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Fix op.translate HCOP URL after EBI FTP drop (#303) #304

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Merged
PauBadiaM merged 2 commits into from
Apr 10, 2026
Merged

Fix op.translate HCOP URL after EBI FTP drop (#303) #304

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f8f1e7c
Fix op.translate HCOP URL after EBI FTP drop (#303)
PauBadiaM Apr 10, 2026
2a54478
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 10, 2026
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,12 @@ and this project adheres to [Semantic Versioning][].
[keep a changelog]: https://keepachangelog.com/en/1.0.0/
[semantic versioning]: https://semver.org/spec/v2.0.0.html

## 2.1.6

### Bugfixes
- Fixed `op.translate` (and every `op.resource` call for non-human organisms) failing with HTTP 404 after HGNC dropped the `genenames/` subtree from the EBI FTP mirror; the HCOP fifteen-column files are now fetched from the new HGNC Google Cloud Storage bucket (#303)
- Removed a redundant `pd.read_csv` call in `op.translate` that re-downloaded the HCOP file a second time and bypassed the retry logic in `_download`

## 2.1.5

### Added
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ requires = [ "hatchling" ]

[project]
name = "decoupler"
version = "2.1.5"
version = "2.1.6"
description = "Python package to perform enrichment analysis from omics data."
readme = "README.md"
license = { file = "LICENSE" }
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7 changes: 4 additions & 3 deletions src/decoupler/op/_translate.py
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Expand Up @@ -130,7 +130,7 @@ def translate(
predictions tool. Briefings in Bioinformatics, 22(6), p.bbab155.

For more information, please visit the HCOP website: https://www.genenames.org/tools/hcop/,
or alternatively check the bulk download FTP links page: https://ftp.ebi.ac.uk/pub/databases/genenames/hcop/
or the HCOP help page for bulk download details: https://www.genenames.org/help/hcop/

Parameters
----------
Expand Down Expand Up @@ -181,10 +181,11 @@ def translate(
elif target_organism == "fruitfly":
target_col = "fruit fly_symbol"
# Process orthologs
url = f"https://ftp.ebi.ac.uk/pub/databases/genenames/hcop/human_{target_organism}_hcop_fifteen_column.txt.gz"
url = (
f"https://storage.googleapis.com/public-download-files/hcop/human_{target_organism}_hcop_fifteen_column.txt.gz"
)
map_df = _download(url, verbose=verbose)
map_df = _bytes_to_pandas(map_df, low_memory=False, compression="gzip", sep="\t")
map_df = pd.read_csv(url, sep="\t", low_memory=False)
map_df["evidence"] = map_df["support"].apply(lambda x: len(x.split(",")))
map_df = map_df[map_df["evidence"] >= min_evidence]
map_df = map_df[["human_symbol", target_col]]
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