Fixed queries

workflows/smokers.py

@@ -159,7 +159,7 @@ class SAM(workflow.Function):
         rpy.r.library("siggenes")
         rpy.r.library("multtest")
         
-        cl = scipy.dot(y.asarray(), scipy.diag([1,2,3]) ).sum(1)
+        cl = scipy.dot(y.asarray(), scipy.diag(scipy.arange(y.shape[1]))).sum(1)
         data = x.asarray().T
         sam = rpy.r.sam(data, cl=cl, B=n_iter, var_equal=False,med=False,s0=scipy.nan,rand=scipy.nan)
         qvals = scipy.asarray(rpy.r.slot(sam, "p.value"))
@@ -297,11 +297,12 @@ class ModKernelFunction(workflow.Function):
 
 
 class NCBIQuery(workflow.Function):
-    def __init__(self, gene_id_name='gene_id'):
+    def __init__(self, gene_id_name='gene_ids'):
         self._gene_id_name = gene_id_name
         workflow.Function.__init__(self, 'query', 'NCBI')
 
-    def run(self, selection):
+    def run(self):
+        selection = main.project.get_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
@@ -309,7 +310,6 @@ class NCBIQuery(workflow.Function):
             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',
@@ -322,7 +322,7 @@ class NCBIQuery(workflow.Function):
 
 
 class KEGGQuery(workflow.Function):
-    def __init__(self, org='hsa', gene_id_name='gene_id'):
+    def __init__(self, org='hsa', gene_id_name='gene_ids'):
         self._org=org
         self._gene_id_name = gene_id_name
         workflow.Function.__init__(self, 'query', 'KEGG')