Rewrite of prepare, list_recipes, list_local_databases, remove and card...

Rewrite of prepare, list_recipes, list_local_databases, remove and card download script\nOther commands will follow

dbman/helper.py

+import wget
+import tarfile
+import json
+import datetime
+import logging
+
+def download(url):
+  logging.info("Downloading " + url)
+  filename = wget.download(url)
+  print("") # wget does not add a newline to its download bar
+  return filename
+
+def extract(filename):
+  logging.info("Extracting " + filename)
+  with tarfile.open(filename, 'r') as tar:
+    tar.extractall()
+
+def create_metadata(name,
+                    tool,
+                    description=None, 
+                    creation_date=datetime.datetime.now().isoformat(), 
+                    version=datetime.date.today().isoformat(),
+                    ):
+  metadata = { 
+    'name': name,
+    'tool': tool,
+    'description': description,
+    'creation_date': creation_date,
+    'version': version
+  }
+
+  with open("metadata.json", "w") as metadata_file:
+    logging.info("Writing metadata " + json.dumps(metadata))
+    json.dump(metadata, metadata_file)

dbman/recipes/download_card.py

+#!/usr/bin/env python3
+import dbman.helper as h
+import json
+
+import logging
+logging.basicConfig(level=logging.INFO)
+
+dbname = "card"
+dbdescription = "The Comprehensive Antibiotic Resistance Database"
+url = "https://card.mcmaster.ca/latest/data"
+
+# the card version is either available on the homepage or inside the card.json file
+# here we use the card.json file
+def lookup_card_version():
+  with open("card.json") as card:
+    data = json.load(card)
+    version = data["_version"]
+    return version
+
+# download archive
+fn = h.download(url)
+
+# extract archive
+h.extract(fn)
+
+# detect version
+version = lookup_card_version()
+
+# write metadata file
+h.create_metadata(dbname, "download", dbdescription, version=version)

requirements.txt

 wget
+sphinx
+s3cmd
+prettytable