From dd04e28a6236e842d614fa221e90ad1650bce7cf Mon Sep 17 00:00:00 2001
From: flatberg <flatberg@pvv.ntnu.no>
Date: Thu, 5 Jul 2007 18:49:24 +0000
Subject: [PATCH] Query fix

---
 workflows/smokers.py | 30 +++++++++++++++++++++---------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/workflows/smokers.py b/workflows/smokers.py
index 3d222cd..5797347 100644
--- a/workflows/smokers.py
+++ b/workflows/smokers.py
@@ -229,15 +229,24 @@ class ModKernelFunction(workflow.Function):
 
 
 class NCBIQuery(workflow.Function):
-    def __init__(self):
+    def __init__(self, gene_id_name='gene_id'):
+        self._gene_id_name = gene_id_name
         workflow.Function.__init__(self, 'query', 'NCBI')
 
     def run(self, selection):
+        if not selection.has_key(self._gene_id_name):
+            logger.log("notice", "Expected gene ids: %s, but got: %s" %(self._gene_id_name, selection.keys()))
+            return None
+        if len(selection[self._gene_id_name])==0:
+            logger.log("notice", "No selected genes to query")
+            return None
+        
+        logger.log("notice", "No selected genes to query")
         base = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?'
         options = {r'&db=' : 'gene',
                    r'&cmd=' : 'retrieve',
                    r'&dopt=' : 'full_report'}
-        gene_str = ''.join([gene + "+" for gene in selection['gene_id']])
+        gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
         options[r'&list_uids='] = gene_str[:-1]
         opt_str = ''.join([key+value for key,value in options.items()])
         web_str = base + opt_str
@@ -245,20 +254,23 @@ class NCBIQuery(workflow.Function):
 
 
 class KEGGQuery(workflow.Function):
-    def __init__(self):
+    def __init__(self, org='hsa', gene_id_name='gene_id'):
+        self._org=org
+        self._gene_id_name = gene_id_name
         workflow.Function.__init__(self, 'query', 'KEGG')
 
     def run(self, selection):
-        if not selection.has_key('genes') \
-               or not selection.has_key('orfs'):
+        if not selection.has_key(self._gene_id_name):
+            logger.log("notice", "Expected gene ids: %s, but got. %s" %(self._gene_id_name, selection.keys()))
+            return None
+        if len(selection[self._gene_id_name])==0:
+            logger.log("notice", "No selected genes to query")
             return None
         
         base = r'http://www.genome.jp/dbget-bin/www_bget?'
-        options = {'org' : 'gene'}
-        org = 'hsa'
-        gene_str = ''.join([gene + "+" for gene in selection['gene_id']])
+        gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
         gene_str = gene_str[:-1]
-        gene_str = org + "+" + gene_str
+        gene_str = self._org + "+" + gene_str
         web_str = base + gene_str
         webbrowser.open(web_str)