diff options
| -rwxr-xr-x | web/css/general_flask.css | 54 | ||||
| -rwxr-xr-x | web/webqtl/collection/ExportSelectionDetailInfoPage.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 13 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 38 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 41 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 43 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 1 |
9 files changed, 146 insertions, 67 deletions
diff --git a/web/css/general_flask.css b/web/css/general_flask.css index d0cffbc4..d40fa267 100755 --- a/web/css/general_flask.css +++ b/web/css/general_flask.css @@ -10,6 +10,8 @@ Blockquote { margin : 14px 18px 14px 18px; } +/********** All this font size stuff, etc. needs to be replaced/removed ********** / + /*Font size*/ .fs10 {font-size : 10px} .fs11 {font-size : 11px} @@ -218,27 +220,47 @@ color: #999999; /*For font style and color of commands and keywords in the scriptable interface page*/ .keywords { -font-family : "CourierNew", Courier, mono; -font-size : 15px; -color : #0000FF; -font-weight : Normal + font-family : "CourierNew", Courier, mono; + font-size : 15px; + color : #0000FF; + font-weight : Normal } + /*For RIsample.html page*/ .strains { -border:1px solid #999999; -border-top:1px solid #940; -border-bottom:1px solid #940; -padding:5; -background-color:#ddf; -font-family:verdana; + border:1px solid #999999; + border-top:1px solid #940; + border-bottom:1px solid #940; + padding:5; + background-color:#ddf; + font-family:verdana; } + .values { -border:1px solid #999999; -border-top:1px solid #940; -border-bottom:1px solid #940; -padding:5; -background-color:#eee; -font-family:courier; + border:1px solid #999999; + border-top:1px solid #940; + border-bottom:1px solid #940; + padding:5; + background-color:#eee; + font-family:courier; } + +/*****************************************/ + +/* Standard table cell */ +.std_cell +{ + border : 1px solid #999999; + color : #222; + font-size : 13px; + padding : 3px; +} + +/*Input field used to enter sample values, SE, etc.*/ +.trait_value_input +{ + font-style : Italic +} + diff --git a/web/webqtl/collection/ExportSelectionDetailInfoPage.py b/web/webqtl/collection/ExportSelectionDetailInfoPage.py index a61b6f6e..7238c797 100755 --- a/web/webqtl/collection/ExportSelectionDetailInfoPage.py +++ b/web/webqtl/collection/ExportSelectionDetailInfoPage.py @@ -128,7 +128,7 @@ class ExportSelectionDetailInfoPage(templatePage): count = count + 1 except: pass - if count = 0: + if count == 0: mean = 0 else: mean = sum/count diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index d39559d3..df0dc61e 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -112,19 +112,6 @@ class SampleList(object): self.attributes[key].distinct_values.sort(key=natural_sort_key) - # exclude_menu = HT.Select(name="exclude_menu") - # dropdown_menus = [] #ZS: list of dropdown menus with the distinct values of each attribute (contained in DIVs so the style parameter can be edited and they can be hidden) - # for this_attr_name in attribute_names: - # exclude_menu.append((this_attr_name.capitalize(), this_attr_name)) - # attr_value_menu_div = HT.Div(style="display:none;", Class="attribute_values") #container used to show/hide dropdown menus - # attr_value_menu = HT.Select(name=this_attr_name) - # attr_value_menu.append(("None", "show_all")) - # for value in distinct_values: - # attr_value_menu.append((str(value[0]), value[0])) - # attr_value_menu_div.append(attr_value_menu) - # dropdown_menus.append(attr_value_menu_div) - - def get_extra_attribute_values(self, sample_name): attribute_values = {} diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 9bad6154..d34ae9a6 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -161,7 +161,12 @@ 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" - js_data = dict(sample_groups = self.sample_group_types, + sample_lists = [] + for group in self.sample_groups: + sample_lists.append(group.sample_list) + print("sample_lists is:", pf(sample_lists)) + js_data = dict(sample_group_types = self.sample_group_types, + sample_lists = sample_lists, attribute_names = self.sample_groups[0].attributes) print("js_data:", pf(js_data)) self.js_data = js_data diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index a91e9681..e22f1c21 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -68,8 +68,8 @@ $ -> make_table = -> header = "<thead><tr><th> </th>" - console.log("js_data.sample_groups:", js_data.sample_groups) - for own key, value of js_data.sample_groups + console.log("js_data.sample_group_types:", js_data.sample_group_types) + for own key, value of js_data.sample_group_types console.log("aa key:", key) console.log("aa value:", value) the_id = process_id("column", key) @@ -107,8 +107,8 @@ $ -> 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) - for own key, value of js_data.sample_groups + console.log("box - js_data.sample_group_types:", js_data.sample_group_types) + for own key, value of js_data.sample_group_types console.log("apple key:", key) the_id = process_id(key, row.vn) console.log("the_id:", the_id) @@ -147,7 +147,7 @@ $ -> console.log("Should be now Hide Outliers") - #Calculate Correlations Code + ##Calculate Correlations Code on_corr_method_change = -> @@ -164,9 +164,9 @@ $ -> $('select[name=corr_method]').change(on_corr_method_change) - #End Calculate Correlations Code + ##End Calculate Correlations Code - #Populate Samples Attribute Values Code + ##Populate Samples Attribute Values Code create_value_dropdown = (value) -> return """<option val=#{value}>#{value}</option>""" @@ -187,9 +187,29 @@ $ -> populate_sample_attributes_values_dropdown() $('#exclude_menu').change(populate_sample_attributes_values_dropdown) + ##End Populate Samples Attribute Values Codess + + ##Block Samples By Attribute Value Code + block_by_attribute_value = -> + console.log("in beginning of bbav code") + attribute_name = $('#exclude_menu').val() + console.log("attribute_name is:", attribute_name) + exclude_by_value = $('#attribute_values').val() + console.log("exclude_by_value is:", exclude_by_value) + sample_lists = js_data['sample_lists'] + console.log("sample_lists is:", sample_lists) + for sample_list in sample_lists + for sample in sample_list + console.log("sample is:", sample) + if sample.extra_attributes[attribute_name] == exclude_by_value + console.log("is exclude_by_value") + sample_row = $('') + + + + $('#exclude_group').click(block_by_attribute_value) - - #End Populate Samples Attribute Values Code + ##End Block Samples By Attribute Value 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 index 039a5e04..65440427 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -11,7 +11,7 @@ }; $(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; + var block_by_attribute_value, 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 = []; @@ -94,8 +94,8 @@ 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; + 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]; @@ -132,8 +132,8 @@ 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; + 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]; @@ -222,6 +222,37 @@ }; populate_sample_attributes_values_dropdown(); $('#exclude_menu').change(populate_sample_attributes_values_dropdown); + block_by_attribute_value = function() { + var attribute_name, exclude_by_value, sample, sample_list, sample_lists, sample_row, _i, _len, _results; + console.log("in beginning of bbav code"); + attribute_name = $('#exclude_menu').val(); + console.log("attribute_name is:", attribute_name); + exclude_by_value = $('#attribute_values').val(); + console.log("exclude_by_value is:", exclude_by_value); + sample_lists = js_data['sample_lists']; + console.log("sample_lists is:", sample_lists); + _results = []; + for (_i = 0, _len = sample_lists.length; _i < _len; _i++) { + sample_list = sample_lists[_i]; + _results.push((function() { + var _j, _len1, _results1; + _results1 = []; + for (_j = 0, _len1 = sample_list.length; _j < _len1; _j++) { + sample = sample_list[_j]; + console.log("sample is:", sample); + if (sample.extra_attributes[attribute_name] === exclude_by_value) { + console.log("is exclude_by_value"); + _results1.push(sample_row = $('')); + } else { + _results1.push(void 0); + } + } + return _results1; + })()); + } + return _results; + }; + $('#exclude_group').click(block_by_attribute_value); console.log("before registering show_hide_outliers"); $('#show_hide_outliers').click(show_hide_outliers); console.log("after registering show_hide_outliers"); diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 572f7fcc..c20efe40 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -171,9 +171,9 @@ <TD class="fs12 fwn ffl b1 c222" nowrap="on">{{ loop.index }} <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox" VALUE="{{ thisTrait }}" onClick="highlight(this)"> </TD> - <TD class="fs12 fwn b1 c222"> + <TD class="stdcell"> {# <A HREF="javascript:showDatabase3('{{ thisFormName }}','{{thisTrait.db.name}}','{{ thisTrait.name }}','{{ thisTrait.cellid }}')" class="fs12 fwn"> - </a> #} - <a href="{{ url_for('show_trait', database=thisTrait.db.name, ProbeSetID=thisTrait.name, incparentsf1='ON', RISet='BXD')}}" class="fs12 fwn"> + <a href="{{ url_for('show_trait_page', database=thisTrait.db.name, ProbeSetID=thisTrait.name, incparentsf1='ON', RISet='BXD')}}" class="fs12 fwn"> {{ thisTrait.name.upper() }} </a> </TD> @@ -182,11 +182,11 @@ {{ thisTrait.symbol }} </A> </TD> - <TD class="fs12 fwn b1 c222">{{ thisTrait.description_display }}</TD> - <TD class="fs12 fwn b1 c222" nowrap="on">{{ thisTrait.trait_location_repr }}</TD> - <TD class="fs12 fwn b1 c222" nowrap="ON" align="right">{{ thisTrait.mean }}</TD> - <TD class="fs12 fwn b1 c222" nowrap="on" align="right">{{ thisTrait.LRS_score_repr }}</TD> - <TD class="fs12 fwn b1 c222" nowrap="on">{{ thisTrait.LRS_location_repr }}</TD> + <TD class="stdcell">{{ thisTrait.description_display }}</TD> + <TD class="stdcell" nowrap="on">{{ thisTrait.trait_location_repr }}</TD> + <TD class="stdcell" nowrap="ON" align="right">{{ thisTrait.mean }}</TD> + <TD class="stdcell" nowrap="on" align="right">{{ thisTrait.LRS_score_repr }}</TD> + <TD class="stdcell" nowrap="on">{{ thisTrait.LRS_location_repr }}</TD> </TR> {% endfor %} </TABLE> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 3d24e738..0ef86685 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1238,7 +1238,7 @@ <select id="attribute_values" size=1> </select> {% endif %} - <input type="button" name="exclude_group" class="button" value=" Block "> + <input type="button" id="exclude_group" class="button" value=" Block "> <br> <strong> Options:</strong> @@ -1253,9 +1253,14 @@ </span> <br> <br> - <span> Outliers highlighted in <strong style="background-color:yellow;"> yellow </strong> can be hidden using - the <strong>Hide Outliers</strong> button,<br> - and samples with no value (x) can be hidden by clicking <strong>Hide No Value</strong> .</span><br> + <span> Outliers highlighted in + <strong style="background-color:yellow;"> yellow </strong> + can be hidden using + the <strong>Hide Outliers</strong> button, + <br> + and samples with no value (x) can be hidden by clicking + <strong>Hide No Value</strong>t. + </span><br> </div><br> <div style="width:80%;margin:0;padding:0;border:none;"> @@ -1280,36 +1285,44 @@ {% endif %} {% for attribute in sample_type.attributes|sort() %} - <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60">{{ sample_type.attributes[attribute].name }}</th> + <th class="fs13 fwb ff1 b1 cw cbrb" align="right" width="60"> + {{ sample_type.attributes[attribute].name }} + </th> {% endfor %} </tr> {% for sample in sample_type.sample_list %} <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}"> - <td class="fs13 b1 c222" align="right" width="45"> + <td class="std_cell" data-column_name="Index" align="right" width="45"> {{ loop.index }} - <input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked"> + <input type="checkbox" name="selectCheck" + class="checkbox edit_sample_checkbox" + value="{{ sample.name }}" checked="checked"> </td> - <td class="fs13 b1 c222" align="right" width="100"> - <span class="fs14 fwn ffl edit_sample_sample_name">{{ sample.name }}</span> + <td class="std_cell" data-column_name="Sample" align="right" width="100"> + <span class="fs14 fwn ffl edit_sample_sample_name"> + {{ sample.name }} + </span> </td> {# Todo: Add IDs #} - <td class="fs13 b1 c222" align="right" width="70"> - <input type="text" name="{{ sample.name }}" class="fs13 b1 c222 edit_sample_value valueField" + <td class="std_cell" data-column_name="Value" align="right" width="70"> + <input type="text" name="{{ sample.name }}" + class="trait_value_input edit_sample_value" value="{{ sample.display_value }}" size="8" maxlength="8" style="text-align:right; background-color:#FFFFFF;"> </td> {% if sample_type.se_exists() %} - <td class="fs13 b1 c222" align="center" width="20"> + <td class="std_cell" align="center" width="20"> ± </td> {# Todo: Add IDs #} - <td class="fs13 b1 c222" align="right" width="80"> - <input type="text" name=""{{ 'V' + sample.name}}" class="fs13 b1 c222 valueField edit_sample_se" + <td class="std_cell" data-column_name="SE" align="right" width="80"> + <input type="text" name=""{{ 'V' + sample.name}}" + class="trait_value_input edit_sample_se" value="{{ sample.display_variance }}" size="8" maxlength="8" style="text-align:right"> </td> @@ -1317,7 +1330,7 @@ {# Loop through each attribute type and input value #} {% for attribute in sample_type.attributes|sort() %} - <td class="fd13 b1 c222" align="right" width="80"> + <td class="std_cell" data-column_name="{{ sample_type.attributes[attribute].name }}" align="right" width="80"> {{ sample.extra_attributes[sample_type.attributes[attribute].name] }} </td> {% endfor %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index c38ecb47..82a08c71 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -94,6 +94,7 @@ def corr_compute_page(): # Todo: Can we simplify this? -Sam def sharing_info_page(): + """Info page displayed when the user clicks the "Info" button next to the dataset selection""" print("In sharing_info_page") fd = webqtlFormData.webqtlFormData(request.args) print("2Have fd") |