diff options
34 files changed, 375 insertions, 47 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 1a9eb695..36aeea83 100644 --- a/test/requests/link_checker.py +++ b/test/requests/link_checker.py @@ -103,6 +103,7 @@ def check_packaged_js_files(args_obj, parser): "/js/DataTablesExtensions/colResize/dataTables.colResize.js", "/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js", "/js/DataTablesExtensions/buttons/js/buttons.colVis.min.js", + "/js/DataTablesExtensions/scroller/js/scroller.dataTables.min.js", "/js/DataTables/js/jquery.dataTables.js", "/css/DataTablesExtensions/scroller/css/scroller.dataTables.min.css", # Datatables plugins: @@ -116,6 +117,16 @@ def check_packaged_js_files(args_obj, parser): "/js/nvd3/nv.d3.min.css", "/js/qtip2/jquery.qtip.min.js", "/js/js_alt/md5.min.js", + "/js/js_alt/jstat.min.js", + "/js/js_alt/parsley.min.js", + "/js/js_alt/timeago.min.js", + "/js/plotly/plotly.min.js", + "/js/ckeditor/ckeditor.js", + "/js/jszip/jszip.min.js", + "/js/jscolor/jscolor.js", + "/js/DataTables/js/jquery.js", + "/css/DataTables/css/jquery.dataTables.css", + "/js/colorbox/jquery.colorbox-min.js", "/css/nouislider/nouislider.min.css", "/js/nouislider/nouislider.js", "/js/purescript-genome-browser/js/purescript-genetics-browser.js", @@ -125,6 +136,8 @@ def check_packaged_js_files(args_obj, parser): "/js/cytoscape-panzoom/cytoscape.js-panzoom.css", "/js/cytoscape-qtip/cytoscape-qtip.js", "/css/d3-tip/d3-tip.css", + "/js/DataTables/images/sort_asc_disabled.png", + "/js/DataTables/images/sort_desc_disabled.png", ] print("Checking links") 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/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/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html index 5a6929fb..38ae834c 100644 --- a/wqflask/wqflask/templates/admin/create_group.html +++ b/wqflask/wqflask/templates/admin/create_group.html @@ -80,7 +80,7 @@ {% 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="/static/packages/underscore/underscore-min.js"></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 faa59deb..bb618294 100644 --- a/wqflask/wqflask/templates/base.html +++ b/wqflask/wqflask/templates/base.html @@ -17,7 +17,7 @@ <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" /> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" /> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/colorbox.css" /> <!--<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" />--> <link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css" /> @@ -254,10 +254,11 @@ <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 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 50e1a792..99a6f2de 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -162,7 +162,7 @@ {% 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 b27a6b06..e3dd03d5 100644 --- a/wqflask/wqflask/templates/comparison_bar_chart.html +++ b/wqflask/wqflask/templates/comparison_bar_chart.html @@ -32,7 +32,7 @@ <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 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 cd1998fa..f44350ab 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -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 fb0380c9..de58c4a1 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="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" /> {% endblock %} {% block content %} @@ -64,6 +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;"> @@ -173,6 +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 ee6c3aae..fb168c32 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -171,7 +171,7 @@ <script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> <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="{{ url_for('js', filename='jszip/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='DataTables/js/jquery.dataTables.min.js') }}"></script> diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index f90ee20c..6f009183 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -64,7 +64,7 @@ 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="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script> 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/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 70df1dde..86aa74b0 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -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 %} diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html index 3c2ec601..2941cb80 100644 --- a/wqflask/wqflask/templates/network_graph.html +++ b/wqflask/wqflask/templates/network_graph.html @@ -139,8 +139,7 @@ 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> diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index d64bb4b4..38dca514 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -64,7 +64,7 @@ <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> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 6be60f64..3be2e395 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -183,7 +183,7 @@ <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> 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 bacab9f4..c95a0522 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -132,9 +132,9 @@ <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='d3-tip/d3-tip.js') }}"></script> - <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script> + <script type="text/javascript" src="{{ url_for('js', filename='js_alt/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='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> @@ -146,9 +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="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> 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/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) |