Closed openpaul closed 11 months ago
hello,
not sure if you want pull requests. I found a bug that currently the download_scorefiles cant download into a folder as the checksums are computed for the filename and not the path.
download_scorefiles
As such this command fails:
mkdir anyfolder download_scorefiles -i PGS000922 -o anyfolder/ -b GRCh37
With the output:
pgscatalog_utils.download.ScoringFileChecksum: 2023-08-25 15:50:13 WARNING File PGS000922_hmPOS_GRCh37.txt.gz not found! pgscatalog_utils.download.ScoringFileDownloader: 2023-08-25 15:50:13 WARNING Scoring file PGS000922_hmPOS_GRCh37.txt.gz fails validation pgscatalog_utils.download.ScoringFileDownloader: 2023-08-25 15:50:13 WARNING Remote checksum: 1c59a24ea5ef65a10db2531ba106d5be pgscatalog_utils.download.ScoringFileDownloader: 2023-08-25 15:50:13 WARNING Local checksum: None pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz exists and overwrite is false, skipping download pgscatalog_utils.download.ScoringFileChecksum: 2023-08-25 15:50:13 WARNING File PGS000922_hmPOS_GRCh37.txt.gz not found! pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz.md5 exists and overwrite is false, skipping download pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz exists and overwrite is false, skipping download pgscatalog_utils.download.ScoringFileChecksum: 2023-08-25 15:50:13 WARNING File PGS000922_hmPOS_GRCh37.txt.gz not found! pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz.md5 exists and overwrite is false, skipping download pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz exists and overwrite is false, skipping download pgscatalog_utils.download.ScoringFileChecksum: 2023-08-25 15:50:13 WARNING File PGS000922_hmPOS_GRCh37.txt.gz not found! pgscatalog_utils.download.download_file: 2023-08-25 15:50:13 WARNING /home/paul/software/pgscatalog_utils/anyfolder/PGS000922_hmPOS_GRCh37.txt.gz.md5 exists and overwrite is false, skipping download
This fixes it hopefully as expected.
after the fix the output I see is as expected:
$ download_scorefiles -i PGS000922 -o anyfolder/ -b GRCh37 $ tree anyfolder anyfolder ├── PGS000922_hmPOS_GRCh37.txt.gz └── PGS000922_hmPOS_GRCh37.txt.gz.md5 1 directory, 2 files
Hi @openpaul, we definitely do appreciate PRs (we usually PR into a dev branch before releasing to main)! @nebfield will take a look soon.
Thanks for the fix 🎉
hello,
not sure if you want pull requests. I found a bug that currently the
download_scorefiles
cant download into a folder as the checksums are computed for the filename and not the path.As such this command fails:
With the output:
This fixes it hopefully as expected.
after the fix the output I see is as expected: