From 8145507d6d617554cf996e6cebf286d30ae64df0 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 4 Apr 2018 16:58:21 +0000 Subject: ES: doc --- wqflask/utility/elasticsearch_tools.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'wqflask/utility') diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index 734379f7..1dba357d 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -12,6 +12,7 @@ def test_elasticsearch_connection(): logger.warning("Elasticsearch is DOWN") def get_elasticsearch_connection(): + """Return a connection to ES. Returns None on failure""" logger.info("get_elasticsearch_connection") es = None try: @@ -20,14 +21,14 @@ def get_elasticsearch_connection(): logger.info("ES HOST",ELASTICSEARCH_HOST) es = Elasticsearch([{ - "host": ELASTICSEARCH_HOST - , "port": ELASTICSEARCH_PORT + "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None es_logger = logging.getLogger("elasticsearch") es_logger.setLevel(logging.INFO) es_logger.addHandler(logging.NullHandler()) except: + logger.error("Failed to get elasticsearch connection") es = None return es @@ -42,9 +43,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): item_details = None try: response = es.search( - index = index - , doc_type = doc_type - , body = { + index = index, doc_type = doc_type, body = { "query": { "match": { column_name: column_value } } }) if len(response["hits"]["hits"]) > 0: -- cgit v1.2.3 From 1debb0849066a31c8538b529536a9a7a12a0a8f9 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 6 Apr 2018 10:21:35 +0000 Subject: See #308. Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE. --- jquery.qtip.css | 623 +++++++++++++++++++++++++++ unused.txt | 610 ++++++++++++++++++++++++++ wqflask/utility/tools.py | 12 +- wqflask/wqflask/templates/ctl_results.html | 22 +- wqflask/wqflask/templates/network_graph.html | 28 +- wqflask/wqflask/views.py | 10 +- 6 files changed, 1283 insertions(+), 22 deletions(-) create mode 100644 jquery.qtip.css create mode 100644 unused.txt (limited to 'wqflask/utility') diff --git a/jquery.qtip.css b/jquery.qtip.css new file mode 100644 index 00000000..c2dcb306 --- /dev/null +++ b/jquery.qtip.css @@ -0,0 +1,623 @@ +/* + * qTip2 - Pretty powerful tooltips - v2.2.0 + * http://qtip2.com + * + * Copyright (c) 2013 Craig Michael Thompson + * Released under the MIT, GPL licenses + * http://jquery.org/license + * + * Date: Thu Nov 21 2013 08:34 GMT+0000 + * Plugins: tips modal viewport svg imagemap ie6 + * Styles: basic css3 + */ +.qtip{ + position: absolute; + left: -28000px; + top: -28000px; + display: none; + + max-width: 280px; + min-width: 50px; + + font-size: 10.5px; + line-height: 12px; + + direction: ltr; + + box-shadow: none; + padding: 0; +} + + .qtip-content{ + position: relative; + padding: 5px 9px; + overflow: hidden; + + text-align: left; + word-wrap: break-word; + } + + .qtip-titlebar{ + position: relative; + padding: 5px 35px 5px 10px; + overflow: hidden; + + border-width: 0 0 1px; + font-weight: bold; + } + + .qtip-titlebar + .qtip-content{ border-top-width: 0 !important; } + + /* Default close button class */ + .qtip-close{ + position: absolute; + right: -9px; top: -9px; + + cursor: pointer; + outline: medium none; + + border-width: 1px; + border-style: solid; + border-color: transparent; + } + + .qtip-titlebar .qtip-close{ + right: 4px; top: 50%; + margin-top: -9px; + } + + * html .qtip-titlebar .qtip-close{ top: 16px; } /* IE fix */ + + .qtip-titlebar .ui-icon, + .qtip-icon .ui-icon{ + display: block; + text-indent: -1000em; + direction: ltr; + } + + .qtip-icon, .qtip-icon .ui-icon{ + -moz-border-radius: 3px; + -webkit-border-radius: 3px; + border-radius: 3px; + text-decoration: none; + } + + .qtip-icon .ui-icon{ + width: 18px; + height: 14px; + + line-height: 14px; + text-align: center; + text-indent: 0; + font: normal bold 10px/13px Tahoma,sans-serif; + + color: inherit; + background: transparent none no-repeat -100em -100em; + } + +/* Applied to 'focused' tooltips e.g. most recently displayed/interacted with */ +.qtip-focus{} + +/* Applied on hover of tooltips i.e. added/removed on mouseenter/mouseleave respectively */ +.qtip-hover{} + +/* Default tooltip style */ +.qtip-default{ + border-width: 1px; + border-style: solid; + border-color: #F1D031; + + background-color: #FFFFA3; + color: #555; +} + + .qtip-default .qtip-titlebar{ + background-color: #FFEF93; + } + + .qtip-default .qtip-icon{ + border-color: #CCC; + background: #F1F1F1; + color: #777; + } + + .qtip-default .qtip-titlebar .qtip-close{ + border-color: #AAA; + color: #111; + } + + + +/*! Light tooltip style */ +.qtip-light{ + background-color: white; + border-color: #E2E2E2; + color: #454545; +} + + .qtip-light .qtip-titlebar{ + background-color: #f1f1f1; + } + + +/*! Dark tooltip style */ +.qtip-dark{ + background-color: #505050; + border-color: #303030; + color: #f3f3f3; +} + + .qtip-dark .qtip-titlebar{ + background-color: #404040; + } + + .qtip-dark .qtip-icon{ + border-color: #444; + } + + .qtip-dark .qtip-titlebar .ui-state-hover{ + border-color: #303030; + } + + +/*! Cream tooltip style */ +.qtip-cream{ + background-color: #FBF7AA; + border-color: #F9E98E; + color: #A27D35; +} + + .qtip-cream .qtip-titlebar{ + background-color: #F0DE7D; + } + + .qtip-cream .qtip-close .qtip-icon{ + background-position: -82px 0; + } + + +/*! Red tooltip style */ +.qtip-red{ + background-color: #F78B83; + border-color: #D95252; + color: #912323; +} + + .qtip-red .qtip-titlebar{ + background-color: #F06D65; + } + + .qtip-red .qtip-close .qtip-icon{ + background-position: -102px 0; + } + + .qtip-red .qtip-icon{ + border-color: #D95252; + } + + .qtip-red .qtip-titlebar .ui-state-hover{ + border-color: #D95252; + } + + +/*! Green tooltip style */ +.qtip-green{ + background-color: #CAED9E; + border-color: #90D93F; + color: #3F6219; +} + + .qtip-green .qtip-titlebar{ + background-color: #B0DE78; + } + + .qtip-green .qtip-close .qtip-icon{ + background-position: -42px 0; + } + + +/*! Blue tooltip style */ +.qtip-blue{ + background-color: #E5F6FE; + border-color: #ADD9ED; + color: #5E99BD; +} + + .qtip-blue .qtip-titlebar{ + background-color: #D0E9F5; + } + + .qtip-blue .qtip-close .qtip-icon{ + background-position: -2px 0; + } + + + +.qtip-shadow{ + -webkit-box-shadow: 1px 1px 3px 1px rgba(0, 0, 0, 0.15); + -moz-box-shadow: 1px 1px 3px 1px rgba(0, 0, 0, 0.15); + box-shadow: 1px 1px 3px 1px rgba(0, 0, 0, 0.15); +} + +/* Add rounded corners to your tooltips in: FF3+, Chrome 2+, Opera 10.6+, IE9+, Safari 2+ */ +.qtip-rounded, +.qtip-tipsy, +.qtip-bootstrap{ + -moz-border-radius: 5px; + -webkit-border-radius: 5px; + border-radius: 5px; +} + +.qtip-rounded .qtip-titlebar{ + -moz-border-radius: 4px 4px 0 0; + -webkit-border-radius: 4px 4px 0 0; + border-radius: 4px 4px 0 0; +} + +/* Youtube tooltip style */ +.qtip-youtube{ + -moz-border-radius: 2px; + -webkit-border-radius: 2px; + border-radius: 2px; + + -webkit-box-shadow: 0 0 3px #333; + -moz-box-shadow: 0 0 3px #333; + box-shadow: 0 0 3px #333; + + color: white; + border-width: 0; + + background: #4A4A4A; + background-image: -webkit-gradient(linear,left top,left bottom,color-stop(0,#4A4A4A),color-stop(100%,black)); + background-image: -webkit-linear-gradient(top,#4A4A4A 0,black 100%); + background-image: -moz-linear-gradient(top,#4A4A4A 0,black 100%); + background-image: -ms-linear-gradient(top,#4A4A4A 0,black 100%); + background-image: -o-linear-gradient(top,#4A4A4A 0,black 100%); +} + + .qtip-youtube .qtip-titlebar{ + background-color: #4A4A4A; + background-color: rgba(0,0,0,0); + } + + .qtip-youtube .qtip-content{ + padding: .75em; + font: 12px arial,sans-serif; + + filter: progid:DXImageTransform.Microsoft.Gradient(GradientType=0,StartColorStr=#4a4a4a,EndColorStr=#000000); + -ms-filter: "progid:DXImageTransform.Microsoft.Gradient(GradientType=0,StartColorStr=#4a4a4a,EndColorStr=#000000);"; + } + + .qtip-youtube .qtip-icon{ + border-color: #222; + } + + .qtip-youtube .qtip-titlebar .ui-state-hover{ + border-color: #303030; + } + + +/* jQuery TOOLS Tooltip style */ +.qtip-jtools{ + background: #232323; + background: rgba(0, 0, 0, 0.7); + background-image: -webkit-gradient(linear, left top, left bottom, from(#717171), to(#232323)); + background-image: -moz-linear-gradient(top, #717171, #232323); + background-image: -webkit-linear-gradient(top, #717171, #232323); + background-image: -ms-linear-gradient(top, #717171, #232323); + background-image: -o-linear-gradient(top, #717171, #232323); + + border: 2px solid #ddd; + border: 2px solid rgba(241,241,241,1); + + -moz-border-radius: 2px; + -webkit-border-radius: 2px; + border-radius: 2px; + + -webkit-box-shadow: 0 0 12px #333; + -moz-box-shadow: 0 0 12px #333; + box-shadow: 0 0 12px #333; +} + + /* IE Specific */ + .qtip-jtools .qtip-titlebar{ + background-color: transparent; + filter:progid:DXImageTransform.Microsoft.gradient(startColorstr=#717171,endColorstr=#4A4A4A); + -ms-filter: "progid:DXImageTransform.Microsoft.gradient(startColorstr=#717171,endColorstr=#4A4A4A)"; + } + .qtip-jtools .qtip-content{ + filter:progid:DXImageTransform.Microsoft.gradient(startColorstr=#4A4A4A,endColorstr=#232323); + -ms-filter: "progid:DXImageTransform.Microsoft.gradient(startColorstr=#4A4A4A,endColorstr=#232323)"; + } + + .qtip-jtools .qtip-titlebar, + .qtip-jtools .qtip-content{ + background: transparent; + color: white; + border: 0 dashed transparent; + } + + .qtip-jtools .qtip-icon{ + border-color: #555; + } + + .qtip-jtools .qtip-titlebar .ui-state-hover{ + border-color: #333; + } + + +/* Cluetip style */ +.qtip-cluetip{ + -webkit-box-shadow: 4px 4px 5px rgba(0, 0, 0, 0.4); + -moz-box-shadow: 4px 4px 5px rgba(0, 0, 0, 0.4); + box-shadow: 4px 4px 5px rgba(0, 0, 0, 0.4); + + background-color: #D9D9C2; + color: #111; + border: 0 dashed transparent; +} + + .qtip-cluetip .qtip-titlebar{ + background-color: #87876A; + color: white; + border: 0 dashed transparent; + } + + .qtip-cluetip .qtip-icon{ + border-color: #808064; + } + + .qtip-cluetip .qtip-titlebar .ui-state-hover{ + border-color: #696952; + color: #696952; + } + + +/* Tipsy style */ +.qtip-tipsy{ + background: black; + background: rgba(0, 0, 0, .87); + + color: white; + border: 0 solid transparent; + + font-size: 11px; + font-family: 'Lucida Grande', sans-serif; + font-weight: bold; + line-height: 16px; + text-shadow: 0 1px black; +} + + .qtip-tipsy .qtip-titlebar{ + padding: 6px 35px 0 10px; + background-color: transparent; + } + + .qtip-tipsy .qtip-content{ + padding: 6px 10px; + } + + .qtip-tipsy .qtip-icon{ + border-color: #222; + text-shadow: none; + } + + .qtip-tipsy .qtip-titlebar .ui-state-hover{ + border-color: #303030; + } + + +/* Tipped style */ +.qtip-tipped{ + border: 3px solid #959FA9; + + -moz-border-radius: 3px; + -webkit-border-radius: 3px; + border-radius: 3px; + + background-color: #F9F9F9; + color: #454545; + + font-weight: normal; + font-family: serif; +} + + .qtip-tipped .qtip-titlebar{ + border-bottom-width: 0; + + color: white; + background: #3A79B8; + background-image: -webkit-gradient(linear, left top, left bottom, from(#3A79B8), to(#2E629D)); + background-image: -webkit-linear-gradient(top, #3A79B8, #2E629D); + background-image: -moz-linear-gradient(top, #3A79B8, #2E629D); + background-image: -ms-linear-gradient(top, #3A79B8, #2E629D); + background-image: -o-linear-gradient(top, #3A79B8, #2E629D); + filter:progid:DXImageTransform.Microsoft.gradient(startColorstr=#3A79B8,endColorstr=#2E629D); + -ms-filter: "progid:DXImageTransform.Microsoft.gradient(startColorstr=#3A79B8,endColorstr=#2E629D)"; + } + + .qtip-tipped .qtip-icon{ + border: 2px solid #285589; + background: #285589; + } + + .qtip-tipped .qtip-icon .ui-icon{ + background-color: #FBFBFB; + color: #555; + } + + +/** + * Twitter Bootstrap style. + * + * Tested with IE 8, IE 9, Chrome 18, Firefox 9, Opera 11. + * Does not work with IE 7. + */ +.qtip-bootstrap{ + /** Taken from Bootstrap body */ + font-size: 14px; + line-height: 20px; + color: #333333; + + /** Taken from Bootstrap .popover */ + padding: 1px; + background-color: #ffffff; + border: 1px solid #ccc; + border: 1px solid rgba(0, 0, 0, 0.2); + -webkit-border-radius: 6px; + -moz-border-radius: 6px; + border-radius: 6px; + -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -moz-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2); + -webkit-background-clip: padding-box; + -moz-background-clip: padding; + background-clip: padding-box; +} + + .qtip-bootstrap .qtip-titlebar{ + /** Taken from Bootstrap .popover-title */ + padding: 8px 14px; + margin: 0; + font-size: 14px; + font-weight: normal; + line-height: 18px; + background-color: #f7f7f7; + border-bottom: 1px solid #ebebeb; + -webkit-border-radius: 5px 5px 0 0; + -moz-border-radius: 5px 5px 0 0; + border-radius: 5px 5px 0 0; + } + + .qtip-bootstrap .qtip-titlebar .qtip-close{ + /** + * Overrides qTip2: + * .qtip-titlebar .qtip-close{ + * [...] + * right: 4px; + * top: 50%; + * [...] + * border-style: solid; + * } + */ + right: 11px; + top: 45%; + border-style: none; + } + + .qtip-bootstrap .qtip-content{ + /** Taken from Bootstrap .popover-content */ + padding: 9px 14px; + } + + .qtip-bootstrap .qtip-icon{ + /** + * Overrides qTip2: + * .qtip-default .qtip-icon { + * border-color: #CCC; + * background: #F1F1F1; + * color: #777; + * } + */ + background: transparent; + } + + .qtip-bootstrap .qtip-icon .ui-icon{ + /** + * Overrides qTip2: + * .qtip-icon .ui-icon{ + * width: 18px; + * height: 14px; + * } + */ + width: auto; + height: auto; + + /* Taken from Bootstrap .close */ + float: right; + font-size: 20px; + font-weight: bold; + line-height: 18px; + color: #000000; + text-shadow: 0 1px 0 #ffffff; + opacity: 0.2; + filter: alpha(opacity=20); + } + + .qtip-bootstrap .qtip-icon .ui-icon:hover{ + /* Taken from Bootstrap .close:hover */ + color: #000000; + text-decoration: none; + cursor: pointer; + opacity: 0.4; + filter: alpha(opacity=40); + } + + +/* IE9 fix - removes all filters */ +.qtip:not(.ie9haxors) div.qtip-content, +.qtip:not(.ie9haxors) div.qtip-titlebar{ + filter: none; + -ms-filter: none; +} + + + +.qtip .qtip-tip{ + margin: 0 auto; + overflow: hidden; + z-index: 10; + +} + + /* Opera bug #357 - Incorrect tip position + https://github.com/Craga89/qTip2/issues/367 */ + x:-o-prefocus, .qtip .qtip-tip{ + visibility: hidden; + } + + .qtip .qtip-tip, + .qtip .qtip-tip .qtip-vml, + .qtip .qtip-tip canvas{ + position: absolute; + + color: #123456; + background: transparent; + border: 0 dashed transparent; + } + + .qtip .qtip-tip canvas{ top: 0; left: 0; } + + .qtip .qtip-tip .qtip-vml{ + behavior: url(#default#VML); + display: inline-block; + visibility: visible; + } + +#qtip-overlay{ + position: fixed; + left: 0; top: 0; + width: 100%; height: 100%; +} + + /* Applied to modals with show.modal.blur set to true */ + #qtip-overlay.blurs{ cursor: pointer; } + + /* Change opacity of overlay here */ + #qtip-overlay div{ + position: absolute; + left: 0; top: 0; + width: 100%; height: 100%; + + background-color: black; + + opacity: 0.7; + filter:alpha(opacity=70); + -ms-filter:"progid:DXImageTransform.Microsoft.Alpha(Opacity=70)"; + } + + + +.qtipmodal-ie6fix{ + position: absolute !important; +} \ No newline at end of file diff --git a/unused.txt b/unused.txt new file mode 100644 index 00000000..8eab64ea --- /dev/null +++ b/unused.txt @@ -0,0 +1,610 @@ +wqflask/base/data_set.py:32: unused import 'itemgetter' (90% confidence) +wqflask/base/data_set.py:271: unused attribute 'genetic_type' (60% confidence) +wqflask/base/data_set.py:273: unused attribute 'genetic_type' (60% confidence) +wqflask/base/data_set.py:281: unused attribute 'accession_id' (60% confidence) +wqflask/base/data_set.py:282: unused attribute 'mapping_id' (60% confidence) +wqflask/base/data_set.py:282: unused attribute 'mapping_names' (60% confidence) +wqflask/base/data_set.py:319: unused function 'get_specified_markers' (60% confidence) +wqflask/base/data_set.py:460: unused variable 'dataset_sub_menu' (60% confidence) +wqflask/base/data_set.py:463: unused variable 'tissue_position' (60% confidence) +wqflask/base/data_set.py:467: unused variable 'tissue_position' (60% confidence) +wqflask/base/data_set.py:660: unused class 'PhenotypeDataSet' (60% confidence) +wqflask/base/data_set.py:722: unused function 'get_trait_list' (60% confidence) +wqflask/base/data_set.py:751: unreachable code after 'continue' (100% confidence) +wqflask/base/data_set.py:773: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/data_set.py:775: unused attribute 'LRS_location_value' (60% confidence) +wqflask/base/data_set.py:794: unused variable 'LRS_location_value' (60% confidence) +wqflask/base/data_set.py:797: unused variable 'LRS_location_value' (60% confidence) +wqflask/base/data_set.py:799: unused variable 'LRS_location_value' (60% confidence) +wqflask/base/data_set.py:802: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/data_set.py:802: unused variable 'LRS_score_value' (60% confidence) +wqflask/base/data_set.py:828: unused class 'GenotypeDataSet' (60% confidence) +wqflask/base/data_set.py:864: unused function 'get_trait_list' (60% confidence) +wqflask/base/data_set.py:884: unused variable 'trait_location_repr' (60% confidence) +wqflask/base/data_set.py:897: unused attribute 'location_value' (60% confidence) +wqflask/base/data_set.py:923: unused class 'MrnaAssayDataSet' (60% confidence) +wqflask/base/data_set.py:992: unused function 'get_trait_list_1' (60% confidence) +wqflask/base/data_set.py:1038: unused variable 'trait_location_repr' (60% confidence) +wqflask/base/data_set.py:1057: unused attribute 'location_value' (60% confidence) +wqflask/base/data_set.py:1079: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/data_set.py:1081: unused attribute 'LRS_location_value' (60% confidence) +wqflask/base/data_set.py:1097: unused variable 'lrs_location_value' (60% confidence) +wqflask/base/data_set.py:1099: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/data_set.py:1115: unused function 'get_sequence' (60% confidence) +wqflask/base/data_set.py:1167: unused class 'TempDataSet' (60% confidence) +wqflask/base/data_set.py:1207: unused function 'get_group' (60% confidence) +wqflask/base/data_set.py:1218: unused attribute 'group_id' (60% confidence) +wqflask/base/mrna_assay_tissue_data.py:21: unused attribute 'have_data' (60% confidence) +wqflask/base/species.py:21: unused attribute 'genome_mb_length' (60% confidence) +wqflask/base/species.py:45: unused function 'set_cm_length' (60% confidence) +wqflask/base/species.py:77: unused attribute 'mb_graph_interval' (60% confidence) +wqflask/base/species.py:79: unused attribute 'mb_graph_interval' (60% confidence) +wqflask/base/species.py:94: unused function 'get_genome_cm_length' (60% confidence) +wqflask/base/species.py:99: unused function 'get_cm_length_list' (60% confidence) +wqflask/base/template.py:27: unused variable 'template' (60% confidence) +wqflask/base/trait.py:28: unused function 'print_mem' (60% confidence) +wqflask/base/trait.py:58: unused attribute 'pvalue' (60% confidence) +wqflask/base/trait.py:66: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/trait.py:68: unused attribute 'LRS_location_value' (60% confidence) +wqflask/base/trait.py:86: unused function 'get_name' (60% confidence) +wqflask/base/trait.py:97: unused function 'get_given_name' (60% confidence) +wqflask/base/trait.py:118: unused function 'display_name' (60% confidence) +wqflask/base/trait.py:148: unused function 'export_data' (60% confidence) +wqflask/base/trait.py:189: unused property 'name_header_fmt' (60% confidence) +wqflask/base/trait.py:201: unused property 'description_fmt' (60% confidence) +wqflask/base/trait.py:220: unused property 'alias_fmt' (60% confidence) +wqflask/base/trait.py:232: unused property 'location_fmt' (60% confidence) +wqflask/base/trait.py:261: unused function 'getSequence' (60% confidence) +wqflask/base/trait.py:309: unused function 'get_sample_data' (60% confidence) +wqflask/base/trait.py:546: unused attribute 'homologeneid' (60% confidence) +wqflask/base/trait.py:575: unused attribute 'homologeneid' (60% confidence) +wqflask/base/trait.py:594: unused attribute 'location_value' (60% confidence) +wqflask/base/trait.py:611: unused attribute 'location_value' (60% confidence) +wqflask/base/trait.py:615: unused attribute 'location_value' (60% confidence) +wqflask/base/trait.py:624: unused attribute 'location_value' (60% confidence) +wqflask/base/trait.py:629: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/trait.py:631: unused attribute 'LRS_location_value' (60% confidence) +wqflask/base/trait.py:646: unused attribute 'pvalue' (60% confidence) +wqflask/base/trait.py:664: unused attribute 'pvalue' (60% confidence) +wqflask/base/trait.py:704: unused 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'r_head' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:44: unused variable 'r_matrix' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:45: unused variable 'r_seq' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:47: unused variable 'r_names' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:48: unused variable 'r_sink' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:49: unused variable 'r_is_NA' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:50: unused variable 'r_file' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:53: unused variable 'r_save_image' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:54: unused variable 'r_class' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:55: unused variable 'r_save' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:56: unused variable 'r_write_table' (60% confidence) +wqflask/wqflask/ctl/ctl_analysis.py:57: unused variable 'r_read_table' (60% confidence) 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confidence) +wqflask/wqflask/marker_regression/rqtl_mapping.py:16: unused variable 'postscript' (60% confidence) +wqflask/wqflask/marker_regression/rqtl_mapping.py:26: unused variable 'read_cross' (60% confidence) +wqflask/wqflask/marker_regression/rqtl_mapping.py:27: unused variable 'write_cross' (60% confidence) +wqflask/wqflask/model.py:9: unused import 'SQLAlchemy' (90% confidence) +wqflask/wqflask/model.py:15: unused import 'Integer' (90% confidence) +wqflask/wqflask/model.py:15: unused import 'String' (90% confidence) +wqflask/wqflask/model.py:15: unused import 'Table' (90% confidence) +wqflask/wqflask/model.py:17: unused import 'backref' (90% confidence) +wqflask/wqflask/model.py:45: unused variable 'active' (60% confidence) +wqflask/wqflask/model.py:47: unused variable 'registration_info' (60% confidence) +wqflask/wqflask/model.py:65: unused function 'display_num_collections' (60% confidence) +wqflask/wqflask/model.py:99: unused property 'login_count' (60% confidence) +wqflask/wqflask/model.py:104: unused property 'confirmed_at' (60% confidence) +wqflask/wqflask/model.py:112: unused property 'superuser_info' (60% confidence) +wqflask/wqflask/model.py:119: unused property 'crowner' (60% confidence) +wqflask/wqflask/model.py:129: unused property 'most_recent_login' (60% confidence) +wqflask/wqflask/model.py:146: unused variable 'ip_address' (60% confidence) +wqflask/wqflask/model.py:147: unused variable 'successful' (60% confidence) +wqflask/wqflask/model.py:155: unused attribute 'ip_address' (60% confidence) +wqflask/wqflask/model.py:195: unused function 'user_uuid' (60% confidence) +wqflask/wqflask/model.py:197: unused variable 'user_uuid' (60% confidence) +wqflask/wqflask/network_graph/network_graph.py:26: unused import 'gc' (90% confidence) +wqflask/wqflask/network_graph/network_graph.py:98: unused attribute 'network_data' (60% confidence) +wqflask/wqflask/news.py:16: unused attribute 'newslist' (60% confidence) +wqflask/wqflask/search_results.py:121: unused attribute 'json_trait_list' (60% confidence) +wqflask/wqflask/send_mail.py:41: unused attribute 'From' (60% confidence) +wqflask/wqflask/send_mail.py:42: unused attribute 'To' (60% confidence) +wqflask/wqflask/send_mail.py:43: unused attribute 'Subject' (60% confidence) +wqflask/wqflask/send_mail.py:44: unused attribute 'Body' (60% confidence) +wqflask/wqflask/show_trait/export_trait_data.py:3: unused import 'operator' (90% confidence) +wqflask/wqflask/show_trait/SampleList.py:28: unused attribute 'sample_group_type' (60% confidence) +wqflask/wqflask/show_trait/SampleList.py:29: unused attribute 'header' (60% confidence) +wqflask/wqflask/show_trait/SampleList.py:66: unused attribute 'this_id' (60% confidence) +wqflask/wqflask/show_trait/SampleList.py:68: unused attribute 'this_id' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:27: unused import 'BasicStatisticsFunctions' (90% confidence) +wqflask/wqflask/show_trait/show_trait.py:123: unused attribute 'UCSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:124: unused attribute 'UTHSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:126: unused attribute 'UCSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:127: unused attribute 'UTHSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:129: unused attribute 'UCSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:130: unused attribute 'UTHSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:132: unused attribute 'UCSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:133: unused attribute 'UTHSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:135: unused attribute 'UCSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:136: unused attribute 'UTHSC_BLAT_URL' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:183: unused attribute 'hddn' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:198: unused attribute 'stats_table_width' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:198: unused attribute 'trait_table_width' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:232: unused attribute 'genofiles' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:233: unused attribute 'use_plink_gemma' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:234: unused attribute 'use_pylmm_rqtl' (60% confidence) +wqflask/wqflask/show_trait/show_trait.py:262: unused attribute 'corr_tools' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:41: unused class 'ShowTraitPage' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:44: unused attribute 'fd' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:67: unused variable 'indId' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:67: unused variable 'indName' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:138: unused attribute 'display_variance' (60% confidence) +wqflask/wqflask/show_trait/show_trait_page.py:139: unused attribute 'formID' (60% confidence) +wqflask/wqflask/tracer.py:37: unused function 'turn_on' (60% confidence) +wqflask/wqflask/user_manager.py:69: unused function 'add_collection' (60% confidence) +wqflask/wqflask/user_manager.py:123: unused function 'display_num_collections' (60% confidence) +wqflask/wqflask/user_manager.py:259: unused attribute 'thank_you_mode' (60% confidence) +wqflask/wqflask/user_manager.py:299: unused attribute 'registration_info' (60% confidence) +wqflask/wqflask/user_manager.py:305: unused attribute 'algorithm' (60% confidence) +wqflask/wqflask/user_manager.py:316: unused attribute 'created_ts' (60% confidence) +wqflask/wqflask/user_manager.py:411: unused function 'verify_email' (60% confidence) +wqflask/wqflask/user_manager.py:425: unused function 'password_reset' (60% confidence) +wqflask/wqflask/user_manager.py:456: unused function 'password_reset_step2' (60% confidence) +wqflask/wqflask/user_manager.py:497: unused function 'reencode_standalone' (60% confidence) +wqflask/wqflask/user_manager.py:519: unused function 'github_oauth2' (60% confidence) +wqflask/wqflask/user_manager.py:549: unused function 'orcid_oauth2' (60% confidence) +wqflask/wqflask/user_manager.py:606: unused attribute 'login_type' (60% confidence) +wqflask/wqflask/user_manager.py:691: unused attribute 'successful' (60% confidence) +wqflask/wqflask/user_manager.py:693: unused attribute 'assumed_by' (60% confidence) +wqflask/wqflask/user_manager.py:715: unused attribute 'successful' (60% confidence) +wqflask/wqflask/user_manager.py:719: unused function 'logout' (60% confidence) +wqflask/wqflask/user_manager.py:730: unused function 'forgot_password' (60% confidence) +wqflask/wqflask/user_manager.py:735: unused function 'forgot_password_submit' (60% confidence) +wqflask/wqflask/user_manager.py:755: unused function 'unauthorized' (60% confidence) +wqflask/wqflask/user_manager.py:770: unused function 'manage_users' (60% confidence) +wqflask/wqflask/user_manager.py:776: unused function 'manage_user' (60% confidence) +wqflask/wqflask/user_manager.py:782: unused function 'manage_groups' (60% confidence) +wqflask/wqflask/user_manager.py:788: unused function 'make_superuser' (60% confidence) +wqflask/wqflask/user_manager.py:801: unused function 'assume_identity' (60% confidence) +wqflask/wqflask/user_manager.py:811: unused function 'register' (60% confidence) +wqflask/wqflask/user_manager.py:921: unused class 'RolesManager' (60% confidence) +wqflask/wqflask/views.py:17: unused import 'gc' (90% confidence) +wqflask/wqflask/views.py:23: unused import 'yaml' (90% confidence) +wqflask/wqflask/views.py:70: unused import 'werkzeug' (90% confidence) +wqflask/wqflask/views.py:77: unused function 'connect_db' (60% confidence) +wqflask/wqflask/views.py:82: unused attribute '_database' (60% confidence) +wqflask/wqflask/views.py:85: unused function 'shutdown_session' (60% confidence) +wqflask/wqflask/views.py:86: unused variable 'exception' (60% confidence) +wqflask/wqflask/views.py:98: unused function 'handle_bad_request' (60% confidence) +wqflask/wqflask/views.py:104: unused variable 'exc_traceback' (60% confidence) +wqflask/wqflask/views.py:104: unused variable 'exc_type' (60% confidence) +wqflask/wqflask/views.py:104: unused variable 'exc_value' (60% confidence) +wqflask/wqflask/views.py:123: unused function 'index_page' (60% confidence) +wqflask/wqflask/views.py:140: unused function 'tmp_page' (60% confidence) +wqflask/wqflask/views.py:154: unused function 'cytoscape' (60% confidence) +wqflask/wqflask/views.py:158: unused function 'twitter' (60% confidence) +wqflask/wqflask/views.py:178: unused function 'search_page' (60% confidence) +wqflask/wqflask/views.py:219: unused function 'gsearchact' (60% confidence) +wqflask/wqflask/views.py:229: unused function 'gsearch_updating' (60% confidence) +wqflask/wqflask/views.py:241: unused function 'docedit' (60% confidence) +wqflask/wqflask/views.py:247: unused function 'generated_file' (60% confidence) +wqflask/wqflask/views.py:252: unused function 'help' (60% confidence) +wqflask/wqflask/views.py:258: unused function 'wcgna_setup' (60% confidence) +wqflask/wqflask/views.py:264: unused function 'wcgna_results' (60% confidence) +wqflask/wqflask/views.py:273: unused function 'ctl_setup' (60% confidence) +wqflask/wqflask/views.py:279: unused function 'ctl_results' (60% confidence) +wqflask/wqflask/views.py:288: unused function 'news_route' (60% confidence) +wqflask/wqflask/views.py:293: unused function 'references' (60% confidence) +wqflask/wqflask/views.py:299: unused function 'intro' (60% confidence) +wqflask/wqflask/views.py:304: unused function 'policies' (60% confidence) +wqflask/wqflask/views.py:309: unused function 'links' (60% confidence) +wqflask/wqflask/views.py:314: unused function 'environments' (60% confidence) +wqflask/wqflask/views.py:319: unused function 'submit_trait_form' (60% confidence) +wqflask/wqflask/views.py:325: unused function 'create_temp_trait' (60% confidence) +wqflask/wqflask/views.py:335: unused function 'export_trait_excel' (60% confidence) +wqflask/wqflask/views.py:361: unused function 'export_trait_csv' (60% confidence) +wqflask/wqflask/views.py:382: unused function 'export_traits_csv' (60% confidence) +wqflask/wqflask/views.py:394: unused function 'export_perm_data' (60% confidence) +wqflask/wqflask/views.py:418: unused function 'show_temp_trait_page' (60% confidence) +wqflask/wqflask/views.py:433: unused function 'show_trait_page' (60% confidence) +wqflask/wqflask/views.py:448: unused function 'heatmap_page' (60% confidence) +wqflask/wqflask/views.py:495: unused function 'mapping_results_container_page' (60% confidence) +wqflask/wqflask/views.py:499: unused function 'loading_page' (60% confidence) +wqflask/wqflask/views.py:556: unused function 'marker_regression_page' (60% confidence) +wqflask/wqflask/views.py:696: unused function 'export' (60% confidence) +wqflask/wqflask/views.py:706: unused function 'export_pdf' (60% confidence) +wqflask/wqflask/views.py:714: unused variable 'filepath' (60% confidence) +wqflask/wqflask/views.py:720: unused function 'network_graph_page' (60% confidence) +wqflask/wqflask/views.py:736: unused function 'corr_compute_page' (60% confidence) +wqflask/wqflask/views.py:744: unused function 'corr_matrix_page' (60% confidence) +wqflask/wqflask/views.py:761: unused function 'corr_scatter_plot_page' (60% confidence) +wqflask/wqflask/views.py:770: unused function 'submit_bnw' (60% confidence) +wqflask/wqflask/views.py:786: unused function 'get_temp_data' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:5: unused import 'sp' (90% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:18: unused variable 'utils' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:23: unused variable 'r_read_csv' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:24: unused variable 'r_dim' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:27: unused variable 'r_paste' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:33: unused variable 'r_matrix' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:34: unused variable 'r_seq' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:36: unused variable 'r_names' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:37: unused variable 'r_sink' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:38: unused variable 'r_is_NA' (60% confidence) +wqflask/wqflask/wgcna/wgcna_analysis.py:39: unused variable 'r_file' (60% confidence) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 59bb49d8..ea216a35 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -285,10 +285,16 @@ TEMPDIR = tempdir() # defaults to UNIX TMPDIR assert_dir(TEMPDIR) # ---- Handle specific JS modules +JS_GUIX_PATH = get_setting("JS_GUIX_PATH") +assert_dir(JS_GUIX_PATH) +assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom') +CSS_PATH = "UNKNOWN" +# assert_dir(JS_PATH) JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) assert_dir(JS_TWITTER_POST_FETCHER_PATH) - -from six import string_types +assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") +JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape")) +assert_dir(JS_CYTOSCAPE_PATH) +assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js') # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html index 969ca18a..d85075a9 100644 --- a/wqflask/wqflask/templates/ctl_results.html +++ b/wqflask/wqflask/templates/ctl_results.html @@ -1,7 +1,7 @@ {% extends "base.html" %} {% block css %} - + {% endblock %} {% block content %} - + {{ header("Network Graph") }}
@@ -39,7 +39,7 @@ {% endfor %} - + Correlation Coefficient ? @@ -69,9 +69,9 @@ - + - +

Download

@@ -102,11 +102,19 @@ - - - - - + + + + + + + + {% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index a65924d8..3c2cca94 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -54,7 +54,7 @@ from wqflask.ctl import ctl_analysis #from wqflask.trait_submission import submit_trait from utility import temp_data -from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH +from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH from utility.helper_functions import get_species_groups from base import webqtlFormData @@ -151,6 +151,14 @@ def tmp_page(img_path): return render_template("show_image.html", img_base64 = bytesarray ) +@app.route("/js/") +def js(filename): + return send_from_directory(JS_GUIX_PATH, filename) + +@app.route("/css/") +def css(filename): + return send_from_directory(CSS_PATH, filename) + @app.route("/twitter/") def twitter(filename): return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) -- cgit v1.2.3