diff options
| -rw-r--r-- | .github/ISSUE_TEMPLATE/bug_report.md | 16 | ||||
| -rw-r--r-- | .github/ISSUE_TEMPLATE/feature_request.md | 23 | ||||
| -rw-r--r-- | .github/ISSUE_TEMPLATE/user_story.md | 8 | ||||
| -rw-r--r-- | .github/PULL_REQUEST_TEMPLATE.md | 9 | ||||
| -rw-r--r-- | jquery.qtip.css | 623 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_export_trait_data.py | 118 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 4 |
10 files changed, 174 insertions, 659 deletions
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 7d7e34a5..48bad39b 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -9,26 +9,26 @@ assignees: '' **Describe the bug** -A clear and concise description of what the bug is. +<!-- A clear and concise description of what the bug is. --> **To Reproduce** -Steps to reproduce the behavior +<!-- Steps to reproduce the behavior --> **Expected behavior** -A clear and concise description of what you expected to happen. +<!-- A clear and concise description of what you expected to happen. --> **Screenshots** -If applicable, add screenshots to help explain your problem. +<!-- If applicable, add screenshots to help explain your problem. --> **Environment setup (please complete the following information):** -- OS: [e.g. Linux] -- Guix Version (optional) -- [Anything else you think is relevant] +<!-- - OS: [e.g. Linux] --> +<!-- - Guix Version (optional) --> +<!-- - [Anything else you think is relevant] --> **Additional context** -Add any other context about the problem here. +<!-- Add any other context about the problem here. --> diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index 254754c6..eb6c3e4b 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -9,26 +9,33 @@ assignees: '' ## Is your feature request related to a problem? Please describe. -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] +<!-- A clear and concise description of what the problem is. --> + +<!-- Example: I'm always frustrated when [...] --> ## Describe the solution you'd like -A clear and concise description of what you want to happen. +<!-- A clear and concise description of what you want to happen. --> ## Describe alternatives you've considered -A clear and concise description of any alternative solutions or features you've considered. +<!-- A clear and concise description of any alternative solutions or features you've considered. --> ## User Stories (optional) -As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ +<!-- Example: --> + +<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ --> + +<!-- **Feature:** _[Brief description of feature]_ --> -**Feature:** _[Brief description of feature]_ +<!-- _[Any additional descriptions on feature]_ --> -_[Any additional descriptions on feature]_ +<!-- **Scenario:** -**Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here +Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ +here --> ## Additional context -Add any other context or screenshots about the feature request here. +<!-- Add any other context or screenshots about the feature request here. --> diff --git a/.github/ISSUE_TEMPLATE/user_story.md b/.github/ISSUE_TEMPLATE/user_story.md index 2682fc98..52ae775d 100644 --- a/.github/ISSUE_TEMPLATE/user_story.md +++ b/.github/ISSUE_TEMPLATE/user_story.md @@ -7,10 +7,10 @@ assignees: '' --- -As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ +<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ --> -**Feature:** _[Brief description of feature]_ +<!-- **Feature:** _[Brief description of feature]_ --> -_[Any additional descriptions on feature]_ +<!-- _[Any additional descriptions on feature]_ --> -**Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here +<!-- **Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here --> diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 223e24ef..f3371183 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,11 +1,20 @@ #### Description +<!--Brief description of the PR. What does this PR do? --> #### How should this be tested? +<!-- What should you do to test this PR? Is there any manual quality +assurance checks that should be done. What are the expectations --> #### Any background context you want to provide? +<!-- Anything the reviewer should be aware of ahead of testing --> + #### What are the relevant pivotal tracker stories? +<!-- Does this PR track anything anywhere? --> + #### Screenshots (if appropriate) #### Questions + +<!-- Are there any questions for the reviewer --> diff --git a/jquery.qtip.css b/jquery.qtip.css deleted file mode 100644 index c2dcb306..00000000 --- a/jquery.qtip.css +++ /dev/null @@ -1,623 +0,0 @@ -/* - * 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/wqflask/tests/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py index 98d599b1..41761944 100644 --- a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py +++ b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py @@ -1,10 +1,128 @@ import unittest +from unittest import mock from wqflask.show_trait.export_trait_data import dict_to_sorted_list from wqflask.show_trait.export_trait_data import cmp_samples +from wqflask.show_trait.export_trait_data import export_sample_table +from wqflask.show_trait.export_trait_data import get_export_metadata + + +class AttributesSetter: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) class TestExportTraits(unittest.TestCase): """Test methods related to converting dict to sortedlist""" + @mock.patch("wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata_no_publish(self, mock_dataset, mock_trait): + """test for exporting metadata with no publish""" + mock_dataset_attributes = AttributesSetter( + {"type": "no_publish", "dataset_name": "Temp", "name": "Temp"}) + + mock_nested_attributes = AttributesSetter({"name": "name"}) + mock_dataset_attributes.group = mock_nested_attributes + mock_dataset.create_dataset.return_value = mock_dataset_attributes + mock_trait.return_value = AttributesSetter({"symbol": "", "description_display": "Description", + "title": "research1", "journal": "", "authors": ""}) + + results = get_export_metadata("random_id", "Temp") + expected = [["Record ID: random_id"], + ["Trait URL: http://genenetwork.org/show_trait?trait_id=random_id&dataset=Temp"], + ["Dataset: Temp"], + ["Group: name"], []] + + mock_dataset.create_dataset.assert_called_with("Temp") + mock_trait.assert_called_with( + dataset=mock_dataset_attributes, name="random_id", cellid=None, get_qtl_info=False) + self.assertEqual(results, expected) + + @mock.patch("wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata_with_publish(self, data_mock, trait_mock): + """test for exporting metadata with dataset.type=Publish""" + mock_dataset_attributes = AttributesSetter({"type": "Publish", "dataset_name": "Temp", + "name": "Temp", "description_display": "Description goes here"}) + + mock_nested_attributes = AttributesSetter({"name": "name"}) + mock_dataset_attributes.group = mock_nested_attributes + data_mock.create_dataset.return_value = mock_dataset_attributes + trait_instance = AttributesSetter({"symbol": "", "description_display": "Description", + "title": "research1", "journal": "", "authors": ""}) + trait_mock.return_value = trait_instance + + results = get_export_metadata( + "29ae0615-0d77-4814-97c7-c9e91f6bfd7b", "Temp") + + expected = [['Phenotype ID: 29ae0615-0d77-4814-97c7-c9e91f6bfd7b'], + ['Phenotype URL: http://genenetwork.org/show_trait?trait_id=29ae0615-0d77-4814-97c7-c9e91f6bfd7b&dataset=Temp'], [ + 'Group: name'], ['Phenotype: Description'], + ['Authors: N/A'], ['Title: research1'], + ['Journal: N/A'], ['Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Temp'], []] + + self.assertEqual(results, expected) + + @mock.patch("wqflask.show_trait.export_trait_data.dict_to_sorted_list") + @mock.patch("wqflask.show_trait.export_trait_data.get_export_metadata") + def test_export_sample_table(self, exp_metadata, dict_list): + """test for exporting sample table""" + targs_obj = { + "export_data": """{ + "primary_samples": [ + { + "other": "germanotta", + "name": "Sauroniops", + "se":{ + "name":"S2" + }, + "num_cases":{ + "k1":"value" + + } + } + ], + "other_samples": [ + { + "se": 1, + "num_cases": 4, + "value": 6, + "name": 3 + } + ] + }""", + "trait_display_name": "Hair_color", + "trait_id": "23177fdc-312e-4084-ad0c-f3eae785fff5", + "dataset": { + } + } + exp_metadata.return_value = [ + ["Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f"], ['Group:gp1'], + ["Phenotype:p1"], [ + "Authors:N/A"], + ["Title:research1"], + ["Journal:N/A"], + ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1"], []] + expected = ('Hair_color', + [['Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f'], + ['Group:gp1'], + ['Phenotype:p1'], + ['Authors:N/A'], + ['Title:research1'], + ['Journal:N/A'], + ['Dataset Link: ' + 'http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1'], + [], + ['Name', 'Value', 'SE', 'N'], + ['Sauroniops', 'germanotta'], + [3, 6, 1, 4]]) + + dict_list.side_effect = [['Sauroniops', 'germanotta'], [3, 6, 1, 4]] + + self.assertEqual(export_sample_table(targs_obj), expected) + exp_metadata.assert_called_with( + "23177fdc-312e-4084-ad0c-f3eae785fff5", {}) + self.assertEqual(dict_list.call_count, 2) def test_dict_to_sortedlist(self): """test for conversion of dict to sorted list""" diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py index d855a7fa..236cc755 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -25,6 +25,10 @@ def is_redis_available(): return True +def load_json_from_redis(item_list, column_value): + return json.loads(item_list[str.encode(column_value)]) + + def get_user_id(column_name, column_value): user_list = Redis.hgetall("users") key_list = [] @@ -46,7 +50,7 @@ def get_user_by_unique_column(column_name, column_value): if column_name in user_ob and user_ob[column_name] == column_value: item_details = user_ob else: - item_details = json.loads(user_list[column_value]) + item_details = load_json_from_redis(user_list, column_value) return item_details @@ -70,7 +74,7 @@ def get_users_like_unique_column(column_name, column_value): if column_value in user_ob[column_name]: matched_users.append(user_ob) else: - matched_users.append(json.loads(user_list[column_value])) + matched_users.append(load_json_from_redis(user_list, column_value)) return matched_users @@ -199,7 +203,7 @@ def get_groups_like_unique_column(column_name, column_value): if column_value in group_info[column_name]: matched_groups.append(group_info) else: - matched_groups.append(json.loads(group_list[column_value])) + matched_groups.append(load_json_from_redis(group_list, column_value)) return matched_groups diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index e710bacd..4c2b64ba 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -184,6 +184,8 @@ class CorrelationResults(object): for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) + if not trait_object: + continue if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": #ZS: Convert trait chromosome to an int for the location range option @@ -434,15 +436,15 @@ class CorrelationResults(object): self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) - #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ - if self.corr_method == 'bicor': - sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) - elif self.corr_method == 'pearson': - sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) - else: - sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) - if num_overlap > 5: + #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ + if self.corr_method == 'bicor': + sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals) + elif self.corr_method == 'pearson': + sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals) + else: + sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals) + if numpy.isnan(sample_r): pass else: @@ -635,3 +637,4 @@ def get_header_fields(data_type, corr_method): 'Sample p(r)'] return header_fields + diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index b5686b70..6d6572ff 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2146,9 +2146,6 @@ class DisplayMappingResults(object): LRSScale = 1.0 LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) - #make sure the user's value appears on the y-axis - #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460 - LRSAxisList.append(ceil(LRS_LOD_Max)) #ZS: Convert to int if all axis values are whole numbers all_int = True diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index edf9638c..25ba1a1d 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -228,8 +228,8 @@ class ShowTrait(object): hddn = OrderedDict() if self.dataset.group.allsamples: - hddn['allsamples'] = ''.join(self.dataset.group.allsamples) - hddn['primary_samples'] = ''.join(self.primary_sample_names) + hddn['allsamples'] = ','.join(self.dataset.group.allsamples) + hddn['primary_samples'] = ','.join(self.primary_sample_names) hddn['trait_id'] = self.trait_id hddn['trait_display_name'] = self.this_trait.display_name hddn['dataset'] = self.dataset.name |