Updated list all metagenomes

Author: Will Trimble

examples/python/list_all_mg.py

@@ -1,24 +1,29 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 '''This script retrieves a list of metagenomes from the MG-RAST API.'''
 from __future__ import print_function
-import urllib
+from __future__ import unicode_literals
 import sys
 
-from mglib import get_auth_token, obj_from_url, API_URL
+from mglib import get_auth_token, obj_from_url, API_URL, urlencode
 
 def printlist(js):
     '''prints essential fields from metagenome list'''
     for item in js["data"]:
         if "public" in item.keys():
-            public = repr(item["public"])
+            public = item["public"]
         else:
-            public = "False"
-        sys.stdout.write( ("\t".join([item["metagenome_id"],
-#                         str(len(item.keys())),
-                          public, item["created_on"],
-                          item["name"]]) + "\n").encode("utf-8"))
+            public = False
+        try:
+            mg_name= item["name"]
+            project_id = item["project_id"]
+            project_name = item["project_name"]
+        except KeyError:
+            sys.stderr.write(repr(item))
+        sys.stdout.write(("\t".join([item["metagenome_id"],
+#                        str(len(item.keys())),
+                         repr(public), item["created_on"],
+                         mg_name, project_id, project_name]) + "\n"))
 
-CALL = "/metagenome"
 CALL = "/search"
 
 key = get_auth_token()
@@ -28,19 +33,21 @@ def printlist(js):
 
 # construct API call
 
-parameters = {"limit": limit, "auth": key, "order":"created_on", "direction": "asc"}
-base_url = API_URL + CALL + "?" + urllib.urlencode(parameters)
+parameters = {"limit": limit, "order":"created_on", "direction": "asc", "public": "1"}
+API_URL= "https://api.mg-rast.org/"
+
+base_url = API_URL + CALL + "?" + urlencode(parameters)
 
 # convert the data from a JSON structure to a python data type, a dict of dicts.
-jsonstructure = obj_from_url(base_url)
+jsonstructure = obj_from_url(base_url, auth=key)
 
 # unpack and display the data table
 total_count = int(jsonstructure["total_count"])
 sys.stderr.write("Total number of records: {:d}\n".format(total_count))
 
-for i in range(0, total_count / limit +1):
+for i in range(0, int(total_count / limit) +1):
     sys.stderr.write("Page {:d}\t".format(i))
-    jsonstructure = obj_from_url(base_url)
+    jsonstructure = obj_from_url(base_url, auth=key)
     printlist(jsonstructure)
     try:
         next_url = jsonstructure["next"]