Mercurial > repos > bebatut > data_manager_humann2_database_downloader

changeset 6:75898d1aabc3 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit b'318eb33ea866441cc9b2f98bdda88dd594037a0e\n'-dirty
author bebatut
date Thu, 02 Mar 2017 04:52:41 -0500
parents 71114ccf1026
children 1c2eb6bd1cd1
files data_manager/data_manager_humann2_download.py
diffstat 1 files changed, 8 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_humann2_download.py	Thu Mar 02 03:24:06 2017 -0500
+++ b/data_manager/data_manager_humann2_download.py	Thu Mar 02 04:52:41 2017 -0500
@@ -108,20 +108,23 @@
       target_dir: directory to put copy or link to the data file
 
     """
-    today = datetime.date.today()
-    db_target_dir = os.path.join(target_dir, database, build)
-    os.makedirs(db_target_dir)
+    value = "%s_%s_%s" % (database, build, datetime.date.today().isoformat())
+    db_target_dir = os.path.join(target_dir, database)
+    build_target_dir = os.path.join(db_target_dir, build)
+    os.makedirs(build_target_dir)
     cmd = "humann2_databases --download %s %s %s" % (database,
                                                      build,
                                                      db_target_dir)
     subprocess.check_call(cmd, shell=True)
+    os.rename(os.path.join(db_target_dir, database), build_target_dir)
     add_data_table_entry(
         data_tables,
         table_name,
         dict(
             dbkey=build,
-            value=today.isoformat(),
-            name=HUMANN2_REFERENCE_DATA[build], path=db_target_dir))
+            value=value,
+            name=HUMANN2_REFERENCE_DATA[build], 
+            path=db_target_dir))
 
 
 if __name__ == "__main__":