: "{{ variables.zone }}"
-    root: "{{ variables.root }}"
-    timeout: "{{ variables.timeout }}"
-    refresh_time: "{{ variables.refresh_time }}"
+    root: "/{{ variables.zone }}/home/{{ variables.username }}{% if variables.get('subpath') %}/{{ variables.get('subpath') | ensure_path_component }}{% endif %}"
+    timeout: 30
+    refresh_time: 300
     writable: "{{ variables.writable }}"
\ No newline at end of file

From 9c01e04557780e6373f03bd432591c6803c95090 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 25 May 2026 13:47:14 +0200
Subject: [PATCH 11/17] Make the SSLContext optional and align it with the SSL
 configuration setting in python-irodsclient

---
 lib/galaxy/files/sources/irods.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 8a28c530216..778479a89bd 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -1,5 +1,4 @@
 import os
-import ssl
 from fnmatch import fnmatch
 from typing import (
     Optional,
@@ -161,8 +160,11 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
             "encryption_salt_size": config.encryption_salt_size,
             "ssl_verify_server": config.ssl_verify_server,
             "ssl_ca_certificate_file": config.ssl_ca_certificate_file,
-            "ssl_context": ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH),
         }
+        ssl_context = getattr(config, "ssl_context", None)
+        if ssl_context is not None:
+            session_kwargs["ssl_context"] = ssl_context
+
         session = iRODSSession(**session_kwargs)
         session.connection_timeout = config.timeout
         if config.resource:

From 770913e6435e881e81a9e857d91d3d5eb7ffb69d Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Mon, 25 May 2026 16:24:16 +0200
Subject: [PATCH 12/17] Make recursive requests explicitly unsupported to
 prevent unbounded traversal

---
 lib/galaxy/files/sources/irods.py | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/lib/galaxy/files/sources/irods.py b/lib/galaxy/files/sources/irods.py
index 778479a89bd..78d649284db 100644
--- a/lib/galaxy/files/sources/irods.py
+++ b/lib/galaxy/files/sources/irods.py
@@ -88,17 +88,6 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
             info = fs_handle.getinfo(entry_path, namespaces=["details"])
             yield entry_path, info
 
-    def _list_recursive(self, fs_handle, path: str) -> tuple[list[AnyRemoteEntry], int]:
-        result: list[AnyRemoteEntry] = []
-        pending = [path]
-        while pending:
-            current_path = pending.pop(0)
-            for entry_path, info in self._iter_directory_entries(fs_handle, current_path):
-                result.append(self._resource_info_to_dict(current_path, info))
-                if info.is_dir:
-                    pending.append(entry_path)
-        return result, len(result)
-
     def _list_non_recursive(
         self,
         fs_handle,
@@ -131,7 +120,7 @@ class IrodsFilesSource(PyFilesystem2FilesSource[IrodsFileSourceTemplateConfigura
         try:
             with self._open_fs(context) as fs_handle:
                 if recursive:
-                    return self._list_recursive(fs_handle, path)
+                    raise MessageException("Recursive listing is not supported for iRODS file sources.")
                 return self._list_non_recursive(fs_handle, path, limit, offset, query)
         except fs.errors.PermissionDenied as e:
             raise AuthenticationRequired(

From 02ced4cb21b1c68646a71af4ef0f8f36c664c300 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 26 May 2026 09:41:49 +0200
Subject: [PATCH 13/17] Remove mock testing and update test to raise
 MessageException on recursive list

---
 test/unit/files/test_irods.py | 63 ++---------------------------------
 1 file changed, 3 insertions(+), 60 deletions(-)

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index 8a6eac4847a..e7b21e88562 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -4,6 +4,7 @@ import socket
 import pytest
 import yaml
 
+from galaxy.exceptions import MessageException
 from galaxy.files.models import (
     FileSourcePluginsConfig,
     FilesSourceRuntimeContext,
@@ -26,21 +27,6 @@ except ImportError:
 ROUNDTRIP_TEST_FILENAME = "numerical_sort_and_write_back_to_irods_v2.tab"
 
 
-class _FakeSession:
-    init_kwargs = None
-
-    def __init__(self, **kwargs):
-        type(self).init_kwargs = kwargs
-        self.connection_timeout = None
-        self.default_resource = None
-
-
-class _FakeIrodsFs:
-    def __init__(self, session, root=None):
-        self.session = session
-        self.root = root
-
-
 def _get_setting(irods_config: dict, env_name: str, key: str, cast=None):
     raw = os.environ.get(env_name)
     if raw is None:
@@ -147,48 +133,6 @@ def test_irods_plugin_registered():
     assert plugin_class is IrodsFilesSource
 
 
-def test_irods_open_fs_builds_session(monkeypatch):
-    monkeypatch.setattr("galaxy.files.sources.irods.iRODSSession", _FakeSession)
-    monkeypatch.setattr("galaxy.files.sources.irods.iRODSFS", _FakeIrodsFs)
-    monkeypatch.setattr(IrodsFilesSource, "required_module", _FakeIrodsFs)
-
-    file_source = IrodsFilesSource(
-        IrodsFilesSource.build_template_config(
-            type="irods",
-            id="test_irods",
-            file_sources_config=FileSourcePluginsConfig(),
-            host="irods.example.org",
-            port=1247,
-            username="rods",
-            password="secret",
-            zone="tempZone",
-            root="/tempZone/home/rods",
-            timeout=42,
-            refresh_time=120,
-            resource="demoResc",
-            writable=True,
-        )
-    )
-
-    resolved_config = file_source._evaluate_template_config(UserData())
-    context = FilesSourceRuntimeContext(user_data=UserData(), config=resolved_config)
-
-    fs = file_source._open_fs(context)
-    init_kwargs = _FakeSession.init_kwargs
-
-    assert isinstance(fs, _FakeIrodsFs)
-    assert fs.root == "/tempZone/home/rods"
-    assert init_kwargs is not None
-    assert init_kwargs["host"] == "irods.example.org"
-    assert init_kwargs["port"] == 1247
-    assert init_kwargs["user"] == "rods"
-    assert init_kwargs["password"] == "secret"
-    assert init_kwargs["zone"] == "tempZone"
-    assert init_kwargs["refresh_time"] == 120
-    assert fs.session.connection_timeout == 42
-    assert fs.session.default_resource == "demoResc"
-
-
 def test_irods_live_touch():
     settings = _irods_live_settings()
     _skip_if_irods_unreachable(settings["host"], settings["port"])
@@ -212,9 +156,8 @@ def test_irods_live_recursive_list():
     file_sources = configured_file_sources(_live_file_source_config(settings, writable=False))
     file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
 
-    entries, count = file_source_pair.file_source.list("/", recursive=True)
-    assert isinstance(entries, list)
-    assert count >= 0
+    with pytest.raises(MessageException):
+        file_source_pair.file_source.list("/", recursive=True)
     _cleanup_live_test_artifacts(settings)
 
 

From cd3df9012f9e4deac3270b77cdf65c46a8147315 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Tue, 26 May 2026 23:29:28 +0200
Subject: [PATCH 14/17] Fix the OpenAPI linting

---
 client/packages/api-client/src/schema/schema.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/packages/api-client/src/schema/schema.ts b/client/packages/api-client/src/schema/schema.ts
index 1ec8b2f8c34..ddc2fb8bb09 100644
--- a/client/packages/api-client/src/schema/schema.ts
+++ b/client/packages/api-client/src/schema/schema.ts
@@ -13044,6 +13044,7 @@ export interface components {
                 | "s3fs"
                 | "azure"
                 | "azureflat"
+                | "irods"
                 | "onedata"
                 | "webdav"
                 | "dropbox"
@@ -25350,6 +25351,7 @@ export interface components {
                 | "s3fs"
                 | "azure"
                 | "azureflat"
+                | "irods"
                 | "onedata"
                 | "webdav"
                 | "dropbox"

From a4c25be83f1cba4d29f8de961e7cef5f6cb21249 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 14:03:48 +0200
Subject: [PATCH 15/17] Add check for iRODS file source and update conditional
 requirements

---
 lib/galaxy/dependencies/__init__.py                  | 3 +++
 lib/galaxy/dependencies/conditional-requirements.txt | 1 +
 test/unit/app/dependencies/test_deps.py              | 2 ++
 3 files changed, 6 insertions(+)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 7153f44105f..b28bf8af973 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -291,6 +291,9 @@ class ConditionalDependencies:
     def check_rspace_client(self):
         return "rspace" in self.file_sources
 
+    def check_fs_irods(self):
+        return "irods" in self.file_sources
+
     def check_watchdog(self):
         install_set = {"auto", "True", "true", "polling", True}
         return self.config["watch_tools"] in install_set or self.config["watch_tool_data_dir"] in install_set
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 8d84205bfd2..2c45fb5ba80 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -35,6 +35,7 @@ adlfs
 huggingface_hub
 omero-py #type: omero
 iiif-fsspec # type: iiif
+fs-irods # type: irods, depends on python-irodsclient
 
 # Vault backend
 hvac
diff --git a/test/unit/app/dependencies/test_deps.py b/test/unit/app/dependencies/test_deps.py
index 7e2f8efa03a..f36e1b929f0 100644
--- a/test/unit/app/dependencies/test_deps.py
+++ b/test/unit/app/dependencies/test_deps.py
@@ -25,6 +25,7 @@ FILES_SOURCES_CONFIG = """
 - type: webdav
 - type: dropbox
 - type: googledrive
+- type: irods
 """
 JOB_CONF_YAML = """
 runners:
@@ -95,6 +96,7 @@ def test_fs_configured():
         assert cds.check_gdrive_fsspec()
         assert cds.check_dropboxdrivefs()
         assert cds.check_webdav4()
+        assert cds.check_fs_irods()
 
 
 def test_yaml_jobconf_runners():

From 8eccf2577a4b0bd39bcf4d97d04cea616e432dae Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 14:10:41 +0200
Subject: [PATCH 16/17] Remove unused imports from test_irods.py

---
 test/unit/files/test_irods.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/test/unit/files/test_irods.py b/test/unit/files/test_irods.py
index e7b21e88562..8396dc108e0 100644
--- a/test/unit/files/test_irods.py
+++ b/test/unit/files/test_irods.py
@@ -5,11 +5,6 @@ import pytest
 import yaml
 
 from galaxy.exceptions import MessageException
-from galaxy.files.models import (
-    FileSourcePluginsConfig,
-    FilesSourceRuntimeContext,
-    UserData,
-)
 from galaxy.files.plugins import FileSourcePluginLoader
 from galaxy.files.sources.irods import IrodsFilesSource
 from ._util import (

From 1fd2a3fad48d8a3fa91560c8d38488110670beb1 Mon Sep 17 00:00:00 2001
From: Jenny Kuo <118450954+fairytalesbykcc@users.noreply.github.com>
Date: Thu, 28 May 2026 16:12:13 +0200
Subject: [PATCH 17/17] Add iRODS file source type to templateTypes

---
 client/src/api/fileSources.ts | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/src/api/fileSources.ts b/client/src/api/fileSources.ts
index e7121c3a270..008775f999b 100644
--- a/client/src/api/fileSources.ts
+++ b/client/src/api/fileSources.ts
@@ -91,6 +91,10 @@ export const templateTypes: FileSourceTypesDetail = {
         icon: faNetworkWired,
         message: "This is a file repository plugin that connects with a remote server over SSH.",
     },
+    irods: {
+        icon: faNetworkWired,
+        message: "This is a file repository plugin that connects with an iRODS server.",
+    },
 };
 
 export const FileSourcesValidFilters = {