# HG changeset patch
# User iuc
# Date 1490803737 14400
# Node ID 80b0bd65cbfbc197de7b051b4abc0872d90afe49
# Parent  4c96b684f0fd1190f6b456ba6f475ea9059b7d1c
Uploaded

diff -r 4c96b684f0fd -r 80b0bd65cbfb data_manager/data_manager_plant_tribes_scaffolds_download.py
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py	Fri Jan 13 10:34:15 2017 -0500
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py	Wed Mar 29 12:08:57 2017 -0400
@@ -31,9 +31,23 @@
         shutil.rmtree(dir)
 
 
-def url_download(target_directory, url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
-    work_directory = os.path.abspath(os.path.join(os.getcwd(), 'scaffolds'))
-    make_directory(work_directory)
+def extract_archive(file_path, work_directory):
+    if tarfile.is_tarfile(file_path):
+        fh = tarfile.open(file_path, 'r:*')
+    elif zipfile.is_zipfile(file_path):
+        fh = zipfile.ZipFile(file_path, 'r')
+    else:
+        return
+    fh.extractall(work_directory)
+
+
+def move_files(source_directory, target_directory):
+    # Move the files into defined output directory.
+    for filename in os.listdir(source_directory):
+        shutil.move(os.path.join(source_directory, filename), target_directory)
+
+
+def url_download(url, work_directory):
     file_path = os.path.join(work_directory, os.path.basename(url))
     src = None
     dst = None
@@ -54,26 +68,43 @@
             src.close()
         if dst:
             dst.close()
-    if tarfile.is_tarfile(file_path):
-        fh = tarfile.open(file_path, 'r:*')
-    elif zipfile.is_zipfile(file_path):
-        fh = zipfile.ZipFile(file_path, 'r')
-    else:
-        return
-    fh.extractall(work_directory)
+    return file_path
+
+
+def download(target_directory, web_url, config_web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+    data_manager_dict = {}
+    data_table_entry = {}
+    # Download the scaffolds data.
+    work_directory = os.path.abspath(os.path.join(os.getcwd(), 'scaffolds'))
+    make_directory(work_directory)
+    file_path = url_download(web_url, work_directory)
+    extract_archive(file_path, work_directory)
     os.remove(file_path)
-    # Move the scaffolds data files into defined output directory.
-    for filename in os.listdir(work_directory):
-        shutil.move(os.path.join(work_directory, filename), target_directory)
+    # Move the scaffolds data files into the defined output directory.
+    move_files(work_directory, target_directory)
     remove_directory(work_directory)
-    data_manager_dict = {}
-    # Populate the data table, there should be a single entry in target_directory.
+    # Populate the data_manager_dict with the scaffolds data entry.
     for file_path in os.listdir(target_directory):
         full_path = os.path.abspath(os.path.join(target_directory, file_path))
         entry_name = "%s" % os.path.basename(file_path)
-        data_table_entry = dict(value=entry_name, name=entry_name, path=full_path, description=description)
+        data_table_entry['value'] = entry_name
+        data_table_entry['name'] = entry_name
+        data_table_entry['path'] = full_path
+        data_table_entry['description'] = description
+        # Populate the data_manager_dict.
         for data_table_name in data_table_names:
             data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+    # Download the default configuration files.
+    work_directory = os.path.abspath(os.path.join(os.getcwd(), 'configs'))
+    make_directory(work_directory)
+    file_path = url_download(config_web_url, work_directory)
+    extract_archive(file_path, work_directory)
+    os.remove(file_path)
+    # Move the default configuration files into the defined output directory.
+    source_configs_directory = os.path.join(work_directory, entry_name)
+    target_configs_directory = os.path.join(target_directory, entry_name)
+    move_files(source_configs_directory, target_configs_directory)
+    remove_directory(work_directory)
     return data_manager_dict
 
 
@@ -81,7 +112,8 @@
 parser.add_argument('--description', dest='description', default=None, help='Description')
 parser.add_argument('--name', dest='name', help='Data table entry unique ID')
 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
-parser.add_argument('--web_url', dest='web_url', help='Web URL')
+parser.add_argument('--web_url', dest='web_url', help='URL for downloading scaffolds')
+parser.add_argument('--config_web_url', dest='config_web_url', help='URL for downloading default configs')
 
 args = parser.parse_args()
 
@@ -97,7 +129,7 @@
     description = args.description.strip()
 
 # Get the scaffolds data.
-data_manager_dict = url_download(target_directory, args.web_url, description)
+data_manager_dict = download(target_directory, args.web_url, args.config_web_url, description)
 # Write the JSON output dataset.
 fh = open(args.out_file, 'wb')
 fh.write(json.dumps(data_manager_dict))