Allow a posix file source to prefer linking.

lib/galaxy/config/__init__.py

@@ -115,6 +115,14 @@
             "level": "INFO",
             "qualname": "watchdog.observers.inotify_buffer",
         },
+        "py.warnings": {
+            "level": "ERROR",
+            "qualname": "py.warnings",
+        },
+        "celery.utils.functional": {
+            "level": "INFO",
+            "qualname": "celery.utils.functional",
+        },
     },
     "filters": {
         "stack": {

lib/galaxy/files/sources/__init__.py

@@ -277,6 +277,10 @@ def to_dict(self, for_serialization=False, user_context: "OptionalUserContext" =
         context doesn't need to be present after the plugin is re-hydrated.
         """
 
+    @abc.abstractmethod
+    def prefer_links(self) -> bool:
+        """Prefer linking to files."""
+
 
 class SupportsBrowsing(metaclass=abc.ABCMeta):
     """An interface indicating that this filesource is browsable.
@@ -351,6 +355,9 @@ def user_has_access(self, user_context: "OptionalUserContext") -> bool:
             or (self._user_has_required_roles(user_context) and self._user_has_required_groups(user_context))
         )
 
+    def prefer_links(self) -> bool:
+        return False
+
     @property
     def user_context_required(self) -> bool:
         return self.requires_roles is not None or self.requires_groups is not None

lib/galaxy/files/sources/posix.py

@@ -26,13 +26,15 @@
 DEFAULT_ENFORCE_SYMLINK_SECURITY = True
 DEFAULT_DELETE_ON_REALIZE = False
 DEFAULT_ALLOW_SUBDIR_CREATION = True
+DEFAULT_PREFER_LINKS = False
 
 
 class PosixFilesSourceProperties(FilesSourceProperties, total=False):
     root: str
     enforce_symlink_security: bool
     delete_on_realize: bool
     allow_subdir_creation: bool
+    prefer_links: bool
 
 
 class PosixFilesSource(BaseFilesSource):
@@ -53,6 +55,10 @@ def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         self.enforce_symlink_security = props.get("enforce_symlink_security", DEFAULT_ENFORCE_SYMLINK_SECURITY)
         self.delete_on_realize = props.get("delete_on_realize", DEFAULT_DELETE_ON_REALIZE)
         self.allow_subdir_creation = props.get("allow_subdir_creation", DEFAULT_ALLOW_SUBDIR_CREATION)
+        self._prefer_links = props.get("prefer_links", DEFAULT_PREFER_LINKS)
+
+    def prefer_links(self) -> bool:
+        return self._prefer_links
 
     def _list(
         self,
@@ -182,6 +188,7 @@ def _serialization_props(self, user_context: OptionalUserContext = None) -> Posi
             "enforce_symlink_security": self.enforce_symlink_security,
             "delete_on_realize": self.delete_on_realize,
             "allow_subdir_creation": self.allow_subdir_creation,
+            "prefer_links": self._prefer_links,
         }
 
     @property

lib/galaxy/files/uris.py

@@ -49,8 +49,7 @@ def stream_url_to_file(
     target_path: Optional[str] = None,
     file_source_opts: Optional[FilesSourceOptions] = None,
 ) -> str:
-    if file_sources is None:
-        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    file_sources = ensure_file_sources(file_sources)
     file_source, rel_path = file_sources.get_file_source_path(url)
     if file_source:
         if not target_path:
@@ -62,6 +61,12 @@ def stream_url_to_file(
         raise NoMatchingFileSource(f"Could not find a matching handler for: {url}")
 
 
+def ensure_file_sources(file_sources: Optional["ConfiguredFileSources"]) -> "ConfiguredFileSources":
+    if file_sources is None:
+        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    return file_sources
+
+
 def stream_to_file(stream, suffix="", prefix="", dir=None, text=False, **kwd):
     """Writes a stream to a temporary file, returns the temporary file's name"""
     fd, temp_name = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir, text=text)

lib/galaxy/tools/data_fetch.py

@@ -23,6 +23,7 @@
     UploadProblemException,
 )
 from galaxy.files.uris import (
+    ensure_file_sources,
     stream_to_file,
     stream_url_to_file,
 )
@@ -97,13 +98,13 @@ def expand_elements_from(target_or_item):
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _directory_to_items(decompressed_directory)
             elif elements_from == "bagit":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _bagit_to_items(elements_from_path)
             elif elements_from == "bagit_archive":
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _bagit_to_items(decompressed_directory)
             elif elements_from == "directory":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _directory_to_items(elements_from_path)
             else:
                 raise Exception(f"Unknown elements from type encountered [{elements_from}]")
@@ -205,7 +206,7 @@ def _resolve_item(item):
                     pass
                 key = keys[composite_item_idx]
                 writable_file = writable_files[key]
-                _, src_target = _has_src_to_path(upload_config, composite_item)
+                _, src_target, _ = _has_src_to_path(upload_config, composite_item)
                 # do the writing
                 sniff.handle_composite_file(
                     datatype,
@@ -238,10 +239,23 @@ def _resolve_item_with_primary(item):
         converted_path = None
 
         deferred = upload_config.get_option(item, "deferred")
+
+        link_data_only = upload_config.link_data_only
+        link_data_only_explicit = upload_config.link_data_only_explicit
+        if "link_data_only" in item:
+            # Allow overriding this on a per file basis.
+            link_data_only, link_data_only_explicit = _link_data_only(item)
+
         name: str
         path: Optional[str]
+        default_in_place = False
         if not deferred:
-            name, path = _has_src_to_path(upload_config, item, is_dataset=True)
+            name, path, is_link = _has_src_to_path(
+                upload_config, item, is_dataset=True, link_data_only_explicitly_set=link_data_only_explicit
+            )
+            if is_link:
+                link_data_only = True
+                default_in_place = True
         else:
             name, path = _has_src_to_name(item) or "Deferred Dataset", None
         sources = []
@@ -266,10 +280,6 @@ def _resolve_item_with_primary(item):
                     item["error_message"] = error_message
 
         dbkey = item.get("dbkey", "?")
-        link_data_only = upload_config.link_data_only
-        if "link_data_only" in item:
-            # Allow overriding this on a per file basis.
-            link_data_only = _link_data_only(item)
 
         ext = "data"
         staged_extra_files = None
@@ -281,7 +291,7 @@ def _resolve_item_with_primary(item):
 
         effective_state = "ok"
         if not deferred and not error_message:
-            in_place = item.get("in_place", False)
+            in_place = item.get("in_place", default_in_place)
             purge_source = item.get("purge_source", True)
 
             registry = upload_config.registry
@@ -339,7 +349,7 @@ def walk_extra_files(items, prefix=""):
                                 item_prefix = os.path.join(prefix, name)
                             walk_extra_files(item.get("elements"), prefix=item_prefix)
                         else:
-                            src_name, src_path = _has_src_to_path(upload_config, item)
+                            src_name, src_path, _ = _has_src_to_path(upload_config, item)
                             if prefix:
                                 rel_path = os.path.join(prefix, src_name)
                             else:
@@ -425,7 +435,7 @@ def _bagit_to_items(directory):
 
 
 def _decompress_target(upload_config: "UploadConfig", target: Dict[str, Any]):
-    elements_from_name, elements_from_path = _has_src_to_path(upload_config, target, is_dataset=False)
+    elements_from_name, elements_from_path, _ = _has_src_to_path(upload_config, target, is_dataset=False)
     # by default Galaxy will check for a directory with a single file and interpret that
     # as the new root for expansion, this is a good user experience for uploading single
     # files in a archive but not great from an API perspective. Allow disabling by setting
@@ -483,13 +493,33 @@ def _has_src_to_name(item) -> Optional[str]:
     return name
 
 
-def _has_src_to_path(upload_config: "UploadConfig", item: Dict[str, Any], is_dataset: bool = False) -> Tuple[str, str]:
+def _has_src_to_path(
+    upload_config: "UploadConfig",
+    item: Dict[str, Any],
+    is_dataset: bool = False,
+    link_data_only: bool = False,
+    link_data_only_explicitly_set: bool = False,
+) -> Tuple[str, str, bool]:
     assert "src" in item, item
     src = item.get("src")
     name = item.get("name")
+    is_link = False
     if src == "url":
         url = item.get("url")
+        file_sources = ensure_file_sources(upload_config.file_sources)
         assert url, "url cannot be empty"
+        if not link_data_only_explicitly_set:
+            file_source, rel_path = file_sources.get_file_source_path(url)
+            prefer_links = file_source.prefer_links()
+            if prefer_links:
+                if rel_path.startswith("/"):
+                    rel_path = rel_path[1:]
+                path = os.path.abspath(os.path.join(file_source.root, rel_path))
+                if name is None:
+                    name = url.split("/")[-1]
+                is_link = True
+                return name, path, is_link
+
         try:
             path = stream_url_to_file(url, file_sources=upload_config.file_sources, dir=upload_config.working_directory)
         except Exception as e:
@@ -513,7 +543,7 @@ def _has_src_to_path(upload_config: "UploadConfig", item: Dict[str, Any], is_dat
         path = item["path"]
         if name is None:
             name = os.path.basename(path)
-    return name, path
+    return name, path, is_link
 
 
 def _handle_hash_validation(hash_function: HashFunctionNameEnum, hash_value: str, path: str):
@@ -564,7 +594,7 @@ def __init__(
         self.space_to_tab = request.get("space_to_tab", False)
         self.auto_decompress = request.get("auto_decompress", False)
         self.deferred = request.get("deferred", False)
-        self.link_data_only = _link_data_only(request)
+        self.link_data_only, self.link_data_only_explicit = _link_data_only(request)
         self.file_sources_dict = file_sources_dict
         self._file_sources = None
 
@@ -616,12 +646,19 @@ def ensure_in_working_directory(self, path, purge_source, in_place):
         return new_path
 
 
-def _link_data_only(has_config_dict):
-    link_data_only = has_config_dict.get("link_data_only", False)
-    if not isinstance(link_data_only, bool):
-        # Allow the older string values of 'copy_files' and 'link_to_files'
-        link_data_only = link_data_only == "copy_files"
-    return link_data_only
+def _link_data_only(has_config_dict) -> Tuple[bool, bool]:
+    if "link_data_only" in has_config_dict:
+        link_data_only_raw = has_config_dict["link_data_only"]
+        if not isinstance(link_data_only_raw, bool):
+            # Allow the older string values of 'copy_files' and 'link_to_files'
+            link_data_only = link_data_only_raw == "copy_files"
+        else:
+            link_data_only = link_data_only_raw
+        link_data_only_explicit = True
+    else:
+        link_data_only = False
+        link_data_only_explicit = False
+    return link_data_only, link_data_only_explicit
 
 
 def _for_each_src(f, obj):

lib/galaxy_test/driver/integration_setup.py

@@ -15,7 +15,9 @@
 REQUIRED_GROUP_EXPRESSION = f"{GROUP_A} or '{GROUP_B}'"
 
 
-def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include_test_data_dir: bool) -> str:
+def get_posix_file_source_config(
+    root_dir: str, roles: str, groups: str, include_test_data_dir: bool, prefer_links: bool = False
+) -> str:
     rval = f"""
 - type: posix
   id: posix_test
@@ -26,6 +28,17 @@ def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include
   requires_roles: {roles}
   requires_groups: {groups}
 """
+    if prefer_links:
+        rval += f"""
+- type: posix
+  id: linking_source
+  label: Posix
+  doc: Files from local path to links
+  root: {root_dir}
+  writable: true
+  prefer_links: true
+"""
+
     if include_test_data_dir:
         rval += """
 - type: posix
@@ -44,9 +57,10 @@ def create_file_source_config_file_on(
     include_test_data_dir,
     required_role_expression,
     required_group_expression,
+    prefer_links: bool = False,
 ):
     file_contents = get_posix_file_source_config(
-        root_dir, required_role_expression, required_group_expression, include_test_data_dir
+        root_dir, required_role_expression, required_group_expression, include_test_data_dir, prefer_links=prefer_links
     )
     file_path = os.path.join(temp_dir, "file_sources_conf_posix.yml")
     with open(file_path, "w") as f:
@@ -67,6 +81,7 @@ def handle_galaxy_config_kwds(
         # Require role for access but do not require groups by default on every test to simplify them
         required_role_expression=REQUIRED_ROLE_EXPRESSION,
         required_group_expression="",
+        prefer_links: bool = False,
     ):
         temp_dir = os.path.realpath(mkdtemp())
         clazz_ = clazz_ or cls
@@ -79,6 +94,7 @@ def handle_galaxy_config_kwds(
             clazz_.include_test_data_dir,
             required_role_expression,
             required_group_expression,
+            prefer_links=prefer_links,
         )
         config["file_sources_config_file"] = file_sources_config_file
 

test/integration/test_remote_files_posix.py

@@ -1,8 +1,8 @@
-# Before running this test, start nginx+webdav in Docker using following command:
-# docker run -v `pwd`/test/integration/webdav/data:/media  -e WEBDAV_USERNAME=alice -e WEBDAV_PASSWORD=secret1234 -p 7083:7083 jmchilton/webdavdev
-# Apache Docker host (shown next) doesn't work because displayname not set in response.
-# docker run -v `pwd`/test/integration/webdav:/var/lib/dav  -e AUTH_TYPE=Basic -e USERNAME=alice -e PASSWORD=secret1234  -e LOCATION=/ -p 7083:80 bytemark/webdav
+import os
 
+from sqlalchemy import select
+
+from galaxy.model import Dataset
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
@@ -108,3 +108,53 @@ def _assert_list_response_matches_fixtures(self, list_response):
 
     def _assert_access_forbidden_response(self, response):
         api_asserts.assert_status_code_is(response, 403)
+
+
+class TestPreferLinksPosixFileSourceIntegration(PosixFileSourceSetup, integration_util.IntegrationTestCase):
+    dataset_populator: DatasetPopulator
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        PosixFileSourceSetup.handle_galaxy_config_kwds(
+            config,
+            cls,
+            prefer_links=True,
+        )
+
+    def setUp(self):
+        super().setUp()
+        self._write_file_fixtures()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    def test_links_by_default(self):
+        with self.dataset_populator.test_history() as history_id:
+            element = dict(src="url", url="gxfiles://linking_source/a")
+            target = {
+                "destination": {"type": "hdas"},
+                "elements": [element],
+            }
+            targets = [target]
+            payload = {
+                "history_id": history_id,
+                "targets": targets,
+            }
+            new_dataset = self.dataset_populator.fetch(payload, assert_ok=True).json()["outputs"][0]
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset)
+            assert content == "a\n", content
+            stmt = select(Dataset).order_by(Dataset.create_time.desc()).limit(1)
+            dataset = self._app.model.session.execute(stmt).unique().scalar_one()
+            assert dataset.external_filename.endswith("/root/a")
+            assert os.path.exists(dataset.external_filename)
+            assert open(dataset.external_filename).read() == "a\n"
+            payload = self.dataset_populator.run_tool(
+                tool_id="cat",
+                inputs={
+                    "input1": {"src": "hda", "id": new_dataset["id"]},
+                },
+                history_id=history_id,
+            )
+            derived_dataset = payload["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            derived_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=derived_dataset)
+            assert derived_content.strip() == "a"