Prevent automatic decompression of gzipped files, fix for #710
Henning Timm
Branch: HenningTimm/snakemake-fork:http-gzip-autodecode
Branch: snakemake/snakemake:http-gzip-autodecode
Merged
Merged pull request
Added clarifying comment.
Added clarifying comment.
This is a fix for Issue #710. It derives from the filename if the target file is a gzip file (i.e. has a .gz suffix) and uses the raw file if that is the case.
I also added a test for it, but could not manage to integrate it into the
tests.py
script. It works when I call snakemake in the test folder and when I importtests.py
and run it (from IPython).For the test I reused the landsat dataset found in the
test_remote_gs
folder. Both files (plain text and gzipped version of the file) are downloaded from bitbucket and compared using diff. I hope this is solid for most use cases.The paths still point to my fork and need to be updated.
Commits
Added test for downloading zipped and unzipped files via http and compare them.
Finished test that fails with the current setup.
Consistent naming of files.
Added fix for the HTTP remote provider automagically decompressing .gz files.
Added comment about test setup