-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added cli tests for 'convert' command.
- Loading branch information
Showing
1 changed file
with
98 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| import os | ||
| import shutil | ||
| import pytest | ||
|
|
||
| from nmrstarlib import nmrstarlib | ||
|
|
||
|
|
||
| def teardown_module(module): | ||
| if os.path.exists("tests/example_data/NMRSTAR3/tmp"): | ||
| shutil.rmtree("tests/example_data/NMRSTAR3/tmp") | ||
| if os.path.exists("tests/example_data/NMRSTAR2/tmp"): | ||
| shutil.rmtree("tests/example_data/NMRSTAR2/tmp") | ||
|
|
||
| @pytest.mark.parametrize("from_path,to_path,from_format,to_format", [ | ||
| # one-to-one file conversions | ||
| ("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR3/tmp/json/bmr18569.json", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/bmr18569.str", "tests/example_data/NMRSTAR2/tmp/json/bmr18569.json", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.gz", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/bmr18569.str", "tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.gz", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.bz2", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/bmr18569.str", "tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.bz2", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json", "tests/example_data/NMRSTAR3/tmp/nmrstar/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json", "tests/example_data/NMRSTAR2/tmp/nmrstar/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/gz/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/gz/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/gz/bmr18569.str.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/gz/bmr18569.str.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/gz/bmr18569.str.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/gz/bmr18569.str.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/bz2/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/bz2/bmr18569.str", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/bz2/bmr18569.str.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/bz2/bmr18569.str.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/bz2/bmr18569.str.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/bmr18569.json.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/bz2/bmr18569.str.bz2", "json", "nmrstar"), | ||
| # many-to-many file conversions | ||
| ("tests/example_data/NMRSTAR3/starfiles_directory", "tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/starfiles_directory", "tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/starfiles_directory", "tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/starfiles_directory", "tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/starfiles_directory", "tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/starfiles_directory", "tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/starfiles_directory", "tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/starfiles_directory", "tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/starfiles_directory", "tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR2/starfiles_directory", "tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "nmrstar", "json"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR3/tmp/nmrstar/zip/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR2/tmp/nmrstar/zip/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR3/tmp/nmrstar/zip/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR2/tmp/nmrstar/zip/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR3/tmp/nmrstar/zip/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR2/tmp/nmrstar/zip/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR3/tmp/nmrstar/zip/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR2/tmp/nmrstar/zip/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR3/tmp/nmrstar/zip/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.zip", "tests/example_data/NMRSTAR2/tmp/nmrstar/zip/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR2/tmp/nmrstar/tar/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR2/tmp/nmrstar/tar/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR2/tmp/nmrstar/tar/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR2/tmp/nmrstar/tar/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar", "tests/example_data/NMRSTAR2/tmp/nmrstar/tar/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/tar/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/targz/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/targz/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/targz/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/targz/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/targz/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/targz/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/targz/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR3/tmp/nmrstar/targz/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.gz", "tests/example_data/NMRSTAR2/tmp/nmrstar/targz/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/tarbz2/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/tarbz2/starfiles_nmrstar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/tarbz2/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/tarbz2/starfiles_nmrstar.zip", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar.gz", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR3/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR3/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar.bz2", "json", "nmrstar"), | ||
| ("tests/example_data/NMRSTAR2/tmp/json/dir/starfiles_files_json.tar.bz2", "tests/example_data/NMRSTAR2/tmp/nmrstar/tarbz2/starfiles_nmrstar.tar.bz2", "json", "nmrstar") | ||
| ]) | ||
| def test_convert_command(from_path, to_path, from_format, to_format): | ||
| command = "python -m nmrstarlib convert {} {} --from_format={} --to_format={}".format(from_path, | ||
| to_path, | ||
| from_format, | ||
| to_format) | ||
| assert os.system(command) == 0 | ||
|
|
||
| starfile_generator = nmrstarlib.read_files(to_path) | ||
| starfiles_list = list(starfile_generator) | ||
| starfiles_ids_set = set(sf.bmrbid for sf in starfiles_list) | ||
| assert starfiles_ids_set.issubset({"15000", "18569"}) |