diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 103 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 236 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 43 |
6 files changed, 361 insertions, 69 deletions
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 62bc63c3..d39559d3 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -24,7 +24,7 @@ class SampleList(object): self.sample_list = [] # The actual list - self.calc_attributes() + self.get_attributes() print("camera: attributes are:", pf(self.attributes)) @@ -85,7 +85,7 @@ class SampleList(object): sample.outlier = False - def calc_attributes(self): + def get_attributes(self): """Finds which extra attributes apply to this dataset""" #ZS: Id and name values for this trait's extra attributes diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 743e4ad6..9bad6154 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -161,7 +161,10 @@ class ShowTrait(templatePage): self.sample_group_types['primary_only'] = fd.RISet + " Only" self.sample_group_types['other_only'] = "Non-" + fd.RISet self.sample_group_types['all_cases'] = "All Cases" - self.js_data = dict(sample_groups = self.sample_group_types) + js_data = dict(sample_groups = self.sample_group_types, + attribute_names = self.sample_groups[0].attributes) + print("js_data:", pf(js_data)) + self.js_data = js_data def get_this_trait(self): @@ -989,55 +992,55 @@ class ShowTrait(templatePage): except: plotTitle = str(this_trait.name) - #normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) - #normalplot.append(HT.TR(HT.TD(normalplot_img))) - #normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ - #normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), - #"More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", - # target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) - #normalplot_container.append(normalplot) - #normalplot_div.append(normalplot_container) - #stats_container.append(normalplot_div) - - #boxplot_div = HT.Div(id="statstabs-2") - #boxplot_container = HT.Paragraph() - #boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - #boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) - #boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) - #boxplot_container.append(boxplot) - #boxplot_div.append(boxplot_container) - #stats_container.append(boxplot_div) - - - #barName_div = HT.Div(id="statstabs-3") - #barName_container = HT.Paragraph() - #barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - #barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") - #barName.append(HT.TR(HT.TD(barName_img))) - #barName_container.append(barName) - #barName_div.append(barName_container) - #stats_container.append(barName_div) - # - #barRank_div = HT.Div(id="statstabs-4") - #barRank_container = HT.Paragraph() - #barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") - #barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") - #barRank.append(HT.TR(HT.TD(barRank_img))) - #barRank_container.append(barRank) - #barRank_div.append(barRank_container) - #stats_container.append(barRank_div) - - # stats_cell.append(stats_container) - # - #stats_script.append(stats_script_text) - # - #submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") - #stats_row.append(stats_cell) - - #submitTable.append(stats_row) - #submitTable.append(stats_script) - - #title2Body.append(submitTable) + #normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains) + #normalplot.append(HT.TR(HT.TD(normalplot_img))) + #normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \ + #normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(), + #"More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot", + # target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary")))) + #normalplot_container.append(normalplot) + #normalplot_div.append(normalplot_container) + #stats_container.append(normalplot_div) + + #boxplot_div = HT.Div(id="statstabs-2") + #boxplot_container = HT.Paragraph() + #boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + #boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals) + #boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left"))) + #boxplot_container.append(boxplot) + #boxplot_div.append(boxplot_container) + #stats_container.append(boxplot_div) + + + #barName_div = HT.Div(id="statstabs-3") + #barName_container = HT.Paragraph() + #barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + #barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name") + #barName.append(HT.TR(HT.TD(barName_img))) + #barName_container.append(barName) + #barName_div.append(barName_container) + #stats_container.append(barName_div) + # + #barRank_div = HT.Div(id="statstabs-4") + #barRank_container = HT.Paragraph() + #barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%") + #barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank") + #barRank.append(HT.TR(HT.TD(barRank_img))) + #barRank_container.append(barRank) + #barRank_div.append(barRank_container) + #stats_container.append(barRank_div) + + # stats_cell.append(stats_container) + # + #stats_script.append(stats_script_text) + # + #submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2") + #stats_row.append(stats_cell) + + #submitTable.append(stats_row) + #submitTable.append(stats_script) + + #title2Body.append(submitTable) def build_correlation_tools(self, fd, this_trait): diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 803045d5..a91e9681 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -69,7 +69,7 @@ $ -> make_table = -> header = "<thead><tr><th> </th>" console.log("js_data.sample_groups:", js_data.sample_groups) - for key, value of js_data.sample_groups + for own key, value of js_data.sample_groups console.log("aa key:", key) console.log("aa value:", value) the_id = process_id("column", key) @@ -108,7 +108,7 @@ $ -> row_line = """<tr>""" row_line += """<td id="#{ row.vn }">#{ row.pretty }</td>""" console.log("box - js_data.sample_groups:", js_data.sample_groups) - for key, value of js_data.sample_groups + for own key, value of js_data.sample_groups console.log("apple key:", key) the_id = process_id(key, row.vn) console.log("the_id:", the_id) @@ -166,6 +166,30 @@ $ -> #End Calculate Correlations Code + #Populate Samples Attribute Values Code + + create_value_dropdown = (value) -> + return """<option val=#{value}>#{value}</option>""" + + populate_sample_attributes_values_dropdown = -> + console.log("in beginning of psavd") + $('#attribute_values').empty() + sample_attributes = {} + for own key, attribute_info of js_data.attribute_names + sample_attributes[attribute_info.name] = attribute_info.distinct_values + console.log("[visa] attributes is:", sample_attributes) + selected_attribute = $('#exclude_menu').val() + for value in sample_attributes[selected_attribute] + $(create_value_dropdown(value)) + .appendTo($('#attribute_values')) + + # Must run once at beginning + populate_sample_attributes_values_dropdown() + $('#exclude_menu').change(populate_sample_attributes_values_dropdown) + + + + #End Populate Samples Attribute Values Code console.log("before registering show_hide_outliers") $('#show_hide_outliers').click(show_hide_outliers) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js new file mode 100644 index 00000000..039a5e04 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -0,0 +1,236 @@ +// Generated by CoffeeScript 1.3.3 +(function() { + var is_number, + __hasProp = {}.hasOwnProperty, + __slice = [].slice; + + console.log("start_b"); + + is_number = function(o) { + return !isNaN((o - 0) && o !== null); + }; + + $(function() { + var change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values; + hide_tabs = function(start) { + var x, _i, _results; + _results = []; + for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) { + _results.push($("#stats_tabs" + x).hide()); + } + return _results; + }; + hide_tabs(1); + stats_mdp_change = function() { + var selected; + selected = $(this).val(); + hide_tabs(0); + return $("#stats_tabs" + selected).show(); + }; + $(".stats_mdp").change(stats_mdp_change); + change_stats_value = function(sample_sets, category, value_type, decimal_places) { + var current_value, id, in_box, the_value; + id = "#" + process_id(category, value_type); + console.log("the_id:", id); + in_box = $(id).html; + current_value = parseFloat($(in_box)).toFixed(decimal_places); + the_value = sample_sets[category][value_type](); + if (decimal_places > 0) { + the_value = the_value.toFixed(decimal_places); + } + if (the_value !== current_value) { + return $(id).html(the_value).effect("highlight"); + } + }; + update_stat_values = function(sample_sets) { + var category, stat, _i, _len, _ref, _results; + _ref = ['primary_only', 'other_only', 'all_cases']; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + category = _ref[_i]; + change_stats_value(sample_sets, category, "n_of_samples", 0); + _results.push((function() { + var _j, _len1, _ref1, _results1; + _ref1 = ["mean", "median", "std_dev", "std_error"]; + _results1 = []; + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + stat = _ref1[_j]; + _results1.push(change_stats_value(sample_sets, category, stat, 2)); + } + return _results1; + })()); + } + return _results; + }; + edit_data_change = function() { + var category, checkbox, checked, real_value, row, sample_sets, value, values, _i, _len; + sample_sets = { + primary_only: new Stats([]), + other_only: new Stats([]), + all_cases: new Stats([]) + }; + console.log("at beginning:", sample_sets); + values = $('#value_table').find(".edit_sample_value"); + for (_i = 0, _len = values.length; _i < _len; _i++) { + value = values[_i]; + real_value = $(value).val(); + row = $(value).closest("tr"); + category = row[0].id; + checkbox = $(row).find(".edit_sample_checkbox"); + checked = $(checkbox).attr('checked'); + if (checked && is_number(real_value) && real_value !== "") { + real_value = parseFloat(real_value); + if (_(category).startsWith("Primary")) { + sample_sets.primary_only.add_value(real_value); + } else if (_(category).startsWith("Other")) { + sample_sets.other_only.add_value(real_value); + } + sample_sets.all_cases.add_value(real_value); + } + } + console.log("towards end:", sample_sets); + return update_stat_values(sample_sets); + }; + make_table = function() { + var header, key, row, row_line, rows, table, the_id, the_rows, value, _i, _len, _ref, _ref1; + header = "<thead><tr><th> </th>"; + console.log("js_data.sample_groups:", js_data.sample_groups); + _ref = js_data.sample_groups; + for (key in _ref) { + if (!__hasProp.call(_ref, key)) continue; + value = _ref[key]; + console.log("aa key:", key); + console.log("aa value:", value); + the_id = process_id("column", key); + header += "<th id=\"" + the_id + "\">" + value + "</th>"; + } + header += "</thead>"; + console.log("windex header is:", header); + rows = [ + { + vn: "n_of_samples", + pretty: "N of Samples" + }, { + vn: "mean", + pretty: "Mean" + }, { + vn: "median", + pretty: "Median" + }, { + vn: "std_error", + pretty: "Standard Error (SE)" + }, { + vn: "std_dev", + pretty: "Standard Deviation (SD)" + } + ]; + console.log("rows are:", rows); + the_rows = "<tbody>"; + console.log("length of rows:", rows.length); + for (_i = 0, _len = rows.length; _i < _len; _i++) { + row = rows[_i]; + console.log("rowing"); + row_line = "<tr>"; + row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>"; + console.log("box - js_data.sample_groups:", js_data.sample_groups); + _ref1 = js_data.sample_groups; + for (key in _ref1) { + if (!__hasProp.call(_ref1, key)) continue; + value = _ref1[key]; + console.log("apple key:", key); + the_id = process_id(key, row.vn); + console.log("the_id:", the_id); + row_line += "<td id=\"" + the_id + "\">foo</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); + return $("#stats_table").append(table); + }; + process_id = function() { + var processed, value, values, _i, _len; + values = 1 <= arguments.length ? __slice.call(arguments, 0) : []; + /* Make an id or a class valid javascript by, for example, eliminating spaces + */ + + processed = ""; + for (_i = 0, _len = values.length; _i < _len; _i++) { + value = values[_i]; + console.log("value:", value); + value = value.replace(" ", "_"); + if (processed.length) { + processed += "-"; + } + processed += value; + } + return processed; + }; + show_hide_outliers = function() { + var label; + console.log("FOOBAR in beginning of show_hide_outliers"); + label = $('#show_hide_outliers').val(); + console.log("lable is:", label); + if (label === "Hide Outliers") { + return $('#show_hide_outliers').val("Show Outliers"); + } else if (label === "Show Outliers") { + console.log("Found Show Outliers"); + $('#show_hide_outliers').val("Hide Outliers"); + return console.log("Should be now Hide Outliers"); + } + }; + on_corr_method_change = function() { + var corr_method; + console.log("in beginning of on_corr_method_change"); + corr_method = $('select[name=corr_method]').val(); + console.log("corr_method is:", corr_method); + $('.correlation_desc').hide(); + $('#' + corr_method + "_r_desc").show().effect("highlight"); + if (corr_method === "lit") { + return $("#corr_sample_method_options").hide(); + } else { + return $("#corr_sample_method_options").show(); + } + }; + $('select[name=corr_method]').change(on_corr_method_change); + create_value_dropdown = function(value) { + return "<option val=" + value + ">" + value + "</option>"; + }; + populate_sample_attributes_values_dropdown = function() { + var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; + console.log("in beginning of psavd"); + $('#attribute_values').empty(); + sample_attributes = {}; + _ref = js_data.attribute_names; + for (key in _ref) { + if (!__hasProp.call(_ref, key)) continue; + attribute_info = _ref[key]; + sample_attributes[attribute_info.name] = attribute_info.distinct_values; + } + console.log("[visa] attributes is:", sample_attributes); + selected_attribute = $('#exclude_menu').val(); + _ref1 = sample_attributes[selected_attribute]; + _results = []; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + value = _ref1[_i]; + _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + } + return _results; + }; + populate_sample_attributes_values_dropdown(); + $('#exclude_menu').change(populate_sample_attributes_values_dropdown); + console.log("before registering show_hide_outliers"); + $('#show_hide_outliers').click(show_hide_outliers); + console.log("after registering show_hide_outliers"); + _.mixin(_.str.exports()); + $('#value_table').change(edit_data_change); + console.log("loaded"); + make_table(); + edit_data_change(); + return console.log("end"); + }); + +}).call(this); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 7d0e671f..3d24e738 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1227,6 +1227,20 @@ </select></span> <input type="button" name="blockSamples" class="button" value=" Block "> <br> + + {% if sample_groups[0].attributes %} + <strong> Block samples by index: </strong> + <select id="exclude_menu" size=1> + {% for attribute in sample_groups[0].attributes %} + <option value="{{ sample_groups[0].attributes[attribute].name }}">{{ sample_groups[0].attributes[attribute].name }}</option> + {% endfor %} + </select> + <select id="attribute_values" size=1> + </select> + {% endif %} + <input type="button" name="exclude_group" class="button" value=" Block "> + <br> + <strong> Options:</strong> <input type="button" id="show_hide_no_value" class="button" value="Hide No Value"> @@ -1335,7 +1349,7 @@ <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script> <script type="text/javascript" src="/static/new/javascript/stats.js"></script> - <script type="text/javascript" src="/static/new/javascript/trait_data_and_analysis.js"></script> + <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> <!-- End of body --> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4da1082f..c38ecb47 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -1,6 +1,6 @@ from __future__ import absolute_import, division, print_function -import json +import simplejson as json import yaml import flask @@ -10,7 +10,7 @@ from wqflask import app from flask import render_template, request from wqflask import search_results -from wqflask.show_trait import DataEditingPage +from wqflask.show_trait import show_trait from wqflask.correlation import CorrelationPage from wqflask.dataSharing import SharingInfo, SharingInfoPage @@ -19,8 +19,6 @@ from base import webqtlFormData from pprint import pformat as pf -print("latest blue") - @app.route("/") def index_page(): @@ -29,7 +27,7 @@ def index_page(): @app.route("/data_sharing") -def data_sharing(): +def data_sharing_page(): print("In data_sharing") fd = webqtlFormData.webqtlFormData(request.args) print("1Have fd") @@ -45,7 +43,7 @@ def data_sharing(): @app.route("/search") -def search(): +def search_page(): if 'info_database' in request.args: print("Going to sharing_info_page") template_vars = sharing_info_page() @@ -60,7 +58,7 @@ def search(): @app.route("/whats_new") -def whats_new(): +def whats_new_page(): #variables = whats_new.whats_new() with open("/home/sam/gene/wqflask/wqflask/yaml_data/whats_new.yaml") as fh: contents = fh.read() @@ -72,19 +70,20 @@ def whats_new(): @app.route("/show_trait") -def show_trait(): +def show_trait_page(): # Here it's currently too complicated not to use an fd that is a webqtlFormData fd = webqtlFormData.webqtlFormData(request.args) - #template_vars = show_trait_page.ShowTraitPage(fd) - template_vars = show_trait.show_trait(fd) - template_vars.js_data = json.dumps(template_vars.js_data) - + template_vars = show_trait.ShowTrait(fd) + template_vars.js_data = json.dumps(template_vars.js_data, + default=json_default_handler, + indent=" ", + sort_keys=True) print("show_trait template_vars:", pf(template_vars.__dict__)) - return render_template("trait_data_and_analysis.html", **template_vars.__dict__) + return render_template("show_trait.html", **template_vars.__dict__) @app.route("/corr_compute", methods=('POST',)) -def corr_compute(): +def corr_compute_page(): #print("In corr_compute, request.args is:", pf(request.form)) fd = webqtlFormData.webqtlFormData(request.form) print("Have fd") @@ -101,3 +100,19 @@ def sharing_info_page(): template_vars = SharingInfoPage.SharingInfoPage(fd) print("2 Made it to rendering") return template_vars + + +def json_default_handler(obj): + '''Based on http://stackoverflow.com/a/2680060/1175849''' + # Handle datestamps + if hasattr(obj, 'isoformat'): + return obj.isoformat() + # Handle integer keys for dictionaries + elif isinstance(obj, int): + return str(int) + # Handle custom objects + if hasattr(obj, '__dict__'): + return obj.__dict__ + else: + raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % ( + type(obj), repr(obj)) |