# HG changeset patch
# User pimarin
# Date 1667576766 0
# Node ID 718080c30a76a26e48cf6ca64ec74e2433569a2a
# Parent  ac4d5e1d1421c913fd015c6c1ea6fe85635c73f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit e7c35e529ae95a2c9f2ecd87a3716e6866feabfa

diff -r ac4d5e1d1421 -r 718080c30a76 data_manager/bakta_build_database.py
--- a/data_manager/bakta_build_database.py	Wed Nov 02 16:21:11 2022 +0000
+++ b/data_manager/bakta_build_database.py	Fri Nov 04 15:46:06 2022 +0000
@@ -2,13 +2,14 @@
 import hashlib
 import json
 import os
-import subprocess as sp
 import sys
 import tarfile
 from datetime import datetime
 from pathlib import Path
 
 import requests
+
+
 class GetBaktaDatabaseInfo:
     """
     Extract bakta database information to make a json file for data_manager
@@ -64,7 +65,6 @@
                 for db_dic in versions:
                     db_date_list.append(datetime.strptime(db_dic["date"],
                                                           '%Y-%m-%d').date())
-                max(db_date_list)
                 filtered_version = next(item for item in versions
                                         if max(db_date_list))
             elif db_version == "test":
@@ -96,17 +96,16 @@
 
     def get_data_manager(self, bakta_database_info, output_path):
         self.bakta_table_list = self.get_data_table_format()
-        bakta_value = f"bakta_{bakta_database_info['major']}." \
-                      f"{bakta_database_info['minor']}"
-        data_info = dict(value=bakta_value,
-                         dbkey=bakta_database_info['date'],
-                         database_record=bakta_database_info['record'],
-                         bakta_version=str(
-                             f"{bakta_database_info['software-min']['major']}."
-                             f"{bakta_database_info['software-min']['minor']}"
-                         ),
-                         path=output_path)
-        self.bakta_table_list["data_tables"][self.data_table_name] = data_info
+        bakta_value = f"V{bakta_database_info['major']}." \
+                      f"{bakta_database_info['minor']}_" \
+                      f"{bakta_database_info['date']}"
+        tool_version = str(f"{bakta_database_info['software-min']['major']}."
+                           f"{bakta_database_info['software-min']['minor']}")
+        data_info = dict(value=bakta_database_info['record'],
+                         dbkey=bakta_value,
+                         bakta_version=tool_version,
+                         path="db")
+        self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
         return self.bakta_table_list
 
 
@@ -148,13 +147,13 @@
                   f' url={self.db_url}, path={self.tarball_name}')
 
     def untar(self):
-        db_path = Path(self.db_dir).joinpath(self.db_name)
+        db_path = Path(self.db_dir).as_posix()
         try:
             with self.tarball_path.open('rb') as fh_in, \
                     tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
-                tar_file.extractall(path=str(db_path))
+                tar_file.extractall(path=db_path)
                 print(f'Untar the database in {db_path}')
-                return db_path.as_posix()
+                return db_path
         except OSError:
             sys.exit(f'ERROR: Could not extract {self.tarball_name} '
                      f'to {self.db_name}')
@@ -175,6 +174,10 @@
                   f"calculated md5 = {md5.hexdigest()}"
                   f" different from {self.md5} ")
 
+
+"""
+This is the method to download the amrfinderplus database need by bakta.
+Deprecated to use the amrfinderplus data_manager
     def update_amrfinderplus_db(self):
         amrfinderplus_db_path = f"{self.db_dir}/{self.db_name}/db/amrfinderplus-db"
         if self.db_version == "test":
@@ -200,6 +203,7 @@
                   f" --database {amrfinderplus_db_path}'")
         else:
             print("AMRFinderPlus database download")
+"""
 
 
 def parse_arguments():
@@ -221,11 +225,9 @@
     all_args = parse_arguments()
 
     with open(all_args.data_manager_json) as fh:
-        data_manager_input = json.load(fh)
-
-    target_dir = data_manager_input['output_data'][0]['extra_files_path']
+        params = json.load(fh)
+    target_dir = params['output_data'][0]['extra_files_path']
     os.makedirs(target_dir)
-
     # init the class to download bakta db
     bakta_upload = InstallBaktaDatabase()
     # extract the version
@@ -242,11 +244,9 @@
     # check md5 sum
     bakta_upload.calc_md5_sum()
     # untar db
-    bakta_extracted_path = bakta_upload.untar()
-    # update for amrfinderplus
-    bakta_upload.update_amrfinderplus_db()
+    bakta_upload.untar()
     # make the data_manager metadata
-    bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=bakta_extracted_path)
+    bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=target_dir)
     with open(all_args.data_manager_json, 'w') as fh:
         json.dump(bakta_data_manager, fh, sort_keys=True)
 
diff -r ac4d5e1d1421 -r 718080c30a76 data_manager/bakta_build_database.xml
--- a/data_manager/bakta_build_database.xml	Wed Nov 02 16:21:11 2022 +0000
+++ b/data_manager/bakta_build_database.xml	Fri Nov 04 15:46:06 2022 +0000
@@ -33,7 +33,7 @@
         <!-- Test download -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
-            <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
+            <output name="output_file" value="bakta_test_data_manager.json" />
         </test>
     </tests>
     <help><![CDATA[
diff -r ac4d5e1d1421 -r 718080c30a76 data_manager/macro.xml
--- a/data_manager/macro.xml	Wed Nov 02 16:21:11 2022 +0000
+++ b/data_manager/macro.xml	Fri Nov 04 15:46:06 2022 +0000
@@ -5,9 +5,9 @@
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="requirements">
-        <requirements>
+        <requirements>w
             <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
-            <requirement type="package" version="@REQUEST_VERSION@">requests</requirement>
+            <requirement type="package" version="@REQUESTS_VERSION@">requests</requirement>
         </requirements>
     </xml>
 </macros>
diff -r ac4d5e1d1421 -r 718080c30a76 data_manager_conf.xml
--- a/data_manager_conf.xml	Wed Nov 02 16:21:11 2022 +0000
+++ b/data_manager_conf.xml	Fri Nov 04 15:46:06 2022 +0000
@@ -4,15 +4,14 @@
             <output>
                 <column name="value"/>
                 <column name="dbkey"/>
-                <column name="database_record"/>
                 <column name="bakta_version"/>
                 <column name="path" output_ref="output_file">
                     <move type="directory" relativize_symlinks="True">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bakta_database/${dbkey}/${path}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bakta_database/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${dbkey}/${path}</value_translation>
-                  <value_translation type="function">abspath</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bakta_database/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
         </data_table>
diff -r ac4d5e1d1421 -r 718080c30a76 test-data/bakta_test.loc
--- a/test-data/bakta_test.loc	Wed Nov 02 16:21:11 2022 +0000
+++ b/test-data/bakta_test.loc	Fri Nov 04 15:46:06 2022 +0000
@@ -1,7 +1,7 @@
 # this is a tab separated file describing the location of bakta database
 #
 # the columns are:
-# value, dbkey, database_record, bakta_version, path
+# value, dbkey, bakta_version, path
 #
 # for example
-bakta_0.0	date_test	7197299	0.0	${__HERE__}
+7197299 V0.0_date_test  0.0 ${__HERE__}
diff -r ac4d5e1d1421 -r 718080c30a76 test-data/bakta_test_data_manager.json
--- a/test-data/bakta_test_data_manager.json	Wed Nov 02 16:21:11 2022 +0000
+++ b/test-data/bakta_test_data_manager.json	Fri Nov 04 15:46:06 2022 +0000
@@ -1,1 +1,1 @@
-{"data_tables":{"bakta_database": [{"bakta_version": "0.0","database_record": "7197299","dbkey": "date_test","path": "/tmp/tmpu_ccwfs9/job_working_directory/000/1/working/dataset_fb48f154-bf1b-4974-8759-e4f0e230e917_files/bakta_test","value": "bakta_0.0"}]}}
+{"data_tables": {"bakta_database": [{"bakta_version": "0.0", "dbkey": "V0.0_date_test", "path": "db", "value": "7197299"}]}}
diff -r ac4d5e1d1421 -r 718080c30a76 tool-data/bakta_database.loc
--- a/tool-data/bakta_database.loc	Wed Nov 02 16:21:11 2022 +0000
+++ b/tool-data/bakta_database.loc	Fri Nov 04 15:46:06 2022 +0000
@@ -1,7 +1,7 @@
 # this is a tab separated file describing the location of bakta database
 #
 # the columns are:
-# value, dbkey, database_record, bakta_version, path
+# value, dbkey, bakta_version, path
 #
 # for example
-#bakta_0.0	date_test	7197299	0.0	path/to/db
+#7197299 V0.0_date_test  0.0 ${__HERE__}
diff -r ac4d5e1d1421 -r 718080c30a76 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Nov 02 16:21:11 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Nov 04 15:46:06 2022 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of bakta database in the required format -->
     <table name="bakta_database" comment_char="#">
-        <columns>value, dbkey, database_record, bakta_version, path</columns>
+        <columns>value, dbkey, bakta_version, path</columns>
         <file path="tool-data/bakta_database.loc" />
     </table>
 </tables>
diff -r ac4d5e1d1421 -r 718080c30a76 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Wed Nov 02 16:21:11 2022 +0000
+++ b/tool_data_table_conf.xml.test	Fri Nov 04 15:46:06 2022 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of bakta database in the required format -->
     <table name="bakta_database" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, database_record, bakta_version, path</columns>
+        <columns>value, dbkey, bakta_version, path</columns>
         <file path="${__HERE__}/test-data/bakta_test.loc" />
     </table>
 </tables>