Mercurial > repos > greg > data_manager_gtdbtk_database_installer

changeset 2:e4fe7259c4e9 draft default tip

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author greg
date Wed, 16 Mar 2022 12:53:21 +0000
parents 7093598fa300
children
files data_manager/gtdbtk_database_installer.py data_manager_conf.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 4 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/gtdbtk_database_installer.py	Tue Mar 15 19:31:23 2022 +0000
+++ b/data_manager/gtdbtk_database_installer.py	Wed Mar 16 12:53:21 2022 +0000
@@ -52,7 +52,7 @@
     data_manager_entry = {}
     data_manager_entry['value'] = database_id
     data_manager_entry['name'] = database_name
-    data_manager_entry['db_path'] = file_path
+    data_manager_entry['path'] = file_path
     data_manager_json["data_tables"]["gtdbtk_database"] = data_manager_entry
 
     with open(out_file, 'w') as fh:
--- a/data_manager_conf.xml	Tue Mar 15 19:31:23 2022 +0000
+++ b/data_manager_conf.xml	Wed Mar 16 12:53:21 2022 +0000
@@ -4,11 +4,11 @@
             <output>
                 <column name="value"/>
                 <column name="name"/>
-                <column name="db_path" output_ref="out_file">
+                <column name="path" output_ref="out_file">
                     <move type="directory" relativize_symlinks="True">
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gtdbtk_database/${value}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gtdbtk_database/${value}/${db_path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gtdbtk_database/${value}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/tool_data_table_conf.xml.sample	Tue Mar 15 19:31:23 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Mar 16 12:53:21 2022 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of GTDB-Tk database versions 202 and higher -->
     <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, db_path</columns>
+        <columns>value, name, path</columns>
         <file path="tool-data/gtdbtk_database.loc" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Tue Mar 15 19:31:23 2022 +0000
+++ b/tool_data_table_conf.xml.test	Wed Mar 16 12:53:21 2022 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of databases for gtdbtk version 202 and higher -->
     <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, db_path</columns>
+        <columns>value, name, path</columns>
         <file path="${__HERE__}/test-data/gtdbtk_database.loc" />
     </table>
 </tables>