fetching abstracts

1 files changed, 22 insertions, 4 deletions

diff --git a/ncbi/dbsnp/ncbiutils.py b/ncbi/dbsnp/ncbiutils.py
index b3c199a..9bc1c94 100644
--- a/ncbi/dbsnp/ncbiutils.py
+++ b/ncbi/dbsnp/ncbiutils.py
@@ -2,10 +2,11 @@
 
 import requests
 
-BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
-
-# Example https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=snp_pubmed_cited[sb]&retmax=200000&retstart=1000&retmode=json
-def db_query(**kwargs):
+"""
+Used to make an esearch and get the results back in json
+"""
+def esearch(**kwargs):
+    BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
     args = []
     for key, value in kwargs.items():
         args.append(key+"="+str(value))
@@ -15,4 +16,21 @@ def db_query(**kwargs):
         results = resp.json()
         return(results)
     else:
+        print("You've encountered an error and we can't return your results")
+
+"""
+Used for an efetch, which is primarily to query specific IDs in dbsnp or pubmed
+Doesn't return json, but must return XML, apparently.  
+"""
+def efetch(**kwargs):
+    BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
+    args = []
+    for key, value in kwargs.items():
+        args.append(key+"="+str(value))
+    qstring = "&".join(args)
+    resp = requests.get(BASE_URL + qstring)
+    if resp.status_code == 200:
+        results = resp.text
+        return(results)
+    else:
         print("You've encountered an error and we can't return your results")
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