galaxy-data 26.0.1.dev0__tar.gz → 26.0.2__tar.gz

galaxy_data-26.0.1.dev0/galaxy_data.egg-info/PKG-INFO → galaxy_data-26.0.2/HISTORY.rst

@@ -1,76 +1,88 @@
-Metadata-Version: 2.4
-Name: galaxy-data
-Version: 26.0.1.dev0
-Summary: Galaxy datatype framework and datatypes
-Home-page: https://github.com/galaxyproject/galaxy
-Author: Galaxy Project and Community
-Author-email: galaxy-committers@lists.galaxyproject.org
-License: MIT
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
-License-File: LICENSE
-Requires-Dist: galaxy-files
-Requires-Dist: galaxy-objectstore
-Requires-Dist: galaxy-schema
-Requires-Dist: galaxy-tool-util
-Requires-Dist: galaxy-util[image-util,template]
-Requires-Dist: alembic
-Requires-Dist: bdbag>=1.6.3
-Requires-Dist: bx-python
-Requires-Dist: dnspython
-Requires-Dist: galaxy-sequence-utils
-Requires-Dist: h5grove>=1.2.1
-Requires-Dist: h5py
-Requires-Dist: ijson
-Requires-Dist: isa-rwval>=0.10.11
-Requires-Dist: isal>=1.7.0
-Requires-Dist: MarkupSafe
-Requires-Dist: msal
-Requires-Dist: mrcfile
-Requires-Dist: numpy
-Requires-Dist: openpyxl>=3.1.5
-Requires-Dist: parsley
-Requires-Dist: pycryptodome
-Requires-Dist: pydantic[email]>=2.7.4
-Requires-Dist: pydicom
-Requires-Dist: pylibmagic
-Requires-Dist: pypng
-Requires-Dist: python-magic
-Requires-Dist: pysam>=0.21
-Requires-Dist: rocrate
-Requires-Dist: social-auth-core>=4.5.0
-Requires-Dist: SQLAlchemy!=2.0.41,<2.1,>=2.0.37
-Requires-Dist: tifffile
-Requires-Dist: typing-extensions
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: roc-validator; extra == "test"
-Dynamic: license-file
-
-
-.. image:: https://badge.fury.io/py/galaxy-data.svg
-   :target: https://pypi.org/project/galaxy-data/
-
-
-Overview
---------
-
-The Galaxy_ models, datatype framework, and datatype implementations.
-
-* Code: https://github.com/galaxyproject/galaxy
-
-.. _Galaxy: http://galaxyproject.org/
-
 History
 -------
 
 .. to_doc
 
------------
-26.0.1.dev0
------------
+-------------------
+26.0.2 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Raise InvalidFileFormatError on short rows in UCSC display by `@guerler <https://github.com/guerler>`_ in `#22524 <https://github.com/galaxyproject/galaxy/pull/22524>`_
+* Fix tag creation self-deadlock under SQLite by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22846 <https://github.com/galaxyproject/galaxy/pull/22846>`_
+* Fix fasta preview rendering for sequences larger than 100 KB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23163 <https://github.com/galaxyproject/galaxy/pull/23163>`_
+* Fix invalid \`\`LN:0\`\` field in \`\`@SQ\`\` header lines in \`\`1.bam\`\` test file by `@nsoranzo <https://github.com/nsoranzo>`_ in `#23474 <https://github.com/galaxyproject/galaxy/pull/23474>`_
+* Don't let extended metadata import set the live job's terminal state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23529 <https://github.com/galaxyproject/galaxy/pull/23529>`_
+* Complete subworkflows before their parent invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23581 <https://github.com/galaxyproject/galaxy/pull/23581>`_
+* Bug fix - Galaxy would delete composite files it shouldn't during data_fetch.py sometimes. by `@jmchilton <https://github.com/jmchilton>`_ in `#23733 <https://github.com/galaxyproject/galaxy/pull/23733>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Bind OIDC account confirmation to the authenticated browser flow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24084 <https://github.com/galaxyproject/galaxy/pull/24084>`_
+* Fix workflow editor map-over onto \`:paired_or_unpaired\` inputs the server rejects by `@jmchilton <https://github.com/jmchilton>`_ in `#24227 <https://github.com/galaxyproject/galaxy/pull/24227>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Fix supports_returning() probe always returning False by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24252 <https://github.com/galaxyproject/galaxy/pull/24252>`_
+* Ignore stale user and history object store preferences by `@davelopez <https://github.com/davelopez>`_ in `#24280 <https://github.com/galaxyproject/galaxy/pull/24280>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Fix ok_to_edit_metadata checking HDA job associations for LDDAs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24306 <https://github.com/galaxyproject/galaxy/pull/24306>`_
+* Lock HDCAs with FOR NO KEY UPDATE when touching update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24404 <https://github.com/galaxyproject/galaxy/pull/24404>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+25.1.3 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
+* Fix \`\`preferred_object_store_id\`\` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
+* Sequence datatypes: only read first character per line for setting metadata by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#22276 <https://github.com/galaxyproject/galaxy/pull/22276>`_
+* Fix timestamp parsing in job import/export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22372 <https://github.com/galaxyproject/galaxy/pull/22372>`_
+* Use correct timezone to compare step scheduling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22446 <https://github.com/galaxyproject/galaxy/pull/22446>`_
+* Sniff spatialdata archives whose directory does not end in .zarr by `@nilchia <https://github.com/nilchia>`_ in `#22802 <https://github.com/galaxyproject/galaxy/pull/22802>`_
+* Don't let extended metadata import set the live job's terminal state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23529 <https://github.com/galaxyproject/galaxy/pull/23529>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Bind OIDC account confirmation to the authenticated browser flow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24084 <https://github.com/galaxyproject/galaxy/pull/24084>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Ignore stale user and history object store preferences by `@davelopez <https://github.com/davelopez>`_ in `#24280 <https://github.com/galaxyproject/galaxy/pull/24280>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Fix ok_to_edit_metadata checking HDA job associations for LDDAs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24306 <https://github.com/galaxyproject/galaxy/pull/24306>`_
+* Lock HDCAs with FOR NO KEY UPDATE when touching update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24404 <https://github.com/galaxyproject/galaxy/pull/24404>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Respect workflow object store preference for mapped step outputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22409 <https://github.com/galaxyproject/galaxy/pull/22409>`_
+* Avoid premature commit when copying MetadataFile by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22422 <https://github.com/galaxyproject/galaxy/pull/22422>`_
+* Fix testing, publishing and dependencies of packages by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22445 <https://github.com/galaxyproject/galaxy/pull/22445>`_
+* Fix \`get_structure\` when it is passed a DCE with nested elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22453 <https://github.com/galaxyproject/galaxy/pull/22453>`_
+* Enforce file source access during dataset materialization by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22486 <https://github.com/galaxyproject/galaxy/pull/22486>`_
+* Fix sample sheet upload without sample-sheet-specific columns  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22488 <https://github.com/galaxyproject/galaxy/pull/22488>`_
+* Truncate dataset name in export arcname to avoid OSError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22518 <https://github.com/galaxyproject/galaxy/pull/22518>`_
+* Catch end of file error when reading corrupted tabular dataset by `@guerler <https://github.com/guerler>`_ in `#22523 <https://github.com/galaxyproject/galaxy/pull/22523>`_
+* Fix data manager URL for managers with '+' version suffix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22525 <https://github.com/galaxyproject/galaxy/pull/22525>`_
+* update the binary.py for spatialdata so it also works if the file has… by `@nilchia <https://github.com/nilchia>`_ in `#22802 <https://github.com/galaxyproject/galaxy/pull/22802>`_
+
+============
+Enhancements
+============
 
+* Replace per-term joins in workflow search with EXISTS subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22548 <https://github.com/galaxyproject/galaxy/pull/22548>`_
+* add TEI XML datatype by `@bgruening <https://github.com/bgruening>`_ in `#22718 <https://github.com/galaxyproject/galaxy/pull/22718>`_
 
 -------------------
 26.0.0 (2026-04-08)

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/PKG-INFO

@@ -1,11 +1,26 @@
 Metadata-Version: 2.4
 Name: galaxy-data
-Version: 26.0.1.dev0
+Version: 26.0.2
 Summary: Galaxy datatype framework and datatypes
 Home-page: https://github.com/galaxyproject/galaxy
 Author: Galaxy Project and Community
 Author-email: galaxy-committers@lists.galaxyproject.org
 License: MIT
+Keywords: Galaxy
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Testing
 Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -37,12 +52,13 @@ Requires-Dist: pylibmagic
 Requires-Dist: pypng
 Requires-Dist: python-magic
 Requires-Dist: pysam>=0.21
-Requires-Dist: rocrate
-Requires-Dist: social-auth-core>=4.5.0
+Requires-Dist: rocrate<0.15.0
+Requires-Dist: social-auth-core<6,>=4.5.0
 Requires-Dist: SQLAlchemy!=2.0.41,<2.1,>=2.0.37
 Requires-Dist: tifffile
 Requires-Dist: typing-extensions
 Provides-Extra: test
+Requires-Dist: galaxy-config; extra == "test"
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: roc-validator; extra == "test"
 Dynamic: license-file
@@ -66,11 +82,86 @@ History
 
 .. to_doc
 
------------
-26.0.1.dev0
------------
+-------------------
+26.0.2 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Raise InvalidFileFormatError on short rows in UCSC display by `@guerler <https://github.com/guerler>`_ in `#22524 <https://github.com/galaxyproject/galaxy/pull/22524>`_
+* Fix tag creation self-deadlock under SQLite by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22846 <https://github.com/galaxyproject/galaxy/pull/22846>`_
+* Fix fasta preview rendering for sequences larger than 100 KB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23163 <https://github.com/galaxyproject/galaxy/pull/23163>`_
+* Fix invalid \`\`LN:0\`\` field in \`\`@SQ\`\` header lines in \`\`1.bam\`\` test file by `@nsoranzo <https://github.com/nsoranzo>`_ in `#23474 <https://github.com/galaxyproject/galaxy/pull/23474>`_
+* Don't let extended metadata import set the live job's terminal state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23529 <https://github.com/galaxyproject/galaxy/pull/23529>`_
+* Complete subworkflows before their parent invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23581 <https://github.com/galaxyproject/galaxy/pull/23581>`_
+* Bug fix - Galaxy would delete composite files it shouldn't during data_fetch.py sometimes. by `@jmchilton <https://github.com/jmchilton>`_ in `#23733 <https://github.com/galaxyproject/galaxy/pull/23733>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Bind OIDC account confirmation to the authenticated browser flow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24084 <https://github.com/galaxyproject/galaxy/pull/24084>`_
+* Fix workflow editor map-over onto \`:paired_or_unpaired\` inputs the server rejects by `@jmchilton <https://github.com/jmchilton>`_ in `#24227 <https://github.com/galaxyproject/galaxy/pull/24227>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Fix supports_returning() probe always returning False by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24252 <https://github.com/galaxyproject/galaxy/pull/24252>`_
+* Ignore stale user and history object store preferences by `@davelopez <https://github.com/davelopez>`_ in `#24280 <https://github.com/galaxyproject/galaxy/pull/24280>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Fix ok_to_edit_metadata checking HDA job associations for LDDAs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24306 <https://github.com/galaxyproject/galaxy/pull/24306>`_
+* Lock HDCAs with FOR NO KEY UPDATE when touching update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24404 <https://github.com/galaxyproject/galaxy/pull/24404>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+25.1.3 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
+* Fix \`\`preferred_object_store_id\`\` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
+* Sequence datatypes: only read first character per line for setting metadata by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#22276 <https://github.com/galaxyproject/galaxy/pull/22276>`_
+* Fix timestamp parsing in job import/export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22372 <https://github.com/galaxyproject/galaxy/pull/22372>`_
+* Use correct timezone to compare step scheduling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22446 <https://github.com/galaxyproject/galaxy/pull/22446>`_
+* Sniff spatialdata archives whose directory does not end in .zarr by `@nilchia <https://github.com/nilchia>`_ in `#22802 <https://github.com/galaxyproject/galaxy/pull/22802>`_
+* Don't let extended metadata import set the live job's terminal state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23529 <https://github.com/galaxyproject/galaxy/pull/23529>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Bind OIDC account confirmation to the authenticated browser flow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24084 <https://github.com/galaxyproject/galaxy/pull/24084>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Ignore stale user and history object store preferences by `@davelopez <https://github.com/davelopez>`_ in `#24280 <https://github.com/galaxyproject/galaxy/pull/24280>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Fix ok_to_edit_metadata checking HDA job associations for LDDAs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24306 <https://github.com/galaxyproject/galaxy/pull/24306>`_
+* Lock HDCAs with FOR NO KEY UPDATE when touching update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24404 <https://github.com/galaxyproject/galaxy/pull/24404>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Respect workflow object store preference for mapped step outputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22409 <https://github.com/galaxyproject/galaxy/pull/22409>`_
+* Avoid premature commit when copying MetadataFile by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22422 <https://github.com/galaxyproject/galaxy/pull/22422>`_
+* Fix testing, publishing and dependencies of packages by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22445 <https://github.com/galaxyproject/galaxy/pull/22445>`_
+* Fix \`get_structure\` when it is passed a DCE with nested elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22453 <https://github.com/galaxyproject/galaxy/pull/22453>`_
+* Enforce file source access during dataset materialization by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22486 <https://github.com/galaxyproject/galaxy/pull/22486>`_
+* Fix sample sheet upload without sample-sheet-specific columns  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22488 <https://github.com/galaxyproject/galaxy/pull/22488>`_
+* Truncate dataset name in export arcname to avoid OSError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22518 <https://github.com/galaxyproject/galaxy/pull/22518>`_
+* Catch end of file error when reading corrupted tabular dataset by `@guerler <https://github.com/guerler>`_ in `#22523 <https://github.com/galaxyproject/galaxy/pull/22523>`_
+* Fix data manager URL for managers with '+' version suffix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22525 <https://github.com/galaxyproject/galaxy/pull/22525>`_
+* update the binary.py for spatialdata so it also works if the file has… by `@nilchia <https://github.com/nilchia>`_ in `#22802 <https://github.com/galaxyproject/galaxy/pull/22802>`_
+
+============
+Enhancements
+============
 
+* Replace per-term joins in workflow search with EXISTS subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22548 <https://github.com/galaxyproject/galaxy/pull/22548>`_
+* add TEI XML datatype by `@bgruening <https://github.com/bgruening>`_ in `#22718 <https://github.com/galaxyproject/galaxy/pull/22718>`_
 
 -------------------
 26.0.0 (2026-04-08)

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/binary.py

@@ -4894,13 +4894,16 @@ class SpatialData(CompressedZarrZipArchive):
 
         try:
             with zipfile.ZipFile(filename) as zf:
-                # Find root zarr directory and detect version
+                # Find root zarr directory and detect version (at any nesting level)
                 root_zarr = is_v3 = None
                 for file in zf.namelist():
-                    if file.endswith(".zarr/zarr.json"):
+                    # Look for zarr.json or .zattrs in any directory
+                    if file.endswith("/zarr.json"):
+                        # Format: <path>/zarr.json (v3)
                         root_zarr, is_v3 = file.rsplit("/", 1)[0], True
                         break
-                    elif file.endswith(".zarr/.zattrs"):
+                    elif file.endswith("/.zattrs"):
+                        # Format: <path>/.zattrs (v2)
                         root_zarr, is_v3 = file.rsplit("/", 1)[0], False
                         break
                 if not root_zarr:
@@ -4992,6 +4995,15 @@ class SpatialData(CompressedZarrZipArchive):
         >>> fname = get_test_fname('Images.zarr.zip')
         >>> SpatialData().sniff(fname)
         False
+        >>> fname = get_test_fname('subsampled_visium_no_extension.spatialdata.zip')
+        >>> SpatialData().sniff(fname)
+        True
+        >>> fname = get_test_fname('subsampled_visium_v3_no_extension.spatialdata.zip')
+        >>> SpatialData().sniff(fname)
+        True
+        >>> fname = get_test_fname('subsampled_visium_v3_no_extension_3lvl_nested.spatialdata.zip')
+        >>> SpatialData().sniff(fname)
+        True
         """
         try:
             with zipfile.ZipFile(filename) as zf:
@@ -5000,7 +5012,7 @@ class SpatialData(CompressedZarrZipArchive):
 
                 # Check root metadata files (.zattrs or zarr.json) for spatialdata_attrs
                 for file in zf.namelist():
-                    if len(file.split("/")) <= 2 and file.endswith((".zattrs", "zarr.json")):
+                    if file.endswith(("/.zattrs", "/zarr.json")):
                         try:
                             with zf.open(file) as f:
                                 meta = json.load(f)

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/interval.py

@@ -43,6 +43,7 @@ from galaxy.datatypes.util.gff_util import (
     parse_gff3_attributes,
     parse_gff_attributes,
 )
+from galaxy.exceptions import InvalidFileFormatError
 from galaxy.util import compression_utils
 from galaxy.util.compression_utils import FileObjType
 from . import (
@@ -274,27 +275,30 @@ class Interval(Tabular):
                 dataset.metadata.nameCol or 0,
             )
             c, s, e, t, n = int(c) - 1, int(s) - 1, int(e) - 1, int(t) - 1, int(n) - 1
-            if t >= 0:  # strand column (should) exists
-                for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
-                    strand = "+"
-                    name = f"region_{i}"
-                    if n >= 0 and n < len(elems):
-                        name = elems[n]
-                    if t < len(elems):
-                        strand = elems[t]
-                    tmp = [elems[c], elems[s], elems[e], name, "0", strand]
-                    fh.write("{}\n".format("\t".join(tmp)))
-            elif n >= 0:  # name column (should) exists
-                for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
-                    name = f"region_{i}"
-                    if n >= 0 and n < len(elems):
-                        name = elems[n]
-                    tmp = [elems[c], elems[s], elems[e], name]
-                    fh.write("{}\n".format("\t".join(tmp)))
-            else:
-                for elems in compression_utils.file_iter(dataset.get_file_name()):
-                    tmp = [elems[c], elems[s], elems[e]]
-                    fh.write("{}\n".format("\t".join(tmp)))
+            try:
+                if t >= 0:  # strand column (should) exists
+                    for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
+                        strand = "+"
+                        name = f"region_{i}"
+                        if n >= 0 and n < len(elems):
+                            name = elems[n]
+                        if t < len(elems):
+                            strand = elems[t]
+                        tmp = [elems[c], elems[s], elems[e], name, "0", strand]
+                        fh.write("{}\n".format("\t".join(tmp)))
+                elif n >= 0:  # name column (should) exists
+                    for i, elems in enumerate(compression_utils.file_iter(dataset.get_file_name())):
+                        name = f"region_{i}"
+                        if n >= 0 and n < len(elems):
+                            name = elems[n]
+                        tmp = [elems[c], elems[s], elems[e], name]
+                        fh.write("{}\n".format("\t".join(tmp)))
+                else:
+                    for elems in compression_utils.file_iter(dataset.get_file_name()):
+                        tmp = [elems[c], elems[s], elems[e]]
+                        fh.write("{}\n".format("\t".join(tmp)))
+            except IndexError:
+                raise InvalidFileFormatError("Dataset row has fewer columns than its metadata declares.")
             return compression_utils.get_fileobj(fh.name, mode="rb")
 
     def display_peek(self, dataset: DatasetProtocol) -> str:

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/sequence.py

@@ -336,12 +336,13 @@ class Sequence(data.Text):
                     chunk = fh.read(max_peek_size + 1)
                 except UnicodeDecodeError:
                     raise InvalidFileFormatError("Dataset appears to contain binary data, cannot display.")
+                # Always serve as text/plain so the browser preserves whitespace/newlines
+                # and does not interpret the content as HTML.
+                self._clean_and_set_mime_type(trans, "text/plain", headers)
                 if len(chunk) <= max_peek_size:
-                    mime = "text/plain"
-                    self._clean_and_set_mime_type(trans, mime, headers)
-                    return chunk[:-1], headers
-                headers["x-content-truncated"] = max_peek_size
-                return util.unicodify(chunk[:-1]), headers
+                    return chunk, headers
+                headers["x-content-truncated"] = str(max_peek_size)
+                return util.unicodify(chunk[:max_peek_size]), headers
         else:
             return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)
 

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/sniff.py

@@ -38,7 +38,11 @@ from galaxy.util.checkers import (
     COMPRESSION_CHECK_FUNCTIONS,
     is_tar,
 )
-from galaxy.util.path import StrPath
+from galaxy.util.path import (
+    safe_contains,
+    safe_relpath,
+    StrPath,
+)
 
 try:
     import pylibmagic  # noqa: F401  # isort:skip
@@ -80,15 +84,31 @@ def sniff_with_cls(cls, fname):
 stream_url_to_file = partial(files_stream_url_to_file, prefix="gx_url_paste")
 
 
-def handle_composite_file(datatype, src_path, extra_files, name, is_binary, tmp_dir, tmp_prefix, upload_opts):
-    if not is_binary:
-        if upload_opts.get("space_to_tab"):
-            convert_newlines_sep2tabs(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix)
-        else:
-            convert_newlines(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix)
-
+def handle_composite_file(
+    datatype, src_path, extra_files, name, is_binary, tmp_dir, tmp_prefix, upload_opts, purge_source=True
+):
+    # ``name`` can be user-controlled (e.g. the ``files_N|NAME`` of an ad-hoc
+    # ``force_composite`` upload), so it must never resolve outside of the
+    # dataset's extra files directory.
     file_output_path = os.path.join(extra_files, name)
-    shutil.move(src_path, file_output_path)
+    if not name or not safe_relpath(name) or not safe_contains(os.path.realpath(extra_files), file_output_path):
+        raise ValueError(
+            f"Invalid composite file name '{name}'; must be a relative path inside the dataset's extra files directory"
+        )
+
+    converted_path = None
+    if not is_binary:
+        convert = convert_newlines_sep2tabs if upload_opts.get("space_to_tab") else convert_newlines
+        # ``purge_source`` is false for a source Galaxy does not own, which must neither be
+        # rewritten in place nor moved out of the caller's directory.
+        converted_path = convert(src_path, in_place=purge_source, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix).converted_path
+
+    if converted_path is not None:
+        shutil.move(converted_path, file_output_path)
+    elif purge_source:
+        shutil.move(src_path, file_output_path)
+    else:
+        shutil.copy(src_path, file_output_path)
 
     # groom the dataset file content if required by the corresponding datatype definition
     if datatype and datatype.dataset_content_needs_grooming(file_output_path):

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/tabular.py

@@ -165,6 +165,10 @@ class TabularData(Text):
                         cursor = f.read(1)
             except UnicodeDecodeError:
                 raise InvalidFileFormatError("Dataset appears to contain binary data, cannot display.")
+            except EOFError:
+                raise InvalidFileFormatError(
+                    "Dataset appears to be a truncated or corrupt compressed file, cannot display."
+                )
             last_read = f.tell()
         return ck_data, last_read
 

{galaxy_data-26.0.1.dev0 → galaxy_data-26.0.2}/galaxy/datatypes/xml.py

@@ -24,6 +24,10 @@ log = logging.getLogger(__name__)
 
 OWL_MARKER = re.compile(r"\<owl:")
 SBML_MARKER = re.compile(r"\<sbml")
+TEI_MARKER = re.compile(
+    r"^\s*(?:<\?xml[^>]*>\s*)?(?:<!--.*?-->\s*)*<([A-Za-z_][\w.-]*:)?TEI(?:\s|>|/)",
+    re.DOTALL,
+)
 
 
 @dataproviders.decorators.has_dataproviders
@@ -113,6 +117,27 @@ class CisML(GenericXml):
             dataset.blurb = "file purged from disk"
 
 
+class Tei(GenericXml):
+    """Text Encoding Initiative XML data."""
+
+    file_ext = "tei"
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.get_file_name())
+            dataset.blurb = "TEI XML data"
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """
+        Determines whether the file is TEI XML.
+        """
+        return bool(file_prefix.search(TEI_MARKER))
+
+
 class Dzi(GenericXml):
     """
     Deep zoom image format, see