# HG changeset patch
# User rhpvorderman
# Date 1624970168 0
# Node ID b17f2fb4a5cb6cf9cbc989d08a88ac613756289d
# Parent  4e2dd090d3ba436b655b4a5d7cf8aef6157c0a25
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 6c115a41a535feff1e805d3d10f3a39940e5d738"

diff -r 4e2dd090d3ba -r b17f2fb4a5cb data_manager/data_manager_fetch_mothur_reference_data.xml
--- a/data_manager/data_manager_fetch_mothur_reference_data.xml	Mon Jun 28 13:02:27 2021 +0000
+++ b/data_manager/data_manager_fetch_mothur_reference_data.xml	Tue Jun 29 12:36:08 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.3.0" tool_type="manage_data" profile="19.05">
+<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.3.1" tool_type="manage_data" profile="19.05">
     <description>Fetch and install reference data for Mothur</description>
     <requirements>
         <requirement type="package" version="3.8">python</requirement>
diff -r 4e2dd090d3ba -r b17f2fb4a5cb data_manager/fetch_mothur_reference_data.py
--- a/data_manager/fetch_mothur_reference_data.py	Mon Jun 28 13:02:27 2021 +0000
+++ b/data_manager/fetch_mothur_reference_data.py	Tue Jun 29 12:36:08 2021 +0000
@@ -11,7 +11,7 @@
 import tempfile
 import urllib.request
 import zipfile
-from typing import Generator, List, Iterable, Union, Optional, Dict
+from typing import Dict, Generator, Iterable, List, Optional, Union
 
 # When extracting files from archives, skip names that
 # start with the following strings
@@ -226,7 +226,7 @@
                 os.makedirs(target, exist_ok=True)
             else:
                 # Extract file
-                print("Extracting {target}")
+                print(f"Extracting {target}")
                 os.makedirs(os.path.dirname(target), exist_ok=True)
                 with open(target, 'wb') as fh:
                     with z.open(name) as zh:
@@ -333,10 +333,14 @@
                     target = os.path.join(target_dir, ref_data_file)
                     print(f"Moving {unpacked_file} to {target}")
                     shutil.move(unpacked_file, target)
-                    print(f"Removing {unpacked_file}")
-                    os.remove(unpacked_file)
                     data_tables['data_tables'][f"mothur_{type_}"].append(
                         dict(name=entry_name, value=ref_data_file))
+                print(f"Removing downloaded file: {filen}")
+                # check if file was not moved and therefore already deleted.
+                if os.path.exists(filen):
+                    # Removing file early here minimizes temporary storage
+                    # needed on the server.
+                    os.remove(filen)
     print(f"Removing {wd}")
     shutil.rmtree(wd)