1 files changed, 93 insertions, 10 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index a2eddfc6..1b1b56fb 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -20,17 +20,18 @@ class DoSearch(object):
     # Used to translate search phrases into classes
     search_types = dict()
 
-    def __init__(self, search_term, search_operator, dataset):
+    def __init__(self, search_term, search_operator=None, dataset=None):
         self.search_term = search_term
         # Make sure search_operator is something we expect
         assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
         self.search_operator = search_operator
         self.dataset = dataset
-        print("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
-        print("self.dataset.group is: ", pf(self.dataset.group))
-
-        #Get group information for dataset and the species id
-        self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)           
+        
+        if self.dataset:
+            print("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
+            print("self.dataset.group is: ", pf(self.dataset.group))
+            #Get group information for dataset and the species id
+            self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)           
 
     def execute(self, query):
         """Executes query and returns results"""
@@ -57,8 +58,42 @@ class DoSearch(object):
 
     @classmethod
     def get_search(cls, search_type):
+        print("search_types are:", pf(cls.search_types))
         return cls.search_types[search_type]
 
+class QuickMrnaAssaySearch(DoSearch):
+    """A general search for mRNA assays"""
+    
+    DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch"
+    
+    base_query = """SELECT ProbeSet.Name as ProbeSet_Name,
+                ProbeSet.Symbol as ProbeSet_Symbol,
+                ProbeSet.description as ProbeSet_Description,
+                ProbeSet.Chr_num as ProbeSet_Chr_Num,
+                ProbeSet.Mb as ProbeSet_Mb,
+                ProbeSet.name_num as ProbeSet_name_num
+                FROM ProbeSet """
+                
+    header_fields = ['',
+                     'Record ID',
+                     'Symbol',
+                     'Location']
+
+    def run(self):
+        """Generates and runs a search for assays across all mRNA expression datasets"""
+
+        print("Running ProbeSetSearch")
+        query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
+                    ProbeSet.description,
+                    ProbeSet.symbol,
+                    ProbeSet.alias)
+                    AGAINST ('%s' IN BOOLEAN MODE))
+                            """ % (escape(self.search_term[0]))
+
+        print("final query is:", pf(query))
+
+        return self.execute(query)
+
 
 class MrnaAssaySearch(DoSearch):
     """A search within an mRNA expression dataset"""
@@ -124,7 +159,7 @@ class MrnaAssaySearch(DoSearch):
 
         return self.execute(query)
 
-
+    
 class PhenotypeSearch(DoSearch):
     """A search within a phenotype dataset"""
 
@@ -198,9 +233,57 @@ class PhenotypeSearch(DoSearch):
 
         query = self.compile_final_query(where_clause = self.get_fields_clause())
 
-        results = self.execute(query)
-        print("in [df] run results are:", results)
-        return results
+        return self.execute(query)
+
+class QuickPhenotypeSearch(PhenotypeSearch):
+    """A search across all phenotype datasets"""
+    
+    DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch"
+    
+    base_query = """SELECT Species.Name as Species_Name,
+                PublishFreeze.FullName as Dataset_Name,
+                PublishFreeze.Name,
+                PublishXRef.Id,
+                PublishFreeze.createtime as thistable,
+                Publication.PubMed_ID as Publication_PubMed_ID,
+                Phenotype.Post_publication_description as Phenotype_Name
+                FROM Phenotype,
+                    PublishFreeze,
+                    Publication,
+                    PublishXRef,
+                    InbredSet,
+                    Species """
+
+    search_fields = ('Phenotype.Post_publication_description',
+                    'Phenotype.Pre_publication_description',
+                    'Phenotype.Pre_publication_abbreviation',
+                    'Phenotype.Post_publication_abbreviation',
+                    'Phenotype.Lab_code',
+                    'Publication.PubMed_ID',
+                    'Publication.Abstract',
+                    'Publication.Title',
+                    'Publication.Authors')    
+    
+    def compile_final_query(self, where_clause = ''):
+        """Generates the final query string"""
+
+        query = (self.base_query +
+                 """WHERE %s
+                    PublishXRef.PhenotypeId = Phenotype.Id and
+                    PublishXRef.PublicationId = Publication.Id and
+                    PublishXRef.InbredSetId = InbredSet.Id and
+                    InbredSet.SpeciesId = Species.Id""" % where_clause)
+
+        print("query is:", pf(query))
+
+        return query
+    
+    def run(self):
+        """Generates and runs a search across all phenotype datasets"""
+
+        query = self.compile_final_query(where_clause = self.get_fields_clause())
+
+        return self.execute(query)
 
 class GenotypeSearch(DoSearch):
     """A search within a genotype dataset"""