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-rw-r--r--wqflask/utility/helper_functions.py1
-rw-r--r--wqflask/utility/temp_data.py27
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py11
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py8
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee10
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js43
-rw-r--r--wqflask/wqflask/templates/show_trait.html4
-rw-r--r--wqflask/wqflask/views.py11
9 files changed, 65 insertions, 54 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index d2567b63..56b409e6 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -4,6 +4,7 @@ from base.trait import GeneralTrait
from base import data_set
from base.species import TheSpecies
+
def get_species_dataset_trait(self, start_vars):
#assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
self.dataset = data_set.create_dataset(start_vars['dataset'])
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
new file mode 100644
index 00000000..192dcc44
--- /dev/null
+++ b/wqflask/utility/temp_data.py
@@ -0,0 +1,27 @@
+from __future__ import print_function, division, absolute_import
+from redis import Redis
+
+import simplejson as json
+
+class TempData(object):
+
+ def __init__(self, temp_uuid):
+ self.temp_uuid = temp_uuid
+ self.redis = Redis()
+ self.key = "tempdata:{}".format(self.temp_uuid)
+
+ def store(self, field, value):
+ print("Storing...")
+ self.redis.hset(self.key, field, value)
+ self.redis.expire(self.key, 60*15) # Expire in 15 minutes
+
+ def get_all(self):
+ return self.redis.hgetall(self.key)
+
+
+
+if __name__ == "__main__":
+ redis = Redis()
+ for key in redis.keys():
+ for field in redis.hkeys(key):
+ print("{}.{}={}".format(key, field, redis.hget(key, field)))
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 40ebc546..412d9e35 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -34,6 +34,7 @@ from dbFunction import webqtlDatabaseFunction
from base.GeneralObject import GeneralObject
from wqflask.my_pylmm.data import prep_data
from wqflask.my_pylmm.pyLMM import lmm
+from utility import temp_data
import reaper
import cPickle
@@ -65,7 +66,13 @@ class MarkerRegression(object):
helper_functions.get_species_dataset_trait(self, start_vars)
+ print("start_vars is:", start_vars)
+
+
self.num_perm = int(start_vars['num_perm'])
+ #self.temp_uuid = start_vars['temp_uuid']
+ self.temp_data = temp_data.TempData(start_vars['temp_uuid'])
+
# Passed in by the form (user might have edited)
#samples = start_vars['allsamples'].split()
@@ -465,7 +472,7 @@ class MarkerRegression(object):
def gen_data(self):
"""Todo: Fill this in here"""
- print("Session UUID: ", self.start_vars[session_uuid])
+ #print("Temp UUID: ", self.temp_uuid)
genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
@@ -476,7 +483,7 @@ class MarkerRegression(object):
genotype_matrix = np.array(trimmed_genotype_data).T
with Bench("Calculate Kinship"):
- kinship_matrix = lmm.calculate_kinship(genotype_matrix)
+ kinship_matrix = lmm.calculate_kinship(genotype_matrix, self.temp_data)
with Bench("Create LMM object"):
lmm_ob = lmm.LMM(pheno_vector, kinship_matrix)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 374452f0..cc2e32a7 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -54,7 +54,7 @@ def matrixMult(A,B):
return linalg.fblas.dgemm(alpha=1.,a=AA,b=BB,trans_a=transA,trans_b=transB)
-def calculate_kinship(genotype_matrix):
+def calculate_kinship(genotype_matrix, temp_data):
"""
genotype_matrix is an n x m matrix encoding SNP minor alleles.
@@ -87,8 +87,10 @@ def calculate_kinship(genotype_matrix):
keep.append(counter)
genotype_matrix[:,counter] = (genotype_matrix[:,counter] - values_mean) / np.sqrt(vr)
- stage = round((counter/m)*45)
- print("Percent complete: ", stage)
+ percent_complete = int(round((counter/m)*45))
+ print("Percent complete: ", percent_complete)
+ temp_data.store("percent_complete", percent_complete)
+
genotype_matrix = genotype_matrix[:,keep]
kinship_matrix = np.dot(genotype_matrix,genotype_matrix.T) * 1.0/float(m)
return kinship_matrix
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 7b2d022c..16aec827 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -122,7 +122,7 @@ class ShowTrait(object):
# We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
self.hddn = hddn
- self.session_uuid = uuid.uuid4()
+ self.temp_uuid = uuid.uuid4()
self.sample_group_types = OrderedDict()
self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only"
@@ -133,7 +133,7 @@ class ShowTrait(object):
js_data = dict(sample_group_types = self.sample_group_types,
sample_lists = sample_lists,
attribute_names = self.sample_groups[0].attributes,
- session_uuid = self.session_uuid)
+ temp_uuid = self.temp_uuid)
#print("js_data:", pf(js_data))
self.js_data = js_data
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 83cdce4d..50b97171 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -11,13 +11,21 @@ $ ->
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit()
+ get_progress () =>
+ console.log("temp_uuid:", $("#temp_uuid").val())
+
$("#marker_regression").click(() =>
$("#progress_bar_container").modal()
+
+ get_progress()
+
url = "/marker_regression"
+ form_data = $('#trait_data_form').serialize()
+ console.log("form_data is:", form_data)
$.ajax(
type: "POST"
url: url
- data: $("#trait_data_form").serialize()
+ data: form_data
success: (data) =>
$('#progress_bar_container').modal('hide')
$("body").html(data)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 9e40a129..c8b0aa7b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,47 +1,6 @@
// Generated by CoffeeScript 1.4.0
(function() {
- $(function() {
- var composite_mapping_fields, submit_special, toggle_enable_disable,
- _this = this;
- submit_special = function() {
- var url;
- console.log("In submit_special");
- console.log("this is:", this);
- console.log("$(this) is:", $(this));
- url = $(this).data("url");
- console.log("url is:", url);
- $("#trait_data_form").attr("action", url);
- return $("#trait_data_form").submit();
- };
- $("#marker_regression").click(function() {
- var url;
- $("#progress_bar_container").modal();
- url = "/marker_regression";
- $.ajax({
- type: "POST",
- url: url,
- data: $("#trait_data_form").serialize(),
- success: function(data) {
- $('#progress_bar_container').modal('hide');
- return $("body").html(data);
- }
- });
- return false;
- });
- composite_mapping_fields = function() {
- return $(".composite_fields").toggle();
- };
- $("#use_composite_choice").change(composite_mapping_fields);
- toggle_enable_disable = function(elem) {
- return $(elem).prop("disabled", !$(elem).prop("disabled"));
- };
- $("#choose_closet_control").change(function() {
- return toggle_enable_disable("#control_locus");
- });
- return $("#display_all_lrs").change(function() {
- return toggle_enable_disable("#suggestive_lrs");
- });
- });
+
}).call(this);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index bb87b4bb..2d569b20 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -21,8 +21,8 @@
{% for key in hddn %}
<input type="hidden" name="{{ key }}" value="{{ hddn[key] }}">
{% endfor %}
-
- <input type="hidden" name="session_uuid" value="{{ session_uuid }}">
+
+ <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
<div class="container">
<div class="page-header">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9a250434..473dfdff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -13,13 +13,14 @@ import sqlalchemy
from wqflask import app
-from flask import render_template, request, make_response, Response, Flask, g, config
+from flask import render_template, request, make_response, Response, Flask, g, config, jsonify
from wqflask import search_results
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.marker_regression import marker_regression
from wqflask.correlation import show_corr_results
+from utility import temp_data
from wqflask.dataSharing import SharingInfo, SharingInfoPage
@@ -178,6 +179,12 @@ def sharing_info_page():
return template_vars
+@app.route("/get_temp_data")
+def get_temp_data():
+ temp_uuid = request.args['key']
+ return flask.jsonify(temp_data.TempData(temp_uuid).get_all())
+
+
def json_default_handler(obj):
'''Based on http://stackoverflow.com/a/2680060/1175849'''
# Handle datestamps
@@ -194,4 +201,4 @@ def json_default_handler(obj):
# return None
else:
raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
- type(obj), repr(obj))
+ type(obj), repr(obj)) \ No newline at end of file