Worked towards correctly passing form data to correlation page and addressed various bugs that arose while doing so

10 files changed, 160 insertions, 115 deletions

diff --git a/misc/byobu_commands.txt b/misc/byobu_commands.txt
deleted file mode 100644
index 48e85396..00000000
--- a/misc/byobu_commands.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-byobu -RD
-control-a then :multiuser on
-control-a then :acladd sam
-
-type: screen -list for sessions
-screen -r zas1024/25679.byobu
diff --git a/misc/find.txt b/misc/find.txt
deleted file mode 100644
index 5c792d80..00000000
--- a/misc/find.txt
+++ /dev/null
@@ -1 +0,0 @@
-find | grep _____
diff --git a/misc/notes.txt b/misc/notes.txt
new file mode 100644
index 00000000..be023c1d
--- /dev/null
+++ b/misc/notes.txt
@@ -0,0 +1,41 @@
+To get server running:
+
+Start up virtual environment:
+source ~/ve27/bin/activate
+
+To set WQFLASK_SETTINGS environment variable:
+export WQFLASK_SETTINGS=~/gene/wqflask/cfg/zach_settings.py (or wherever file is located)
+
+To search for commands in history if necessary:
+history | grep "(whatever is being searched for)"
+
+Run server:
+python runserver.py
+
+===========================================
+
+Start screen session 
+byobu -RD (to start)
+control-a then :multiuser on
+control-a then :acladd sam
+
+type: screen -list for sessions
+screen -r zas1024/25679.byobu
+
+or if only one:
+
+screen -r zas1024/
+
+===========================================
+
+Coffeescript Stuff:
+
+coffee -c (filename)
+coffee -c -w (to watch for changes and recompile)
+coffee --help (for information about setting options)
+
+===========================================
+
+Python stuff:
+
+Classes should always inherit "object"
\ No newline at end of file
diff --git a/misc/python_stuff.txt b/misc/python_stuff.txt
deleted file mode 100644
index f36fe338..00000000
--- a/misc/python_stuff.txt
+++ /dev/null
@@ -1 +0,0 @@
-Classes should always inherit "object"
\ No newline at end of file
diff --git a/misc/runserver.txt b/misc/runserver.txt
deleted file mode 100644
index 71e3dfd7..00000000
--- a/misc/runserver.txt
+++ /dev/null
@@ -1 +0,0 @@
-python runserver.py
diff --git a/misc/virtual_env.txt b/misc/virtual_env.txt
deleted file mode 100644
index 7a8f20be..00000000
--- a/misc/virtual_env.txt
+++ /dev/null
@@ -1 +0,0 @@
-source ~/ve27/bin/activate
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index a9e3b7d4..177c72a2 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -60,17 +60,12 @@ class webqtlFormData:
         print("in webqtlFormData start_vars are:", pf(start_vars))
         for item in webqtlFormData.attrs:
             self.__dict__[item] = None
-        #self.__dict__.update(start_vars)
+
         for item in start_vars:
             self.__dict__[item] = start_vars[item]
-        print("  Now self.dict is:", pf(self.__dict__))
-        #for item in self.attrs:
-        #    if getattr(self, item, None):
-        #        print("Setting item %s to None" % (item,))
-        #        self.attrs[item] = None
-        #    else:
-        #        self.attrs[item] = self.attrs[item].strip()
+        #print("  Now self.dict is:", pf(self.__dict__))
 
+        #Todo: This can't be good below...rework
         try:
             self.remote_ip = req.connection.remote_ip
         except:
@@ -151,23 +146,32 @@ class webqtlFormData:
 
 
     def readGenotype(self):
-        'read genotype from .geno file'
+        '''read genotype from .geno file'''
         if self.RISet == 'BXD300':
             self.RISet = 'BXD'
-        else:
-            pass
-        assert self.RISet
+    
+        assert self.RISet, "self.RISet needs to be set"
+        
         #genotype_1 is Dataset Object without parents and f1
         #genotype_2 is Dataset Object with parents and f1 (not for intercross)
+        
         self.genotype_1 = reaper.Dataset()
-        self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
+        
+        full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')
+        
+        # reaper barfs on unicode filenames, so here we ensure it's a string
+        full_filename = str(full_filename)
+        self.genotype_1.read(full_filename)
+        
+        print("Got to after read")
+        
         try:
             # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
             _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
-        except:
+        except KeyError:
             _f1 = _f12 = _mat = _pat = None
 
-        self.genotype_2 =self.genotype_1
+        self.genotype_2 = self.genotype_1
         if self.genotype_1.type == "riset" and _mat and _pat:
             self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat)       #, F1=_f1)
 
@@ -177,78 +181,83 @@ class webqtlFormData:
         else:
             self.incparentsf1 = 0
             self.genotype = self.genotype_1
+            
         self.strainlist = list(self.genotype.prgy)
-        self.f1list = self.parlist = []
+        self.f1list = []
+        self.parlist = []
+        
         if _f1 and _f12:
             self.f1list = [_f1, _f12]
         if _mat and _pat:
             self.parlist = [_mat, _pat]
+            
 
-    def readData(self, strainlst=[], incf1=[]):
-        'read user input data or from trait data and analysis form'
+    def readData(self, strainlist, incf1=None):
+        '''read user input data or from trait data and analysis form'''
+
+        if incf1 == None:
+            incf1 = []
 
         if not self.genotype:
             self.readGenotype()
-        if not strainlst:
+        if not strainlist:
             if incf1:
-                strainlst = self.f1list + self.strainlist
+                strainlist = self.f1list + self.strainlist
             else:
-                strainlst = self.strainlist
+                strainlist = self.strainlist
 
+        #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
 
-        traitfiledata = self.formdata.getfirst('traitfile')
-        traitpastedata = self.formdata.getfirst('traitpaste')
-        variancefiledata = self.formdata.getfirst('variancefile')
-        variancepastedata = self.formdata.getfirst('variancepaste')
-        Nfiledata = self.formdata.getfirst('Nfile')
+        traitfiledata = getattr(self, "traitfile", None) 
+        traitpastedata = getattr(self, "traitpaste", None) 
+        variancefiledata = getattr(self, "variancefile", None) 
+        variancepastedata = getattr(self, "variancepaste", None) 
+        Nfiledata = getattr(self, "Nfile", None) 
 
+        #### Todo: Rewrite below when we get to someone submitting their own trait #####
 
         if traitfiledata:
-            tt = string.split(traitfiledata)
-            vals = map(webqtlUtil.StringAsFloat, tt)
+            tt = traitfiledata.split()
+            values = map(webqtlUtil.StringAsFloat, tt)
         elif traitpastedata:
-            tt = string.split(traitpastedata)
-            vals = map(webqtlUtil.StringAsFloat, tt)
+            tt = traitpastedata.split()
+            values = map(webqtlUtil.StringAsFloat, tt)
         else:
-            vals = map(self.FormDataAsFloat, strainlst)
-
-        if len(vals) < len(strainlst):
-            vals += [None]*(len(strainlst) - len(vals))
-        elif len(vals) > len(strainlst):
-            vals = vals[:len(strainlst)]
-        else:
-            pass
+            values = map(self.FormDataAsFloat, strainlist)
 
+        if len(values) < len(strainlist):
+            values += [None] * (len(strainlist) - len(values))
+        elif len(values) > len(strainlist):
+            values = values[:len(strainlist)]
+            
 
         if variancefiledata:
-            tt = string.split(variancefiledata)
-            vars = map(webqtlUtil.StringAsFloat, tt)
+            tt = variancefiledata.split()
+            variances = map(webqtlUtil.StringAsFloat, tt)
         elif variancepastedata:
-            tt = string.split(variancepastedata)
-            vars = map(webqtlUtil.StringAsFloat, tt)
+            tt = variancepastedata.split()
+            variances = map(webqtlUtil.StringAsFloat, tt)
         else:
-            vars = map(self.FormVarianceAsFloat, strainlst)
+            variances = map(self.FormVarianceAsFloat, strainlist)
 
-        if len(vars) < len(strainlst):
-            vars += [None]*(len(strainlst) - len(vars))
-        elif len(vars) > len(strainlst):
-            vars = vars[:len(strainlst)]
-        else:
-            pass
+        if len(variances) < len(strainlist):
+            variances += [None]*(len(strainlist) - len(variances))
+        elif len(variances) > len(strainlist):
+            variances = variances[:len(strainlist)]
 
         if Nfiledata:
             tt = string.split(Nfiledata)
             nstrains = map(webqtlUtil.IntAsFloat, tt)
-            if len(nstrains) < len(strainlst):
-                nstrains += [None]*(len(strainlst) - len(nstrains))
+            if len(nstrains) < len(strainlist):
+                nstrains += [None]*(len(strainlist) - len(nstrains))
         else:
-            nstrains = map(self.FormNAsFloat, strainlst)
+            nstrains = map(self.FormNAsFloat, strainlist)
 
-        ##vals, vars, nstrains is obsolete
+        ##values, variances, nstrains is obsolete
         self.allTraitData = {}
-        for i, _strain in enumerate(strainlst):
-            if vals[i] != None:
-                self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i])
+        for i, _strain in enumerate(strainlist):
+            if values[i] != None:
+                self.allTraitData[_strain] = webqtlCaseData(values[i], variances[i], nstrains[i])
 
 
 
diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py
index 9caf6595..62e4c4ab 100644
--- a/wqflask/wqflask/correlation/CorrelationPage.py
+++ b/wqflask/wqflask/correlation/CorrelationPage.py
@@ -177,42 +177,37 @@ 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(form_data):
-    if form_data.allstrainlist:
-        mdpchoice = form_data.formdata.getvalue('MDPChoice')
-        #XZ, in HTML source code, it is "BXD Only" or "BXH only", and so on
+def get_sample_data(fd):
+    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
         if mdpchoice == "1":
-            strainlist = form_data.f1list + form_data.strainlist
-        #XZ, in HTML source code, it is "MDP Only"
+            strainlist = fd.f1list + fd.strainlist
+        #XZ, in HTML source code, it is "Non-BXD Only", "Non-BXD Only", etc
         elif mdpchoice == "2":
             strainlist = []
-            strainlist2 = form_data.f1list + form_data.strainlist
-            for strain in form_data.allstrainlist:
+            strainlist2 = fd.f1list + fd.strainlist
+            for strain in fd.allstrainlist:
                 if strain not in strainlist2:
                     strainlist.append(strain)
             #So called MDP Panel
             if strainlist:
-                strainlist = form_data.f1list+form_data.parlist+strainlist
+                strainlist = fd.f1list + fd.parlist+strainlist
         #XZ, in HTML source code, it is "All Cases"
         else:
-            strainlist = form_data.allstrainlist
-        #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
-        form_data.readData(form_data.allstrainlist)
+            strainlist = fd.allstrainlist
+        #XZ, 09/18/2008: put the trait data into dictionary fd.allTraitData
+        fd.readData(fd.allstrainlist)
     else:
         mdpchoice = None
-        strainlist = form_data.strainlist
-        #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
-        form_data.readData()
+        strainlist = fd.strainlist
+        #XZ, 09/18/2008: put the trait data into dictionary fd.allTraitData
+        fd.readData()
 
     return strainlist
 
 
-def get_mdp_choice(form_data):
-    if form_data.allstrainlist:
-        return form_data.formdata.getvalue("MDPChoice")
-    else:
-        return None
-
 
 def get_species(fd, cursor):
     #XZ, 3/16/2010: variable RISet must be pass by the form
@@ -277,7 +272,7 @@ class CorrelationPage(templatePage):
     RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
 
 
-    def error(self, message, error="Error", heading = None):
+    def error(self, message, *args, **kw):
         heading = heading or self.PAGE_HEADING
         return templatePage.error(heading = heading, detail = [message], error=error)
 
@@ -295,23 +290,30 @@ class CorrelationPage(templatePage):
             fd.readGenotype()
 
         sample_list = get_sample_data(fd)
-        mdp_choice = get_mdp_choice(fd) # No idea what this is yet
+        
+        # Whether the user chose BXD Only, Non-BXD Only, or All Strains
+        # (replace BXD with whatever the group/inbredset name is)
+        # "mdp" stands for "mouse diversity panel" This is outdated; it now represents any
+        # cases/strains from the non-primary group
+        mdp_choice = fd.MDPChoice if fd.allstrainlist else None 
+        
         self.species = get_species(fd, self.cursor)
 
         #XZ, 09/18/2008: get all information about the user selected database.
-        target_db_name = fd.formdata.getvalue('database')
-        self.target_db_name = target_db_name
+        #target_db_name = fd.corr_dataset
+        self.target_db_name = fd.corr_dataset
 
-        try:
-            self.db = webqtlDataset(target_db_name, self.cursor)
-        except:
-            detail = ["The database you just requested has not been established yet."]
-            self.error(detail)
-            return
+        #try:
+        #print("target_db_name is:", target_db_name)
+        self.db = webqtlDataset(self.target_db_name, self.cursor)
+        #except:
+        #    detail = ["The database you just requested has not been established yet."]
+        #    self.error(detail)
+        #    return
 
          # Auth if needed
         try:
-            auth_user_for_db(self.db, self.cursor, target_db_name, self.privilege, self.userName)
+            auth_user_for_db(self.db, self.cursor, self.target_db_name, self.privilege, self.userName)
         except AuthException, e:
             detail = [e.message]
             return self.error(detail)
@@ -322,7 +324,7 @@ class CorrelationPage(templatePage):
          #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=PAGE_HEADING,detail=detail)
+            self.error(heading=None, detail=detail)
 
 
         self.method = get_correlation_method_key(fd)
@@ -330,15 +332,16 @@ class CorrelationPage(templatePage):
         rankOrder = self.RANK_ORDERS[self.method]
 
          # CF - Number of results returned
-        self.returnNumber = int(fd.formdata.getvalue('criteria'))
+        self.returnNumber = int(fd.criteria)
 
         self.record_count = 0
 
         myTrait = get_custom_trait(fd, self.cursor)
 
 
-        # We will not get Literature Correlations if there is no GeneId because there is nothing to look against
-        self.gene_id = int(fd.formdata.getvalue('GeneId') or 0)
+        # We will not get Literature Correlations if there is no GeneId because there is nothing
+        # to look against
+        self.gene_id = int(fd.GeneId)
 
         # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
         self.trait_symbol = myTrait.symbol
@@ -359,7 +362,8 @@ class CorrelationPage(templatePage):
         TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
 
         mainfmName = webqtlUtil.genRandStr("fm_")
-        form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden'))
+        form = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
+                       enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden'))
         hddn = {'FormID': 'showDatabase',
                 'ProbeSetID': '_',
                 'database': self.target_db_name,
@@ -369,9 +373,9 @@ class CorrelationPage(templatePage):
                 'identification': fd.identification}
 
         if myTrait:
-            hddn['fullname']=fd.formdata.getvalue('fullname')
+            hddn['fullname'] = fd.fullname
         if mdp_choice:
-            hddn['MDPChoice']=mdp_choice
+            hddn['MDPChoice']= mdp_choice
 
 
         #XZ, 09/18/2008: pass the trait data to next page by hidden parameters.
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 3ea90b9c..7bfa6d01 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -170,10 +170,14 @@ $ ->
         console.log("in beginning of on_corr_submit")
         values = $('#trait_data_form').serialize()
         console.log("in on_corr_submit, values are:", values)
-        $.ajax "/corr_compute",
-            type: 'GET'
-            dataType: 'html'
-            data: 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)
 
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 0de0297b..e1f870d9 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -200,15 +200,12 @@
     };
     $('select[name=corr_method]').change(on_corr_method_change);
     on_corr_submit = function() {
-      var values;
+      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);
-      return $.ajax("/corr_compute", {
-        type: 'GET',
-        dataType: 'html',
-        data: values
-      });
+      params = $.param(values);
+      return window.location.href = "/corr_compute?" + params;
     };
     $('#corr_compute').click(on_corr_submit);
     /*