diff data_manager/plasmidfinder_fetch_database.py @ 0:b56071bdecad draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/plasmidfinder_fetch_database.py	Thu Jun 15 09:14:08 2023 +0000
@@ -0,0 +1,154 @@
+import argparse
+import json
+import os
+import time
+from pathlib import Path
+
+
+import git
+
+
+class GetPlasmidfinderDataManager:
+    """
+    Create the json file with database information for galaxy data manager
+    """
+
+    def __init__(self,
+                 plasmidfinder_database="plasmidfinder_database",
+                 db_name="plasmidfinder_database",
+                 plasmidfinder_version="latest"):
+        self.data_table_name = plasmidfinder_database
+        self._db_name = db_name
+        self._plasmidfinder_version = plasmidfinder_version
+        self._plasmidfinder_date_version = None
+        self.data_table_entry = None
+        self.plasmidfinder_table_list = None
+        self._commit_number = None
+
+    def get_data_table_format(self):
+        """
+        Skeleton of a data_table format
+        return: a data table formatted for json output
+        """
+        self.data_table_entry = {
+            "data_tables": {
+                self.data_table_name: {}
+            }
+        }
+        return self.data_table_entry
+
+    def get_data_manager(self):
+        """
+        Create the empty data table format and add all the information into
+        Commit number is added if latest is required instead of version number
+        return: The data table with database information
+        """
+        self.plasmidfinder_table_list = self.get_data_table_format()
+        if self._plasmidfinder_version == "latest":
+            version_value = self._commit_number
+        else:
+            version_value = self._plasmidfinder_version
+        plasmidfinder_value = f"plasmidfinder_{self._commit_number}" \
+                              f"_{self._plasmidfinder_date_version}"
+        plasmidfinder_name = f"{version_value}" \
+                             f"_{self._plasmidfinder_date_version}"
+        data_info = dict(value=plasmidfinder_value,
+                         name=plasmidfinder_name,
+                         date=self._plasmidfinder_date_version,
+                         path=self._db_name)
+        self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]
+        return self.plasmidfinder_table_list
+
+
+class DownloadPlasmidfinderDatabase(GetPlasmidfinderDataManager):
+    """
+    Download the plasmidfinder database from the bitbucket repository.
+    Build the data manager info for galaxy
+    """
+
+    def __init__(self,
+                 output_dir=Path.cwd(),
+                 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master",
+                 db_name="plasmidfinder_database",
+                 db_tmp="tmp_database",
+                 plasmidfinder_version="latest",
+                 json_file_path=None,
+                 date_version=None):
+
+        super().__init__()
+        self.json_file_path = json_file_path
+        self._output_dir = output_dir
+        self._plasmidfinder_url = plasmidfinder_url
+        self._temporary_folder = db_tmp
+        self._db_name = db_name
+        self._db_name_tar = f'{db_name}.gz'
+        self._plasmidfinder_version = plasmidfinder_version
+        self._plasmidfinder_date_version = date_version
+        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)
+
+    def get_commit_number(self):
+        sha = self._plasmidfinder_repository.head.commit.hexsha
+        short_sha = self._plasmidfinder_repository.git.rev_parse(sha, short=7)
+        self._commit_number = short_sha
+
+    def get_commit_date(self):
+        self._plasmidfinder_date_version = time.strftime("%Y_%m_%d", time.gmtime(self._plasmidfinder_repository.head.commit.committed_date))
+
+    def download_database(self):
+        """
+        Download the plasmidfinder database using git lib
+        Extract commit and commit date
+        """
+        self._output_dir = Path(self._output_dir)
+        self.git_clone()
+        if self._plasmidfinder_version != "latest":
+            self._plasmidfinder_repository.git.checkout(self._plasmidfinder_version)
+        self.get_commit_number()
+        self.get_commit_date()
+
+    def read_json_input_file(self):
+        """
+        Import the json file
+        """
+        with open(self.json_file_path) as fh:
+            params = json.load(fh)
+        target_dir = params['output_data'][0]['extra_files_path']
+        os.makedirs(target_dir)
+        self._output_dir = target_dir
+
+    def write_json_infos(self):
+        """
+        Write in the imported json file
+        """
+        with open(self.json_file_path, 'w') as fh:
+            json.dump(self.get_data_manager(), fh, sort_keys=True)
+
+
+def parse_arguments():
+    """
+    List of arguments provided by the user
+    return: parsed arguments
+    """
+    # parse options and arguments
+    arg_parser = argparse.ArgumentParser()
+    arg_parser.add_argument("data_manager_json",
+                            help="json file from galaxy")
+    arg_parser.add_argument("-v", "--db_version",
+                            help="version of the plasmidfinder (latest or 2.1)")
+    return arg_parser.parse_args()
+
+
+def main():
+    all_args = parse_arguments()
+    plasmidfinder_download = DownloadPlasmidfinderDatabase(json_file_path=all_args.data_manager_json, plasmidfinder_version=all_args.db_version)
+    plasmidfinder_download.read_json_input_file()
+    plasmidfinder_download.download_database()
+    plasmidfinder_download.write_json_infos()
+
+
+if __name__ == '__main__':
+    main()