From 34286093ec2324ac3573a0bfa311349e87abe143 Mon Sep 17 00:00:00 2001 From: Kevin Velghe Date: Thu, 8 Aug 2024 14:06:13 +0200 Subject: [PATCH 1/2] download models using https There is a checksum check, and server-side there is a redirect to https, but that also means there is no point in not using https right away. --- ms2pip/_utils/xgb_models.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ms2pip/_utils/xgb_models.py b/ms2pip/_utils/xgb_models.py index c1e7233..165b92b 100644 --- a/ms2pip/_utils/xgb_models.py +++ b/ms2pip/_utils/xgb_models.py @@ -97,7 +97,7 @@ def _download_model(model, model_hash, model_dir): logger.info(f"Downloading {model} to {filename}...") urllib.request.urlretrieve( - os.path.join("http://genesis.ugent.be/uvpublicdata/ms2pip/", model), filename + os.path.join("https://genesis.ugent.be/uvpublicdata/ms2pip/", model), filename ) if not _check_model_integrity(filename, model_hash): raise InvalidXGBoostModelError() From 5d46707c32a860b9cb390c79944aac6fc86b2b74 Mon Sep 17 00:00:00 2001 From: Kevin Velghe Date: Fri, 20 Sep 2024 18:48:49 +0200 Subject: [PATCH 2/2] download models from zenodo --- ms2pip/_utils/xgb_models.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/ms2pip/_utils/xgb_models.py b/ms2pip/_utils/xgb_models.py index 165b92b..a880433 100644 --- a/ms2pip/_utils/xgb_models.py +++ b/ms2pip/_utils/xgb_models.py @@ -53,7 +53,7 @@ def get_predictions_xgb(features, num_ions, model_params, model_dir, processes=1 for ion_type, xgb_model in xgboost_models.items(): # Get predictions from XGBoost model preds = xgb_model.predict(features) - preds = preds.clip(min=np.log2(0.001)) # Clip negative intensities + preds = preds.clip(min=np.log2(0.001)) # Clip negative intensities xgb_model.__del__() # Reshape into arrays for each peptide @@ -96,9 +96,7 @@ def _download_model(model, model_hash, model_dir): filename = os.path.join(model_dir, model) logger.info(f"Downloading {model} to {filename}...") - urllib.request.urlretrieve( - os.path.join("https://genesis.ugent.be/uvpublicdata/ms2pip/", model), filename - ) + urllib.request.urlretrieve(f"https://zenodo.org/records/13270668/files/{model}", filename) if not _check_model_integrity(filename, model_hash): raise InvalidXGBoostModelError()