# HG changeset patch # User blankenberglab # Date 1631278614 0 # Node ID aec9bc48cdb70ac8eb18b144f8b0b688681604b3 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306" diff -r 000000000000 -r aec9bc48cdb7 data_manager/data_manager_refgenie_pull.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_refgenie_pull.py Fri Sep 10 12:56:54 2021 +0000 @@ -0,0 +1,42 @@ +#!/usr/bin/env python + + +import argparse +import logging +from base64 import urlsafe_b64encode +from urllib.parse import urljoin + +import refgenconf +import requests + + +log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull") + + +def galaxy_code_get_refgenie_assets(refgenie_config_file): + rgc = refgenconf.RefGenConf(refgenie_config_file) + rval = [] + for urlname, genomes in rgc.listr().items(): + urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8') + ul = [] + for genome, assets in genomes.items(): + al = [] + for name in assets: + al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False}) + ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False}) + rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False}) + return rval + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload') + parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload') + parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key') + + args = parser.parse_args() + if not args.names: + tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json() + args.names = [d.get('name') for d in tables] + for name in args.names: + print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json()) diff -r 000000000000 -r aec9bc48cdb7 data_manager/data_manager_refgenie_pull.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_refgenie_pull.xml Fri Sep 10 12:56:54 2021 +0000 @@ -0,0 +1,69 @@ + + from remote resource + + macros.xml + + + refgenie + +


+    
+        
+    
+    > '${out_log}' 2>&1
+         &&
+       #end for
+       echo '{}' > '${out_file}'
+       #if $api_refresh:
+         && python '${__tool_directory__}/data_manager_refgenie_pull.py' -k "\$API_KEY" -u '${__galaxy_url__}' >> '${out_log}'
+       #end if
+    ]]>
+    
+        
+            .+/.+/.+
+        
+        
+        
+    
+    
+        
+        
+    
+    
+        
+            
+            
+            
+            
+                
+                    
+                
+            
+            
+                
+                    
+                
+            
+        
+    
+    
+    
+        10.1093/gigascience/giz149
+        10.1101/2020.10.09.327114
+    
+


diff -r 000000000000 -r aec9bc48cdb7 data_manager/macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml	Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,4 @@
+
+    0.9.1
+
+
diff -r 000000000000 -r aec9bc48cdb7 data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,5 @@
+
+
+    
+    
+
diff -r 000000000000 -r aec9bc48cdb7 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,3 @@
+
+    
+
diff -r 000000000000 -r aec9bc48cdb7 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Sep 10 12:56:54 2021 +0000
@@ -0,0 +1,3 @@
+
+    
+