From 29b51444acbc6fa7c839bb588d7985c79364dc3d Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 5 Jun 2015 22:14:38 +0000 Subject: Added back in some of the options on the trait page; Add, Find, and Verify now work. I'll get the other 4 working next. --- wqflask/wqflask/show_trait/show_trait.py | 21 +-- .../static/new/javascript/show_trait.coffee | 8 + .../wqflask/static/new/javascript/show_trait.js | 163 +++++++++++---------- wqflask/wqflask/templates/show_trait.html | 1 + wqflask/wqflask/templates/show_trait_details.html | 24 +-- .../wqflask/templates/show_trait_edit_data.html | 8 +- 6 files changed, 123 insertions(+), 102 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 7ad824fa..adb12b7b 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -362,34 +362,35 @@ class ShowTrait(object): #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A' #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. - self.cursor.execute("""SELECT Probe.Sequence, Probe.Name + query = """SELECT Probe.Sequence, Probe.Name FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND - ProbeSetFreeze.Name = '%s' AND - ProbeSet.Name = '%s' AND - Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (this_trait.dataset.name, this_trait.name) ) + ProbeSetFreeze.Name = '{}' AND + ProbeSet.Name = '{}' AND + Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""".format(this_trait.dataset.name, this_trait.name) + + seqs = g.db.execute(query).fetchall() - seqs = self.cursor.fetchall() for seqt in seqs: if int(seqt[1][-1]) %2 == 1: blatsequence += '%3EProbe_'+string.strip(seqt[1])+'%0A'+string.strip(seqt[0])+'%0A' #XZ: Pay attention to the parameter of version (rn, mm, hg). They need to be changed if necessary. if _Species == "rat": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('rat', 'rn3', blatsequence) UTHSC_BLAT_URL = "" elif _Species == "mouse": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('mouse', 'mm9', blatsequence) UTHSC_BLAT_URL = webqtlConfig.UTHSC_BLAT % ('mouse', 'mm9', blatsequence) elif _Species == "human": - UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) + self.UCSC_BLAT_URL = webqtlConfig.UCSC_BLAT % ('human', 'hg19', blatsequence) UTHSC_BLAT_URL = "" else: - UCSC_BLAT_URL = "" + self.UCSC_BLAT_URL = "" UTHSC_BLAT_URL = "" - if UCSC_BLAT_URL: + if self.UCSC_BLAT_URL != "": verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL) verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;") diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 3dedd7d5..91aa15ba 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -61,6 +61,14 @@ Stat_Table_Rows = [ ] $ -> + + add = -> + trait = $("input[name=trait_hmac]").val() + console.log("trait is:", trait) + $.colorbox({href:"/collections/add?traits=#{trait}"}) + + $('#add_to_collection').click(add) + sample_lists = js_data.sample_lists sample_group_types = js_data.sample_group_types diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 7311d0a8..302d5ec4 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -1,8 +1,8 @@ -// Generated by CoffeeScript 1.9.2 +// Generated by CoffeeScript 1.8.0 (function() { var Stat_Table_Rows, is_number, - hasProp = {}.hasOwnProperty, - slice = [].slice; + __hasProp = {}.hasOwnProperty, + __slice = [].slice; console.log("start_b"); @@ -56,7 +56,16 @@ ]; $(function() { - var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; + var add, block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; + add = function() { + var trait; + trait = $("input[name=trait_hmac]").val(); + console.log("trait is:", trait); + return $.colorbox({ + href: "/collections/add?traits=" + trait + }); + }; + $('#add_to_collection').click(add); sample_lists = js_data.sample_lists; sample_group_types = js_data.sample_group_types; d3.select("#select_compare_trait").on("click", (function(_this) { @@ -82,12 +91,12 @@ })(this)); }; hide_tabs = function(start) { - var i, ref, results, x; - results = []; - for (x = i = ref = start; ref <= 10 ? i <= 10 : i >= 10; x = ref <= 10 ? ++i : --i) { - results.push($("#stats_tabs" + x).hide()); + 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; + return _results; }; stats_mdp_change = function() { var selected; @@ -124,36 +133,36 @@ } }; update_stat_values = function(sample_sets) { - var category, i, len, ref, results, row, show_effects; + var category, row, show_effects, _i, _len, _ref, _results; show_effects = $(".tab-pane.active").attr("id") === "stats_tab"; - ref = ['samples_primary', 'samples_other', 'samples_all']; - results = []; - for (i = 0, len = ref.length; i < len; i++) { - category = ref[i]; - results.push((function() { - var j, len1, results1; - results1 = []; - for (j = 0, len1 = Stat_Table_Rows.length; j < len1; j++) { - row = Stat_Table_Rows[j]; + _ref = ['samples_primary', 'samples_other', 'samples_all']; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + category = _ref[_i]; + _results.push((function() { + var _j, _len1, _results1; + _results1 = []; + for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) { + row = Stat_Table_Rows[_j]; console.log("Calling change_stats_value"); - results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects)); + _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects)); } - return results1; + return _results1; })()); } - return results; + return _results; }; redraw_histogram = function() { var x; return root.histogram.redraw((function() { - var i, len, ref, results; - ref = _.values(root.selected_samples[root.histogram_group]); - results = []; - for (i = 0, len = ref.length; i < len; i++) { - x = ref[i]; - results.push(x.value); + var _i, _len, _ref, _results; + _ref = _.values(root.selected_samples[root.histogram_group]); + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + x = _ref[_i]; + _results.push(x.value); } - return results; + return _results; })()); }; redraw_bar_chart = function() { @@ -163,13 +172,13 @@ return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group); }; make_table = function() { - var header, i, key, len, ref, ref1, row, row_line, table, the_id, the_rows, value; + var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; header = " "; console.log("js_data.sample_group_types:", js_data.sample_group_types); - ref = js_data.sample_group_types; - for (key in ref) { - if (!hasProp.call(ref, key)) continue; - value = ref[key]; + _ref = js_data.sample_group_types; + 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); @@ -178,8 +187,8 @@ header += ""; console.log("windex header is:", header); the_rows = ""; - for (i = 0, len = Stat_Table_Rows.length; i < len; i++) { - row = Stat_Table_Rows[i]; + for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { + row = Stat_Table_Rows[_i]; console.log("rowing"); row_line = ""; if (row.url != null) { @@ -188,10 +197,10 @@ row_line += "" + row.pretty + ""; } console.log("box - js_data.sample_group_types:", js_data.sample_group_types); - ref1 = js_data.sample_group_types; - for (key in ref1) { - if (!hasProp.call(ref1, key)) continue; - value = ref1[key]; + _ref1 = js_data.sample_group_types; + 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); @@ -207,13 +216,13 @@ return $("#stats_table").append(table); }; process_id = function() { - var i, len, processed, value, values; - values = 1 <= arguments.length ? slice.call(arguments, 0) : []; + 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]; + for (_i = 0, _len = values.length; _i < _len; _i++) { + value = values[_i]; console.log("value:", value); value = value.replace(" ", "_"); if (processed.length) { @@ -224,7 +233,7 @@ return processed; }; edit_data_change = function() { - var already_seen, checkbox, checked, i, j, len, len1, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables; + var already_seen, checkbox, checked, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; already_seen = {}; sample_sets = { samples_primary: new Stats([]), @@ -238,11 +247,11 @@ }; console.log("at beginning:", sample_sets); tables = ['samples_primary', 'samples_other']; - for (i = 0, len = tables.length; i < len; i++) { - table = tables[i]; + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; rows = $("#" + table).find('tr'); - for (j = 0, len1 = rows.length; j < len1; j++) { - row = rows[j]; + for (_j = 0, _len1 = rows.length; _j < _len1; _j++) { + row = rows[_j]; name = $(row).find('.edit_sample_sample_name').html(); name = $.trim(name); real_value = $(row).find('.edit_sample_value').val(); @@ -310,26 +319,26 @@ return ""; }; populate_sample_attributes_values_dropdown = function() { - var attribute_info, i, key, len, ref, ref1, results, sample_attributes, selected_attribute, value; + 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]; + _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 = $('#exclude_menu').val().replace("_", " "); console.log("selected_attribute is:", selected_attribute); - ref1 = sample_attributes[selected_attribute]; - results = []; - for (i = 0, len = ref1.length; i < len; i++) { - value = ref1[i]; - results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + _ref1 = sample_attributes[selected_attribute]; + _results = []; + for (_i = 0, _len = _ref1.length; _i < _len; _i++) { + value = _ref1[_i]; + _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); } - return results; + return _results; }; if (js_data.attribute_names.length > 0) { populate_sample_attributes_values_dropdown(); @@ -352,17 +361,17 @@ }; $('#exclude_group').click(block_by_attribute_value); block_by_index = function() { - var end_index, error, i, index, index_list, index_set, index_string, j, k, len, len1, ref, ref1, ref2, results, start_index; + var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results; index_string = $('#remove_samples_field').val(); index_list = []; - ref = index_string.split(","); - for (i = 0, len = ref.length; i < len; i++) { - index_set = ref[i]; + _ref = index_string.split(","); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + index_set = _ref[_i]; if (index_set.indexOf('-') !== -1) { try { start_index = parseInt(index_set.split("-")[0]); end_index = parseInt(index_set.split("-")[1]); - for (index = j = ref1 = start_index, ref2 = end_index; ref1 <= ref2 ? j <= ref2 : j >= ref2; index = ref1 <= ref2 ? ++j : --j) { + for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) { index_list.push(index); } } catch (_error) { @@ -376,22 +385,22 @@ } } console.log("index_list:", index_list); - results = []; - for (k = 0, len1 = index_list.length; k < len1; k++) { - index = index_list[k]; + _results = []; + for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { + index = index_list[_k]; if ($('#block_group').val() === "primary") { console.log("block_group:", $('#block_group').val()); console.log("row:", $('#Primary_' + index.toString())); - results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x")); + _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x")); } else if ($('#block_group').val() === "other") { console.log("block_group:", $('#block_group').val()); console.log("row:", $('#Other_' + index.toString())); - results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x")); + _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x")); } else { - results.push(void 0); + _results.push(void 0); } } - return results; + return _results; }; $('#block_by_index').click(block_by_index); hide_no_value = function() { @@ -428,17 +437,17 @@ samples = []; $('#' + table_name).find('.value_se').each((function(_this) { return function(_index, element) { - var attribute_info, key, ref, row_data; + var attribute_info, key, row_data, _ref; row_data = {}; row_data.name = $.trim($(element).find('.column_name-Sample').text()); row_data.value = $(element).find('.edit_sample_value').val(); if ($(element).find('.edit_sample_se').length !== -1) { row_data.se = $(element).find('.edit_sample_se').val(); } - ref = js_data.attribute_names; - for (key in ref) { - if (!hasProp.call(ref, key)) continue; - attribute_info = ref[key]; + _ref = js_data.attribute_names; + for (key in _ref) { + if (!__hasProp.call(_ref, key)) continue; + attribute_info = _ref[key]; row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_")).text()); } console.log("row_data is:", row_data); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 559650f3..c0a404d9 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -26,6 +26,7 @@
+ {% for key in hddn %} {% endfor %} diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index ffedbd5f..c938c683 100755 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -60,38 +60,40 @@ - +
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 585165bb..a02dc409 100755 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -44,11 +44,11 @@ {% endif %}
- - - + + + - +