# HG changeset patch
# User iuc
# Date 1594973975 14400
# Node ID 93253aebaf2e386d6db765446f9d198aff4026f3
# Parent  5833ef61c1f870f6301b031e9bd9b3498e8ab77f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"

diff -r 5833ef61c1f8 -r 93253aebaf2e data_manager/data_manager_plant_tribes_scaffolds_download.py
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py	Fri Aug 17 07:04:08 2018 -0400
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py	Fri Jul 17 04:19:35 2020 -0400
@@ -7,9 +7,8 @@
 import shutil
 import sys
 import tarfile
-import urllib2
 import zipfile
-
+from urllib.request import Request, urlopen
 
 DEFAULT_DATA_TABLE_NAMES = ["plant_tribes_scaffolds"]
 
@@ -52,22 +51,20 @@
     src = None
     dst = None
     try:
-        req = urllib2.Request(url)
-        src = urllib2.urlopen(req)
-        dst = open(file_path, 'wb')
-        while True:
-            chunk = src.read(2**10)
-            if chunk:
-                dst.write(chunk)
-            else:
-                break
+        req = Request(url)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
     except Exception as e:
-        print >>sys.stderr, str(e)
+        sys.exit(str(e))
     finally:
         if src:
             src.close()
-        if dst:
-            dst.close()
     return file_path
 
 
@@ -117,9 +114,8 @@
 
 args = parser.parse_args()
 
-# Some magic happens with tools of type "manage_data" in that the output
-# file contains some JSON data that allows us to define the target directory.
-params = json.loads(open(args.out_file).read())
+with open(args.out_file) as fh:
+    params = json.loads(fh.read())
 target_directory = params['output_data'][0]['extra_files_path']
 make_directory(target_directory)
 
@@ -131,6 +127,5 @@
 # Get the scaffolds data.
 data_manager_dict = download(target_directory, args.web_url, args.config_web_url, description)
 # Write the JSON output dataset.
-fh = open(args.out_file, 'wb')
-fh.write(json.dumps(data_manager_dict))
-fh.close()
+with open(args.out_file, 'w') as fh:
+    fh.write(json.dumps(data_manager_dict, sort_keys=True))
diff -r 5833ef61c1f8 -r 93253aebaf2e data_manager/data_manager_plant_tribes_scaffolds_download.xml
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Fri Aug 17 07:04:08 2018 -0400
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.xml	Fri Jul 17 04:19:35 2020 -0400
@@ -1,18 +1,15 @@
-<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.0" tool_type="manage_data">
+<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.1" tool_type="manage_data">
     <description></description>
-    <stdio>
-        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
-    <command>
-        <![CDATA[
-            python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
-            --name '$name'
-            --description '$description'
-            --web_url '$web_url'
-            --config_web_url '$config_web_url'
-            --out_file '$out_file'
-        ]]>
+    <requirements>
+        <requirement type="package" version="3.8.3">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
+--name '$name'
+--description '$description'
+--web_url '$web_url'
+--config_web_url '$config_web_url'
+--out_file '$out_file']]>
     </command>
     <inputs>
         <param name="name" type="text" value="" label="Data table entry unique ID"/>
@@ -24,6 +21,13 @@
         <data name="out_file" format="data_manager_json" />
     </outputs>
     <tests>
+        <test>
+            <param name="name" value="12Gv1.0"/>
+            <param name="description" value="12 plant genomes (Monocots, version 1.0)"/>
+            <param name="web_url" value="https://github.com/gregvonkuster/galaxy_tools/raw/master/test/plant_tribes/scaffolds/12Gv1.0.tar.bz2"/>
+            <param name="config_web_url" value="http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/12Gv1.0.tar.gz"/>
+            <output name="out_file" value="plant_tribes_scaffolds.json" compare="contains"/>
+        </test>
     </tests>
     <help>
 .. class:: infomark
diff -r 5833ef61c1f8 -r 93253aebaf2e data_manager_conf.xml
--- a/data_manager_conf.xml	Fri Aug 17 07:04:08 2018 -0400
+++ b/data_manager_conf.xml	Fri Jul 17 04:19:35 2020 -0400
@@ -3,17 +3,17 @@
     <data_manager tool_file="data_manager/data_manager_plant_tribes_scaffolds_download.xml" id="data_manager_plant_tribes_scaffolds_download" >
         <data_table name="plant_tribes_scaffolds">
             <output>
-                <column name="value" />
+                <column name="value"/>
                 <column name="name"/>
                 <column name="path" output_ref="out_file">
-                    <move type="file">
+                    <move type="file" relativize_symlinks="True">>
                         <source>${path}</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">plant_tribes/scaffolds/${value}</target>
                     </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/plant_tribes/scaffolds/${value}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
-                <column name="description" />
+                <column name="description"/>
             </output>
         </data_table>
     </data_manager>
diff -r 5833ef61c1f8 -r 93253aebaf2e test-data/plant_tribes_scaffolds.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plant_tribes_scaffolds.json	Fri Jul 17 04:19:35 2020 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"plant_tribes_scaffolds": [{"description": "12 plant genomes (Monocots, version 1.0)", "name": "12Gv1.0", "path": 
diff -r 5833ef61c1f8 -r 93253aebaf2e test-data/plant_tribes_scaffolds.loc
diff -r 5833ef61c1f8 -r 93253aebaf2e tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Jul 17 04:19:35 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of scaffolds files for plant_tribes_scaffolds version 1.1.0 -->
+    <table name="plant_tribes_scaffolds" comment_char="#">
+        <columns>value, name, path, description</columns>
+        <file path="${__HERE__}/test-data/plant_tribes_scaffolds.loc" />
+    </table>
+</tables>