From 92129dd26649c4e8be4726fdbdd2a294c7988c64 Mon Sep 17 00:00:00 2001 From: WassimG Date: Tue, 10 Mar 2026 08:13:33 +0000 Subject: [PATCH 1/4] fix weights prosit-irt40PTM --- models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo index bad3bbd..14e3fe2 100755 --- a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo +++ b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/record/17798825/files/model.savedmodel.zip?download=1 -md5:bfdb1b153911388793f11b240455d076 -https://ndownloader.figshare.com/files/61465183 \ No newline at end of file +https://zenodo.org/record/18934365/files/model.savedmodel.zip?download=1 +md5:b6f286a30d45083f63117539e4ad6066 +https://ndownloader.figshare.com/files/62587186 \ No newline at end of file From 1e5bab589269b8fa554643e62132fd336f802666 Mon Sep 17 00:00:00 2001 From: WassimG Date: Tue, 10 Mar 2026 09:09:23 +0000 Subject: [PATCH 2/4] use figshare link first for bigger models --- models/3dmolms/3dmolms_orbitrap_core/1/.zenodo | 4 ++-- models/3dmolms/3dmolms_qtof_core/1/.zenodo | 4 ++-- models/Altimeter/Altimeter_2024_core/1/.zenodo | 4 ++-- models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo | 5 +++-- models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo | 4 ++-- models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo | 4 ++-- models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo | 4 ++-- models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo | 4 ++-- models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo | 4 ++-- 9 files changed, 19 insertions(+), 18 deletions(-) diff --git a/models/3dmolms/3dmolms_orbitrap_core/1/.zenodo b/models/3dmolms/3dmolms_orbitrap_core/1/.zenodo index 2710c32..5accd1a 100644 --- a/models/3dmolms/3dmolms_orbitrap_core/1/.zenodo +++ b/models/3dmolms/3dmolms_orbitrap_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/records/13928958/files/model_orbitrap.zip?download=1 md5:0b3beb45d6ca6e7c82271bf3be9e3eee -https://ndownloader.figshare.com/files/61421536 \ No newline at end of file +https://ndownloader.figshare.com/files/61421536 +https://zenodo.org/records/13928958/files/model_orbitrap.zip?download=1 \ No newline at end of file diff --git a/models/3dmolms/3dmolms_qtof_core/1/.zenodo b/models/3dmolms/3dmolms_qtof_core/1/.zenodo index d280b70..a03aa93 100644 --- a/models/3dmolms/3dmolms_qtof_core/1/.zenodo +++ b/models/3dmolms/3dmolms_qtof_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/records/13928958/files/model_qtof.zip?download=1 md5:8ac637326f9378c6c3d2535183ae439a -https://ndownloader.figshare.com/files/61458817 \ No newline at end of file +https://ndownloader.figshare.com/files/61458817 +https://zenodo.org/records/13928958/files/model_qtof.zip?download=1 \ No newline at end of file diff --git a/models/Altimeter/Altimeter_2024_core/1/.zenodo b/models/Altimeter/Altimeter_2024_core/1/.zenodo index 0c7673d..9a49e07 100644 --- a/models/Altimeter/Altimeter_2024_core/1/.zenodo +++ b/models/Altimeter/Altimeter_2024_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/records/14894501/files/model.pt.zip?download=1 md5:714e2cd897171e42e61cce94bba28f8e -https://ndownloader.figshare.com/files/61459279 \ No newline at end of file +https://ndownloader.figshare.com/files/61459279 +https://zenodo.org/records/14894501/files/model.pt.zip?download=1 \ No newline at end of file diff --git a/models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo b/models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo index 3462488..c7ae7ca 100644 --- a/models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo +++ b/models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo @@ -1,2 +1,3 @@ -https://zenodo.org/records/14896508/files/model.onnx.zip?download=1 -md5:98d179ccb6f46d8eee540044e18203b1 \ No newline at end of file +md5:98d179ccb6f46d8eee540044e18203b1 +https://ndownloader.figshare.com/files/62589634 +https://zenodo.org/records/14896508/files/model.onnx.zip?download=1 \ No newline at end of file diff --git a/models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo b/models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo index ca544d0..c4fdf40 100755 --- a/models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo +++ b/models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/record/17798879/files/model.savedmodel.zip?download=1 md5:0f9196ee4b4cf381de476afccb38c61e -https://ndownloader.figshare.com/files/61465183 \ No newline at end of file +https://ndownloader.figshare.com/files/61465183 +https://zenodo.org/record/17798879/files/model.savedmodel.zip?download=1 \ No newline at end of file diff --git a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo index 14e3fe2..e7e0d11 100755 --- a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo +++ b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/record/18934365/files/model.savedmodel.zip?download=1 md5:b6f286a30d45083f63117539e4ad6066 -https://ndownloader.figshare.com/files/62587186 \ No newline at end of file +https://ndownloader.figshare.com/files/62587186 +https://zenodo.org/record/18934365/files/model.savedmodel.zip?download=1 \ No newline at end of file diff --git a/models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo b/models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo index 9d23ca3..2873ced 100644 --- a/models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo +++ b/models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_B.json.zip?download=1 md5:b3a644da2b026deed832730f8ec53b02 -https://ndownloader.figshare.com/files/61461328 \ No newline at end of file +https://ndownloader.figshare.com/files/61461328 +https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_B.json.zip?download=1 \ No newline at end of file diff --git a/models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo b/models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo index f2c1860..5f5c61f 100644 --- a/models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo +++ b/models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_Y.json.zip?download=1 md5:379bd15fa12cbec627d172a949b26aed -https://ndownloader.figshare.com/files/61461364 \ No newline at end of file +https://ndownloader.figshare.com/files/61461364 +https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_Y.json.zip?download=1 \ No newline at end of file diff --git a/models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo b/models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo index f4068ae..25a8889 100644 --- a/models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo +++ b/models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo @@ -1,3 +1,3 @@ -https://zenodo.org/record/7576711/files/xgboost.json.zip?download=1 md5:8fc9a3a075a90fee10ec22942dceb123 -https://ndownloader.figshare.com/files/61461475 \ No newline at end of file +https://ndownloader.figshare.com/files/61461475 +https://zenodo.org/record/7576711/files/xgboost.json.zip?download=1 \ No newline at end of file From 980daeef47027436bcc2c440ddadb195169aba4f Mon Sep 17 00:00:00 2001 From: WassimG Date: Tue, 10 Mar 2026 09:25:07 +0000 Subject: [PATCH 3/4] fix start script to read checksum first --- models/start.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/models/start.py b/models/start.py index 82022df..cd48258 100755 --- a/models/start.py +++ b/models/start.py @@ -104,6 +104,9 @@ def find_and_download(): for line in content: if line[:3] == "md5": checksum_algorithm, checksum = line.split(":") + for line in content: + if line[:3] == "md5": + continue else: url_zip = line From dc55b7cd7c0fb7c09b7f7860cbb6bc9ef8b5163e Mon Sep 17 00:00:00 2001 From: WassimG Date: Tue, 10 Mar 2026 10:06:35 +0000 Subject: [PATCH 4/4] fix start script and assign correct checksum --- models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo | 6 +++--- models/start.py | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo index e7e0d11..5a4ffc0 100755 --- a/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo +++ b/models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo @@ -1,3 +1,3 @@ -md5:b6f286a30d45083f63117539e4ad6066 -https://ndownloader.figshare.com/files/62587186 -https://zenodo.org/record/18934365/files/model.savedmodel.zip?download=1 \ No newline at end of file +md5:412556912991b4b190b3215b825858e1 +https://ndownloader.figshare.com/files/62592103 +https://zenodo.org/record/18935907/files/model.savedmodel.zip?download=1 \ No newline at end of file diff --git a/models/start.py b/models/start.py index cd48258..cfb1b46 100755 --- a/models/start.py +++ b/models/start.py @@ -98,12 +98,13 @@ def find_and_download(): path_zen = Path(path_zen) target_zip = Path(f"{path_zen.parent}/zenodo.zip") with open(path_zen) as f: - url_zip = f.readline() content = [line.strip() for line in f.readlines()] checksum_matches = False + checksum = '' for line in content: if line[:3] == "md5": checksum_algorithm, checksum = line.split(":") + break for line in content: if line[:3] == "md5": continue