diff options
Diffstat (limited to 'wqflask')
52 files changed, 619 insertions, 257 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index ec8c40a0..50bd8874 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -25,19 +25,19 @@ def create_trait(**kw): assert bool(kw.get('dataset')) != bool( kw.get('dataset_name')), "Needs dataset ob. or name" - if kw.get('name'): - if kw.get('dataset_name'): - if kw.get('dataset_name') != "Temp": - dataset = create_dataset(kw.get('dataset_name')) - else: - dataset = kw.get('dataset') + assert bool(kw.get('name')), "Needs trait name" + if kw.get('dataset_name'): if kw.get('dataset_name') != "Temp": - if dataset.type == 'Publish': - permissions = check_resource_availability( - dataset, kw.get('name')) - else: - permissions = check_resource_availability(dataset) + dataset = create_dataset(kw.get('dataset_name')) + else: + dataset = kw.get('dataset') + + if dataset.type == 'Publish': + permissions = check_resource_availability( + dataset, kw.get('name')) + else: + permissions = check_resource_availability(dataset) if "view" in permissions['data']: the_trait = GeneralTrait(**kw) diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 6ab8c3d8..c87776bb 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -29,6 +29,8 @@ class CorrScatterPlot(object): self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2) #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3) + self.method = params['method'] + primary_samples = self.dataset_1.group.samplelist if self.dataset_1.group.parlist != None: primary_samples += self.dataset_1.group.parlist diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 0c1cea0e..7d3b9b9f 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -493,14 +493,15 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['description'] = "N/A" results_dict['location'] = trait.location_repr results_dict['mean'] = "N/A" - results_dict['lrs_score'] = "N/A" results_dict['additive'] = "N/A" if bool(trait.description_display): results_dict['description'] = trait.description_display if bool(trait.mean): results_dict['mean'] = f"{float(trait.mean):.3f}" - if trait.LRS_score_repr != "N/A": - results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}" + try: + results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}" + except: + results_dict['lod_score'] = "N/A" results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): results_dict['additive'] = f"{float(trait.additive):.3f}" @@ -544,8 +545,10 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap else: results_dict['pubmed_link'] = trait.pubmed_link results_dict['pubmed_text'] = trait.pubmed_text - - results_dict['lrs_score'] = trait.LRS_score_repr + try: + results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}" + except: + results_dict['lod_score'] = "N/A" results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): results_dict['additive'] = f"{float(trait.additive):.3f}" diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index 0269ce68..a77877d2 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -20,24 +20,23 @@ import datetime import math +import random +import string + import numpy as np import scipy import rpy2.robjects as robjects -import utility.webqtlUtil # this is for parallel computing only. -import utility.logger +from rpy2.robjects.packages import importr from base import data_set +from base.webqtlConfig import GENERATED_TEXT_DIR from functools import reduce from functools import cmp_to_key -from rpy2.robjects.packages import importr - from utility import webqtlUtil from utility import helper_functions from utility import corr_result_helpers from utility.redis_tools import get_redis_conn -logger = utility.logger.getLogger(__name__) - Redis = get_redis_conn() THIRTY_DAYS = 60 * 60 * 24 * 30 @@ -135,6 +134,8 @@ class CorrelationMatrix(object): self.corr_results.append(corr_result_row) self.pca_corr_results.append(pca_corr_result_row) + self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results) + self.trait_data_array = [] for trait_db in self.trait_list: this_trait = trait_db[0] @@ -232,6 +233,36 @@ class CorrelationMatrix(object): loadings_array.append(loadings_row) return loadings_array +def export_corr_matrix(corr_results): + corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename) + with open(matrix_export_path, "w+") as output_file: + output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n") + output_file.write("\n") + output_file.write("Correlation ") + for i, item in enumerate(corr_results[0]): + output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("\n") + for i, row in enumerate(corr_results): + output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + for item in row: + output_file.write(str(item[1]) + "\t") + output_file.write("\n") + + output_file.write("\n") + output_file.write("\n") + output_file.write("N ") + for i, item in enumerate(corr_results[0]): + output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t") + output_file.write("\n") + for i, row in enumerate(corr_results): + output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t") + for item in row: + output_file.write(str(item[2]) + "\t") + output_file.write("\n") + + return corr_matrix_filename, matrix_export_path + def zScore(trait_data_array): NN = len(trait_data_array[0]) if NN < 10: diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 505ae295..8341ee55 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -33,8 +33,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo ) opt_list.append("-b") - opt_list.append(f"--n_bootstrap{str(num_bootstrap)}") - opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") + opt_list.append(f"--n_bootstrap {str(num_bootstrap)}") + opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: permu_filename =("{this_dataset.group.name}_PERM_" + ''.join(random.choice(string.ascii_uppercase + diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c474e0e0..891fcc66 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -426,6 +426,8 @@ class RunMapping(object): marker['display_pos'] = "N/A" self.qtl_results.append(marker) + total_markers = len(self.qtl_results) + with Bench("Exporting Results"): export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type) @@ -489,13 +491,15 @@ class RunMapping(object): perm_results = self.perm_output, significant = significant_for_browser, browser_files = browser_files, - selected_chr = this_chr + selected_chr = this_chr, + total_markers = total_markers ) else: self.js_data = dict( chr_lengths = chr_lengths, browser_files = browser_files, - selected_chr = this_chr + selected_chr = this_chr, + total_markers = total_markers ) def run_rqtl_plink(self): diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index ce836ce2..0d0894a4 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -126,11 +126,14 @@ views.py). trait_dict['mean'] = "N/A" trait_dict['additive'] = "N/A" if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['mean'] = f"{this_trait.mean:.3f}" + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" trait_dict['lrs_location'] = this_trait.LRS_location_repr if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive + trait_dict['additive'] = f"{this_trait.additive:.3f}" elif this_trait.dataset.type == "Geno": trait_dict['location'] = this_trait.location_repr elif this_trait.dataset.type == "Publish": @@ -143,12 +146,15 @@ views.py). trait_dict['pubmed_text'] = this_trait.pubmed_text trait_dict['mean'] = "N/A" if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['mean'] = f"{this_trait.mean:.3f}" + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" trait_dict['lrs_location'] = this_trait.LRS_location_repr trait_dict['additive'] = "N/A" if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive + trait_dict['additive'] = f"{this_trait.additive:.3f}" # Convert any bytes in dict to a normal utf-8 string for key in trait_dict.keys(): if isinstance(trait_dict[key], bytes): diff --git a/wqflask/wqflask/static/new/css/colorbox.css b/wqflask/wqflask/static/new/css/colorbox.css new file mode 100644 index 00000000..8b9fb388 --- /dev/null +++ b/wqflask/wqflask/static/new/css/colorbox.css @@ -0,0 +1,238 @@ +/* + Colorbox Core Style: + The following CSS is consistent between example themes and should not be altered. +*/ +#colorbox, +#cboxOverlay, +#cboxWrapper { + position: absolute; + top: 0; + left: 0; + z-index: 9999; + overflow: hidden; +} + +#cboxOverlay { + position: fixed; + width: 100%; + height: 100%; +} + +#cboxMiddleLeft, +#cboxBottomLeft { + clear: left; +} + +#cboxContent { + position: relative; +} + +#cboxLoadedContent { + overflow: auto; + -webkit-overflow-scrolling: touch; +} + +#cboxTitle { + margin: 0; +} + +#cboxLoadingOverlay, +#cboxLoadingGraphic { + position: absolute; + top: 0; + left: 0; + width: 100%; + height: 100%; +} + +#cboxPrevious, +#cboxNext, +#cboxClose, +#cboxSlideshow { + cursor: pointer; +} + +.cboxPhoto { + float: left; + margin: auto; + border: 0; + display: block; + max-width: none; + -ms-interpolation-mode: bicubic; +} + +.cboxIframe { + width: 100%; + height: 100%; + display: block; + border: 0; +} + +#colorbox, +#cboxContent, +#cboxLoadedContent { + box-sizing: content-box; + -moz-box-sizing: content-box; + -webkit-box-sizing: content-box; +} + +/* + User Style: + Change the following styles to modify the appearance of Colorbox. They are + ordered & tabbed in a way that represents the nesting of the generated HTML. +*/ +#cboxOverlay { + background: #fff; +} + +#colorbox { + outline: 0; +} + +#cboxTopLeft { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat 0 0; +} + +#cboxTopCenter { + height: 25px; + background: url(images/border1.png) repeat-x 0 -50px; +} + +#cboxTopRight { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat -25px 0; +} + +#cboxBottomLeft { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat 0 -25px; +} + +#cboxBottomCenter { + height: 25px; + background: url(images/border1.png) repeat-x 0 -75px; +} + +#cboxBottomRight { + width: 25px; + height: 25px; + background: url(images/border1.png) no-repeat -25px -25px; +} + +#cboxMiddleLeft { + width: 25px; + background: url(images/border2.png) repeat-y 0 0; +} + +#cboxMiddleRight { + width: 25px; + background: url(images/border2.png) repeat-y -25px 0; +} + +#cboxContent { + background: #fff; + overflow: hidden; +} + +.cboxIframe { + background: #fff; +} + +#cboxError { + padding: 50px; + border: 1px solid #ccc; +} + +#cboxLoadedContent { + margin-bottom: 20px; +} + +#cboxTitle { + position: absolute; + bottom: 0px; + left: 0; + text-align: center; + width: 100%; + color: #999; +} + +#cboxCurrent { + position: absolute; + bottom: 0px; + left: 100px; + color: #999; +} + +#cboxLoadingOverlay { + background: #fff url(images/loading.gif) no-repeat 5px 5px; +} + +/* these elements are buttons, and may need to have additional styles reset to avoid unwanted base styles */ +#cboxPrevious, +#cboxNext, +#cboxSlideshow, +#cboxClose { + border: 0; + padding: 0; + margin: 0; + overflow: visible; + width: auto; + background: none; +} + +/* avoid outlines on :active (mouseclick), but preserve outlines on :focus (tabbed navigating) */ +#cboxPrevious:active, +#cboxNext:active, +#cboxSlideshow:active, +#cboxClose:active { + outline: 0; +} + +#cboxSlideshow { + position: absolute; + bottom: 0px; + right: 42px; + color: #444; +} + +#cboxPrevious { + position: absolute; + bottom: 0px; + left: 0; + color: #444; +} + +#cboxNext { + position: absolute; + bottom: 0px; + left: 63px; + color: #444; +} + +#cboxClose { + position: absolute; + bottom: 0; + right: 0; + display: block; + color: #444; +} + +/* + The following fixes a problem where IE7 and IE8 replace a PNG's alpha transparency with a black fill + when an alpha filter (opacity change) is set on the element or ancestor element. This style is not applied to or needed in IE9. + See: http://jacklmoore.com/notes/ie-transparency-problems/ +*/ +.cboxIE #cboxTopLeft, +.cboxIE #cboxTopCenter, +.cboxIE #cboxTopRight, +.cboxIE #cboxBottomLeft, +.cboxIE #cboxBottomCenter, +.cboxIE #cboxBottomRight, +.cboxIE #cboxMiddleLeft, +.cboxIE #cboxMiddleRight { + filter: progid:DXImageTransform.Microsoft.gradient(startColorstr=#00FFFFFF, endColorstr=#00FFFFFF); +}
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index e0a5ceea..9f56b63d 100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css @@ -48,10 +48,10 @@ table.dataTable thead th{ } table.dataTable thead .sorting_asc { - background-image: url("../packages/DataTables/images/sort_asc_disabled.png"); + background-image: url("/js/DataTables/images/sort_asc_disabled.png"); } table.dataTable thead .sorting_desc { - background-image: url("../packages/DataTables/images/sort_desc_disabled.png"); + background-image: url("/js/DataTables/images/sort_desc_disabled.png"); } table.dataTable thead th { diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index 39c6ba53..27404801 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -25,10 +25,10 @@ table.dataTable thead th, table.dataTable tfoot th{ } table.dataTable thead .sorting_asc { - background-image: url("../packages/DataTables/images/sort_asc_disabled.png"); + background-image: url("/js/DataTables/images/sort_asc_disabled.png"); } table.dataTable thead .sorting_desc { - background-image: url("../packages/DataTables/images/sort_desc_disabled.png"); + background-image: url("/js/DataTables/images/sort_desc_disabled.png"); } table.dataTable thead th, table.dataTable tfoot { diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js new file mode 100644 index 00000000..1a4dc039 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js @@ -0,0 +1,21 @@ + function filterDatatable(datatable){ + let invalidColumns=[] + let columnCount=datatable.columns().header().length; + let numberOfRows=datatable.rows().count(); + for (let col=0; col<columnCount; col++){ + colObj = datatable.column(col).nodes().to$(); + allNAs = true; + for (let i=0;i<numberOfRows;i++){ + cellContent = colObj[i].childNodes[0].data + if (cellContent != "N/A" && cellContent != ""){ + allNAs = false; + break; + } + } + if (allNAs){ + invalidColumns.push(col) + } + } + return datatable.columns(invalidColumns).visible(false); + + }
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 87c35984..5dc9e456 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -731,14 +731,36 @@ filter_by_value = function() { } }; +hide_no_value_filter = function( settings, data, dataIndex ) { + this_value = table_api.column(3).nodes().to$()[dataIndex].childNodes[0].value; + if (this_value == "x"){ + return false + } else { + return true + } +} + hide_no_value = function() { - return $('.value_se').each((function(_this) { - return function(_index, element) { - if ($(element).find('.trait-value-input').val() === 'x') { - return $(element).hide(); + tables = ['samples_primary', 'samples_other']; + filter_active = $(this).data("active"); + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + table_api = $('#' + table).DataTable(); + if (filter_active == "true"){ + $(this).val("Hide No Value") + table_api.draw(); + $(this).data("active", "false"); + } else { + $(this).val("Show No Value") + $.fn.dataTable.ext.search.push(hide_no_value_filter); + table_api.search(); + table_api.draw(); + $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hide_no_value_filter, 1)); + $(this).data("active", "true"); } - }; - })(this)); + } + } }; $('#hide_no_value').click(hide_no_value); @@ -754,6 +776,7 @@ $('#block_outliers').click(block_outliers); reset_samples_table = function() { $('input[name="transform"]').val(""); $('span[name="transform_text"]').text("") + $('#hide_no_value').val("Hide No Value") tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; @@ -771,6 +794,7 @@ reset_samples_table = function() { this_node.value = this_node.attributes["data-value"].value; } } + table_api.draw(); } } }; diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html index 5a6929fb..21ef5653 100644 --- a/wqflask/wqflask/templates/admin/create_group.html +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -80,9 +80,9 @@ {% endblock %} {% block js %} - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> <script type="text/javascript" charset="utf-8"> </script> diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html index c8ed6851..c0b99e75 100644 --- a/wqflask/wqflask/templates/admin/group_manager.html +++ b/wqflask/wqflask/templates/admin/group_manager.html @@ -2,7 +2,7 @@ {% block title %}Group Manager{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/admin/ind_user_manager.html b/wqflask/wqflask/templates/admin/ind_user_manager.html index e859b442..b821e5d5 100644 --- a/wqflask/wqflask/templates/admin/ind_user_manager.html +++ b/wqflask/wqflask/templates/admin/ind_user_manager.html @@ -103,7 +103,7 @@ {% block js %} - <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script> <script> $('body').timeago(); </script> diff --git a/wqflask/wqflask/templates/admin/manage_user.html b/wqflask/wqflask/templates/admin/manage_user.html index 7afe075f..3ef90b90 100644 --- a/wqflask/wqflask/templates/admin/manage_user.html +++ b/wqflask/wqflask/templates/admin/manage_user.html @@ -2,7 +2,7 @@ {% block title %}View and Edit Group{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html index f304a172..0e1ec720 100644 --- a/wqflask/wqflask/templates/admin/search_for_groups.html +++ b/wqflask/wqflask/templates/admin/search_for_groups.html @@ -63,7 +63,7 @@ {% endblock %} {% block js %} - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html index bc52788f..04842453 100644 --- a/wqflask/wqflask/templates/admin/set_group_privileges.html +++ b/wqflask/wqflask/templates/admin/set_group_privileges.html @@ -2,7 +2,7 @@ {% block title %}Set Group Privileges{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html index 9e3cce7b..26692fe8 100644 --- a/wqflask/wqflask/templates/admin/view_group.html +++ b/wqflask/wqflask/templates/admin/view_group.html @@ -2,7 +2,7 @@ {% block title %}View and Edit Group{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html index bfa95805..a86b9ea9 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -239,8 +239,8 @@ <!--</div>--> </div> - <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script> - <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> + <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script> + <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> <script> //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working var $window = $(window) @@ -251,14 +251,15 @@ } }) </script> - <script src="/static/new/js_external/jquery.cookie.js"></script> + <script src="{{ url_for('js', filename='jquery-cookie/jquery.cookie.js') }}" type="text/javascript"></script> <script type="text/javascript" src="/static/new/js_external/json2.js"></script> - <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script> + <script src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script> - <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script> <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>--> - <script type="text/javascript" src="/static/new/js_external/parsley.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script> + {% block js %} {% endblock %} diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 9e0c0f07..2ff7b2fd 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -66,10 +66,10 @@ {% endblock %} {% block js %} - <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script> diff --git a/wqflask/wqflask/templates/collections/not_logged_in.html b/wqflask/wqflask/templates/collections/not_logged_in.html index a4c8747e..49b0e07d 100644 --- a/wqflask/wqflask/templates/collections/not_logged_in.html +++ b/wqflask/wqflask/templates/collections/not_logged_in.html @@ -5,7 +5,7 @@ {{ header("Not logged in") }} - <div id "collections_holder" class="container"> + <div id="collections_holder" class="container"> <div class="page-header"> <h1>Please log in in order to use this feature.</h1> </div> @@ -16,7 +16,7 @@ {% endblock %} {% block js %} - <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script> <script> $('body').timeago(); </script> diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index ccec495b..66945ed7 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -28,41 +28,7 @@ {{ this_trait.name }}:{{ this_trait.dataset.name }}:{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}, {% endfor %}" > - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > - BNW - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> + {% include 'tool_buttons.html' %} </form> </div> @@ -162,7 +128,7 @@ {% endblock %} {% block js %} - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html index f791457f..d77e0515 100644 --- a/wqflask/wqflask/templates/comparison_bar_chart.html +++ b/wqflask/wqflask/templates/comparison_bar_chart.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Comparison Bar Chart{% endblock %} {% block css %} - <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -31,8 +31,8 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script> {% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index 1133fcd2..f44350ab 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -118,17 +118,17 @@ {% endif %} <ul class="nav nav-tabs"> - <li class="active"> + <li {% if method == 'pearson' %}class="active"{% endif %}> <a href="#tp1" data-toggle="tab">Pearson</a> </li> - <li> + <li {% if method == 'spearman' %}class="active"{% endif %}> <a href="#tp2" data-toggle="tab">Spearman Rank</a> </li> </ul> <div class="tab-content" style="min-width: 800px;"> - <div class="tab-pane active" id="tp1"> + <div class="tab-pane {% if method == 'pearson' %}active{% endif %}" id="tp1"> <br> <div id="scatterplot2"></div> <br> @@ -243,7 +243,7 @@ </div> </div> - <div class="tab-pane" id="tp2"> + <div class="tab-pane {% if method == 'spearman' %}active{% endif %}" id="tp2"> <br> <div id="srscatterplot2"></div> <br> @@ -349,11 +349,11 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jscolor.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jscolor/jscolor.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <!--<script language="javascript" type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>--> - <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 4e150618..8275f1dd 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -1,10 +1,11 @@ {% extends "base.html" %} +{% block title %}Correlation Matrix{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> {% endblock %} {% block content %} @@ -32,6 +33,7 @@ {% endfor %} </tr> {% for trait in traits %} + {% set outer_loop = loop.index %} <tr> <td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td> <td align="right" style="padding-right: 4px;" > @@ -54,7 +56,7 @@ {% if result[1] == 0 %} <td nowrap="ON" align="middle" bgcolor="#eeeeee" style="padding: 3px; line-height: 1.1;">N/A</td> {% else %} - <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> + <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?method={% if loop.index > outer_loop %}spearman{% else %}pearson{% endif %}&dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td> {% endif %} {% endif %} {% endfor %} @@ -63,6 +65,12 @@ </tbody> </table> <br> +<form method="post" target="_blank" action="/export_corr_matrix" id="matrix_export_form"> + <input type="hidden" name="export_filepath" value="{{ export_filepath }}"> + <input type="hidden" name="export_filename" value="{{ export_filename }}"> + <button class="btn btn-default" id="export">Download <span class="glyphicon glyphicon-download"></span></button> +</form> +<br> {% if pca_works == "True" %} <h2>PCA Traits</h2> <div style="margin-bottom: 20px; overflow:hidden;"> @@ -133,7 +141,7 @@ <script type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='chroma/chroma.min.js') }}"></script> @@ -172,6 +180,14 @@ "paging": false, "orderClasses": true } ); + + export_corr_matrix = function() { + $('#matrix_export_form').attr('action', '/export_corr_matrix'); + return $('#matrix_export_form').submit(); + } + + $('#export').click(export_corr_matrix); + </script> {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 06ee9056..8e2a23fd 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -32,43 +32,7 @@ {% for this_trait in trait_list %} {{ this_trait.name }}:{{ this_trait.dataset }}, {% endfor %}" > - - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > - BNW - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> - + {% include 'tool_buttons.html' %} </form> </div> <br /> @@ -120,14 +84,12 @@ <div class="show-hide-container" style="float: left; clear: left;"> <b>Show/Hide Columns:</b> <br> - <button class="toggle-vis" data-column="1">Index</button> - <button class="toggle-vis" data-column="2">Record</button> {% if target_dataset.type == 'ProbeSet' %} <button class="toggle-vis" data-column="3">Symbol</button> <button class="toggle-vis" data-column="4">Description</button> <button class="toggle-vis" data-column="5">Location</button> <button class="toggle-vis" data-column="6">Mean</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% elif target_dataset.type == 'Publish' %} @@ -138,7 +100,7 @@ <button class="toggle-vis" data-column="7">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button> <button class="toggle-vis" data-column="8">N</button> <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button> - <button class="toggle-vis" data-column="10">High P</button> + <button class="toggle-vis" data-column="10">Peak LOD</button> <button class="toggle-vis" data-column="11">Peak Location</button> <button class="toggle-vis" data-column="12">Effect Size</button> {% else %} @@ -172,8 +134,9 @@ <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script> @@ -345,8 +308,15 @@ 'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}", 'type': "natural-minus-na", 'width': "40px", - 'data': "sample_r", - 'orderSequence': [ "desc", "asc"] + 'data': null, + 'orderSequence': [ "desc", "asc"], + 'render': function(data, type, row, meta) { + if (data.sample_r != "N/A") { + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + } else { + return data.sample_r + } + } }, { 'title': "N", @@ -357,7 +327,7 @@ }, { 'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})", - 'type': "natural-minus-na", + 'type': "scientific", 'width': "65px", 'data': "sample_p", 'orderSequence': [ "desc", "asc"] @@ -384,9 +354,9 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", + 'data': "lod_score", 'width': "60px", 'orderSequence': [ "desc", "asc"] }, @@ -459,8 +429,15 @@ 'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}", 'type': "natural-minus-na", 'width': "40px", - 'data': "sample_r", - 'orderSequence': [ "desc", "asc"] + 'data': null, + 'orderSequence': [ "desc", "asc"], + 'render': function(data, type, row, meta) { + if (data.sample_r != "N/A") { + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + } else { + return data.sample_r + } + } }, { 'title': "N", @@ -471,15 +448,15 @@ }, { 'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})", - 'type': "natural-minus-na", + 'type': "scientific", 'width': "65px", 'data': "sample_p", 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", + 'data': "lod_score", 'width': "60px", 'orderSequence': [ "desc", "asc"] }, @@ -506,8 +483,15 @@ 'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}", 'type': "natural-minus-na", 'width': "40px", - 'data': "sample_r", - 'orderSequence': [ "desc", "asc"] + 'data': null, + 'orderSequence': [ "desc", "asc"], + 'render': function(data, type, row, meta) { + if (data.sample_r != "N/A") { + return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>" + } else { + return data.sample_r + } + } }, { 'title': "N", @@ -518,7 +502,7 @@ }, { 'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})", - 'type': "natural-minus-na", + 'type': "scientific", 'width': "65px", 'data': "sample_p", 'orderSequence': [ "desc", "asc"] diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index e374eb4e..6f009183 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" /> - <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}"> <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}"> <style> /* The Cytoscape Web container must have its dimensions set. */ @@ -64,13 +64,13 @@ gn2_url = "{{ gn2_url | safe }}" </script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/js/cytoscape/cytoscape.min.js"></script> - <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script> <!-- should be using cytoscape-popper for tips, see docs --> - <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script> <!-- Loads flash - who wants that? diff --git a/wqflask/wqflask/templates/docedit.html b/wqflask/wqflask/templates/docedit.html index b87c5b41..50bb96c0 100644 --- a/wqflask/wqflask/templates/docedit.html +++ b/wqflask/wqflask/templates/docedit.html @@ -16,7 +16,7 @@ {{content|safe}} </textarea> <button class="submit_changes" style="margin-top: 20px;">Submit Changes</button> - <script src="/static/packages/ckeditor/ckeditor.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='ckeditor/ckeditor.js') }}"></script> <script type="text/javascript"> CKEDITOR.replace('ckcontent', { height: '650px', diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index d5bc4141..6fd0abe8 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -48,7 +48,7 @@ {% block js %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script> diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index ccd4a9d9..0dc6fe5f 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -48,7 +48,7 @@ {% block js %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script> diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html index 497838dd..92754266 100644 --- a/wqflask/wqflask/templates/heatmap.html +++ b/wqflask/wqflask/templates/heatmap.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block title %}Heatmap{% endblock %} {% block css %} - <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -39,6 +39,6 @@ <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> {% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html index 13ca52df..7efbdccf 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -326,7 +326,7 @@ } </script> - <script type="text/javascript" src="/twitter/js/twitterFetcher_min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script> <script type="text/javascript"> var configProfile = { diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 1716b095..926f258d 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -39,8 +39,8 @@ </div> </div> </form> -<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script> - <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> +<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script> +<script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script> <script type="text/javascript"> $("#loading_form").attr("action", "{{ start_vars.form_url }}"); diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 5533ecf3..1a601bef 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -4,7 +4,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous"> - <link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='purescript-genome-browser/css/purescript-genetics-browser.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" /> @@ -350,7 +350,7 @@ <script type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script> <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> {% if manhattan_plot == True and selectedChr == -1 %} <script type="text/javascript" src="/static/new/js_external/jscolor.js"></script> {% endif %} @@ -359,7 +359,7 @@ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script> <script> js_data = {{ js_data | safe }} @@ -388,8 +388,11 @@ "targets": 0, "orderable": false } ], + "language": { + "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records", + }, "order": [[1, "asc" ]], - "sDom": "RZtir", + "sDom": "iRZtir", "iDisplayLength": -1, "autoWidth": false, "deferRender": true, diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html index be3d0402..2941cb80 100644 --- a/wqflask/wqflask/templates/network_graph.html +++ b/wqflask/wqflask/templates/network_graph.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" /> - <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}"> <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}"> <style> /* The Cytoscape Web container must have its dimensions set. */ @@ -139,15 +139,14 @@ elements_list = {{ elements | safe }} gn2_url = "{{ gn2_url | safe }}" </script> - - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/js/cytoscape/cytoscape.min.js"></script> - <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script> <!-- should be using cytoscape-popper for tips, see docs --> - <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script> <!-- Loads flash - who wants that? diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html index 473fa377..5dc424e5 100644 --- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html +++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html @@ -21,6 +21,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html index 7110dc79..4e3ea59f 100644 --- a/wqflask/wqflask/templates/new_security/password_reset.html +++ b/wqflask/wqflask/templates/new_security/password_reset.html @@ -74,6 +74,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html index 325d8aa5..2506f4ee 100644 --- a/wqflask/wqflask/templates/new_security/register_user.html +++ b/wqflask/wqflask/templates/new_security/register_user.html @@ -101,6 +101,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html index e71d5598..eaed3ed0 100644 --- a/wqflask/wqflask/templates/new_security/registered.html +++ b/wqflask/wqflask/templates/new_security/registered.html @@ -20,6 +20,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html index 459bd66a..f492fb51 100644 --- a/wqflask/wqflask/templates/new_security/thank_you.html +++ b/wqflask/wqflask/templates/new_security/thank_you.html @@ -19,6 +19,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html index 3aa24e37..91768eb9 100644 --- a/wqflask/wqflask/templates/new_security/verification_still_needed.html +++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html @@ -22,6 +22,6 @@ {% block js %} {% include "new_security/_scripts.html" %} - <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script> {% endblock %} diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index acafe3a0..d6c7da4a 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -4,7 +4,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> {% endblock %} @@ -64,11 +64,11 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> {% endblock %}
\ No newline at end of file diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 87c97c50..f2334512 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -75,42 +75,7 @@ {{ this_trait.name }}:{{ this_trait.dataset }}, {% endfor %}" > - - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > - BNW - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> + {% include 'tool_buttons.html' %} </form> </div> @@ -141,14 +106,12 @@ <div class="show-hide-container"> <b>Show/Hide Columns:</b> <br> - <button class="toggle-vis" data-column="1">Index</button> - <button class="toggle-vis" data-column="2">Record</button> {% if dataset.type == 'ProbeSet' %} <button class="toggle-vis" data-column="3">Symbol</button> <button class="toggle-vis" data-column="4">Description</button> <button class="toggle-vis" data-column="5">Location</button> <button class="toggle-vis" data-column="6">Mean</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% elif dataset.type == 'Publish' %} @@ -156,7 +119,7 @@ <button class="toggle-vis" data-column="4">Mean</button> <button class="toggle-vis" data-column="5">Authors</button> <button class="toggle-vis" data-column="6">Year</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% endif %} @@ -183,7 +146,7 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> @@ -314,10 +277,10 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", - 'width': "65px", + 'data': "lod_score", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { @@ -383,10 +346,10 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", - 'width': "80px", + 'data': "lod_score", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/wqflask/wqflask/templates/set_group_privileges.html index 98b0cc12..a0a53292 100644 --- a/wqflask/wqflask/templates/set_group_privileges.html +++ b/wqflask/wqflask/templates/set_group_privileges.html @@ -2,7 +2,7 @@ {% block title %}Set Group Privileges{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 7b74a3f6..c881eb76 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -5,10 +5,9 @@ <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> - <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" /> - <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" /> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} @@ -131,11 +130,11 @@ <script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script> <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script> - <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script> <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> - <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script> - <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script> - <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='shapiro-wilk/shapiro-wilk.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script> <script type="text/javascript" src="/static/new/javascript/stats.js"></script> @@ -147,9 +146,8 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script> - + <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.3/js/dataTables.scroller.min.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script> <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script> <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script> <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> @@ -221,6 +219,33 @@ primary_table.search($(this).val()).draw(); } ); + $('.toggle-vis').on('click', function (e) { + e.preventDefault(); + + function toggle_column(column) { + //ZS: Toggle column visibility + column.visible( ! column.visible() ); + if (column.visible()){ + $(this).removeClass("active"); + } else { + $(this).addClass("active"); + } + } + + // Get the column API object + var target_cols = $(this).attr('data-column').split(",") + for (let i = 0; i < target_cols.length; i++){ + console.log("THE COL:", target_cols[i]) + var column = primary_table.column( target_cols[i] ); + toggle_column(column); + + {% if sample_groups|length != 1 %} + var column2 = other_table.column( target_cols[i] ); + toggle_column(column2); + {% endif %} + } + } ); + {% if sample_groups|length != 1 %} $('#other_searchbox').on( 'keyup', function () { other_table.search($(this).val()).draw(); diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 4f25e90a..ba72ff27 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -38,7 +38,7 @@ </div> <div class="form-group"> - <label for="corr_return_results" class="col-xs-2 control-label">Return</label> + <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label> <div class="col-xs-4 controls"> <select name="corr_return_results" class="form-control"> {% for return_result in corr_tools.return_results_menu %} diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 2e730248..4ad11a5e 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -1,6 +1,36 @@ <div> {% for sample_type in sample_groups %} <div class="sample-table-container"> + {% if loop.index == 1 %} + <b>Show/Hide Columns:</b> + <br> + <button class="toggle-vis" data-column="1">ID</button> + <button class="toggle-vis" data-column="2">Sample</button> + <button class="toggle-vis" data-column="3">Value</button> + {% if sample_groups[0].se_exists %} + <button class="toggle-vis" data-column="4,5">SE</button> + {% if has_num_cases %} + <button class="toggle-vis" data-column="6">N</button> + {% set attr_start_pos = 7 %} + {% else %} + {% set attr_start_pos = 6 %} + {% endif %} + {% else %} + {% if has_num_cases %} + <button class="toggle-vis" data-column="4">N</button> + {% set attr_start_pos = 5 %} + {% else %} + {% set attr_start_pos = 4 %} + {% endif %} + {% endif %} + {% if sample_groups[0].attributes %} + {% for attribute in sample_groups[0].attributes %} + <button class="toggle-vis" data-column="{{ loop.index + attr_start_pos - 1 }}">{{ sample_groups[0].attributes[attribute].name }}</button> + {% endfor %} + {% endif %} + <br> + <br> + {% endif %} <div class="sample-table-search-container"> <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control sample-table-search" placeholder="Search This Table For ..."> </div> diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index d7eac378..b70ca590 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -80,7 +80,7 @@ <input type="button" id="filter_by_value" class="btn btn-danger" value="Filter"> </div> <div> - <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> + <input data-active="false" type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers"> <input type="button" class="btn btn-success reset" value="Reset"> <span class="input-append"> diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html index fb564b28..a96b8e3b 100644 --- a/wqflask/wqflask/templates/snp_browser.html +++ b/wqflask/wqflask/templates/snp_browser.html @@ -217,7 +217,7 @@ {% block js %} <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/typeahead.bundle.js"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='typeahead/typeahead.bundle.js') }}"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script> diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html new file mode 100644 index 00000000..5b2dbf3d --- /dev/null +++ b/wqflask/wqflask/templates/tool_buttons.html @@ -0,0 +1,35 @@ +<button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+ Correlations
+</button>
+
+<button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
+ Networks
+</button>
+
+<button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+ WebGestalt
+</button>
+
+<button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
+ GeneWeaver
+</button>
+
+<button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
+ BNW
+</button>
+
+<button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+ WGCNA
+</button>
+
+<button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+ CTL Maps
+</button>
+
+<button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+ MultiMap
+</button>
+
+<button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+ Comparison Bar Chart
+</button>
\ No newline at end of file diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3557a62a..25563e86 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -799,6 +799,17 @@ def export_mapping_results(): return response +@app.route("/export_corr_matrix", methods = ('POST',)) +def export_corr_matrix(): + file_path = request.form.get("export_filepath") + file_name = request.form.get("export_filename") + results_csv = open(file_path, "r").read() + response = Response(results_csv, + mimetype='text/csv', + headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + + return response + @app.route("/export", methods = ('POST',)) def export(): logger.info("request.form:", request.form) |