diff options
| -rw-r--r-- | wqflask/utility/helper_functions.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/temp_data.py | 27 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 8 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 43 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 11 |
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 |