# HG changeset patch
# User iuc
# Date 1717597259 0
# Node ID baceff842902bc802d2b771e9fe7d8f2496ab161
# Parent  d74850cf4e425e81e47775bc347663971cfaf437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2

diff -r d74850cf4e42 -r baceff842902 data_manager/bakta_build_database.py
--- a/data_manager/bakta_build_database.py	Fri Aug 25 23:34:04 2023 +0000
+++ b/data_manager/bakta_build_database.py	Wed Jun 05 14:20:59 2024 +0000
@@ -1,9 +1,7 @@
 import argparse
 import hashlib
 import json
-import os
 import re
-import shutil
 import sys
 import tarfile
 from datetime import datetime
@@ -34,7 +32,7 @@
         self.tar_name = tarball_name
         self.db_version = db_version
         self.DB_VERSIONS_URL = "https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json"
-        self.DB_TEST_URL = "https://zenodo.org/record/8021032/files/db-versions.json"
+        self.DB_TEST_URL = "https://zenodo.org/record/11381156/files/db-versions.json"
         self.test_mode = test_mode
 
     def get_database_type(self):
@@ -162,22 +160,22 @@
                 print(f"Untar the database in {db_path}")
 
             if not self.test_mode:
-                self.moove_files(db_path=db_path)
+                self.move_files(db_path=db_path)
 
         except OSError:
             sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {db_path}")
 
-    def moove_files(self, db_path):
-        if os.path.isdir(db_path.joinpath("db-light")):
+    def move_files(self, db_path):
+        if db_path.joinpath("db-light").is_dir():
             input_dir = db_path.joinpath("db-light")
-        elif os.path.isdir(db_path.joinpath("db")):
+        elif db_path.joinpath("db").is_dir():
             input_dir = db_path.joinpath("db")
-        file_list = os.listdir(input_dir)
         output_dir = db_path
-        for file in file_list:
-            input = input_dir.joinpath(file)
-            output = output_dir.joinpath(file)
-            shutil.move(input, output)
+        for file in input_dir.iterdir():
+            if file.is_file():  # to avoid moving amrfinder-plus folder
+                input = input_dir.joinpath(file)
+                output = output_dir.joinpath(file)
+                input.rename(output)
 
     def calc_md5_sum(self, buffer_size=1048576):
         tarball_path = Path(self.db_dir).joinpath(self.tar_name)
@@ -223,15 +221,15 @@
     all_args = parse_arguments()
     with open(all_args.data_manager_json) as fh:
         params = json.load(fh)
-    target_dir = params["output_data"][0]["extra_files_path"]
-    os.makedirs(target_dir)
+    target_dir = Path(params["output_data"][0]["extra_files_path"])
+    target_dir.mkdir(parents=True, exist_ok=True)
     # init the class to download bakta db
     bakta_upload = InstallBaktaDatabase(
         test_mode=all_args.test, db_version=all_args.database_version
     )
     bakta_db = bakta_upload.fetch_db_versions()
     # update the path for galaxy
-    bakta_upload.db_dir = target_dir
+    bakta_upload.db_dir = target_dir.absolute()
     # download the database
     bakta_upload.download()
     # check md5 sum
diff -r d74850cf4e42 -r baceff842902 data_manager/bakta_build_database.xml
--- a/data_manager/bakta_build_database.xml	Fri Aug 25 23:34:04 2023 +0000
+++ b/data_manager/bakta_build_database.xml	Wed Jun 05 14:20:59 2024 +0000
@@ -4,24 +4,24 @@
         <import>macro.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="exit_code">
-      <![CDATA[
-        python '$__tool_directory__/bakta_build_database.py'
-        '$output_file'
-        --database_version '$database_select'
-        $test_data_manager
-      ]]></command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/bakta_build_database.py'
+    '$output_file'
+    --database_version '$database_select'
+    $test_data_manager
+]]></command>
     <inputs>
         <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
-            <option value="latest" selected="true">Latest available version</option>
-            <option value="1.0">V1.0_2020-11-20</option>
-            <option value="1.1">V1.1_2020-12-18</option>
-            <option value="2.0">V2.0_2021-04-05</option>
-            <option value="3.0">V3.0_2021-08-05</option>
-            <option value="3.1">V3.1_2022-02-03</option>
-            <option value="4.0">V4.0_2022-08-29</option>
-            <option value="5.0">V5.0_2023-02-20</option>
-            <option value="5.0_light">V5.0_light_2023-02-20</option>
+            <option value="5.1" selected="true">V5.1 (2024-01-19)</option>
+            <option value="5.1_light">V5.1 light (2024-01-19)</option>
+            <option value="5.0">V5.0 (2023-02-20)</option>
+            <option value="5.0_light">V5.0 light (2023-02-20)</option>
+            <option value="4.0">V4.0 (2022-08-29)</option>
+            <option value="3.1">V3.1 (2022-02-03)</option>
+            <option value="3.0">V3.0 (2021-08-05)</option>
+            <option value="2.0">V2.0 (2021-04-05)</option>
+            <option value="1.1">V1.1 (2020-12-18)</option>
+            <option value="1.0">V1.0 (2020-11-20)</option>
         </param>
         <param name="test_data_manager" type="hidden" value=""/>
     </inputs>
@@ -33,19 +33,40 @@
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <param name="database_select" value="1.0"/>
-            <output name="output_file" value="bakta_test_data_manager1.json" />
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V1.0_2022-10-12"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test 2 with the latest option -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
-            <param name="database_select" value="latest"/>
-            <output name="output_file" value="bakta_test_data_manager2.json" />
+            <param name="database_select" value="5.1_light"/>
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V5.1light_2024-01-19"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test 3 with light db -->
         <test expect_num_outputs="1">
             <param name="test_data_manager" value="--test"/>
             <param name="database_select" value="5.0_light"/>
-            <output name="output_file" value="bakta_test_data_manager3.json" />
+            <output name="output_file" ftype="data_manager_json">
+                <assert_contents>
+                    <has_text text="data_tables"/>
+                    <has_text text="bakta_database"/>
+                    <has_text text="bakta_version"/>
+                    <has_text text="V5.0light_2023-06-08"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff -r d74850cf4e42 -r baceff842902 data_manager/macro.xml
--- a/data_manager/macro.xml	Fri Aug 25 23:34:04 2023 +0000
+++ b/data_manager/macro.xml	Wed Jun 05 14:20:59 2024 +0000
@@ -1,13 +1,14 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.8.1</token>
+    <token name="@TOOL_VERSION@">1.9.3</token>
     <token name="@REQUESTS_VERSION@">2.27.1</token>
     <token name="@PYTHON_VERSION@">3.8</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
             <requirement type="package" version="@REQUESTS_VERSION@">requests</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bakta</requirement>
         </requirements>
     </xml>
 </macros>
diff -r d74850cf4e42 -r baceff842902 test-data/bakta_test.loc
--- a/test-data/bakta_test.loc	Fri Aug 25 23:34:04 2023 +0000
+++ b/test-data/bakta_test.loc	Wed Jun 05 14:20:59 2024 +0000
@@ -1,3 +1,34 @@
 V1.0_2022-10-12	7197299	1.4	bakta-db
 V5.0_2023-06-08	8021027	1.8	bakta-db
 V5.0light_2023-06-08	8021027	1.8	bakta-db
+V1.0_2022-10-12	7197299	1.4	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpmw3oj2pm/galaxy-dev/tool-data/bakta_database/7197299
+V5.0light_2023-06-08	8021027	1.8	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpmw3oj2pm/galaxy-dev/tool-data/bakta_database/8021027
+V1.0_2022-10-12	7197299	1.4	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpe_k2ghko/galaxy-dev/tool-data/bakta_database/7197299
+V5.0light_2023-06-08	8021027	1.8	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpe_k2ghko/galaxy-dev/tool-data/bakta_database/8021027
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpfggmpn80/galaxy-dev/tool-data/bakta_database/4247253
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpcp1hbj74/galaxy-dev/tool-data/bakta_database/4247253
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpcp1hbj74/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpch1mha23/galaxy-dev/tool-data/bakta_database/4247253
+V5.1_2024-01-19	10522951	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpch1mha23/galaxy-dev/tool-data/bakta_database/10522951
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpch1mha23/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdntg5lkb/galaxy-dev/tool-data/bakta_database/4247253
+V5.1light_2024-01-19	10522951	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdntg5lkb/galaxy-dev/tool-data/bakta_database/10522951
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdntg5lkb/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp2dxsmaz6/galaxy-dev/tool-data/bakta_database/4247253
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp2dxsmaz6/galaxy-dev/tool-data/bakta_database/7669534
+V5.1light_2024-01-19	10522951	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpxo577qsb/galaxy-dev/tool-data/bakta_database/10522951
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpxo577qsb/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpw560binc/galaxy-dev/tool-data/bakta_database/4247253
+V5.1light_2024-01-19	10522951	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpw560binc/galaxy-dev/tool-data/bakta_database/10522951
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpw560binc/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpaehfoqch/galaxy-dev/tool-data/bakta_database/4247253
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpaehfoqch/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2020-11-20	4247253	0.3	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpj53k33oy/galaxy-dev/tool-data/bakta_database/4247253
+V5.1light_2024-01-19	10522951	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpj53k33oy/galaxy-dev/tool-data/bakta_database/10522951
+V5.0light_2023-02-20	7669534	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpj53k33oy/galaxy-dev/tool-data/bakta_database/7669534
+V1.0_2022-10-12	7197299	1.4	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdn_di5v_/galaxy-dev/tool-data/bakta_database/7197299
+V5.1light_2024-01-19	11371737	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdn_di5v_/galaxy-dev/tool-data/bakta_database/11371737
+V5.0light_2023-06-08	8021027	1.8	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmpdn_di5v_/galaxy-dev/tool-data/bakta_database/8021027
+V1.0_2022-10-12	7197299	1.4	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp7n51m5jb/galaxy-dev/tool-data/bakta_database/7197299
+V5.1light_2024-01-19	11371737	1.7	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp7n51m5jb/galaxy-dev/tool-data/bakta_database/11371737
+V5.0light_2023-06-08	8021027	1.8	/private/var/folders/7j/21czvpk170zcyjdbqrp0hmsh0000gn/T/tmp7n51m5jb/galaxy-dev/tool-data/bakta_database/8021027