Got basic statistics in show_trait to display the correct number

of samples for each group

Got show_trait page to display for genotype traits

7 files changed, 72 insertions, 172 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index d0158ebd..8c9e3b10 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -258,113 +258,15 @@ class GeneralTrait:
         #else:
         results = self.dataset.retrieve_sample_data(self)
 
-        #if self.dataset.type == 'Temp':
-        #    query = '''
-        #            SELECT
-        #                    Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
-        #            FROM
-        #                    TempData, Temp, Strain
-        #            WHERE
-        #                    TempData.StrainId = Strain.Id AND
-        #                    TempData.Id = Temp.DataId AND
-        #                    Temp.name = '%s'
-        #            Order BY
-        #                    Strain.Name
-        #            ''' % self.name
-        ##XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
-        #elif self.dataset.type == 'Publish':
-        #    query = '''
-        #            SELECT
-        #                    Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
-        #            FROM
-        #                    (PublishData, Strain, PublishXRef, PublishFreeze)
-        #            left join PublishSE on
-        #                    (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
-        #            left join NStrain on
-        #                    (NStrain.DataId = PublishData.Id AND
-        #                    NStrain.StrainId = PublishData.StrainId)
-        #            WHERE
-        #                    PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-        #                    PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
-        #                    PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
-        #            Order BY
-        #                    Strain.Name
-        #            ''' % (self.name, self.dataset.id)
-
-        #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
-        #elif self.cellid:
-           
-        #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
-        #elif self.dataset.type == 'ProbeSet':
-        #    #ProbeSet Data
-        #    query = '''
-        #            SELECT
-        #                    Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
-        #            FROM
-        #                    (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
-        #            left join ProbeSetSE on
-        #                    (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
-        #            WHERE
-        #                    ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-        #                    ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-        #                    ProbeSetFreeze.Name = '%s' AND
-        #                    ProbeSetXRef.DataId = ProbeSetData.Id AND
-        #                    ProbeSetData.StrainId = Strain.Id
-        #            Order BY
-        #                    Strain.Name
-        #            ''' % (self.name, self.dataset.name)
-        ##XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
-        #else:
-        #    #Geno Data
-        #    #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
-        #    query = '''
-        #            SELECT
-        #                    Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
-        #            FROM
-        #                    (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
-        #            left join GenoSE on
-        #                    (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
-        #            WHERE
-        #                    Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
-        #                    GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-        #                    GenoFreeze.Name = '%s' AND
-        #                    GenoXRef.DataId = GenoData.Id AND
-        #                    GenoData.StrainId = Strain.Id
-        #            Order BY
-        #                    Strain.Name
-        #            ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group), self.name, self.dataset.name)
-
-
-        #self.cursor.execute(query)
-        #results = self.cursor.fetchall()
-        
         # Todo: is this necessary? If not remove
         self.data.clear()
 
         if results:
-            #self.mysqlid = results[0][-1]
-            #if samplelist:
             for item in results:
                 #name, value, variance, num_cases = item
                 if not samplelist or (samplelist and name in samplelist):
-                    #if value != None:
-                    #    num_cases = None
-                    #    if self.dataset.type in ('Publish', 'Temp'):
-                    #        ndata = item[3]
                     name = item[0]
                     self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
-                #end for
-        #    else:
-        #        for item in results:
-        #            val = item[1]
-        #            if val != None:
-        #                var = item[2]
-        #                ndata = None
-        #                if self.dataset.type in ('Publish', 'Temp'):
-        #                    ndata = item[3]
-        #                self.data[item[0]] = webqtlCaseData(val, var, ndata)
-        #        #end for
-        #    #end if
 
     #def keys(self):
     #    return self.__dict__.keys()
@@ -429,7 +331,9 @@ class GeneralTrait:
                             GenoXRef.GenoId = Geno.Id AND
                             GenoFreeze.Name = '%s' AND
                             Geno.Name = '%s'
-                    """ % (escape(display_fields_string), escape(self.dataset.name), escape(self.name))
+                    """ % (escape(display_fields_string),
+                           escape(self.dataset.name),
+                           escape(self.name))
             traitInfo = g.db.execute(query).fetchone()
             print("traitInfo is: ", pf(traitInfo))
         else: #Temp type
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 3ce613e9..fc45395c 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -60,7 +60,7 @@ class DoSearch(object):
         return cls.search_types[search_type]
 
 
-class ProbeSetSearch(DoSearch):
+class MrnaAssaySearch(DoSearch):
     """A search within an mRNA expression dataset"""
 
     DoSearch.search_types['ProbeSet'] = "ProbeSetSearch"
@@ -265,7 +265,7 @@ class GenotypeSearch(DoSearch):
 
         return self.execute(self.query)
 
-class RifSearch(ProbeSetSearch):
+class RifSearch(MrnaAssaySearch):
     """Searches for traits with a Gene RIF entry including the search term."""
 
     DoSearch.search_types['RIF'] = "RifSearch"
@@ -280,7 +280,7 @@ class RifSearch(ProbeSetSearch):
 
         return self.execute(query)
 
-class WikiSearch(ProbeSetSearch):
+class WikiSearch(MrnaAssaySearch):
     """Searches GeneWiki for traits other people have annotated"""
 
     DoSearch.search_types['WIKI'] =  "WikiSearch"
@@ -298,7 +298,7 @@ class WikiSearch(ProbeSetSearch):
 
         return self.execute(query)
 
-class GoSearch(ProbeSetSearch):
+class GoSearch(MrnaAssaySearch):
     """Searches for synapse-associated genes listed in the Gene Ontology."""
 
     DoSearch.search_types['GO'] =  "GoSearch"
@@ -323,7 +323,7 @@ class GoSearch(ProbeSetSearch):
         return self.execute(query)
 
 #ZS: Not sure what the best way to deal with LRS searches is
-class LrsSearch(ProbeSetSearch):
+class LrsSearch(MrnaAssaySearch):
     """Searches for genes with a QTL within the given LRS values
 
     LRS searches can take 3 different forms:
@@ -484,7 +484,7 @@ class TransLrsSearch(CisTransLrsSearch):
         return self.real_run(">")
 
 
-class MeanSearch(ProbeSetSearch):
+class MeanSearch(MrnaAssaySearch):
     """Searches for genes expressed within an interval (log2 units) determined by the user"""
 
     DoSearch.search_types['MEAN'] = "MeanSearch"
@@ -514,7 +514,7 @@ class MeanSearch(ProbeSetSearch):
 
         return self.execute(self.query)
 
-class RangeSearch(ProbeSetSearch):
+class RangeSearch(MrnaAssaySearch):
     """Searches for genes with a range of expression varying between two values"""
     
     DoSearch.search_types['RANGE'] = "RangeSearch"
@@ -571,7 +571,7 @@ class PositionSearch(DoSearch):
 
         return self.execute(self.query)        
 
-class MrnaPositionSearch(ProbeSetSearch, PositionSearch):
+class MrnaPositionSearch(MrnaAssaySearch, PositionSearch):
     """Searches for genes located within a specified range on a specified chromosome"""
     
     def run(self):
@@ -591,7 +591,7 @@ class GenotypePositionSearch(GenotypeSearch, PositionSearch):
 
         return self.execute(self.query)
     
-class PvalueSearch(ProbeSetSearch):
+class PvalueSearch(MrnaAssaySearch):
     """Searches for traits with a permutationed p-value between low and high"""
     
     def run(self):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index f991d8c7..be92014d 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -73,6 +73,23 @@ def parse(pstring):
     print("* items are:", pf(items) + "\n")
     return(items)
 
+    #def encregexp(self,str):
+    #    if not str:
+    #        return []
+    #    else:
+    #        wildcardkeyword = str.strip()
+    #        wildcardkeyword = string.replace(wildcardkeyword,',',' ')
+    #        wildcardkeyword = string.replace(wildcardkeyword,';',' ')
+    #        wildcardkeyword = wildcardkeyword.split()
+    #    NNN = len(wildcardkeyword)
+    #    for i in range(NNN):
+    #        keyword = wildcardkeyword[i]
+    #        keyword = string.replace(keyword,"*",".*")
+    #        keyword = string.replace(keyword,"?",".")
+    #        wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
+    #    return wildcardkeyword
+
+
 if __name__ == '__main__':
     parse("foo=[3 2 1]")
     parse("WIKI=ho*")
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5cb8e314..d986a2e0 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -54,11 +54,6 @@ class SearchResultPage(templatePage):
         # change back to self.dataset
         #if not self.dataset or self.dataset == 'spacer':
         #    #Error, No dataset selected
-        #    heading = "Search Result"
-        #    detail = ['''No dataset was selected for this search, please
-        #        go back and SELECT at least one dataset.''']
-        #    self.error(heading=heading,detail=detail,error="No dataset Selected")
-        #    return
 
         ###########################################
         #   Names and IDs of group / F2 set
@@ -144,21 +139,3 @@ class SearchResultPage(templatePage):
             print("in the search results are:", self.results)
 
         self.header_fields = the_search.header_fields
-
-
-    #ZS: This should be handled in the parser
-    def encregexp(self,str):
-        if not str:
-            return []
-        else:
-            wildcardkeyword = str.strip()
-            wildcardkeyword = string.replace(wildcardkeyword,',',' ')
-            wildcardkeyword = string.replace(wildcardkeyword,';',' ')
-            wildcardkeyword = wildcardkeyword.split()
-        NNN = len(wildcardkeyword)
-        for i in range(NNN):
-            keyword = wildcardkeyword[i]
-            keyword = string.replace(keyword,"*",".*")
-            keyword = string.replace(keyword,"?",".")
-            wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
-        return wildcardkeyword
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 0f593216..836d37ea 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -828,35 +828,34 @@ class ShowTrait(object):
 
         elif this_trait and this_trait.dataset and this_trait.dataset.type == 'Geno': #Check if trait is genotype
 
-            GenoInfo = HT.Paragraph()
             if this_trait.chr and this_trait.mb:
                 location = ' Chr %s @ %s Mb' % (this_trait.chr,this_trait.mb)
             else:
                 location = "not available"
 
-            if this_trait.sequence and len(this_trait.sequence) > 100:
-                if _Species == "rat":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence)
-                    UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence)
-                elif _Species == "mouse":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
-                    UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
-                elif _Species == "human":
-                    UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
-                    UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence)
-                else:
-                    UCSC_BLAT_URL = ""
-                    UTHSC_BLAT_URL = ""
-                if UCSC_BLAT_URL:
-                    #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
-                    verifyButton = HT.Href(url="#")
-                    verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
-                    verifyButton.append(verifyButtonImg)
-                    verifyText = "Verify"
-                    rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
-                    rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
-                    rnaseqButton.append(rnaseqButtonImg)
-                    rnaseqText = "RNA-seq"
+            #if this_trait.sequence and len(this_trait.sequence) > 100:
+            #    if _Species == "rat":
+            #        UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', this_trait.sequence)
+            #        UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('rat', 'rn3', this_trait.sequence)
+            #    elif _Species == "mouse":
+            #        UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
+            #        UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', this_trait.sequence)
+            #    elif _Species == "human":
+            #        UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence)
+            #        UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('human', 'hg19', this_trait.sequence)
+            #    else:
+            #        UCSC_BLAT_URL = ""
+            #        UTHSC_BLAT_URL = ""
+            #    if UCSC_BLAT_URL:
+            #        #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
+            #        verifyButton = HT.Href(url="#")
+            #        verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+            #        verifyButton.append(verifyButtonImg)
+            #        verifyText = "Verify"
+            #        rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
+            #        rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+            #        rnaseqButton.append(rnaseqButtonImg)
+            #        rnaseqText = "RNA-seq"
 
             #tbl.append(HT.TR(
             #                HT.TD('Location: ', Class="fs13 fwb",
@@ -872,7 +871,7 @@ class ShowTrait(object):
             #                        valign="top", width=740)
             #                ))
 
-            menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1")
+            #menuTable = HT.TableLite(cellpadding=2, Class="collap", width="275", id="target1")
             #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(verifyButton, align="center"),HT.TD(rnaseqButton, align="center"), HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
             #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(verifyText, align="center"),HT.TD(rnaseqText, align="center"), HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;"))
 
@@ -1629,7 +1628,6 @@ class ShowTrait(object):
                                         header="%s Only" % (self.dataset.group.name))
         print("primary_samples is: ", pf(primary_samples))
 
-
         other_sample_names = []
         for sample in this_trait.data.keys():
             if sample not in all_samples_ordered:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 278a134b..04d55be7 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -110,6 +110,7 @@ $ ->
                 change_stats_value(sample_sets, category, row.vn, row.digits)
 
     edit_data_change = ->
+        already_seen = {}
         sample_sets =
             samples_primary: new Stats([])
             samples_other: new Stats([])
@@ -117,21 +118,14 @@ $ ->
 
         console.log("at beginning:", sample_sets)
 
-        # ##########
-        # Bug here #value_table doesn't exist and why is it a class?
-        # ##########
-
-        #values = $('.value_table').find(".edit_sample_value")
-
-
         tables = ['samples_primary', 'samples_other']
         for table in tables
             rows = $("#" + table).find('tr')
             console.log("[fuji3] rows:", rows)
             for row in rows
+                name = $(row).find('.edit_sample_sample_name').html()
+                name = $.trim(name)
                 real_value = $(row).find('.edit_sample_value').val()
-                #row = $(value).closest("tr")
-                #category = row[0].id
                 console.log("real_value:", real_value)
                 checkbox = $(row).find(".edit_sample_checkbox")
                 checked = $(checkbox).attr('checked')
@@ -139,11 +133,13 @@ $ ->
                 if checked and is_number(real_value) and real_value != ""
                     console.log("in the iffy if")
                     real_value = parseFloat(real_value)
-                    #if _(category).startsWith("Primary")
+
                     sample_sets[table].add_value(real_value)
-                    #else if _(category).startsWith("Other")
-                    #    sample_sets.other_only.add_value(real_value)
-                    sample_sets['samples_all'].add_value(real_value)
+                    console.log("checking name of:", name)
+                    if not (name of already_seen)
+                        console.log("haven't seen")
+                        sample_sets['samples_all'].add_value(real_value)
+                        already_seen[name] = true
         console.log("towards end:", sample_sets)
         update_stat_values(sample_sets)
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 3a7bc387..1037c890 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -115,7 +115,8 @@
       return _results;
     };
     edit_data_change = function() {
-      var checkbox, checked, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
+      var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
+      already_seen = {};
       sample_sets = {
         samples_primary: new Stats([]),
         samples_other: new Stats([]),
@@ -129,6 +130,8 @@
         console.log("[fuji3] rows:", rows);
         for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
           row = rows[_j];
+          name = $(row).find('.edit_sample_sample_name').html();
+          name = $.trim(name);
           real_value = $(row).find('.edit_sample_value').val();
           console.log("real_value:", real_value);
           checkbox = $(row).find(".edit_sample_checkbox");
@@ -137,7 +140,12 @@
             console.log("in the iffy if");
             real_value = parseFloat(real_value);
             sample_sets[table].add_value(real_value);
-            sample_sets['samples_all'].add_value(real_value);
+            console.log("checking name of:", name);
+            if (!(name in already_seen)) {
+              console.log("haven't seen");
+              sample_sets['samples_all'].add_value(real_value);
+              already_seen[name] = true;
+            }
           }
         }
       }