Made small change to parser to have it detect square brackets '[' along with

round ones '('; need to ask Sam about rewriting the regular expression stuff

Trimmed a lot of code from search_results.py

3 files changed, 99 insertions, 73 deletions

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 4517d9f5..ac6014e7 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -19,6 +19,10 @@ class DoSearch(object):
         self.dataset = dataset
         self.db_conn = db_conn
         self.cursor = cursor
+        
+        #Get group information for dataset and the species id
+        self.dataset.get_group()
+        self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group)           
 
     def execute(self, query):
         """Executes query and returns results"""
@@ -47,10 +51,6 @@ class ProbeSetSearch(DoSearch):
     
     DoSearch.search_types['ProbeSet'] = "ProbeSetSearch"
     
-    #Get group information for dataset and the species id
-    self.dataset.get_group()
-    self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group)
-    
     base_query = """SELECT ProbeSet.Name as TNAME,
                 0 as thistable,
                 ProbeSetXRef.Mean as TMEAN,
@@ -62,6 +62,7 @@ class ProbeSetSearch(DoSearch):
                 ProbeSet.name_num as TNAME_NUM
                 FROM ProbeSetXRef, ProbeSet """
 
+
     def compile_final_query(self, from_clause, where_clause):
         """Generates the final query string"""
         
@@ -268,7 +269,7 @@ class LrsSearch(ProbeSetSearch):
     
     LRS searches can take 2 different forms:
     - LRS=(min_LRS max_LRS)
-    - LRS=(mine_LRS max_LRS chromosome start_Mb end_Mb)
+    - LRS=(min_LRS max_LRS chromosome start_Mb end_Mb)
     where min/max_LRS represent the range of LRS scores and start/end_Mb represent
     the range in megabases on the given chromosome
     
@@ -276,9 +277,6 @@ class LrsSearch(ProbeSetSearch):
     
     DoSearch.search_types['LRS'] = 'LrsSearch'
     
-    self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor,
-                                                               self.dataset.group)
-    
 class CisLrsSearch(LrsSearch):
     """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
     
@@ -290,8 +288,10 @@ class CisLrsSearch(LrsSearch):
     mb_buffer will default to 5 megabases.
     
     A QTL is a cis-eQTL if a gene's expression is regulated by a QTL in roughly the same area
-    (where the area is determined by the mb_buffer that the user can choose.
+    (where the area is determined by the mb_buffer that the user can choose).
+    
     """
+    
     # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps
     # between this and the LrsSearch code. In the original code, commands are divided by
     # the number of inputs they take, so these commands are completely separate
@@ -300,7 +300,7 @@ class CisLrsSearch(LrsSearch):
 
     def run(self):
         if len(self.search_term) == 3:
-            lower_limit, upper_limit, min_threshold = int(value) for value in self.search_term
+            lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term]
             
             where_clause = """ %sXRef.LRS > %s and
                 %sXRef.LRS < %s  and
@@ -309,16 +309,65 @@ class CisLrsSearch(LrsSearch):
                 %s.Chr = Geno.Chr and
                 ABS(%s.Mb-Geno.Mb) < %s """ % (
                     self.dataset.type,
-                    min(lower_limit, upper_limit)
+                    min(lower_limit, upper_limit),
+                    self.dataset.type,
+                    max(lower_limit, upper_limit),
+                    self.dataset.type,
+                    self.species_id,
                     self.dataset.type,
-                    max(lower_limit, upper_limit,
                     self.dataset.type,
-                    
+                    min_threshold
                     )
 
         else:
-            NeedSomeErrorHere
-        
+            NeedSomeErrorHere            
+
+        return None
+    
+class TransLrsSearch(LrsSearch):
+    """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
+    
+    A transLRS search can take 2 forms:
+    - transLRS=(min_LRS max_LRS)
+    - transLRS=(min_LRS max_LRS mb_buffer)
+    where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
+    a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
+    mb_buffer will default to 5 megabases.
+    
+    A QTL is a trans-eQTL if a gene's expression is regulated by a QTL in a different location/area
+    (where the area is determined by the mb_buffer that the user can choose). Opposite of cis-eQTL.
+    
+    """
+    
+    # This is tentatively a child of LrsSearch; I'll need to check what code, if any, overlaps
+    # between this and the LrsSearch code. In the original code, commands are divided by
+    # the number of inputs they take, so these commands are completely separate
+    
+    DoSearch.search_types['TRANSLRS'] = "TransLrsSearch"
+
+    def run(self):
+        if len(self.search_term) == 3:
+            lower_limit, upper_limit, min_threshold = [int(value) for value in self.search_term]
+            
+            where_clause = """ %sXRef.LRS > %s and
+                %sXRef.LRS < %s  and
+                %sXRef.Locus = Geno.name and
+                Geno.SpeciesId = %s and
+                (%s.Chr != Geno.Chr or
+                ABS(%s.Mb-Geno.Mb) > %s) """ % (
+                    self.dataset.type,
+                    min(lower_limit, upper_limit),
+                    self.dataset.type,
+                    max(lower_limit, upper_limit),
+                    self.dataset.type,
+                    self.species_id,
+                    self.dataset.type,
+                    self.dataset.type,
+                    min_threshold
+                    )
+
+        else:
+            NeedSomeErrorHere            
 
         return None
     
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index e693b2b8..b220f837 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -27,6 +27,13 @@ def parse(pstring):
                 value = value[1:-1] # Get rid of the parenthesis
                 values = re.split(r"""\s+|,""", value)
                 value = [value.strip() for value in values if value.strip()]
+            # Brackets can also be used to encapsulate values
+            elif '[' in value:
+                assert value.startswith("["), "Invalid token"
+                assert value.endswith("]"), "Invalid token"
+                value = value[1:-1] # Get rid of the brackets
+                values = re.split(r"""\s+|,""", value)
+                value = [value.strip() for value in values if value.strip()]                
             term = dict(key=key,
                         seperator=seperator,
                         search_term=value)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 6ba4d94a..4aa1f2bc 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -213,56 +213,49 @@ class SearchResultPage(templatePage):
             #### Excel file stuff stops
 
             if self.dataset.type == "ProbeSet":
-                #for item in result:
                 print("foo locals are:", locals())
                 probe_set_id = result[0]
-                print("probe_set_id is:", pf(probe_set_id))
                 this_trait = webqtlTrait(db=self.dataset, name=probe_set_id, cursor=self.cursor)
                 this_trait.retrieveInfo(QTL=True)
                 print("this_trait is:", pf(this_trait))
                 self.trait_list.append(this_trait)
-            elif self.dataset.type == "Publish":
-                newrow += 1
-                tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
-            elif self.dataset.type == "Geno":
-                newrow += 1
-                tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet, newrow=newrow)
+            #elif self.dataset.type == "Publish":
+            #    tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, species=species)
+            #elif self.dataset.type == "Geno":
+            #    tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet)
 
             #traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
             hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group}
             hddn['incparentsf1']='ON'
-            #    for key in hddn.keys():
-            #        traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-            #
-            #    traitForm.append(HT.P(),pageTable)
-            #
-            #    TD_LR.append(traitForm)
-            #    if len(self.results) > 1 and i < len(self.results) - 1:
-            #        last_result = True
-            #if last_result:
-            #    TD_LR.contents.pop()
-            
+
         if self.dataset.type == "ProbeSet":
-            tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, newrow=newrow, species=species)            
+            tblobj['body'] = self.getTableBodyForProbeSet(trait_list=self.trait_list, formName=self.form_name, species=species)            
         elif self.dataset.type == "Publish":
-            tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=mainfmName, worksheet=worksheet, newrow=newrow, species=species)
+            tblobj['body'] = self.getTableBodyForPublish(trait_list=self.trait_list, formName=self.form_name, species=species)
         elif self.dataset.type == "Geno":
-            tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=form_name, worksheet=worksheet, newrow=newrow)
+            tblobj['body'] = self.getTableBodyForGeno(trait_list=self.trait_list, form_name=self.form_name)
 
 
     def search(self):
         print("fd.search_terms:", self.fd['search_terms'])
         self.search_terms = parser.parse(self.fd['search_terms'])
         print("After parsing:", self.search_terms)
-                
+
         self.results = []
         for a_search in self.search_terms:
             print("[kodak] item is:", pf(a_search))
             search_term = a_search['search_term']
-            search_type = string.upper(a_search['key'])
-            if not search_type:
+            if a_search['key']:
+                search_type = string.upper(a_search['key'])
+            else:
                 # We fall back to the dataset type as the key to get the right object
-                search_type = self.dataset.type                
+                search_type = self.dataset.type
+                
+            # This is throwing an error when a_search['key'] is None, so I changed above    
+            #search_type = string.upper(a_search['key'])
+            #if not search_type:
+            #    # We fall back to the dataset type as the key to get the right object
+            #    search_type = self.dataset.type
 
             search_ob = do_search.DoSearch.get_search(search_type)
             search_class = getattr(do_search, search_ob)
@@ -289,26 +282,9 @@ class SearchResultPage(templatePage):
             keyword = string.replace(keyword,"?",".")
             wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
         return wildcardkeyword
+    
 
-
-    def getTableHeaderForGeno(self, worksheet=None, newrow=None, headingStyle=None):
-
-        tblobj_header = []
-
-        className = "fs13 fwb ffl b1 cw cbrb"
-
-        tblobj_header = [[THCell(HT.TD(' ', Class=className), sort=0),
-            THCell(HT.TD('Record', HT.BR(), 'ID', HT.BR(), Class=className), text='record_id', idx=1),
-            THCell(HT.TD('Location', HT.BR(), 'Chr and Mb', HT.BR(), Class=className), text='location', idx=2)]]
-
-        for ncol, item in enumerate(['Record ID', 'Location (Chr, Mb)']):
-            worksheet.write([newrow, ncol], item, headingStyle)
-            worksheet.set_column([ncol, ncol], 2*len(item))
-
-        return tblobj_header
-
-
-    def getTableBodyForGeno(self, trait_list, formName=None, worksheet=None, newrow=None):
+    def getTableBodyForGeno(self, trait_list, formName=None):
 
         tblobj_body = []
 
@@ -345,15 +321,13 @@ class SearchResultPage(templatePage):
 
             tblobj_body.append(tr)
 
-            for ncol, item in enumerate([this_trait.name, trait_location_repr]):
-                worksheet.write([newrow, ncol], item)
-
-            newrow += 1
+            #for ncol, item in enumerate([this_trait.name, trait_location_repr]):
+            #    worksheet.write([newrow, ncol], item)
 
         return tblobj_body
-    
 
-    def getTableBodyForPublish(self, trait_list, formName=None, worksheet=None, newrow=None, species=''):
+
+    def getTableBodyForPublish(self, trait_list, formName=None, species=''):
 
         tblobj_body = []
 
@@ -438,15 +412,13 @@ class SearchResultPage(templatePage):
 
             tblobj_body.append(tr)
 
-            for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]):
-                worksheet.write([newrow, ncol], item)
-
-            newrow += 1
+            #for ncol, item in enumerate([this_trait.name, PhenotypeString, this_trait.authors, this_trait.year, this_trait.pubmed_id, LRS_score_repr, LRS_location_repr]):
+            #    worksheet.write([newrow, ncol], item)
 
         return tblobj_body
 
 
-    def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, worksheet=None, newrow=None, species=''):
+    def getTableBodyForProbeSet(self, trait_list=None, primaryTrait=None, formName=None, species=''):
         #  Note: setting trait_list to [] is probably not a great idea.
         tblobj_body = []
 
@@ -590,8 +562,6 @@ class SearchResultPage(templatePage):
 
             tblobj_body.append(tr)
 
-            newrow += 1
-
         return tblobj_body