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| author | AndreaGuarracino | 2021-01-06 14:09:59 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2021-01-06 14:09:59 +0100 |
| commit | 430090a65786b0b9dde9e1319a740f95579d0275 (patch) | |
| tree | 0d59bcb0e4ca0986b42cda966fec60df02ab8686 | |
| parent | e9f73388c810c678a69ce23c925d7914ba99a251 (diff) | |
| download | bh20-seq-resource-430090a65786b0b9dde9e1319a740f95579d0275.tar.gz bh20-seq-resource-430090a65786b0b9dde9e1319a740f95579d0275.tar.lz bh20-seq-resource-430090a65786b0b9dde9e1319a740f95579d0275.zip | |
avoided using resource_stream, now check_format.py works in CWL
| -rw-r--r-- | workflows/yamlfa2ttl/check_format.py | 10 |
1 files changed, 3 insertions, 7 deletions
diff --git a/workflows/yamlfa2ttl/check_format.py b/workflows/yamlfa2ttl/check_format.py index a1b1f14..4472b18 100644 --- a/workflows/yamlfa2ttl/check_format.py +++ b/workflows/yamlfa2ttl/check_format.py @@ -1,22 +1,18 @@ import gzip import tempfile -import pkg_resources import magic import io - import sys path_fasta = sys.argv[1] format_to_check = sys.argv[2] path_valid_formats = sys.argv[3] - -# ../../bh20sequploader/validation/formats - -schema_resource = pkg_resources.resource_stream(__name__, path_valid_formats) with tempfile.NamedTemporaryFile() as tmp: - tmp.write(schema_resource.read()) + with open(path_valid_formats, 'rb') as f: + tmp.write(f.read()) tmp.flush() + check_format = magic.Magic(magic_file=tmp.name, uncompress=False, mime=True) with open(path_fasta, "rb") as f: |