Merge branch 'release_24.0' into dev

client/src/components/History/HistoryView.vue

@@ -25,7 +25,9 @@
             </b-button>
         </div>
 
-        <b-alert :show="copySuccess"> History imported and set to your active history. </b-alert>
+        <b-alert :show="copySuccess">
+            History imported and is now your active history. <b-link to="/histories/list">View here</b-link>.
+        </b-alert>
 
         <CollectionPanel
             v-if="selectedCollections.length && selectedCollections[0].history_id == id"

client/src/components/Tags/model.js

@@ -7,7 +7,7 @@ import { keyedColorScheme } from "utils/color";
 
 // Valid tag regex. The basic format here is a tag name with optional subtags
 // separated by a period, and then an optional value after a colon.
-export const VALID_TAG_RE = /^([^\s.:])+(.[^\s.:]+)*(:[^\s.:]+)?$/;
+export const VALID_TAG_RE = /^([^\s.:])+(\.[^\s.:]+)*(:\S+)?$/;
 
 export class TagModel {
     /**

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -12,9 +12,14 @@
 )
 
 import fs
+import fs.errors
 from fs.base import FS
 from typing_extensions import Unpack
 
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
 from . import (
     BaseFilesSource,
     FilesSourceOptions,
@@ -42,19 +47,25 @@ def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None)
 
     def _list(self, path="/", recursive=False, user_context=None, opts: Optional[FilesSourceOptions] = None):
         """Return dictionary of 'Directory's and 'File's."""
-
-        with self._open_fs(user_context=user_context, opts=opts) as h:
-            if recursive:
-                res: List[Dict[str, Any]] = []
-                for p, dirs, files in h.walk(path):
-                    to_dict = functools.partial(self._resource_info_to_dict, p)
-                    res.extend(map(to_dict, dirs))
-                    res.extend(map(to_dict, files))
-                return res
-            else:
-                res = h.scandir(path, namespaces=["details"])
-                to_dict = functools.partial(self._resource_info_to_dict, path)
-                return list(map(to_dict, res))
+        try:
+            with self._open_fs(user_context=user_context, opts=opts) as h:
+                if recursive:
+                    res: List[Dict[str, Any]] = []
+                    for p, dirs, files in h.walk(path):
+                        to_dict = functools.partial(self._resource_info_to_dict, p)
+                        res.extend(map(to_dict, dirs))
+                        res.extend(map(to_dict, files))
+                    return res
+                else:
+                    res = h.scandir(path, namespaces=["details"])
+                    to_dict = functools.partial(self._resource_info_to_dict, path)
+                    return list(map(to_dict, res))
+        except fs.errors.PermissionDenied as e:
+            raise AuthenticationRequired(
+                f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
+            )
+        except fs.errors.FSError as e:
+            raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
 
     def _realize_to(self, source_path, native_path, user_context=None, opts: Optional[FilesSourceOptions] = None):
         with open(native_path, "wb") as write_file:

lib/galaxy/files/sources/dropbox.py

@@ -8,6 +8,10 @@
     Union,
 )
 
+from galaxy.exceptions import (
+    AuthenticationRequired,
+    MessageException,
+)
 from . import (
     FilesSourceOptions,
     FilesSourceProperties,
@@ -27,8 +31,17 @@ def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None)
         if "accessToken" in props:
             props["access_token"] = props.pop("accessToken")
 
-        handle = DropboxFS(**{**props, **extra_props})
-        return handle
+        try:
+            handle = DropboxFS(**{**props, **extra_props})
+            return handle
+        except Exception as e:
+            # This plugin might raise dropbox.dropbox_client.BadInputException
+            # which is not a subclass of fs.errors.FSError
+            if "OAuth2" in str(e):
+                raise AuthenticationRequired(
+                    f"Permission Denied. Reason: {e}. Please check your credentials in your preferences for {self.label}."
+                )
+            raise MessageException(f"Error connecting to Dropbox. Reason: {e}")
 
 
 __all__ = ("DropboxFilesSource",)

lib/galaxy/managers/remote_files.py

@@ -9,6 +9,7 @@
 from galaxy import exceptions
 from galaxy.files import (
     ConfiguredFileSources,
+    FileSourcePath,
     ProvidesUserFileSourcesUserContext,
 )
 from galaxy.files.sources import (
@@ -94,10 +95,10 @@ def index(
                 opts=opts,
             )
         except exceptions.MessageException:
-            log.warning(f"Problem listing file source path {file_source_path}", exc_info=True)
+            log.warning(self._get_error_message(file_source_path), exc_info=True)
             raise
         except Exception:
-            message = f"Problem listing file source path {file_source_path}"
+            message = self._get_error_message(file_source_path)
             log.warning(message, exc_info=True)
             raise exceptions.InternalServerError(message)
         if format == RemoteFilesFormat.flat:
@@ -131,6 +132,9 @@ def index(
 
         return index
 
+    def _get_error_message(self, file_source_path: FileSourcePath) -> str:
+        return f"Problem listing file source path {file_source_path.file_source.get_uri_root()}{file_source_path.path}"
+
     def get_files_source_plugins(
         self,
         user_context: ProvidesUserContext,
@@ -162,6 +166,9 @@ def create_entry(self, user_ctx: ProvidesUserContext, entry_data: CreateEntryPay
         file_source = file_source_path.file_source
         try:
             result = file_source.create_entry(entry_data.dict(), user_context=user_file_source_context)
+        except exceptions.MessageException:
+            log.warning(f"Problem creating entry {entry_data.name} in file source {entry_data.target}", exc_info=True)
+            raise
         except Exception:
             message = f"Problem creating entry {entry_data.name} in file source {entry_data.target}"
             log.warning(message, exc_info=True)

lib/galaxy/model/tags.py

@@ -296,7 +296,14 @@ def get_tag_by_name(self, tag_name):
         return None
 
     def _create_tag(self, tag_str: str):
-        """Create a Tag object from a tag string."""
+        """
+        Create or retrieve one or more Tag objects from a tag string. If there are multiple
+        hierarchical tags in the tag string, the string will be split along `self.hierarchy_separator` chars.
+        A Tag instance will be created for each non-empty prefix. If a prefix corresponds to the
+        name of an existing tag, that tag will be retrieved; otherwise, a new Tag object will be created.
+        For example, for the tag string `a.b.c` 3 Tag instances will be created: `a`, `a.b`, `a.b.c`.
+        Return the last tag created (`a.b.c`).
+        """
         tag_hierarchy = tag_str.split(self.hierarchy_separator)
         tag_prefix = ""
         parent_tag = None

lib/galaxy/schema/schema.py

@@ -66,6 +66,8 @@
 
 OptionalNumberT = Annotated[Optional[Union[int, float]], Field(None)]
 
+TAG_ITEM_PATTERN = r"^([^\s.:])+(\.[^\s.:]+)*(:\S+)?$"
+
 
 class DatasetState(str, Enum):
     NEW = "new"
@@ -527,7 +529,7 @@ class HistoryContentSource(str, Enum):
 DatasetCollectionInstanceType = Literal["history", "library"]
 
 
-TagItem = Annotated[str, Field(..., pattern=r"^([^\s.:])+(.[^\s.:]+)*(:[^\s.:]+)?$")]
+TagItem = Annotated[str, Field(..., pattern=TAG_ITEM_PATTERN)]
 
 
 class TagCollection(RootModel):

lib/galaxy_test/api/test_item_tags.py

@@ -135,9 +135,9 @@ def _create_valid_tag(self, prefix: str):
         return response
 
     def _create_history_contents(self, history_id):
-        history_content_id = self.dataset_collection_populator.create_list_in_history(
-            history_id, contents=["test_dataset"], direct_upload=True, wait=True
-        ).json()["outputs"][0]["id"]
+        history_content_id = self.dataset_populator.new_dataset(
+            history_id, contents="test_dataset", direct_upload=True, wait=True
+        )["id"]
         return history_content_id
 
     def _create_history(self):

test/unit/app/managers/test_TagHandler.py

@@ -112,3 +112,15 @@ def test_item_has_tag(self):
         # Tag
         assert self.tag_handler.item_has_tag(self.user, item=hda, tag=hda.tags[0].tag)
         assert not self.tag_handler.item_has_tag(self.user, item=hda, tag="tag2")
+
+    def test_get_name_value_pair(self):
+        """Verify that parsing a single tag string correctly splits it into name/value pairs."""
+        assert self.tag_handler.parse_tags("a") == [("a", None)]
+        assert self.tag_handler.parse_tags("a.b") == [("a.b", None)]
+        assert self.tag_handler.parse_tags("a.b:c") == [("a.b", "c")]
+        assert self.tag_handler.parse_tags("a.b:c.d") == [("a.b", "c.d")]
+        assert self.tag_handler.parse_tags("a.b:c.d:e.f") == [("a.b", "c.d:e.f")]
+        assert self.tag_handler.parse_tags("a.b:c.d:e.f.") == [("a.b", "c.d:e.f.")]
+        assert self.tag_handler.parse_tags("a.b:c.d:e.f..") == [("a.b", "c.d:e.f..")]
+        assert self.tag_handler.parse_tags("a.b:c.d:e.f:") == [("a.b", "c.d:e.f:")]
+        assert self.tag_handler.parse_tags("a.b:c.d:e.f::") == [("a.b", "c.d:e.f::")]

test/unit/schema/test_schema.py

@@ -1,8 +1,12 @@
+import re
 from uuid import uuid4
 
 from pydantic import BaseModel
 
-from galaxy.schema.schema import DatasetStateField
+from galaxy.schema.schema import (
+    DatasetStateField,
+    TAG_ITEM_PATTERN,
+)
 from galaxy.schema.tasks import (
     GenerateInvocationDownload,
     RequestUser,
@@ -34,3 +38,43 @@ class StateModel(BaseModel):
 def test_dataset_state_coercion():
     assert StateModel(state="ok").state == "ok"
     assert StateModel(state="deleted").state == "discarded"
+
+
+class TestTagPattern:
+
+    def test_valid(self):
+        tag_strings = [
+            "a",
+            "aa",
+            "aa.aa",
+            "aa.aa.aa",
+            "~!@#$%^&*()_+`-=[]{};'\",./<>?",
+            "a.b:c",
+            "a.b:c.d:e.f",
+            "a.b:c.d:e..f",
+            "a.b:c.d:e.f:g",
+            "a.b:c.d:e.f::g",
+            "a.b:c.d:e.f::g:h",
+            "a::a",  # leading colon for tag value
+            "a:.a",  # leading period for tag value
+            "a:a:",  # trailing colon OK for tag value
+            "a:a.",  # trailing period OK for tag value
+        ]
+        for t in tag_strings:
+            assert re.match(TAG_ITEM_PATTERN, t)
+
+    def test_invalid(self):
+        tag_strings = [
+            " a",  # leading space for tag name
+            ":a",  # leading colon for tag name
+            ".a",  # leading period for tag name
+            "a ",  # trailing space for tag name
+            "a a",  # space inside tag name
+            "a: a",  # leading space for tag value
+            "a:a a",  # space inside tag value
+            "a:",  # trailing colon for tag name
+            "a.",  # trailing period for tag name
+            "a:b ",  # trailing space for tag value
+        ]
+        for t in tag_strings:
+            assert not re.match(TAG_ITEM_PATTERN, t)