Merge branch 'release_25.0' into release_25.1

nsoranzo · nsoranzo · commit ba0bf2e86824 · 2025-11-12T12:15:23.000Z
diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py
@@ -225,8 +225,8 @@ def _try_to_locate_refresh_token_expiration(self, extra_data):
         return (
             extra_data.get("expires", None)
             or extra_data.get("expires_in", None)
-            or extra_data["refresh_token"].get("expires", None)
-            or extra_data["refresh_token"].get("expires_in", None)
+            or (extra_data.get("refresh_token") or {}).get("expires", None)
+            or (extra_data.get("refresh_token") or {}).get("expires_in", None)
         )
 
     def authenticate(self, trans, idphint=None):
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -1190,6 +1190,7 @@
     <!-- rdeval types -->
     <datatype extension="rd" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" subclass="true" description="Rdeval read sketch"/>
     <datatype extension="safetensors" type="galaxy.datatypes.binary:Safetensors" mimetype="application/octet-stream" display_in_upload="true" description="A simple format for storing tensors safely (as opposed to pickle) and that is still fast (zero-copy)" description_url="https://huggingface.co/docs/safetensors/index"/>
+    <datatype extension="spatialdata.zip" type="galaxy.datatypes.binary:SpatialData" mimetype="application/octet-stream" display_in_upload="true" description="A data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets" description_url="https://github.com/scverse/spatialdata"/>
   </registration>
 
   <sniffers>
@@ -1297,6 +1298,7 @@
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Metadata"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Artifact"/>
     <sniffer type="galaxy.datatypes.qiime2:QIIME2Visualization"/>
+    <sniffer type="galaxy.datatypes.binary:SpatialData"/>
     <sniffer type="galaxy.datatypes.binary:CompressedOMEZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZarrZipArchive"/>
     <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -487,6 +487,12 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
                     dataset.metadata.zarr_format = format_version
 
     def sniff(self, filename: str) -> bool:
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('Images.zarr.zip')
+        >>> CompressedZarrZipArchive().sniff(fname)
+        True
+        """
         # Check if the zip file contains a zarr store.
         # In theory, the zarr store must be in the root of the zip file.
         # See: https://github.com/zarr-developers/zarr-python/issues/756#issuecomment-852134901
@@ -4874,6 +4880,322 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         dataset.metadata.version = struct.unpack("<i", header_bytes[4:8])[0]
 
 
+class SpatialData(CompressedZarrZipArchive):
+    """
+    Class for SpatialData file: https://spatialdata.scverse.org/
+
+    SpatialData: an open and universal framework for processing spatial omics data.
+    SpatialData aims at implementing a performant in-memory representation in Python
+    and an on-disk representation based on the Zarr and Parquet data formats
+    and following, when applicable, the OME-NGFF specification
+
+    The format stores multi-modal spatial omics datasets including:
+    - Images (2D/3D multi-scale)
+    - Labels (segmentation masks)
+    - Shapes (polygons, circles)
+    - Points (transcript locations, point clouds)
+    - Tables (annotations)
+    """
+
+    file_ext = "spatialdata.zip"
+
+    # Minimal metadata for elements
+    MetadataElement(
+        name="images_count",
+        desc="Number of SpatialData image elements",
+        default=0,
+        readonly=True,
+        visible=True,
+        no_value=0,
+    )
+
+    MetadataElement(
+        name="labels_count",
+        desc="Number of SpatialData label elements",
+        default=0,
+        readonly=True,
+        visible=True,
+        no_value=0,
+    )
+
+    MetadataElement(
+        name="shapes_count",
+        desc="Number of SpatialData shape elements",
+        default=0,
+        readonly=True,
+        visible=True,
+        no_value=0,
+    )
+
+    MetadataElement(
+        name="points_count",
+        desc="Number of SpatialData point elements",
+        default=0,
+        readonly=True,
+        visible=True,
+        no_value=0,
+    )
+
+    MetadataElement(
+        name="tables",
+        desc="SpatialData table elements",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+        visible=True,
+    )
+
+    MetadataElement(
+        name="table_shapes",
+        desc="SpatialData table shapes (n_obs, n_vars)",
+        default={},
+        param=metadata.DictParameter,
+        readonly=True,
+        visible=False,
+    )
+
+    MetadataElement(
+        name="coordinate_systems",
+        desc="SpatialData coordinate systems",
+        default=[],
+        param=metadata.SelectParameter,
+        multiple=True,
+        readonly=True,
+        visible=True,
+    )
+
+    MetadataElement(
+        name="spatialdata_version",
+        desc="SpatialData software version",
+        default="",
+        readonly=True,
+        visible=True,
+        no_value="",
+    )
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            # Try to make a metadata like spatialdata file itself
+            peek_lines = ["SpatialData object"]
+
+            # Show zarr format if available
+            if dataset.metadata.zarr_format:
+                peek_lines[0] += f" (Zarr Format v{dataset.metadata.zarr_format})"
+
+            # Show counts for each element type
+            if getattr(dataset.metadata, "images_count", 0):
+                peek_lines.append(f"├── Images ({dataset.metadata.images_count})")
+
+            if getattr(dataset.metadata, "labels_count", 0):
+                peek_lines.append(f"├── Labels ({dataset.metadata.labels_count})")
+
+            if getattr(dataset.metadata, "shapes_count", 0):
+                peek_lines.append(f"├── Shapes ({dataset.metadata.shapes_count})")
+
+            if getattr(dataset.metadata, "points_count", 0):
+                peek_lines.append(f"├── Points ({dataset.metadata.points_count})")
+
+            if dataset.metadata.tables:
+                peek_lines.append(f"└── Tables ({len(dataset.metadata.tables)})")
+                for tbl in dataset.metadata.tables:
+                    # Add shape information if available
+                    if dataset.metadata.table_shapes and tbl in dataset.metadata.table_shapes:
+                        shape = dataset.metadata.table_shapes[tbl]
+                        peek_lines.append(f"      └── '{tbl}': AnnData {shape}")
+                    else:
+                        peek_lines.append(f"      └── '{tbl}'")
+
+            # Show coordinate systems if available
+            if dataset.metadata.coordinate_systems:
+                peek_lines.append("")
+                peek_lines.append("with coordinate systems:")
+                for cs in dataset.metadata.coordinate_systems:
+                    peek_lines.append(f"  • {cs}")
+
+            dataset.peek = "\n".join(peek_lines)
+            dataset.blurb = f"SpatialData file ({nice_size(dataset.get_size())})"
+            if dataset.metadata.spatialdata_version:
+                dataset.blurb += f"\nVersion: {dataset.metadata.spatialdata_version}"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        super().set_meta(dataset, overwrite=overwrite, **kwd)
+        try:
+            with zipfile.ZipFile(dataset.get_file_name()) as zf:
+                # Initialize element dictionaries to track elements by type
+                images = set()
+                labels = set()
+                shapes = set()
+                points = set()
+                tables = set()
+                coordinate_systems = set()
+                spatialdata_version = ""
+
+                # Find the root zarr directory
+                root_zarr = None
+                for file in zf.namelist():
+                    if file.endswith(".zarr/.zattrs"):
+                        root_zarr = file.replace("/.zattrs", "")
+                        break
+
+                # Read root attributes for version info
+                if root_zarr:
+                    root_attrs_path = f"{root_zarr}/.zattrs"
+                    try:
+                        with zf.open(root_attrs_path) as f:
+                            root_attrs = json.load(f)
+                            if "spatialdata_attrs" in root_attrs:
+                                spatialdata_attrs = root_attrs["spatialdata_attrs"]
+                                spatialdata_version = spatialdata_attrs.get("spatialdata_software_version", "")
+                    except Exception:
+                        pass
+
+                # Parse all files to extract elements and coordinate systems
+                for file in zf.namelist():
+                    # Extract elements based on directory structure
+                    # Expected structure: <root>.zarr/<element_type>/<element_name>/...
+                    if root_zarr and file.startswith(root_zarr + "/"):
+                        rel_parts = file[len(root_zarr) + 1 :].split("/")
+                        if len(rel_parts) >= 2:
+                            element_type = rel_parts[0]
+                            element_name = rel_parts[1]
+
+                            # Skip metadata files and empty names
+                            if element_name and not element_name.startswith("."):
+                                if element_type == "images":
+                                    images.add(element_name)
+                                elif element_type == "labels":
+                                    labels.add(element_name)
+                                elif element_type == "shapes":
+                                    shapes.add(element_name)
+                                elif element_type == "points":
+                                    points.add(element_name)
+                                elif element_type == "tables":
+                                    tables.add(element_name)
+
+                    # Extract coordinate system information from .zattrs files
+                    if file.endswith(".zattrs"):
+                        try:
+                            with zf.open(file) as f:
+                                attrs = json.load(f)
+
+                                # Check for coordinate transformations
+                                if "coordinateTransformations" in attrs:
+                                    transforms = attrs["coordinateTransformations"]
+                                    if isinstance(transforms, list):
+                                        for transform in transforms:
+                                            if isinstance(transform, dict) and "output" in transform:
+                                                output = transform["output"]
+                                                if isinstance(output, dict) and "name" in output:
+                                                    coordinate_systems.add(output["name"])
+                                                elif isinstance(output, str):
+                                                    coordinate_systems.add(output)
+
+                                # Check for multiscales (images/labels)
+                                if "multiscales" in attrs:
+                                    multiscales = attrs["multiscales"]
+                                    if isinstance(multiscales, list):
+                                        for ms in multiscales:
+                                            if isinstance(ms, dict) and "coordinateTransformations" in ms:
+                                                for ct in ms["coordinateTransformations"]:
+                                                    if isinstance(ct, dict) and "output" in ct:
+                                                        output = ct["output"]
+                                                        if isinstance(output, dict) and "name" in output:
+                                                            coordinate_systems.add(output["name"])
+                                                        elif isinstance(output, str):
+                                                            coordinate_systems.add(output)
+
+                                # Check for spatialdata transform attribute (legacy)
+                                if "transform" in attrs:
+                                    transform_dict = attrs["transform"]
+                                    if isinstance(transform_dict, dict):
+                                        coordinate_systems.update(transform_dict.keys())
+                        except Exception:
+                            pass
+
+                # Set metadata: counts for most elements, but keep tables and
+                # coordinate system names and table shapes for compatibility.
+                dataset.metadata.images_count = len(images)
+                dataset.metadata.labels_count = len(labels)
+                dataset.metadata.shapes_count = len(shapes)
+                dataset.metadata.points_count = len(points)
+
+                # Preserve table names and shapes (as before)
+                dataset.metadata.tables = sorted(tables)
+                table_shapes = {}
+                for table_name in tables:
+                    try:
+                        obs_index_path = f"{root_zarr}/tables/{table_name}/obs/_index/.zarray"
+                        var_index_path = f"{root_zarr}/tables/{table_name}/var/_index/.zarray"
+                        n_obs = None
+                        n_vars = None
+                        if obs_index_path in zf.namelist():
+                            with zf.open(obs_index_path) as f:
+                                obs_array = json.load(f)
+                                n_obs = obs_array.get("shape", [None])[0]
+                        if var_index_path in zf.namelist():
+                            with zf.open(var_index_path) as f:
+                                var_array = json.load(f)
+                                n_vars = var_array.get("shape", [None])[0]
+                        if n_obs is not None and n_vars is not None:
+                            table_shapes[table_name] = (n_obs, n_vars)
+                    except Exception:
+                        pass
+                dataset.metadata.table_shapes = table_shapes
+                dataset.metadata.coordinate_systems = sorted(coordinate_systems)
+                dataset.metadata.spatialdata_version = spatialdata_version
+        except Exception:
+            pass
+
+    def sniff(self, filename: str) -> bool:
+        """
+        Check if the file is a valid SpatialData zarr archive.
+
+        SpatialData files are Zarr archives with specific structure containing
+        a root .zattrs file with spatialdata_attrs metadata and element directories
+        like images/, labels/, shapes/, points/, or tables/.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('subsampled_visium.spatialdata.zip')
+        >>> SpatialData().sniff(fname)
+        True
+        >>> fname = get_test_fname('Images.zarr.zip')
+        >>> SpatialData().sniff(fname)
+        False
+        """
+
+        try:
+            with zipfile.ZipFile(filename) as zf:
+                # First, check if this is a zarr archive at all
+                if not super().sniff(filename):
+                    return False
+
+                # Look for the root .zattrs file with spatialdata_attrs.
+                # This can distinguish spatialdata from other zarr archives.
+                for file in zf.namelist():
+                    # Look for .zattrs file at the root of the zarr store
+                    # The zarr store can be at root or one level deeper
+                    parts = file.split("/")
+                    # Root level: .zattrs or one level deep: <name>.zarr/.zattrs
+                    if file == ".zattrs" or (len(parts) == 2 and parts[0].endswith(".zarr") and parts[1] == ".zattrs"):
+                        try:
+                            with zf.open(file) as f:
+                                attrs = json.load(f)
+                                # Check for SpatialData-specific metadata
+                                if "spatialdata_attrs" in attrs:
+                                    return True
+                        except Exception:
+                            pass
+
+                return False
+        except Exception:
+            # Any exception during parsing means it's not a valid spatialdata file
+            return False
+
+
 @build_sniff_from_prefix
 class Safetensors(Binary):
     """
diff --git a/lib/galaxy/datatypes/test/Images.zarr.zip b/lib/galaxy/datatypes/test/Images.zarr.zip
diff --git a/lib/galaxy/datatypes/test/subsampled_visium.spatialdata.zip b/lib/galaxy/datatypes/test/subsampled_visium.spatialdata.zip
diff --git a/lib/galaxy/tool_util/toolbox/base.py b/lib/galaxy/tool_util/toolbox/base.py
@@ -802,7 +802,7 @@ def get_tool(
 
                 # if we don't have a lineage_map for this tool we need to sort by version,
                 # so that the last tool in rval is the newest tool.
-                rval.sort(key=lambda t: t.version)
+                rval.sort(key=lambda t: t.version_object)
             if rval:
                 if get_all_versions:
                     return rval
diff --git a/test/functional/tools/multiple_versions_sorting_v110.xml b/test/functional/tools/multiple_versions_sorting_v110.xml
@@ -0,0 +1,11 @@
+<tool id="multiple_versions_sorted" name="multiple_versions_sorted" version="1.10">
+    <command><![CDATA[
+        echo "Version 1.10" > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="inttest" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/multiple_versions_sorting_v19.xml b/test/functional/tools/multiple_versions_sorting_v19.xml
@@ -0,0 +1,11 @@
+<tool id="multiple_versions_sorted" name="multiple_versions_sorted" version="1.9">
+    <command><![CDATA[
+        echo "Version 1.9" > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="inttest" value="1" type="integer" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
