# HG changeset patch
# User chrisw
# Date 1573675077 0
# Node ID 0d90ce4ea724de892de49db746a0301876128539
# Parent  0299ada36cce793477d8d151cd5e50470280585a
Uploaded

diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/.data_manager_conf.xml.swp
Binary file data_manager_monorail_index/.data_manager_conf.xml.swp has changed
diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/data_manager/.data_manager.py.swp
Binary file data_manager_monorail_index/data_manager/.data_manager.py.swp has changed
diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/data_manager/.monorail_index_fetcher.xml.swp
Binary file data_manager_monorail_index/data_manager/.monorail_index_fetcher.xml.swp has changed
diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/data_manager/data_manager.py
--- a/data_manager_monorail_index/data_manager/data_manager.py	Tue Nov 12 01:18:47 2019 -0500
+++ b/data_manager_monorail_index/data_manager/data_manager.py	Wed Nov 13 19:57:57 2019 +0000
@@ -20,18 +20,16 @@
     workdir = os.path.join(os.getcwd(), 'monorail_index')
     data_manager_entry = {}
     ref = args.url.split('/')[-1]
-    if args.name is None:
-        args.name = ref
-    data_manager_entry['value'] = args.name.lower()
-    data_manager_entry['name'] = args.name
+    data_manager_entry['dbkey'] = ref
+    data_manager_entry['value'] = ref.lower()
     jsonin = open(args.output).read()
-    sys.stdout.write(jsonin)
     params = json.loads(jsonin)
     target_directory = params['output_data'][0]['extra_files_path']
-    data_manager_entry['path'] = params['output_data'][0]['extra_files_path']
-    data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + ref + os.sep + 'gtf' + os.sep + 'exons.bed'
+    #data_manager_entry['path'] = params['output_data'][0]['extra_files_path']
+    data_manager_entry['path'] = ref
+    data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed'
     data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry))
-    file(args.output, 'a').write(json.dumps(data_manager_json))
+    file(args.output, 'w').write(json.dumps(data_manager_json))
 
 if __name__ == '__main__':
     main(args)
diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/data_manager/monorail_index_fetcher.xml
--- a/data_manager_monorail_index/data_manager/monorail_index_fetcher.xml	Tue Nov 12 01:18:47 2019 -0500
+++ b/data_manager_monorail_index/data_manager/monorail_index_fetcher.xml	Wed Nov 13 19:57:57 2019 +0000
@@ -14,12 +14,8 @@
         #if $monorail_index_url:
             --url "${monorail_index_url}"
         #end if
-        #if $index_name:
-            --name "${index_name}"
-        #end if
         ]]></command>
     <inputs>
-        <param help="Enter a unique identifier, or leave blank to use the reference ID at end of base URL below" label="Name for this Monorail index set" name="index_name" type="text" optional="True" />
         <param label="Enter base URL for Monorail index directories (e.g. http://snaptron.cs.jhu.edu/data/monorail/ath10)" name="monorail_index_url" type="text" />
     </inputs>
     <outputs>
diff -r 0299ada36cce -r 0d90ce4ea724 data_manager_monorail_index/data_manager_conf.xml
--- a/data_manager_monorail_index/data_manager_conf.xml	Tue Nov 12 01:18:47 2019 -0500
+++ b/data_manager_monorail_index/data_manager_conf.xml	Wed Nov 13 19:57:57 2019 +0000
@@ -6,20 +6,19 @@
 			<output>
                 <column name="value"/>
 				<column name="dbkey"/>
-                <column name="name"/>
                 <column name="path" output_ref="out_file">
                     <move relativize_symlinks="True" type="directory">
                         <!-- <source>${path}</source>
                             out_file.extra_files_path is used as base by default
-                            if no source, eg for type=directory, then refers to base 
+                            if no source, eg for type=directory, then refers to base
                         -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${name}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${dbkey}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${name}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${dbkey}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
 				<column name="exons_path">
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${name}/gtf/exons.bed</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/monorail_index/${dbkey}/gtf/exons.bed</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
 			</output>