diff data_manager/data_manager_eggnog.py @ 1:46d2e3ed9530 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"

--- a/data_manager/data_manager_eggnog.py	Mon Nov 11 11:47:57 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Fri Feb 19 18:52:23 2021 +0000
@@ -11,7 +11,7 @@
 
 
 def _get_db_version(sqlitedb_path):
-    version = '4.5'
+    version = '5.0'
     try:
         query = 'select version from version'
         conn = sqlite3.connect(sqlitedb_path)
@@ -28,7 +28,6 @@
     parser = argparse.ArgumentParser()
     parser.add_argument('--config_file')
     parser.add_argument('--install_path')
-    parser.add_argument('--dbs', default='')
     args = parser.parse_args()
 
     eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
@@ -40,25 +39,22 @@
     # params = json.loads(open(args.config_file).read())
     dm_dict = {}
     dm_dict['data_tables'] = dm_dict.get('data_tables', {})
-    data_table = 'eggnog_mapper_db'
-    dm_dict['data_tables'][data_table]\
-        = dm_dict['data_tables'].get(data_table, [])
-    data_table_entry = dict(value=db_version, name=db_version,
-                            path=args.install_path)
-    dm_dict['data_tables'][data_table].append(data_table_entry)
-    data_table = 'eggnog_mapper_hmm_dbs'
+    data_table = 'eggnog_mapper_db_versioned'
     dm_dict['data_tables'][data_table]\
         = dm_dict['data_tables'].get(data_table, [])
-    if args.dbs:
-        dbs = [x.strip() for x in args.dbs.split(',')]
-        for db in dbs:
-            key = '%s_%s' % (db_version, db)
-            data_table_entry = dict(key=key, db_version=db_version,
-                                    value=db, name=db, path=db)
-            dm_dict['data_tables'][data_table].append(data_table_entry)
+    # Versionning is super confusing:
+    # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
+    # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
+    # db v4.5 are not compatible with eggnog-mapper 2.0
+    version = "2.0"
+    if "4.5" in db_version:
+        version = "1.0"
+    data_table_entry = dict(value=db_version, name=db_version,
+                            path=args.install_path, version=version)
+    dm_dict['data_tables'][data_table].append(data_table_entry)
 
     # save info to json file
-    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+    open(args.config_file, 'w').write(json.dumps(dm_dict))
 
 
 if __name__ == "__main__":