changeset 1:7093598fa300 draft

Uploaded

--- a/data_manager/gtdbtk_database_installer.py	Tue Mar 15 15:32:31 2022 +0000
+++ b/data_manager/gtdbtk_database_installer.py	Tue Mar 15 19:31:23 2022 +0000
@@ -9,15 +9,15 @@
 from urllib.parse import urlparse
 
 
-def url_download(url, work_dir):
+def url_download(url, target_directory):
     url_parts = urlparse(url)
-    file_path = os.path.abspath(os.path.join(work_dir, os.path.basename(url_parts.path)))
+    tarball = os.path.abspath(os.path.join(target_directory, os.path.basename(url_parts.path)))
     src = None
     dst = None
     try:
         req = Request(url)
         src = urlopen(req)
-        with open(file_path, 'wb') as dst:
+        with open(tarball, 'wb') as dst:
             while True:
                 chunk = src.read(2**10)
                 if chunk:
@@ -27,15 +27,16 @@
     except Exception as e:
         sys.exit(str(e))
     finally:
-        if src:
+        if src is not None:
             src.close()
-    if tarfile.is_tarfile(file_path):
-        fh = tarfile.open(file_path, 'r:*')
+    if tarfile.is_tarfile(tarball):
+        fh = tarfile.open(tarball, 'r:*')
     else:
-        return file_path
-    fh.extractall(work_dir)
-    os.remove(file_path)
-    return work_dir
+        return tarball
+    fh.extractall(target_directory)
+    fh.close()
+    os.remove(tarball)
+    return target_directory
 
 
 def download(database_id, database_name, url, out_file):
@@ -43,15 +44,15 @@
     with open(out_file) as fh:
         params = json.load(fh)
 
-    work_dir = params['output_data'][0]['extra_files_path']
-    os.makedirs(work_dir)
-    file_path = url_download(url, work_dir)
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.makedirs(target_directory)
+    file_path = url_download(url, target_directory)
 
     data_manager_json = {"data_tables": {}}
     data_manager_entry = {}
     data_manager_entry['value'] = database_id
     data_manager_entry['name'] = database_name
-    data_manager_entry['path'] = file_path
+    data_manager_entry['db_path'] = file_path
     data_manager_json["data_tables"]["gtdbtk_database"] = data_manager_entry
 
     with open(out_file, 'w') as fh:

--- a/data_manager/gtdbtk_database_installer.xml	Tue Mar 15 15:32:31 2022 +0000
+++ b/data_manager/gtdbtk_database_installer.xml	Tue Mar 15 19:31:23 2022 +0000
@@ -23,7 +23,7 @@
         <param name="url" type="text" value="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz" label="URL for downloading the selected version of the GTDB-Tk database"/>
     </inputs>
     <outputs>
-        <data name="out_file" format="data_manager_json" />
+        <data name="out_file" format="data_manager_json"/>
     </outputs>
     <tests>
         <test>

--- a/tool-data/gtdbtk_database.loc.sample	Tue Mar 15 15:32:31 2022 +0000
+++ b/tool-data/gtdbtk_database.loc.sample	Tue Mar 15 19:31:23 2022 +0000
@@ -23,4 +23,3 @@
 #drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
 #drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
 #drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
-release202		GTDB-Tk database release 202	/depot/data2/galaxy/tool-data/gtdbtk_database/release202