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Migrate obfs datatype from basic to auto_primary_file composite type #23366

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Merged
mvdbeek merged 2 commits into from
Sep 1, 2026
Merged

Migrate obfs datatype from basic to auto_primary_file composite type #23366

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61d305d
Migrate obfs datatype from basic to auto_primary_file composite type
bgruening Aug 25, 2026
c31fb9b
Fix ruff UP032 in OBFS.generate_primary_file
jmchilton Aug 25, 2026
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34 changes: 32 additions & 2 deletions lib/galaxy/datatypes/molecules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,10 @@
Text,
)
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.protocols import (
DatasetProtocol,
HasExtraFilesAndMetadata,
)
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
FilePrefix,
Expand Down Expand Up @@ -628,7 +631,7 @@ class OBFS(Binary):
"""OpenBabel Fastsearch format (fs)."""

file_ext = "obfs"
composite_type = "basic"
composite_type = "auto_primary_file"

MetadataElement(
name="base_name",
Expand All @@ -651,6 +654,33 @@ def __init__(self, **kwd):
self.add_composite_file("molecule.mol2", optional=True, is_binary=False, description="Molecule File")
self.add_composite_file("molecule.cml", optional=True, is_binary=False, description="Molecule File")

def generate_primary_file(self, dataset: HasExtraFilesAndMetadata) -> str:
rval = ["<html><head><title>OpenBabel Fastsearch Index</title></head><p/>"]
rval.append("<div>This composite dataset is composed of the following files:<p/><ul>")
for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
description = composite_file.get("description")
if description:
rval.append(
f'<li><a href="{composite_name}" type="application/binary">{composite_name} ({description})</a></li>'
)
else:
rval.append(f'<li><a href="{composite_name}" type="application/binary">{composite_name}</a></li>')
rval.append("</ul></div></html>")
return "\n".join(rval)

def regenerate_primary_file(self, dataset: DatasetProtocol) -> None:
efp = dataset.extra_files_path
flist = os.listdir(efp)
rval = [
f"<html><head><title>Files for Composite Dataset {dataset.name}</title></head><body><p/>Composite {dataset.name} contains:<p/><ul>"
]
for fname in flist:
sfname = os.path.split(fname)[-1]
rval.append(f'<li><a href="{sfname}">{sfname}</a></li>')
rval.append("</ul></body></html>")
with open(dataset.get_file_name(), "w") as f:
f.write("\n".join(rval))

def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
"""Set the peek and blurb text."""
if not dataset.dataset.purged:
Expand Down
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