diff options
| author | Pjotr Prins | 2018-04-06 10:21:35 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2018-04-06 10:21:35 +0000 |
| commit | 1debb0849066a31c8538b529536a9a7a12a0a8f9 (patch) | |
| tree | ed1e4292add486535ba66517bf77c8c5fcf0499b | |
| parent | b579c97c58f4c5fe55a1dc100747699219b1c66e (diff) | |
| download | genenetwork2-1debb0849066a31c8538b529536a9a7a12a0a8f9.tar.gz | |
See #308.
Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
| -rw-r--r-- | jquery.qtip.css | 623 | ||||
| -rw-r--r-- | unused.txt | 610 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/ctl_results.html | 22 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/network_graph.html | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 10 |
6 files changed, 1283 insertions, 22 deletions
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 variable 'LRS_location_value' (60% confidence) +wqflask/base/trait.py:707: unused variable 'LRS_location_value' (60% confidence) +wqflask/base/trait.py:709: unused variable 'LRS_location_value' (60% confidence) +wqflask/base/trait.py:714: unused attribute 'LRS_score_value' (60% confidence) +wqflask/base/trait.py:714: unused variable 'LRS_score_value' (60% confidence) +wqflask/base/webqtlCaseData.py:42: unused attribute 'this_id' (60% confidence) +wqflask/base/webqtlCaseData.py:59: unused property 'class_outlier' (60% confidence) +wqflask/base/webqtlCaseData.py:67: unused property 'display_value' (60% confidence) +wqflask/base/webqtlCaseData.py:74: unused property 'display_variance' (60% confidence) +wqflask/base/webqtlConfig.py:24: unused variable 'MULTIPLEMAPPINGLIMIT' (60% confidence) +wqflask/base/webqtlConfig.py:27: unused variable 'MAXCORR' (60% confidence) +wqflask/base/webqtlConfig.py:36: unused variable 'MAXLIFE' (60% confidence) +wqflask/base/webqtlConfig.py:42: unused variable 'NCBI_LOCUSID' (60% confidence) +wqflask/base/webqtlConfig.py:43: unused variable 'UCSC_REFSEQ' (60% confidence) +wqflask/base/webqtlConfig.py:44: unused variable 'GENBANK_ID' (60% confidence) +wqflask/base/webqtlConfig.py:45: unused variable 'OMIM_ID' (60% confidence) +wqflask/base/webqtlConfig.py:46: unused variable 'UNIGEN_ID' 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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 %} <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/cytoscape/css/cytoscape.js-panzoom.css" /> + <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" /> <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.css"> <style> /* The Cytoscape Web container must have its dimensions set. */ @@ -24,7 +24,7 @@ {% print("%c"|format(elem)) %} {%- endfor %} " /></a> --> - + <h3>CTL/QTL Plots for individual traits</h3> {% for r in range(2, (request.form['trait_list'].split(',')|length +1)) %} <a href="/tmp/{{ results['imgurl' + r|string] }}"> @@ -66,12 +66,18 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> <script language="javascript" type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/cytoscape.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/AC_OETags.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/json2.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-panzoom.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-qtip.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> + <!-- should be using cytoscape-popper for tips, see docs --> + <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script> + <!-- + Loads flash - who wants that? + <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/AC_OETags.min.js"></script> + Disabled because it is standard JS now: + <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/json2.min.js"></script> +t> + --> <script language="javascript" type="text/javascript" src="/static/new/javascript/ctl_graph.js"></script> -{% endblock %} +{% endblock %} diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html index 24293de6..ad5dee9d 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="/static/packages/cytoscape/css/cytoscape.js-panzoom.css" /> + <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" /> <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.css"> <style> /* The Cytoscape Web container must have its dimensions set. */ @@ -10,7 +10,7 @@ </style> {% endblock %} {% block content %} - + {{ header("Network Graph") }} <div class="container-fluid"> @@ -39,7 +39,7 @@ {% endfor %} </select> </td> - </tr> + </tr> <tr> <td colspan="1"> Correlation Coefficient<sup title="Filter edges to only show correlations less than the negative value specified with the slider and greater than the positive value. For example, moving the slider half way will display correlations less than -0.5 and greater than 0.5" style="color:#f00"> ?</sup> @@ -69,9 +69,9 @@ <option value="random">Random</option> </select> </td> - </tr> + </tr> </tbody> - </table> + </table> <h3 style="margin-bottom: 5px;"> Download</h3> <table> <tbody> @@ -102,11 +102,19 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script> <script language="javascript" type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/cytoscape.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/AC_OETags.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/json2.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-panzoom.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-qtip.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> + <!-- should be using cytoscape-popper for tips, see docs --> + <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script> + + <!-- + Loads flash - who wants that? + <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/AC_OETags.min.js"></script> + Disabled because it is standard JS now: + <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/json2.min.js"></script> + --> <script language="javascript" type="text/javascript" src="/static/new/javascript/network_graph.js"></script> + {% 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/<path:filename>") +def js(filename): + return send_from_directory(JS_GUIX_PATH, filename) + +@app.route("/css/<path:filename>") +def css(filename): + return send_from_directory(CSS_PATH, filename) + @app.route("/twitter/<path:filename>") def twitter(filename): return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) |