Worked on improving readData and informativeStrains functions in webqtlFormData while trying to get correlation page running

7 files changed, 83 insertions, 70 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index be023c1d..9d31fb5d 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -36,6 +36,12 @@ coffee --help (for information about setting options)
 
 ===========================================
 
+Unset ASKPASS when trying to git push
+
+unset SSH_ASKPASS
+
+===========================================
+
 Python stuff:
 
 Classes should always inherit "object"
\ No newline at end of file
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 177c72a2..9f58d437 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -63,7 +63,7 @@ class webqtlFormData:
 
         for item in start_vars:
             self.__dict__[item] = start_vars[item]
-        #print("  Now self.dict is:", pf(self.__dict__))
+        print("  Now self.dict is:", pf(self.__dict__))
 
         #Todo: This can't be good below...rework
         try:
@@ -216,6 +216,13 @@ class webqtlFormData:
 
         #### Todo: Rewrite below when we get to someone submitting their own trait #####
 
+        def to_float(item):
+            try:
+                return float(item)
+            except ValueError:
+                return None
+
+        print("bottle strainlist is:", strainlist)
         if traitfiledata:
             tt = traitfiledata.split()
             values = map(webqtlUtil.StringAsFloat, tt)
@@ -223,12 +230,17 @@ class webqtlFormData:
             tt = traitpastedata.split()
             values = map(webqtlUtil.StringAsFloat, tt)
         else:
-            values = map(self.FormDataAsFloat, strainlist)
+            print("mapping formdataasfloat")
+            #values = map(self.FormDataAsFloat, strainlist)
+            values = [to_float(getattr(self, key)) for key in strainlist]
+        print("rocket values is:", values)
+
 
         if len(values) < len(strainlist):
             values += [None] * (len(strainlist) - len(values))
         elif len(values) > len(strainlist):
             values = values[:len(strainlist)]
+        print("now values is:", values)
             
 
         if variancefiledata:
@@ -257,40 +269,48 @@ class webqtlFormData:
         self.allTraitData = {}
         for i, _strain in enumerate(strainlist):
             if values[i] != None:
-                self.allTraitData[_strain] = webqtlCaseData(values[i], variances[i], nstrains[i])
+                self.allTraitData[_strain] = webqtlCaseData(
+                    _strain, values[i], variances[i], nstrains[i])
+        print("allTraitData is:", pf(self.allTraitData))
 
 
 
-    def informativeStrains(self, strainlst=[], incVars = 0):
-        '''if readData was called, use this to output the informative strains
-           (strain with values)'''
-        if not strainlst:
-            strainlst = self.strainlist
+    def informativeStrains(self, strainlist=None, include_variances = None):
+        '''if readData was called, use this to output informative strains (strain with values)'''
+        
+        if not strainlist:
+            strainlist = self.strainlist
+            
         strains = []
-        vals = []
-        vars = []
-        for _strain in strainlst:
-            if self.allTraitData.has_key(_strain):
-                _val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var
+        values = []
+        variances = []
+        
+        #print("self.allTraitData is:", pf(self.allTraitData))
+        
+        for strain in strainlist:
+            if strain in self.allTraitData:
+                _val, _var = self.allTraitData[strain].value, self.allTraitData[strain].variance
                 if _val != None:
-                    if incVars:
+                    if include_variances:
                         if _var != None:
-                            strains.append(_strain)
-                            vals.append(_val)
-                            vars.append(_var)
+                            strains.append(strain)
+                            values.append(_val)
+                            variances.append(_var)
                     else:
-                        strains.append(_strain)
-                        vals.append(_val)
-                        vars.append(None)
-        return strains, vals, vars, len(strains)
+                        strains.append(strain)
+                        values.append(_val)
+                        variances.append(None)
+                        
+        return strains, values, variances, len(strains)
 
 
 
-    def FormDataAsFloat(self, key):
-        try:
-            return float(self.formdata.getfirst(key))
-        except:
-            return None
+    #def FormDataAsFloat(self, key):
+    #    
+    #    #try:
+    #    #    return float(self.key)
+    #    #except:
+    #    #    return None
 
 
     def FormVarianceAsFloat(self, key):
diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py
index 62e4c4ab..0af5297a 100644
--- a/wqflask/wqflask/correlation/CorrelationPage.py
+++ b/wqflask/wqflask/correlation/CorrelationPage.py
@@ -157,7 +157,7 @@ def get_correlation_method_key(form_data):
     #XZ, 09/28/2008: if user select "4", then display 1, 3 and 4.
     #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
 
-    method = form_data.formdata.getvalue("method")
+    method = form_data.method
     if method not in ["1", "2", "3" ,"4", "5"]:
         return "1"
 
@@ -166,7 +166,7 @@ def get_correlation_method_key(form_data):
 
 def get_custom_trait(form_data, cursor):
     """Pulls the custom trait, if it exists, out of the form data"""
-    trait_name = form_data.formdata.getvalue('fullname')
+    trait_name = form_data.fullname
 
     if trait_name:
         trait = webqtlTrait(fullname=trait_name, cursor=cursor)
@@ -178,7 +178,7 @@ def get_custom_trait(form_data, cursor):
 
 #XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
 def get_sample_data(fd):
-    print("fd is:", pf(fd.__dict__))
+    #print("fd is:", pf(fd.__dict__))
     if fd.allstrainlist:
         mdpchoice = fd.MDPChoice
         #XZ, in HTML source code, it is "BXD Only", "BXH Only", and so on
@@ -277,10 +277,10 @@ class CorrelationPage(templatePage):
         return templatePage.error(heading = heading, detail = [message], error=error)
 
     def __init__(self, fd):
-        print("in CorrelationPage __init__ fd is:", pf(fd.__dict__))
+        #print("in CorrelationPage __init__ fd is:", pf(fd.__dict__))
         # Call the superclass constructor
         templatePage.__init__(self, fd)
-        print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__))
+        #print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__))
         # Connect to the database
         if not self.openMysql():
             return
@@ -290,6 +290,7 @@ class CorrelationPage(templatePage):
             fd.readGenotype()
 
         sample_list = get_sample_data(fd)
+        print("sample_list is", pf(sample_list))
         
         # Whether the user chose BXD Only, Non-BXD Only, or All Strains
         # (replace BXD with whatever the group/inbredset name is)
@@ -321,17 +322,18 @@ class CorrelationPage(templatePage):
         #XZ, 09/18/2008: filter out the strains that have no value.
         self.sample_names, vals, vars, N = fd.informativeStrains(sample_list)
 
-         #CF - If less than a minimum number of strains/cases in common, don't calculate anything
+        print("samplenames is:", pf(self.sample_names))
+        #CF - If less than a minimum number of strains/cases in common, don't calculate anything
         if len(self.sample_names) < self.corrMinInformative:
             detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corrMinInformative, fd.RISet)]
             self.error(heading=None, detail=detail)
 
 
-        self.method = get_correlation_method_key(fd)
+        self.method = fd.method
         correlation_method = self.CORRELATION_METHODS[self.method]
         rankOrder = self.RANK_ORDERS[self.method]
 
-         # CF - Number of results returned
+        # CF - Number of results returned
         self.returnNumber = int(fd.criteria)
 
         self.record_count = 0
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
index 7bfa6d01..5c153ccb 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -166,20 +166,20 @@ $ ->
 
     $('select[name=corr_method]').change(on_corr_method_change)
     
-    on_corr_submit = ->
-        console.log("in beginning of on_corr_submit")
-        values = $('#trait_data_form').serialize()
-        console.log("in on_corr_submit, values are:", values)
-        
-        params = $.param(values)
-        window.location.href = "/corr_compute?" + params
-        
-        #$.ajax "/corr_compute",
-        #    type: 'GET'
-        #    dataType: 'html'
-        #    data: values
-            
-    $('#corr_compute').click(on_corr_submit)
+    #on_corr_submit = ->
+    #    console.log("in beginning of on_corr_submit")
+    #    values = $('#trait_data_form').serialize()
+    #    console.log("in on_corr_submit, values are:", values)
+    #    
+    #    params = $.param(values)
+    #    window.location.href = "/corr_compute?" + params
+    #    
+    #    #$.ajax "/corr_compute",
+    #    #    type: 'GET'
+    #    #    dataType: 'html'
+    #    #    data: values
+    #        
+    #$('#corr_compute').click(on_corr_submit)
 
     ###
     End Calculate Correlations Code
diff --git a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
index e1f870d9..55acbada 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -10,7 +10,7 @@
   };
 
   $(function() {
-    var edit_data_change, hide_tabs, make_table, on_corr_method_change, on_corr_submit, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
+    var edit_data_change, hide_tabs, make_table, on_corr_method_change, process_id, show_hide_outliers, stats_mdp_change, update_stat_values;
     hide_tabs = function(start) {
       var x, _i, _results;
       _results = [];
@@ -199,15 +199,6 @@
       return $('#' + corr_method + "_r_desc").show().effect("highlight");
     };
     $('select[name=corr_method]').change(on_corr_method_change);
-    on_corr_submit = function() {
-      var params, values;
-      console.log("in beginning of on_corr_submit");
-      values = $('#trait_data_form').serialize();
-      console.log("in on_corr_submit, values are:", values);
-      params = $.param(values);
-      return window.location.href = "/corr_compute?" + params;
-    };
-    $('#corr_compute').click(on_corr_submit);
     /*
         End Calculate Correlations Code
     */
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index a5d0e05c..c25db7c4 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -8,7 +8,7 @@
         <table width="100%" cellspacing="0" cellpadding="5">
           <tr>
             <td valign="top" width="100%" bgcolor="#FAFAFA">
-              <form method="post" action="/webqtl/main.py" name="dataInput" id="trait_data_form">
+              <form method="post" action="/corr_compute" name="dataInput" id="trait_data_form">
             {#    <input type="hidden" name="isSE" value="yes">
                 <input type="hidden" name="permCheck">
                 <input type="hidden" name="otherStrainVals" value="_">
@@ -683,13 +683,7 @@
 
                 <p class="sectionheader" id="title3" style="border-radius: 5px;">&nbsp;&nbsp;Calculate Correlations</p>
 
-                <p id="sectionbody3"></p><script language="Javascript" type="text/javascript">
-<!--
-
-                $(function() { $("#corr_tabs").tabs(); });
-
-                //-->
-                </script>
+                <p id="sectionbody3"></p>
 
                 <table class="target4" cellpadding="0" cellspacing="0" width="100%">
                   <tr>
@@ -771,7 +765,7 @@
                                 "sample_method" value="spearman"><br>
                                 <br>
                                     
-                                <input type="button" name="corr_compute" id="corr_compute" class="button" value="Compute"><br><br>
+                                <input type="submit" name="corr_compute" id="corr_compute" class="button" value="Compute"><br><br>
                                 
                                 <span id="sample_r_desc" class="correlation_desc fs12">
                                     The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 114ec458..677c7f43 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -75,10 +75,10 @@ def showDatabaseBXD():
     print("showDatabaseBXD template_vars:", pf(template_vars.__dict__))
     return render_template("trait_data_and_analysis.html", **template_vars.__dict__)
 
-@app.route("/corr_compute")
+@app.route("/corr_compute", methods=('POST',))
 def corr_compute():
-    print("In corr_compute")
-    fd = webqtlFormData.webqtlFormData(request.args)
+    #print("In corr_compute, request.args is:", pf(request.form))
+    fd = webqtlFormData.webqtlFormData(request.form)
     print("Have fd")
     template_vars = CorrelationPage.CorrelationPage(fd)
     print("Made it to  rendering")