diff options
48 files changed, 849 insertions, 309 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py index 6ac26ba7..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 +117,27 @@ 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", + "/js/purescript-genome-browser/css/purescript-genetics-browser.css", + "/js/cytoscape/cytoscape.min.js", + "/js/cytoscape-panzoom/cytoscape-panzoom.js", + "/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/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/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index 5b621264..b8c13ab4 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -43,22 +43,22 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco): """add tests for run_gemma where first run is set to true""" - chromosomes = [] + this_chromosomes={} for i in range(1, 5): - chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) + this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) + chromosomes = AttributeSetter({"chromosomes": this_chromosomes}) + dataset_group = MockGroup( {"name": "GP1", "genofile": "file_geno"}) dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", - "species": AttributeSetter({"chromosomes": chromo})}) + "species": AttributeSetter({"chromosomes": chromosomes})}) trait = AttributeSetter({"name": "trait1"}) samples = [] mock_gen_pheno_txt.return_value = None @@ -76,7 +76,6 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) self.assertEqual(mock_flat_files.call_count, 4) self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 1b801b1d..0c1cea0e 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" @@ -497,7 +498,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap if bool(trait.description_display): results_dict['description'] = trait.description_display if bool(trait.mean): - results_dict['mean'] = float(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}" results_dict['lrs_location'] = trait.LRS_location_repr 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 601845d7..ebf75807 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -4,7 +4,12 @@ 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 send_from_directory from flask import Blueprint from flask import render_template @@ -16,18 +21,25 @@ 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 +47,14 @@ 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 +71,40 @@ 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) + + +@environments_blueprint.route('/svg-dependency-graph') +def svg_graph(): + directory, file_name, _ = get_file_from_python_search_path( + "wqflask/dependency-graph.svg").partition("dependency-graph.svg") + return send_from_directory(directory, file_name) @links_blueprint.route("/") @@ -64,7 +117,7 @@ def links(): @policies_blueprint.route("/") def policies(): return render_template( - "links.html", + "policies.html", rendered_markdown=render_markdown("general/policies/policies.md")), 200 diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 02f91a32..61e4897c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -31,7 +31,8 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) this_chromosomes = this_dataset.species.chromosomes.chromosomes - this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes] + this_chromosomes_name=[this_chromosomes[chromosome].name for chromosome in this_chromosomes] + chr_list_string=",".join(this_chromosomes_name) if covariates != "": @@ -45,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf genofile_name, TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -77,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -93,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf else: gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename) - - logger.debug("gemma_command:" + gemma_command) os.system(gemma_command) else: gwa_output_filename = output_files 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/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/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index dca3e31d..859fe7fc 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -57,8 +57,52 @@ word-spacing: 0.2em; } +.graph-legend h1 { + text-align: center; +} + +.graph-legend, +#guix-graph, +#guix-svg-graph{ + width: 90%; + margin: 10px auto; +} + +#guix-graph { + border: solid 2px black; +} + +#guix-svg-graph img { + width: 100%; +} + +#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/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/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/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 e37f8104..99a6f2de 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -44,7 +44,7 @@ GeneWeaver </button> - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > + <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> @@ -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 }}"> @@ -165,7 +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> @@ -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/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html index f791457f..e3dd03d5 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 --> @@ -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 1133fcd2..a0436ade 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 4e150618..96ad9c35 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -4,7 +4,7 @@ <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 %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 6419b185..7acccc25 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -49,7 +49,7 @@ GeneWeaver </button> - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > + <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> @@ -75,23 +75,26 @@ <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=""> <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation"> - <button class="btn btn-default" id="export_traits">Download CSV</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> <button id="redraw" class="btn btn-default" type="button">Reset Columns</button> </form> <br /> + <div id="export_options"></div> {% if target_dataset.type != "Publish" %} <br /> - <button id="more_options" class="btn btn-primary">More Options...</button> + <div style="float: left; clear: left; margin-top: 10px; margin-bottom: 20px;"> + <button id="more_options" class="btn btn-primary">More Options...</button> + </div> <br /> <br /> - <div id="filter_options" style="display: none;"> + <div id="filter_options" style="display: none; float: left; clear: left;"> <span style="border: 1px dashed #999999; padding: 8px; background-color: #ddf; font-size: 12px;"> <button id="select_traits" class="btn btn-primary" style="font-size: 12px; padding: 2px 3px;">Select Traits</button> with r > <input type="text" name="r_greater_select" value="-1.0" size="6" maxlength="10"> @@ -114,7 +117,7 @@ </div> {% endif %} </div> - <div class="show-hide-container"> + <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> @@ -168,12 +171,12 @@ <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> <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> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.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="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script> @@ -256,55 +259,31 @@ {% 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: [ - { - extend: 'columnsToggle', - columns: function( idx, data, node ) { - if (idx != 0) { - return true; - } else { - return false; - } - }, - postfixButtons: [ 'colvisRestore' ] + { + extend: 'csvHtml5', + text: 'Download <span class="glyphicon glyphicon-download"></span>', + className: 'btn btn-default', + exportOptions: { + columns: 'th:not(:first-child)' } + } ], + '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": [ { @@ -366,8 +345,15 @@ '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?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", @@ -378,7 +364,7 @@ }, { '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"] @@ -480,8 +466,15 @@ '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?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", @@ -492,7 +485,7 @@ }, { '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"] @@ -527,8 +520,15 @@ '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?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", @@ -539,7 +539,7 @@ }, { '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"] @@ -557,21 +557,23 @@ "sDom": "itir", "autoWidth": true, "bSortClasses": false, - "scrollY": "50vh", + "scrollY": "100vh", "scroller": true, "scrollCollapse": true } trait_table = $('#trait_table').DataTable(table_conf); + trait_table.buttons().container().appendTo('#export_options') + + $('.buttons-csv').removeClass('dt-button') + trait_table.on( 'order.dt search.dt draw.dt', function () { trait_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { cell.innerHTML = i+1; } ); } ).draw(); - console.timeEnd("Creating table"); - $('.toggle-vis').on('click', function (e) { e.preventDefault(); 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/environment.html b/wqflask/wqflask/templates/environment.html index 94b31464..89e805ce 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -8,33 +8,153 @@ {% 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> + +<!-- Display the svg graph --> + +<div id="guix-svg-graph"> + <h1>The dependency graph is shown below</h1> + + <p>To explore this image SVG you may want to open it in new browser page and zoom in. Or use an SVG viewing application.</p> + + <img alt="Dependency graph of the tools needed to build python3-genenetwork2" src="{{url_for('environments_blueprint.svg_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/facilities.html b/wqflask/wqflask/templates/facilities.html index a022b657..56b127f9 100644 --- a/wqflask/wqflask/templates/facilities.html +++ b/wqflask/wqflask/templates/facilities.html @@ -10,7 +10,7 @@ <div class="github-btn-container"> <div class="github-btn"> - <a href="https://github.com/genenetwork/gn-docs"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/help/facilities.md"> Edit Text <img src="/static/images/edit.png"> </a> diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html index 752c4b12..aaee7c5a 100644 --- a/wqflask/wqflask/templates/glossary.html +++ b/wqflask/wqflask/templates/glossary.html @@ -10,7 +10,7 @@ <div class="github-btn-container"> <div class="github-btn"> - <a href="https://github.com/genenetwork/gn-docs"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/glossary/glossary.md"> Edit Text <img src="/static/images/edit.png"> </a> 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..b16de42e 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 --> diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html index 072e8429..6e91adae 100644 --- a/wqflask/wqflask/templates/links.html +++ b/wqflask/wqflask/templates/links.html @@ -10,7 +10,7 @@ <div class="github-btn-container"> <div class="github-btn "> - <a href="https://github.com/genenetwork/gn-docs"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/links/links.md"> Edit Text <img src="/static/images/edit.png"> </a> diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 9542c29d..86aa74b0 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" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.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/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index f1646af7..38dca514 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/DT_bootstrap/DT_bootstrap.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 %} @@ -64,7 +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/policies.html b/wqflask/wqflask/templates/policies.html index 4e0985d3..e36c9e08 100644 --- a/wqflask/wqflask/templates/policies.html +++ b/wqflask/wqflask/templates/policies.html @@ -10,7 +10,7 @@ <div class="github-btn-container"> <div class="github-btn "> - <a href="https://github.com/genenetwork/gn-docs"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/policies/policies.md"> Edit Text <img src="/static/images/edit.png"> </a> diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html index f723a1e8..04e60361 100644 --- a/wqflask/wqflask/templates/references.html +++ b/wqflask/wqflask/templates/references.html @@ -6,7 +6,7 @@ {% block content %} <div class="github-btn-container"> <div class="github-btn"> - <a href="https://github.com/genenetwork/gn-docs"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/references/references.md"> Edit Text <img src="/static/images/edit.png"> </a> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 2a8d6931..3be2e395 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -92,7 +92,7 @@ GeneWeaver </button> - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" > + <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> @@ -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 ..."> @@ -182,7 +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> @@ -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;"); 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..b02f8140 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 %} @@ -133,9 +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> @@ -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="{{ url_for('js', filename='DataTablesExtensions/scroller/js/scroller.dataTables.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_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> |