Mercurial > repos > iuc > data_manager_fetch_plasmidfinder

comparison data_manager/plasmidfinder_fetch_database.py @ 1:3542cd220bc3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 1fa130238d58da20df9eee4e960dd794224400a5
author iuc
date Fri, 25 Aug 2023 23:34:04 +0000
parents b56071bdecad
children
comparison
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0:b56071bdecad 1:3542cd220bc3
13 Create the json file with database information for galaxy data manager 13 Create the json file with database information for galaxy data manager
14 """ 14 """
15 15
16 def __init__(self, 16 def __init__(self,
17 plasmidfinder_database="plasmidfinder_database", 17 plasmidfinder_database="plasmidfinder_database",
18 db_name="plasmidfinder_database", 18 db_name="plasmidfinder-db",
19 plasmidfinder_version="latest"): 19 plasmidfinder_version="latest"):
20 self.data_table_name = plasmidfinder_database 20 self.data_table_name = plasmidfinder_database
21 self._db_name = db_name 21 self._db_name = db_name
22 self._plasmidfinder_version = plasmidfinder_version 22 self._plasmidfinder_version = plasmidfinder_version
23 self._plasmidfinder_date_version = None 23 self._plasmidfinder_date_version = None
67 """ 67 """
68 68
69 def __init__(self, 69 def __init__(self,
70 output_dir=Path.cwd(), 70 output_dir=Path.cwd(),
71 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master", 71 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master",
72 db_name="plasmidfinder_database", 72 db_name="plasmidfinder-db",
73 db_tmp="tmp_database", 73 db_tmp="tmp_database",
74 plasmidfinder_version="latest", 74 plasmidfinder_version="latest",
75 json_file_path=None, 75 json_file_path=None,
76 date_version=None): 76 date_version=None):
77 77
85 self._plasmidfinder_version = plasmidfinder_version 85 self._plasmidfinder_version = plasmidfinder_version
86 self._plasmidfinder_date_version = date_version 86 self._plasmidfinder_date_version = date_version
87 self._commit_number = None 87 self._commit_number = None
88 88
89 def git_clone(self): 89 def git_clone(self):
90 git.Repo.clone_from(url=self._plasmidfinder_url, to_path=self._output_dir) 90 self.plasmidfinder_db_path = f'{self._output_dir}/{self._db_name}'
91 self._plasmidfinder_repository = git.Repo(path=self._output_dir) 91 git.Repo.clone_from(url=self._plasmidfinder_url, to_path=self.plasmidfinder_db_path)
92 self._plasmidfinder_repository = git.Repo(path=self.plasmidfinder_db_path)
92 93
93 def get_commit_number(self): 94 def get_commit_number(self):
94 sha = self._plasmidfinder_repository.head.commit.hexsha 95 sha = self._plasmidfinder_repository.head.commit.hexsha
95 short_sha = self._plasmidfinder_repository.git.rev_parse(sha, short=7) 96 short_sha = self._plasmidfinder_repository.git.rev_parse(sha, short=7)
96 self._commit_number = short_sha 97 self._commit_number = short_sha