diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/export_traits.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/markdown_routes.py | 55 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/markdown.css | 41 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lodheatmap.js | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.js | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/search_results.js | 165 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 54 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/environment.html | 152 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 46 |
11 files changed, 368 insertions, 194 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1b801b1d..51aa1622 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -487,6 +487,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['index'] = i + 1 results_dict['trait_id'] = trait.name results_dict['dataset'] = trait.dataset.name + results_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) if target_dataset.type == "ProbeSet": results_dict['symbol'] = trait.symbol results_dict['description'] = "N/A" diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py index 3a886537..6fb760e0 100644 --- a/wqflask/wqflask/export_traits.py +++ b/wqflask/wqflask/export_traits.py @@ -44,7 +44,7 @@ def export_search_results_csv(targs): if targs['filter_term'] != "None": metadata.append(["Search Filter Terms: " + targs['filter_term']]) metadata.append(["Exported Row Number: " + str(len(table_rows))]) - metadata.append(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"]) + metadata.append(["Funding for The GeneNetwork: NIGMS (R01 GM123489, 2017-2021), NIDA (P30 DA044223, 2017-2022), NIA (R01AG043930, 2013-2018), NIAAA (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017), NIDA/NIMH/NIAAA (P20-DA 21131, 2001-2012), NCI MMHCC (U01CA105417), NCRR/BIRN (U24 RR021760)"]) metadata.append([]) trait_list = [] @@ -54,7 +54,7 @@ def export_search_results_csv(targs): trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True) trait_list.append(trait_ob) - table_headers = ['Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] + table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression'] traits_by_group = sort_traits_by_group(trait_list) @@ -77,7 +77,7 @@ def export_search_results_csv(targs): csv_rows.append(full_headers) - for trait in group_traits: + for i, trait in enumerate(group_traits): if getattr(trait, "symbol", None): trait_symbol = getattr(trait, "symbol") elif getattr(trait, "abbreviation", None): @@ -85,6 +85,8 @@ def export_search_results_csv(targs): else: trait_symbol = "N/A" row_contents = [ + i + 1, + "https://genenetwork.org/show_trait?trait_id=" + str(trait.name) + "&dataset=" + str(trait.dataset.name), trait.dataset.group.species, trait.dataset.group.name, trait.dataset.name, diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 3109a352..3b60bc96 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -4,6 +4,10 @@ Render pages from github, or if they are unavailable, look for it else where """ import requests import markdown +import os +import sys + +from bs4 import BeautifulSoup from flask import Blueprint from flask import render_template @@ -16,18 +20,25 @@ policies_blueprint = Blueprint("policies_blueprint", __name__) facilities_blueprint = Blueprint("facilities_blueprint", __name__) -def render_markdown(file_name): +def render_markdown(file_name, is_remote_file=True): """Try to fetch the file name from Github and if that fails, try to look for it inside the file system """ github_url = ("https://raw.githubusercontent.com/" "genenetwork/gn-docs/master/") + if not is_remote_file: + text = "" + with open(file_name, "r", encoding="utf-8") as input_file: + text = input_file.read() + return markdown.markdown(text, + extensions=['tables']) + md_content = requests.get(f"{github_url}{file_name}") + if md_content.status_code == 200: + return markdown.markdown(md_content.content.decode("utf-8"), + extensions=['tables']) - return markdown.markdown(md_content.content.decode("utf-8"), extensions=['tables']) - # TODO: Add fallback on our git server by checking the mirror. - # Content not available return (f"\nContent for {file_name} not available. " "Please check " "(here to see where content exists)" @@ -35,6 +46,14 @@ look for it inside the file system """ "Please reach out to the gn2 team to have a look at this") +def get_file_from_python_search_path(pathname_suffix): + cands = [os.path.join(d, pathname_suffix) for d in sys.path] + try: + return list(filter(os.path.exists, cands))[0] + except IndexError: + return None + + @glossary_blueprint.route('/') def glossary(): return render_template( @@ -51,7 +70,33 @@ def references(): @environments_blueprint.route("/") def environments(): - return render_template("environment.html", rendered_markdown=render_markdown("general/environments/environments.md")), 200 + + md_file = get_file_from_python_search_path("wqflask/DEPENDENCIES.md") + svg_file = get_file_from_python_search_path( + "wqflask/dependency-graph.html") + svg_data = None + if svg_file: + with open(svg_file, 'r') as f: + svg_data = "".join( + BeautifulSoup(f.read(), + 'lxml').body.script.contents) + + if md_file is not None: + return ( + render_template("environment.html", + svg_data=svg_data, + rendered_markdown=render_markdown( + md_file, + is_remote_file=False)), + 200 + ) + # Fallback: Fetch file from server + return (render_template( + "environment.html", + svg_data=None, + rendered_markdown=render_markdown( + "general/environments/environments.md")), + 200) @links_blueprint.route("/") diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index dca3e31d..38d664e2 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -57,8 +57,47 @@ word-spacing: 0.2em; } +.graph-legend h1 { + text-align: center; +} + +.graph-legend, +#guix-graph { + width: 90%; + margin: 10px auto; +} + +#guix-graph { + border: solid 2px black; +} + +#markdown table { + width: 100%; +} + +#markdown td { + padding: 1em; + text-align: left; +} + +#markdown th { + text-align: center; +} + +#markdown table, +#markdown td, +#markdown th { + border: solid 2px black; +} + +#markdown td, +#markdown th { + padding-top: 8px; + padding-bottom: 8px; +} + @media(max-width:650px) { .container { width: 100vw; } -}
\ No newline at end of file +} diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js index 965a1d53..b82c95ad 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.js +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js @@ -44,7 +44,9 @@ lodheatmap = function() { _ref = data.chrnames; for (_i = 0, _len = _ref.length; _i < _len; _i++) { chr = _ref[_i]; - xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + if (data.posByChr[chr[0]].length > 0){ + xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + } } zmin = 0; zmax = 0; @@ -144,7 +146,7 @@ lodheatmap = function() { }).attr("stroke", "none").attr("stroke-width", "1").on("mouseover.paneltip", function(d) { yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 1); d3.select(this).attr("stroke", "black"); - return celltip.show(d); + return celltip.show(d, this); }).on("mouseout.paneltip", function(d) { yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 0); d3.select(this).attr("stroke", "none"); diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 3c715c81..ea55a7cf 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -159,7 +159,6 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) if (mappingScale == "morgan") { max_pos = d3.max(data.posByChr[chr[0]]) - console.log("max_pos:", max_pos) data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); } else { diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 86660126..9ffef4f8 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -1,42 +1,87 @@ +change_buttons = function() { + var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2; + buttons = ["#add", "#remove"]; + + num_checked = 0 + table_api = $('#trait_table').DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[0].checked){ + num_checked += 1 + } + } + + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } +}; + $(function() { - var add, change_buttons, checked_traits, deselect_all, invert, remove, removed_traits, select_all; + var add, checked_traits, deselect_all, invert, remove, removed_traits, select_all; checked_traits = null; select_all = function() { - console.log("selected_all"); - $(".trait_checkbox").each(function() { - $(this).prop('checked', true); - if (!$(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').addClass('selected') - } - }); + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = true; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.add("selected"); + } + + change_buttons(); }; deselect_all = function() { - $(".trait_checkbox").each(function() { - $(this).prop('checked', false); - if ($(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').removeClass('selected') - } - }); + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = false; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.remove("selected") + } + + change_buttons(); }; invert = function() { - $(".trait_checkbox").each(function() { - if ($(this).prop('checked') == true) { - $(this).prop('checked', false) - } - else { - $(this).prop('checked', true) - } - - if ($(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').removeClass('selected') - } - else { - $(this).closest('tr').addClass('selected') - } - }); + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[0].checked){ + check_cells[i].childNodes[0].checked = false; + } else { + check_cells[i].childNodes[0].checked = true; + } + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + if (check_rows[i].classList.contains("selected")){ + check_rows[i].classList.remove("selected") + } else { + check_rows[i].classList.add("selected") + } + } + + change_buttons(); }; $('#searchbox').keyup(function(){ @@ -77,22 +122,6 @@ $(function() { change_buttons(); }); - $('.trait_checkbox:checkbox').change(function() { - change_buttons() - - if ($(this).is(":checked")) { - if (!$(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').addClass('selected') - } - } - else { - if ($(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').removeClass('selected') - } - } - - }); - add_to_collection = function() { var traits; traits = $("#trait_table input:checked").map(function() { @@ -117,25 +146,8 @@ $(function() { }; removed_traits = function() { - console.log('in removed_traits with checked_traits:', checked_traits); return checked_traits.closest("tr").fadeOut(); }; - change_buttons = function() { - var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2; - buttons = ["#add", "#remove"]; - num_checked = $('.trait_checkbox:checked').length; - if (num_checked === 0) { - for (_i = 0, _len = buttons.length; _i < _len; _i++) { - button = buttons[_i]; - $(button).prop("disabled", true); - } - } else { - for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { - button = buttons[_j]; - $(button).prop("disabled", false); - } - } - }; submit_bnw = function() { trait_data = submit_traits_to_export_or_bnw("trait_table", "submit_bnw") @@ -157,18 +169,23 @@ $(function() { }); table_dict['headers'] = headers; - rows = []; - trait_table.find('tbody tr').each(function (i, tr) { - if (trait_table.find('input[name="searchResult"]:checked').length > 0) { - if ($(this).find('input[name="searchResult"]').is(':checked')){ - rows.push($(this).find('input[name="searchResult"]:checked').val()) - } - } - else { - rows.push($(this).find('input[name="searchResult"]').val()) + selected_rows = []; + all_rows = []; //ZS: If no rows are checked, export all + table_api = $('#' + table_name).DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + this_node = check_cells[i].childNodes[0]; + all_rows.push(this_node.value) + if (this_node.checked){ + selected_rows.push(this_node.value) } - }); - table_dict['rows'] = rows; + } + + if (selected_rows.length > 0){ + table_dict['rows'] = selected_rows; + } else { + table_dict['rows'] = all_rows; + } json_table_dict = JSON.stringify(table_dict); $('input[name=export_data]').val(json_table_dict); @@ -253,8 +270,6 @@ $(function() { $("#add").click(add_to_collection); $("#submit_bnw").click(submit_bnw); $("#export_traits").click(export_traits); - $('.trait_checkbox, .btn').click(change_buttons); - let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index e37f8104..ccec495b 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -73,7 +73,7 @@ <form id="export_form" method="POST" action="/export_traits_csv"> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button> <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button> - <button class="btn btn-success" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button> + <button class="btn btn-success" id="add" type="button" disabled><i class="icon-plus-sign"></i> Copy</button> <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> <input type="hidden" name="file_name" id="file_name" value="collection_table"> @@ -81,7 +81,7 @@ <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> - <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button> + <button id="remove" class="btn btn-danger" data-url="/collections/remove" type="button" disabled><i class="icon-minus-sign"></i> Delete Rows</button> <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button> </form> </div> @@ -109,10 +109,7 @@ <tbody> {% for this_trait in trait_obs %} <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> - <TD align="center" style="padding: 0px;"> - <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" - VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"> - </TD> + <TD align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></TD> <TD data-export="{{ loop.index }}" align="right">{{ loop.index }}</TD> <TD title="{{ this_trait.dataset.fullname }}" data-export="{{ this_trait.dataset.fullname }}">{{ this_trait.dataset.fullname }}</TD> <TD data-export="{{ this_trait.name }}"> @@ -178,15 +175,21 @@ <script language="javascript" type="text/javascript"> $(document).ready( function () { - - $('#trait_table tr').click(function(event) { - if (event.target.type !== 'checkbox') { - $(':checkbox', this).trigger('click'); - } - }); - - console.time("Creating table"); $('#trait_table').dataTable( { + 'drawCallback': function( settings ) { + $('#trait_table tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected")){ + $(this).removeClass("selected") + } else { + $(this).addClass("selected") + } + change_buttons() + }); + }, "columns": [ { "orderDataType": "dom-checkbox", @@ -220,7 +223,7 @@ "paging": false, "orderClasses": true } ); - console.timeEnd("Creating table"); + submit_special = function(url) { $("#collection_form").attr("action", url); diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 6419b185..aa74abf5 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -75,6 +75,7 @@ <div> <form id="export_form" method="POST" action="/export_traits_csv"> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button> + <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-adjust"></span> Invert</button> <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> @@ -256,41 +257,6 @@ {% endif %} $(document).ready( function () { - - $('#trait_table tr').click(function(event) { - if (event.target.type !== 'checkbox') { - $(':checkbox', this).trigger('click'); - } - }); - - function change_buttons() { - buttons = ["#add", "#remove"]; - num_checked = $('.trait_checkbox:checked').length; - if (num_checked === 0) { - for (_i = 0, _len = buttons.length; _i < _len; _i++) { - button = buttons[_i]; - $(button).prop("disabled", true); - } - } else { - for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { - button = buttons[_j]; - $(button).prop("disabled", false); - } - } - if ($(this).is(":checked")) { - if (!$(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').addClass('selected') - } - } - else { - if ($(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').removeClass('selected') - } - } - } - - console.time("Creating table"); - table_conf = { buttons: [ { @@ -305,6 +271,20 @@ postfixButtons: [ 'colvisRestore' ] } ], + 'drawCallback': function( settings ) { + $('#trait_table tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected")){ + $(this).removeClass("selected") + } else { + $(this).addClass("selected") + } + }); + $('.trait_checkbox:checkbox').on("change", change_buttons); + }, "data": table_json, "columns": [ { @@ -557,7 +537,7 @@ "sDom": "itir", "autoWidth": true, "bSortClasses": false, - "scrollY": "50vh", + "scrollY": "100vh", "scroller": true, "scrollCollapse": true } @@ -570,8 +550,6 @@ } ); } ).draw(); - console.timeEnd("Creating table"); - $('.toggle-vis').on('click', function (e) { e.preventDefault(); diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html index 94b31464..5fe01dad 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -8,33 +8,143 @@ {% block content %} - <div class="github-btn-container"> - <div class="github-btn "> - <a href="https://github.com/genenetwork/gn-docs"> - Edit Text - <img src="/static/images/edit.png"> - </a> - </div> -</div> <div id="markdown" class="container"> <div class="cls-table-style">{{ rendered_markdown|safe }} </div> </div> -<style type="text/css"> -table { - width: 100%; -} -table, th, td { - border: 1px solid black; +{% if svg_data %} + +<div class="graph-legend"> + <h1>Chord dependency Graph of Genenetwork2</h1> + Graph generated from <a href="http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/branch/master/gn/packages/genenetwork.scm">genenetwork.scm</a>. You can zoom in and out within the bounding box. +</div> + +<div id="guix-graph"></div> +{% endif %} + +{% endblock %} + +{% block js %} + +{% if svg_data %} +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> +<script type="text/javascript"> + {{ svg_data|safe }} + // based on http://bl.ocks.org/mbostock/1046712 under GPLv3 + // Adapted from: https://elephly.net/graph.html + var outerRadius = (nodeArray.length * 10) / 2, + innerRadius = outerRadius - 100, + width = outerRadius * 2, + height = outerRadius * 2, + colors = d3.scale.category20c(), + matrix = []; + + function neighborsOf (node) { + return links.filter(function (e) { + return e.source === node; + }).map(function (e) { + return e.target; + }); + } + + function zoomed () { + zoomer.attr("transform", + "translate(" + d3.event.translate + ")" + + "scale(" + d3.event.scale + ")"); + } + + function fade (opacity, root) { + return function (g, i) { + root.selectAll("g path.chord") + .filter(function (d) { + return d.source.index != i && d.target.index != i; + }) + .transition() + .style("opacity", opacity); + }; + } + + // Now that we have all nodes in an object we can replace each reference + // with the actual node object. + links.forEach(function (link) { + link.target = nodes[link.target]; + link.source = nodes[link.source]; + }); + + // Construct a square matrix for package dependencies + nodeArray.forEach(function (d, index, arr) { + var source = index, + row = matrix[source]; + if (!row) { + row = matrix[source] = []; + for (var i = -1; ++i < arr.length;) row[i] = 0; + } + neighborsOf(d).forEach(function (d) { row[d.index]++; }); + }); + + // chord layout + var chord = d3.layout.chord() + .padding(0.01) + .sortSubgroups(d3.descending) + .sortChords(d3.descending) + .matrix(matrix); + + var arc = d3.svg.arc() + .innerRadius(innerRadius) + .outerRadius(innerRadius + 20); + + var zoom = d3.behavior.zoom() + .scaleExtent([0.1, 10]) + .on("zoom", zoomed); + + var svg = d3.select("#guix-graph").append("svg") + .attr("width", "100%") + .attr("height", "100%") + .attr('viewBox','0 0 '+Math.min(width,height)+' '+Math.min(width,height)) + .attr('preserveAspectRatio','xMinYMin') + .call(zoom); + + var zoomer = svg.append("g"); + + var container = zoomer.append("g") + .attr("transform", "translate(" + outerRadius + "," + outerRadius + ")"); + + // Group for arcs and labels + var g = container.selectAll(".group") + .data(chord.groups) + .enter().append("g") + .attr("class", "group") + .on("mouseout", fade(1, container)) + .on("mouseover", fade(0.1, container)); + + // Draw one segment per package + g.append("path") + .style("fill", function (d) { return colors(d.index); }) + .style("stroke", function (d) { return colors(d.index); }) + .attr("d", arc); -} + // Add circular labels + g.append("text") + .each(function (d) { d.angle = (d.startAngle + d.endAngle) / 2; }) + .attr("dy", ".35em") + .attr("transform", function (d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + (innerRadius + 26) + ")" + + (d.angle > Math.PI ? "rotate(180)" : ""); + }) + .style("text-anchor", function (d) { return d.angle > Math.PI ? "end" : null; }) + .text(function (d) { return nodeArray[d.index].label; }); -td,th{ - padding-top:8px; - padding-bottom: 8px; - text-align: center; -} + // Draw chords from source to target; color by source. + container.selectAll(".chord") + .data(chord.chords) + .enter().append("path") + .attr("class", "chord") + .style("stroke", function (d) { return d3.rgb(colors(d.source.index)).darker(); }) + .style("fill", function (d) { return colors(d.source.index); }) + .attr("d", d3.svg.chord().radius(innerRadius)); +</script> +{% endif %} -</style> {% endblock %} diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 2a8d6931..87c97c50 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -129,6 +129,7 @@ {% endif %} <input type="hidden" name="export_data" id="export_data" value=""> <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button> + <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-adjust"></span> Invert</button> <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ..."> @@ -203,42 +204,21 @@ } }); - function change_buttons() { - buttons = ["#add", "#remove"]; - num_checked = $('.trait_checkbox:checked').length; - if (num_checked === 0) { - for (_i = 0, _len = buttons.length; _i < _len; _i++) { - button = buttons[_i]; - $(button).prop("disabled", true); - } - } else { - for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { - button = buttons[_j]; - $(button).prop("disabled", false); - } - } - //}); - if ($(this).is(":checked")) { - if (!$(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').addClass('selected') - } - } - else { - if ($(this).closest('tr').hasClass('selected')) { - $(this).closest('tr').removeClass('selected') - } - } - } - //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters trait_table = $('#trait_table').DataTable( { 'drawCallback': function( settings ) { - $('#trait_table tr').click(function(event) { - if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { - $(':checkbox', this).trigger('click'); - } - }); - $('.trait_checkbox:checkbox').on("change", change_buttons); + $('#trait_table tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected")){ + $(this).removeClass("selected") + } else { + $(this).addClass("selected") + } + change_buttons() + }); }, 'createdRow': function ( row, data, index ) { $('td', row).eq(0).attr("style", "text-align: center; padding: 0px 10px 2px 10px;"); |