Most of the top fields working

4 files changed, 105 insertions, 66 deletions

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 812d112a..23b98238 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -590,3 +590,69 @@ class webqtlTrait:
             setDescription.append( ' --- FROM : ')
             setDescription.append(self.db.genHTML(Class='cori'))
         return setDescription
+
+    @property
+    def description_fmt(self):
+        '''Return a text formated description'''
+        if self.description:
+            formatted = self.description
+            if self.probe_target_description:
+                formatted += "; " + self.probe_target_description
+        else:
+            formatted = "Not available"
+        return formatted
+
+    @property
+    def alias_fmt(self):
+        '''Return a text formatted alias'''
+        if self.alias:
+            alias = string.replace(self.alias, ";", " ")
+            alias = string.join(string.split(alias), ", ")
+        return alias
+
+
+    @property
+    def location_fmt(self):
+        '''Return a text formatted location
+
+        While we're at it we set self.location in case we need it later (do we?)
+
+        '''
+
+        if self.chr and self.mb:
+            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
+        elif self.chr:
+            self.location = 'Chr %s @ Unknown position' % (self.chr)
+        else:
+            self.location = 'Not available'
+
+        fmt = self.location
+        ##XZ: deal with direction
+        if self.strand_probe == '+':
+            fmt += (' on the plus strand ')
+        elif self.strand_probe == '-':
+            fmt += (' on the minus strand ')
+
+        return fmt
+
+
+    def get_database(self):
+        """
+        Returns the database, and the url referring to the database if it exists
+
+        We're going to to return two values here, and we don't want to have to call this twice from
+        the template. So it's not a property called from the template, but instead is called from the view
+
+        """
+        if self.cellid:
+            self.cursor.execute("""
+                            select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
+                                    where
+                            ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+                            ProbeSetFreeze.Id = %d""" % thisTrait.db.id)
+            probeDBName = self.cursor.fetchone()[0]
+            return dict(name = probeDBName,
+                        url = None)
+        else:
+            return dict(name = self.db.fullname,
+                        url = webqtlConfig.INFOPAGEHREF % self.db.name)
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 1aef0349..fda26322 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -345,44 +345,7 @@ class DataEditingPage(templatePage):
                         HT.TD(HT.Span('Not available', Class="fs13 fsI"), valign="top")
                         ))
 
-            #XZ: Gene Alias
-            if thisTrait.alias:
-                alias = string.replace(thisTrait.alias, ";", " ")
-                alias = string.join(string.split(alias), ", ")
-                thisTrait.alias_fmt = alias
-
-
-            #XZ: Description
-            if thisTrait.description:
-                thisTrait.description_fmt = thisTrait.description
-                if thisTrait.probe_target_description:
-                    thisTrait.description_fmt += "; " + this.trait.probe_target_description
-            else:
-                thisTrait.description_fmt = "Not available"
-
-            #XZ: Location
-
-            #XZ: deal with Chr and Mb
-            if thisTrait.chr and thisTrait.mb:
-                thisTrait.location = 'Chr %s @ %s Mb'  % (thisTrait.chr,thisTrait.mb)
-            elif thisTrait.chr:
-                thisTrait.location = 'Chr %s @ Unknown position' % (thisTrait.chr)
-            else:
-                thisTrait.location = 'Not available'
 
-            ##XZ: deal with direction
-            #if thisTrait.strand_probe == '+':
-            #    tSpan.append(' on the plus strand ')
-            #elif thisTrait.strand_probe == '-':
-            #    tSpan.append(' on the minus strand ')
-            #else:
-            #    pass
-            #
-            #tbl.append(HT.TR(
-            #        HT.TD('Location: ', Class="fwb fs13", valign="top", nowrap="on"),
-            #        HT.TD(width=10, valign="top"),
-            #        HT.TD(tSpan, valign="top")
-            #        ))
 
             ##display Verify Location button
             try:
@@ -474,18 +437,18 @@ class DataEditingPage(templatePage):
                     #probeButton.append(probeButton_img)
                     probeText = "Probes"
 
-            tSpan = HT.Span(Class="fs13")
+            #tSpan = HT.Span(Class="fs13")
 
             #XZ: deal with blat score and blat specificity.
-            if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score:
-                if thisTrait.probe_set_specificity:
-                    pass
-                    #tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3)
-                if thisTrait.probe_set_blat_score:
-                    pass
-                    #tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2)
+            #if thisTrait.probe_set_specificity or thisTrait.probe_set_blat_score:
+            #    if thisTrait.probe_set_specificity:
+            #        pass
+            #        #tSpan.append(HT.Href(url="/blatInfo.html", target="_blank", title="Values higher than 2 for the specificity are good", text="BLAT specificity", Class="non_bold"),": %.1f" % float(thisTrait.probe_set_specificity), " "*3)
+            #    if thisTrait.probe_set_blat_score:
+            #        pass
+            #        #tSpan.append("Score: %s" % int(thisTrait.probe_set_blat_score), " "*2)
 
-            onClick="openNewWin('/blatInfo.html')"
+            #onClick="openNewWin('/blatInfo.html')"
 
             #tbl.append(HT.TR(
             #        HT.TD('Target Score: ', Class="fwb fs13", valign="top", nowrap="on"),
@@ -502,26 +465,28 @@ class DataEditingPage(templatePage):
             #        HT.TD(tSpan, valign="top")
             #        ))
 
-            if thisTrait.cellid:
-                self.cursor.execute("""
-                                select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
-                                        where
-                                ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                                ProbeSetFreeze.Id = %d""" % thisTrait.db.id)
-                probeDBName = self.cursor.fetchone()[0]
-                tbl.append(HT.TR(
-                        HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
-                        HT.TD(width=10, valign="top"),
-                        HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top")
-                        ))
-            else:
+            #if thisTrait.cellid:
+            #    self.cursor.execute("""
+            #                    select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze
+            #                            where
+            #                    ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+            #                    ProbeSetFreeze.Id = %d""" % thisTrait.db.id)
+            #    probeDBName = self.cursor.fetchone()[0]
+            #    tbl.append(HT.TR(
+            #            HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
+            #            HT.TD(width=10, valign="top"),
+            #            HT.TD(HT.Span('%s' % probeDBName, Class="non_bold"), valign="top")
+            #            ))
+            #else:
                 #tbl.append(HT.TR(
                 #        HT.TD('Database: ', Class="fs13 fwb", valign="top", nowrap="on"),
                 #        HT.TD(width=10, valign="top"),
                 #        HT.TD(HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name,
                 #        target='_blank', Class="fs13 fwn non_bold"), valign="top")
                 #        ))
-                pass
+                #pass
+
+            thisTrait.database = thisTrait.get_database()
 
             #XZ: ID links
             if thisTrait.genbankid or thisTrait.geneid or thisTrait.unigeneid or thisTrait.omim or thisTrait.homologeneid:
@@ -534,7 +499,7 @@ class DataEditingPage(templatePage):
                 if thisTrait.omim:
                     gurl = HT.Href(text= 'OMIM', target='_blank', \
                             url= webqtlConfig.OMIM_ID % thisTrait.omim,Class="fs14 fwn", title="Summary from On Mendelian Inheritance in Man")
-                    tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
+                    #tSpan.append(HT.Span(gurl, style=idStyle), " "*2)
                 if thisTrait.unigeneid:
                     try:
                         gurl = HT.Href(text= 'UniGene',target='_blank',\
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
index 57c68a1c..b1f71e55 100644
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ b/wqflask/wqflask/show_trait/show_trait_page.py
@@ -43,6 +43,7 @@ class ShowTraitPage(DataEditingPage):
     def __init__(self, fd, traitInfos = None):
 
         #templatePage.__init__(self, fd)
+        self.fd = fd
 
         if not self.openMysql():
             return
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 0eb1e012..1e67834c 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -68,7 +68,7 @@
 
                     <td valign="top" width="10"></td>
 
-                    <td valign="top"><span class="fs13">{{ thisTrait.location }}<br></span></td>
+                    <td valign="top"><span class="fs13">{{ thisTrait.location_fmt }}<br></span></td>
                   </tr>
 
                   <tr>
@@ -76,8 +76,14 @@
 
                     <td valign="top" width="10"></td>
 
-                    <td valign="top"><span class="fs13"><a href="/blatInfo.html" target="_blank" class="non_bold" title=
-                    "Values higher than 2 for the specificity are good">BLAT specificity</a>: 12.0&nbsp;&nbsp;&nbsp;Score: 240&nbsp;&nbsp;</span></td>
+                    <td valign="top">
+						<span class="fs13">
+							<a href="/blatInfo.html" target="_blank" class="non_bold" title="Values higher than 2 for the specificity are good">
+								BLAT specificity
+							</a>: {{ "%.1f" % (thisTrait.probe_set_specificity) }}&nbsp;&nbsp;&nbsp;
+							Score: {{ "%i" % (thisTrait.probe_set_blat_score) }}&nbsp;&nbsp;
+						</span>
+					</td>
                   </tr>
 
                   <tr>
@@ -93,8 +99,9 @@
 
                     <td valign="top" width="10"></td>
 
-                    <td valign="top"><a href="/dbdoc/HC_M2_0606_P.html" target="_blank" class="fs13 fwn non_bold">Hippocampus Consortium M430v2 (Jun06)
-                    PDNN</a></td>
+                    <td valign="top">
+						<a href="{{ thisTrait.database.url }}" target="_blank" class="fs13 fwn non_bold">{{ thisTrait.database.name }}</a>
+					</td>
                   </tr>
 
                   <tr>