# HG changeset patch
# User chrisw
# Date 1573678591 0
# Node ID 79f33bace3da99e38e562d58b969e2c3713aa081
# Parent  b7ad296c88370db91202bdc16ed504df80b35d61
Uploaded

diff -r b7ad296c8837 -r 79f33bace3da data_manager_monorail_index/data_manager/data_manager.py
--- a/data_manager_monorail_index/data_manager/data_manager.py	Wed Nov 13 20:22:23 2019 +0000
+++ b/data_manager_monorail_index/data_manager/data_manager.py	Wed Nov 13 20:56:31 2019 +0000
@@ -20,16 +20,16 @@
     workdir = os.path.join(os.getcwd(), 'monorail_index')
     data_manager_entry = {}
     ref = args.url.split('/')[-1]
-    data_manager_entry['dbkey'] = ref
+    data_manager_entry['dbkey'] = 'mrail.'+ref
     data_manager_entry['value'] = ref.lower()
     jsonin = open(args.output).read()
     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['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, 'w').write(json.dumps(data_manager_json))
+    data_manager_entry['path'] = target_directory
+    #data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed'
+    data_manager_json = dict(data_tables={'monorail_index': [data_manager_entry]})
+    file(args.output, 'wb').write(json.dumps(data_manager_json))
 
 if __name__ == '__main__':
     main(args)
diff -r b7ad296c8837 -r 79f33bace3da data_manager_monorail_index/data_manager_conf.xml
--- a/data_manager_monorail_index/data_manager_conf.xml	Wed Nov 13 20:22:23 2019 +0000
+++ b/data_manager_monorail_index/data_manager_conf.xml	Wed Nov 13 20:56:31 2019 +0000
@@ -3,21 +3,14 @@
     <data_manager tool_file="data_manager/monorail_index_fetcher.xml" id="monorail_index_fetcher" version="1.0.0">
     <data_table name="monorail_index">
             <output>
-                <column name="value"/>
-                <column name="dbkey"/>
+                <column name="value" />
+                <column name="dbkey" />
                 <column name="path" output_ref="out_file">
-                    <move relativize_symlinks="True" type="directory">
-                        <!-- <source>${path}</source>
-                            out_file.extra_files_path is used as base by default
-                            if no source, eg for type=directory, then refers to base
-                        -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">monorail_index/${dbkey}</target>
+                    <move relative_symlinks="True" type="directory">
+                        <!-- no need to set source, gets taken from out_dir.extra_files_path -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/</target>
                     </move>
-                    <value_translation>${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/${dbkey}/gtf/exons.bed</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>