Merge branch '56-pass-oidc-token-to-object-store' into 'dev' (407ff0b4) · Commits · NDIP / Galaxy

lib/galaxy/datatypes/binary.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -543,9 +543,9 @@ class BamNative(CompressedArchive, _BamOrSam):
		except Exception:
		return f"Binary bam alignments file ({nice_size(dataset.get_size())})"

		def to_archive(self, dataset, name=""):
		def to_archive(self, dataset, name="", trans=None):
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)

		rel_paths = []
		file_paths = []
		@@ -631,13 +631,13 @@ class BamNative(CompressedArchive, _BamOrSam):
		preview = util.string_as_bool(preview)
		if offset is not None:
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)
		return self.get_chunk(trans, dataset, offset, ck_size), headers
		elif to_ext or not preview:
		return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)
		else:
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)

		column_names = dataset.metadata.column_names
		if not column_names:
		@@ -2007,7 +2007,7 @@ class H5MLM(H5):
		return self._serve_raw(dataset, to_ext, headers, **kwd)

		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)

		rval = {}
		try:

lib/galaxy/datatypes/blast.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -211,7 +211,7 @@ class _BlastDb(Data):
		)

		if data.dataset.object_store:
		data.dataset.object_store.update_cache(data.dataset)
		data.dataset.object_store.update_cache(data.dataset, trans=trans)

		if self.file_ext == "blastdbn":
		title = "This is a nucleotide BLAST database"

lib/galaxy/datatypes/data.py

+8 −6

Original line number	Diff line number	Diff line
		@@ -429,7 +429,7 @@ class Data(metaclass=DataMeta):
		headers["Content-Disposition"] = f'attachment; filename="{filename}"'
		return open(dataset.file_name, mode="rb"), headers

		def to_archive(self, dataset, name=""):
		def to_archive(self, dataset, name="", trans=None):
		"""
		Collect archive paths and file handles that need to be exported when archiving `dataset`.

		@@ -443,7 +443,7 @@ class Data(metaclass=DataMeta):
		main_file = f"{name}.html"
		rel_paths.append(main_file)
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)

		file_paths.append(dataset.file_name)
		for fpath, rpath in self.__archive_extra_files_path(dataset.extra_files_path):
		@@ -451,7 +451,7 @@ class Data(metaclass=DataMeta):
		file_paths.append(fpath)
		else:
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)
		rel_paths.append(f"{name or dataset.file_name}.{dataset.extension}")
		file_paths.append(dataset.file_name)
		return zip(file_paths, rel_paths)
		@@ -525,7 +525,8 @@ class Data(metaclass=DataMeta):
		# For files in extra_files_path
		extra_dir = data.dataset.extra_files_path_name
		if data.dataset.object_store:
		data.dataset.object_store.update_cache(data.dataset, extra_dir=extra_dir, alt_name=filename)
		data.dataset.object_store.update_cache(data.dataset, extra_dir=extra_dir, alt_name=filename,
		trans=trans)
		file_path = trans.app.object_store.get_filename(data.dataset, extra_dir=extra_dir, alt_name=filename)
		if os.path.exists(file_path):
		if os.path.isdir(file_path):
		@@ -574,7 +575,7 @@ class Data(metaclass=DataMeta):
		return _serve_large_file_warning(headers, data, trans, file_size)

		if data.dataset.object_store:
		data.dataset.object_store.update_cache(data.dataset)
		data.dataset.object_store.update_cache(data.dataset, trans=trans)

		if not os.path.exists(data.file_name):
		raise ObjectNotFound(f"File Not Found ({data.file_name}).")
		@@ -585,7 +586,8 @@ class Data(metaclass=DataMeta):
		else: # displaying
		trans.log_event(f"Display dataset id: {str(data.id)}")
		max_peek_size = _get_peak_size(data)
		if _is_binary_file(data) and preview: # preview file which format is unknown (to Galaxy), we still try to display this as text
		if _is_binary_file(
		data) and preview: # preview file which format is unknown (to Galaxy), we still try to display this as text
		return self._serve_binary_file_contents_as_text(trans, data, headers, file_size, max_peek_size)
		else: # text/html, or image, or display was called without preview flag
		return self._serve_file_contents(trans, data, headers, preview, file_size, max_peek_size)

lib/galaxy/datatypes/isa.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -262,7 +262,7 @@ class _Isa(data.Data):
		return super().display_data(trans, dataset, preview, filename, to_ext, **kwd)

		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)

		# prepare the preview of the ISA dataset
		investigation = self._get_investigation(dataset)

lib/galaxy/datatypes/sequence.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -749,7 +749,7 @@ class BaseFastq(Sequence):

		def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
		if dataset.dataset.object_store:
		dataset.dataset.object_store.update_cache(dataset.dataset)
		dataset.dataset.object_store.update_cache(dataset.dataset, trans=trans)
		headers = kwd.get("headers", {})
		if preview:
		with compression_utils.get_fileobj(dataset.file_name) as fh: