# HG changeset patch
# User pimarin
# Date 1668438309 0
# Node ID 02a159f061a17da72b18de7766270d351cc94772
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
diff -r 000000000000 -r 02a159f061a1 data_manager/data_manager_build_amrfinderplus.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.py Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,107 @@
+import argparse
+import json
+import os
+import re
+import subprocess as sp
+
+from datetime import datetime
+from pathlib import Path
+
+
+class GetDataManager:
+
+ def __init__(self):
+ self.data_table_name = "amrfinderplus_database"
+ self._db_name = "amrfinderplus-db"
+ self._db_path = Path().absolute()
+ self._today = datetime.now().strftime("%Y-%m-%d_%H:%M")
+
+ 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, amrfinderplus_version):
+ self.amrfinderplus_table_list = self.get_data_table_format()
+
+ data_info = dict(value=self._today,
+ name=amrfinderplus_version,
+ path=self._db_name)
+ self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
+ return self.amrfinderplus_table_list
+
+ def update_amrfinderplus_db(self):
+ amrfinderplus_db_path = Path(self._db_path).joinpath(self._db_name)
+ cmd = [
+ 'amrfinder_update',
+ '--database', str(amrfinderplus_db_path),
+ '--force_update'
+ ]
+ print(cmd)
+ proc = sp.run(
+ cmd,
+ stdout=sp.PIPE,
+ stderr=sp.PIPE,
+ universal_newlines=True
+ )
+ if (proc.returncode != 0):
+ print(
+ f"ERROR: AMRFinderPlus failed! command: 'amrfinder_update --force_update --database {amrfinderplus_db_path}', error code: {proc.returncode}")
+ else:
+ return amrfinderplus_db_path
+
+ def get_amrfinderplus_version(self, amrfinderplus_path):
+ version_file = Path(f'{amrfinderplus_path}/latest/version.txt')
+ with open(version_file, "r") as version:
+ version_value = version.read()
+ version_value = re.sub("\n", "", version_value)
+ return version_value
+
+ def parse_arguments(self):
+ # parse options and arguments
+ arg_parser = argparse.ArgumentParser()
+ arg_parser.add_argument("data_manager_json")
+ arg_parser.add_argument("-t", "--test", action='store_true',
+ help="option to test the script with an lighted database")
+ return arg_parser.parse_args()
+
+ def read_json_input_file(self, json_file_path):
+ with open(json_file_path) as fh:
+ params = json.load(fh)
+ target_dir = params['output_data'][0]['extra_files_path']
+ os.makedirs(target_dir)
+ return Path(target_dir)
+
+ def write_json_infos(self, json_file_path, data_manager_infos):
+ with open(json_file_path, 'w') as fh:
+ json.dump(data_manager_infos, fh, sort_keys=True)
+
+
+def main():
+ # init the class
+ amrfinderplus_download = GetDataManager()
+ # import the arguments
+ all_args = amrfinderplus_download.parse_arguments()
+ # read the json input from galaxy to define the db path
+ path_to_download = amrfinderplus_download.read_json_input_file(json_file_path=all_args.data_manager_json)
+ # change the path to th json information
+ amrfinderplus_download._db_path = path_to_download
+ # download the last amrfinderplus database
+ amrfinder_output = amrfinderplus_download.update_amrfinderplus_db()
+ # extract the version number of the database
+ amrfinder_version = amrfinderplus_download.get_amrfinderplus_version(amrfinder_output)
+ # make a dic with database information
+ amrfinderplus_json_output = amrfinderplus_download.get_data_manager(amrfinder_version)
+ amrfinderplus_download.write_json_infos(json_file_path=all_args.data_manager_json,
+ data_manager_infos=amrfinderplus_json_output)
+
+
+if __name__ == '__main__':
+ main()
diff -r 000000000000 -r 02a159f061a1 data_manager/data_manager_build_amrfinderplus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_build_amrfinderplus.xml Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,32 @@
+
+ AMRfinderplus database builder
+
+ macro.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/s41598-021-91456-0
+
+
diff -r 000000000000 -r 02a159f061a1 data_manager/macro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macro.xml Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,13 @@
+
+
+ 3.10.45
+ 3.10.6
+ 0
+ 21.05
+
+
+ ncbi-amrfinderplus
+ python
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 02a159f061a1 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 02a159f061a1 test-data/amrfinderplus.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus.loc Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, path
+#
+# for example
+2022-11-10_15:48 2022-10-11.2 ${__HERE__}
\ No newline at end of file
diff -r 000000000000 -r 02a159f061a1 test-data/amrfinderplus_test_data_manager.json
diff -r 000000000000 -r 02a159f061a1 tool-data/amrfinderplus.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/amrfinderplus.loc Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of amrfinderplus database
+#
+# the columns are:
+# value, name, path
+#
+# for example
+2022-11-10_15:48 2022-10-11.2 ${__HERE__}
\ No newline at end of file
diff -r 000000000000 -r 02a159f061a1 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 02a159f061a1 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Nov 14 15:05:09 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+
\ No newline at end of file