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-rwxr-xr-xwqflask/wqflask/dataSharing/SharingInfo.py46
-rw-r--r--wqflask/wqflask/static/new/javascript/trait_data_and_analysis.coffee32
-rw-r--r--wqflask/wqflask/static/new/javascript/trait_data_and_analysis.js24
-rw-r--r--wqflask/wqflask/templates/base.html1
-rw-r--r--wqflask/wqflask/templates/trait_data_and_analysis.html2
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%">