# HG changeset patch
# User iuc
# Date 1571213774 14400
# Node ID 5ca251be823648fb074ad793ba651c7e82fe6040
# Parent  872d7cf608f90feb08616f56d615d65cd98c740d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit b56485a8b386fc6f17219850e30e5656c159f231"

diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/.pytest_cache/README.md
--- a/data_manager/.pytest_cache/README.md	Mon Aug 13 08:43:15 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-# pytest cache directory #
-
-This directory contains data from the pytest's cache plugin,
-which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
-
-**Do not** commit this to version control.
-
-See [the docs](https://docs.pytest.org/en/latest/cache.html) for more information.
diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/.pytest_cache/v/cache/lastfailed
--- a/data_manager/.pytest_cache/v/cache/lastfailed	Mon Aug 13 08:43:15 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-{
-  "data_manager_fetch_genome_all_fasta_dbkeys.py::data_manager_fetch_genome_all_fasta_dbkeys.download_from_url": true
-}
\ No newline at end of file
diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/.pytest_cache/v/cache/nodeids
--- a/data_manager/.pytest_cache/v/cache/nodeids	Mon Aug 13 08:43:15 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-[
-  "data_manager_fetch_genome_all_fasta_dbkeys.py::data_manager_fetch_genome_all_fasta_dbkeys.download_from_url"
-]
\ No newline at end of file
diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/__pycache__/data_manager_fetch_genome_all_fasta_dbkeys.cpython-36-PYTEST.pyc
Binary file data_manager/__pycache__/data_manager_fetch_genome_all_fasta_dbkeys.cpython-36-PYTEST.pyc has changed
diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Mon Aug 13 08:43:15 2018 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Wed Oct 16 04:16:14 2019 -0400
@@ -3,6 +3,7 @@
 
 import bz2
 import gzip
+import json
 import optparse
 import os
 import shutil
@@ -11,7 +12,6 @@
 import tempfile
 import zipfile
 from ftplib import FTP
-from json import dumps, loads
 
 try:
     # For Python 3.0 and later
@@ -452,7 +452,8 @@
 
     filename = args[0]
 
-    params = loads(open(filename).read())
+    with open(filename) as fh:
+        params = json.load(fh)
     target_directory = params['output_data'][0]['extra_files_path']
     os.mkdir(target_directory)
     data_manager_dict = {}
@@ -488,7 +489,8 @@
     finally:
         cleanup_before_exit(tmp_dir)
     # save info to json file
-    open(filename, 'w').write(dumps(data_manager_dict))
+    with open(filename, 'w') as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
 
 
 if __name__ == "__main__":
diff -r 872d7cf608f9 -r 5ca251be8236 data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Mon Aug 13 08:43:15 2018 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Wed Oct 16 04:16:14 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.2" tool_type="manage_data">
+<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.3" tool_type="manage_data">
     <description>fetching</description>
     <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/data_manager_fetch_genome_all_fasta_dbkeys.py'
@@ -78,9 +78,10 @@
     <tests>
         <!-- TODO: need some way to test that new entry was added to data table -->
         <test>
-            <param name="dbkey" value="anoGam1"/>
-            <param name="sequence_name" value=""/>
-            <param name="sequence_id" value=""/>
+            <param name="dbkey" value="phiX174"/>
+            <param name="dbkey_source|dbkey_source_selector" value="new"/>
+            <param name="sequence_name" value="phiX174 sequence name"/>
+            <param name="sequence_id" value="phix174"/>
             <param name="reference_source_selector" value="history"/>
             <param name="input_fasta" value="phiX174.fasta"/>
             <param name="sort_selector" value="as_is"/>
diff -r 872d7cf608f9 -r 5ca251be8236 test-data/phiX174.data_manager_json
--- a/test-data/phiX174.data_manager_json	Mon Aug 13 08:43:15 2018 -0400
+++ b/test-data/phiX174.data_manager_json	Wed Oct 16 04:16:14 2019 -0400
@@ -1,1 +1,1 @@
-{"data_tables": {"all_fasta": [{"path": "anoGam1.fa", "dbkey": "anoGam1", "name": "A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)", "value": "anoGam1"}]}}
\ No newline at end of file
+{"data_tables": {"__dbkeys__": [{"len_path": "phiX174.len", "name": "phiX174", "value": "phiX174"}], "all_fasta": [{"dbkey": "phiX174", "name": "phiX174 sequence name", "path": "phix174.fa", "value": "phix174"}]}}
\ No newline at end of file
diff -r 872d7cf608f9 -r 5ca251be8236 tool-data/dbkeys.loc.sample
--- a/tool-data/dbkeys.loc.sample	Mon Aug 13 08:43:15 2018 -0400
+++ b/tool-data/dbkeys.loc.sample	Wed Oct 16 04:16:14 2019 -0400
@@ -1,1 +1,1 @@
-#<dbkey>		<display_name>	<len_file_path>
\ No newline at end of file
+#<dbkey>		<display_name>	<len_file_path>