From 0f6f0030439acfce43babfed516262bc78354d71 Mon Sep 17 00:00:00 2001
From: Sam Ockman
Date: Wed, 18 Jul 2012 18:55:43 -0400
Subject: latest changes

---
 wqflask/wqflask/dataSharing/SharingInfo.py         | 46 ++++++++++++++--------
 .../new/javascript/trait_data_and_analysis.coffee  | 32 +++++++--------
 .../new/javascript/trait_data_and_analysis.js      | 24 ++++++++---
 wqflask/wqflask/templates/base.html                |  1 +
 .../wqflask/templates/trait_data_and_analysis.html |  2 +
 5 files changed, 64 insertions(+), 41 deletions(-)

diff --git a/wqflask/wqflask/dataSharing/SharingInfo.py b/wqflask/wqflask/dataSharing/SharingInfo.py
index 289754d0..befc158a 100755
--- a/wqflask/wqflask/dataSharing/SharingInfo.py
+++ b/wqflask/wqflask/dataSharing/SharingInfo.py
@@ -29,11 +29,19 @@ from __future__ import print_function, division
 from pprint import pformat as pf
 from collections import namedtuple
 
-import httplib
+import requests
 
 from dbFunction import webqtlDatabaseFunction
 import SharingBody
 
+import logging
+logging.basicConfig(filename="/tmp/flask_gn_log", level=logging.INFO)
+
+_log = logging.getLogger("search")
+_ch = logging.StreamHandler()
+_log.addHandler(_ch)
+
+
 
 #########################################
 #      Sharing Info
@@ -62,30 +70,34 @@ class SharingInfo(object):
 
         # We can use string interpolation here cause we own the string
         sql = """select %s from InfoFiles where """ % (field_names)
-        if(self.GN_AccessionId):
+        if self.GN_AccessionId:
             sql += "GN_AccesionId = %s"
             cursor.execute(sql, self.GN_AccessionId)
-        elif (self.InfoPageName):
+        elif self.InfoPageName:
             sql += "InfoPageName = %s"
             cursor.execute(sql, self.InfoPageName)
         else:
-            raise 'No correct parameter found'
+            raise Exception('No correct parameter found')
         info = cursor.fetchone()
 
         info = todict(field_names, info)
 
         # fetch datasets file list
-        try:
-            conn = httplib.HTTPConnection("atlas.uthsc.edu")
-            conn.request("GET", "/scandatasets.php?GN_AccesionId=%s" % (info[32]))
-            response = conn.getresponse()
-            data = response.read()
-            filelist = data.split()
-            conn.close()
-        except Exception:
-            filelist = []
+        filelist = []
+        if info["GN_AccesionId"]:
+            url = "http://atlas.uthsc.edu/scandatasets.php?GN_AccesionId=%s" % (
+                info["GN_AccesionId"])
+            try:
+                response = requests.get(url)
+            except Exception as why:
+                log.exception("Problem conneting to:", url)
+            if response:
+                data = response.text
+                filelist = data.split()
+
         return info, filelist
 
+
     def getBody(self, infoupdate=""):
         info, filelist = self.getInfo()
         if filelist:
@@ -99,16 +111,16 @@ class SharingInfo(object):
                     htmlfilelist += '   '
                     #r=re.compile(r'(?<=\d)(?=(\d\d\d)+(?!\d))')
                     #htmlfilelist += '[%s&nbsp;B]' % r.sub(r',',filesize)
-                    if 12<len(filesize):
+                    if 12 < len(filesize):
                         filesize=filesize[0:-12]
                         filesize += ' T'
-                    elif 9<len(filesize):
+                    elif 9 < len(filesize):
                         filesize=filesize[0:-9]
                         filesize += ' G'
-                    elif 6<len(filesize):
+                    elif 6 < len(filesize):
                         filesize=filesize[0:-6]
                         filesize += ' M'
-                    elif 3<len(filesize):
+                    elif 3 < len(filesize):
                         filesize=filesize[0:-3]
                         filesize += ' K'
                     htmlfilelist += '[%sB]' % filesize
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 d3817f99..2c912f05 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee
@@ -56,7 +56,7 @@ $ ->
         mean(the_values)
 
     make_table = ->
-        header = "<thead><tr>"
+        header = "<thead><tr><th>&nbsp;</th>"
         for column in basic_table['columns']
             the_id = process_id("column_" + column)
             header += """<th id="#{ the_id }">#{ column }</th>"""
@@ -73,7 +73,7 @@ $ ->
                 },
                 {
                     vn: "median"
-                    pretty: "median"
+                    pretty: "Median"
                 },
                 {
                     vn: "se"
@@ -86,30 +86,26 @@ $ ->
         console.log("length of rows:", rows.length)
         for row in rows
             console.log("rowing")
-            #row_line = key
-            row_line = """<tr><td id="#{ row.vn  }">#{ row.pretty }</td></tr>"""
+            row_line = """<tr>"""
+            row_line += """<td id="#{ row.vn  }">#{ row.pretty }</td>"""
+            for column in basic_table['columns']
+                console.log("apple:", column)
+                the_id = process_id(column + "_" + row.vn)
+                console.log("the_id:", the_id)
+                row_line += """<td id="#{ the_id }">&nbsp;</td>"""
+            row_line += """</tr>"""
             console.log("row line:", row_line)
             the_rows += row_line
         the_rows += "</tbody>"
+        table = header + the_rows
+        console.log("table is:", table)
+        $("#stats_table").append(table)
 
 
-        #                                  - N of Samples
-        #                                  - Mean
-        #                                  - Median
-        #                                  - Standard Error (SE)
-        #                                  - Standard Deviation (SD)
-        #                                  - Minimum
-        #                                  - Maximum
-        #                                  - Range (log2)
-        #                                  - Range (fold)
-        #                                  - Interquartile Range
-        #                                  """)
-
-        console.log("header:", header)
-        console.log("the_rows:", the_rows)
 
     process_id = (value) ->
         ### Make an id or a class valid javascript by, for example, eliminating spaces ###
+        console.log("value:", value)
         value = value.replace(" ", "_")
         return value
 
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 abf98b9b..c288f11f 100644
--- a/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
+++ b/wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js
@@ -68,8 +68,8 @@
       return mean(the_values);
     };
     make_table = function() {
-      var column, header, row, row_line, rows, the_id, the_rows, _i, _j, _len, _len1, _ref;
-      header = "<thead><tr>";
+      var column, header, row, row_line, rows, table, the_id, the_rows, _i, _j, _k, _len, _len1, _len2, _ref, _ref1;
+      header = "<thead><tr><th>&nbsp;</th>";
       _ref = basic_table['columns'];
       for (_i = 0, _len = _ref.length; _i < _len; _i++) {
         column = _ref[_i];
@@ -86,7 +86,7 @@
           pretty: "Mean"
         }, {
           vn: "median",
-          pretty: "median"
+          pretty: "Median"
         }, {
           vn: "se",
           pretty: "Standard Error (SE)"
@@ -98,17 +98,29 @@
       for (_j = 0, _len1 = rows.length; _j < _len1; _j++) {
         row = rows[_j];
         console.log("rowing");
-        row_line = "<tr><td id=\"" + row.vn + "\">" + row.pretty + "</td></tr>";
+        row_line = "<tr>";
+        row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
+        _ref1 = basic_table['columns'];
+        for (_k = 0, _len2 = _ref1.length; _k < _len2; _k++) {
+          column = _ref1[_k];
+          console.log("apple:", column);
+          the_id = process_id(column + "_" + row.vn);
+          console.log("the_id:", the_id);
+          row_line += "<td id=\"" + the_id + "\">&nbsp;</td>";
+        }
+        row_line += "</tr>";
         console.log("row line:", row_line);
         the_rows += row_line;
       }
       the_rows += "</tbody>";
-      console.log("header:", header);
-      return console.log("the_rows:", the_rows);
+      table = header + the_rows;
+      console.log("table is:", table);
+      return $("#stats_table").append(table);
     };
     process_id = function(value) {
       /* Make an id or a class valid javascript by, for example, eliminating spaces
       */
+      console.log("value:", value);
       value = value.replace(" ", "_");
       return value;
     };
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index d7154a5b..4050164d 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -14,6 +14,7 @@
     <LINK REL="stylesheet" TYPE="text/css" HREF='/css/general_flask.css'>
     <LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
     <link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" />
+	<link rel="stylesheet" media="all" type="text/css" href="/static/new/css/table.css" />
     <LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
     <link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' />
     <link type="text/css" href='/css/tab_style.css' rel='Stylesheet' />
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 97fee3ea..47d0827b 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -3014,6 +3014,8 @@
 
                 <p class="sectionheader" id="title5" style="border-radius: 5px;">&nbsp;&nbsp;Review and Edit Data</p>
 
+				<table id="stats_table" class="one-column-emphasis" />
+
                 <p id="sectionbody5"></p>
 
                 <table class="target5" cellpadding="0" cellspacing="0" width="100%">
-- 
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