Refactor stream_to_file out of galaxy.datatypes.sniff.

Doesn't do anything datatype specific, can be pushed into a lower package. galaxy.files.uris is better I think.

lib/galaxy/datatypes/sniff.py

@@ -26,6 +26,7 @@ from typing_extensions import Protocol
 
 from galaxy import util
 from galaxy.files import ConfiguredFileSources
+from galaxy.files.uris import stream_to_file
 from galaxy.util import (
     compression_utils,
     file_reader,
@@ -81,12 +82,6 @@ def stream_url_to_file(path: str, file_sources: Optional[ConfiguredFileSources]
         return temp_name
 
 
-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)
-    return stream_to_open_named_file(stream, fd, temp_name, **kwd)
-
-
 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"):

lib/galaxy/files/uris.py

@@ -1,6 +1,7 @@
 import ipaddress
 import logging
 import socket
+import tempfile
 from typing import (
     List,
     Union,
@@ -11,10 +12,21 @@ from galaxy.exceptions import (
     AdminRequiredException,
     ConfigDoesNotAllowException,
 )
-from galaxy.util import unicodify
+from galaxy.util import (
+    stream_to_open_named_file,
+    unicodify,
+)
+
 
 log = logging.getLogger(__name__)
 
+
+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)
+    return stream_to_open_named_file(stream, fd, temp_name, **kwd)
+
+
 IpAddressT = Union[ipaddress.IPv4Address, ipaddress.IPv6Address]
 IpNetwrokT = Union[ipaddress.IPv4Network, ipaddress.IPv6Network]
 IpAllowedListEntryT = Union[IpAddressT, IpNetwrokT]

lib/galaxy/tools/actions/upload_common.py

@@ -17,9 +17,8 @@ from sqlalchemy.orm import joinedload
 from webob.compat import cgi_FieldStorage
 
 from galaxy import util
-from galaxy.datatypes.sniff import stream_to_file
 from galaxy.exceptions import RequestParameterInvalidException
-from galaxy.files.uris import validate_non_local
+from galaxy.files.uris import stream_to_file, validate_non_local
 from galaxy.model import (
     FormDefinition,
     LibraryDataset,

lib/galaxy/tools/data_fetch.py

@@ -21,6 +21,7 @@ from galaxy.datatypes.upload_util import (
     handle_upload,
     UploadProblemException,
 )
+from galaxy.files.uris import stream_to_file
 from galaxy.util import (
     in_directory,
     safe_makedirs,
@@ -154,7 +155,7 @@ def _fetch_target(upload_config, target):
             dataset_bunch = Bunch(
                 name=name,
             )
-            primary_file = sniff.stream_to_file(
+            primary_file = stream_to_file(
                 StringIO(datatype.generate_primary_file(dataset_bunch)), prefix="upload_auto_primary_file", dir="."
             )
             extra_files_path = f"{primary_file}_extra"
@@ -436,7 +437,7 @@ def _has_src_to_path(upload_config, item, is_dataset=False) -> Tuple[str, str]:
         if name is None:
             name = url.split("/")[-1]
     elif src == "pasted":
-        path = sniff.stream_to_file(StringIO(item["paste_content"]))
+        path = stream_to_file(StringIO(item["paste_content"]))
         if name is None:
             name = "Pasted Entry"
     else:

lib/galaxy/tools/parameters/grouping.py

@@ -15,14 +15,12 @@ from typing import (
     TYPE_CHECKING,
 )
 
-from galaxy.datatypes import (
-    data,
-    sniff,
-)
+from galaxy.datatypes import data
 from galaxy.exceptions import (
     AdminRequiredException,
     ConfigDoesNotAllowException,
 )
+from galaxy.files.uris import stream_to_file
 from galaxy.util import (
     asbool,
     inflector,
@@ -656,7 +654,7 @@ class UploadDataset(Group):
             dataset.name = self.get_composite_dataset_name(context)
             if dataset.datatype.composite_type == "auto_primary_file":
                 # replace sniff here with just creating an empty file
-                temp_name = sniff.stream_to_file(
+                temp_name = stream_to_file(
                     io.StringIO(d_type.generate_primary_file(dataset)), prefix="upload_auto_primary_file"
                 )
                 dataset.primary_file = temp_name