diff data_manager/bigg_model_sbml_fetcher.py @ 0:262b8d79bc08 draft

"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 19ad973add8651c1a18c1bda789e9296a57044b1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bigg_model_sbml_fetcher.py	Wed Feb 23 14:33:49 2022 +0000
@@ -0,0 +1,62 @@
+import argparse
+import json
+import os
+import sys
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+
+def url_download(url, workdir):
+    file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    except Exception as e:
+        sys.exit(str(e))
+    finally:
+        if src:
+            src.close()
+    return file_path
+
+
+def download(model_id, out_file):
+
+    with open(out_file) as fh:
+        params = json.load(fh)
+
+    workdir = params['output_data'][0]['extra_files_path']
+    os.makedirs(workdir)
+    file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml' % (model_id,), workdir)
+    entry_name = os.path.basename(file_path)
+
+    data_manager_json = {"data_tables": {}}
+    data_manager_entry = {}
+    data_manager_entry['value'] = model_id
+    data_manager_entry['name'] = entry_name
+    data_manager_entry['path'] = file_path
+
+    with open(out_file, 'w') as fh:
+        json.dump(data_manager_json, fh, sort_keys=True)
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--model-id', help='Model id')
+parser.add_argument('--out-file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.model_id, args.out_file)