Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder
changeset 9:464ffa0526c6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 8146dca92a35830d7e83d8eff031a92cdc7591bd-dirty
| author | pimarin |
|---|---|
| date | Wed, 23 Aug 2023 12:42:32 +0000 |
| parents | f99089461adb |
| children | |
| files | data_manager/plasmidfinder_fetch_database.py test-data/plasmidfinder.loc.test test-data/plasmidfinder_test_data_manager_2.1.json |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/plasmidfinder_fetch_database.py Wed Aug 23 12:17:01 2023 +0000 +++ b/data_manager/plasmidfinder_fetch_database.py Wed Aug 23 12:42:32 2023 +0000 @@ -87,8 +87,9 @@ self._commit_number = None def git_clone(self): - git.Repo.clone_from(url=self._plasmidfinder_url, to_path=self._output_dir) - self._plasmidfinder_repository = git.Repo(path=self._output_dir) + self.plasmidfinder_db_path = f'{self._output_dir}/{self._db_name}' + git.Repo.clone_from(url=self._plasmidfinder_url, to_path=self.plasmidfinder_db_path) + self._plasmidfinder_repository = git.Repo(path=self.plasmidfinder_db_path) def get_commit_number(self): sha = self._plasmidfinder_repository.head.commit.hexsha
--- a/test-data/plasmidfinder.loc.test Wed Aug 23 12:17:01 2023 +0000 +++ b/test-data/plasmidfinder.loc.test Wed Aug 23 12:42:32 2023 +0000 @@ -1,1 +1,4 @@ plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 plasmidfinder-db +plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpimkqnsxv/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 +plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpbqa_r7hv/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28 +plasmidfinder_1307168_2019_08_28 2.1_2019_08_28 2019_08_28 /tmp/tmpp_z4mmla/galaxy-dev/tool-data/plasmidfinder-db/2.1_2019_08_28
--- a/test-data/plasmidfinder_test_data_manager_2.1.json Wed Aug 23 12:17:01 2023 +0000 +++ b/test-data/plasmidfinder_test_data_manager_2.1.json Wed Aug 23 12:42:32 2023 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"plasmidfinder_database": [{"date": "2019_08_28", "name": "2.1_2019_08_28", "path": "plasmidfinder_database", "value": "plasmidfinder_1307168_2019_08_28"}]}} \ No newline at end of file +{"data_tables": {"plasmidfinder_database": [{"date": "2019_08_28", "name": "2.1_2019_08_28", "path": "plasmidfinder-db", "value": "plasmidfinder_1307168_2019_08_28"}]}} \ No newline at end of file