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-- | wqflask/base/GeneralObject.py | 2 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_show_trait.py | 242 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/show_trait.css | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/trait_list.css | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 72 |
15 files changed, 378 insertions, 80 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/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0122ee32..249195e2 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -28,7 +28,7 @@ class GeneralObject: """ Base class to define an Object. a = [Spam(1, 4), Spam(9, 3), Spam(4,6)] - a.sort(lambda x, y: cmp(x.eggs, y.eggs)) + a.sort(key = lambda x: x.eggs) """ def __init__(self, *args, **kw): diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py new file mode 100644 index 00000000..24150738 --- /dev/null +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -0,0 +1,242 @@ +"""test for wqflask/show_trait/test_show_trait.py""" +import unittest +from unittest import mock +from wqflask import app +from wqflask.show_trait.show_trait import check_if_attr_exists +from wqflask.show_trait.show_trait import get_ncbi_summary +from wqflask.show_trait.show_trait import has_num_cases +from wqflask.show_trait.show_trait import get_table_widths +from wqflask.show_trait.show_trait import get_categorical_variables +from wqflask.show_trait.show_trait import get_trait_units +from wqflask.show_trait.show_trait import get_nearest_marker +from wqflask.show_trait.show_trait import get_genotype_scales +from wqflask.show_trait.show_trait import requests + + +class TraitObject: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + + +class TestTraits(unittest.TestCase): + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + def test_check_if_attr_exists_truthy(self): + """"test if attributes exists with true return""" + trait_obj = TraitObject({"id_type": "id"}) + trait_obj2 = TraitObject({"sample_name": ['samp1']}) + results = check_if_attr_exists(trait_obj, "id_type") + result2 = check_if_attr_exists(trait_obj2, "sample_name") + self.assertIsInstance(trait_obj, TraitObject) + self.assertTrue(results) + self.assertTrue(result2) + + def test_check_if_attr_exists_empty_attr(self): + """test if attributes exists with false return""" + trait_obj = TraitObject({"sample": ""}) + trait_obj2 = TraitObject({"group": None}) + result = check_if_attr_exists(trait_obj, "sample") + result2 = check_if_attr_exists(trait_obj, "group") + self.assertFalse(result) + self.assertFalse(result2) + + def test_check_if_attr_exists_falsey(self): + """check if attribute exists with empty attributes""" + trait_obj = TraitObject({}) + results = check_if_attr_exists(trait_obj, "any") + self.assertFalse(results) + + @mock.patch("wqflask.show_trait.show_trait.requests.get") + @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists") + def test_get_ncbi_summary_request_success(self, mock_exists, mock_get): + """test for getting ncbi summary with + successful request""" + trait = TraitObject({"geneid": "id"}) + mock_exists.return_value = True + content_json_string = """{ + "result":{ + "id":{ + "summary":"this is a summary of the geneid" + } + } + } + """ + get_return_obj = TraitObject({"content": content_json_string}) + mock_get.return_value = get_return_obj + results = get_ncbi_summary(trait) + mock_exists.assert_called_once() + mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json") + + self.assertEqual(results, "this is a summary of the geneid") + + @mock.patch("wqflask.show_trait.show_trait.requests.get") + @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists") + def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail): + """test for getting ncbi summary with request fail""" + trait = TraitObject({"geneid": "id"}) + mock_exists.return_value = True + mock_get_fail.side_effect = Exception("an error occurred") + content_json_string = """{ + "result":{ + "id":{ + "summary":"this is a summary of the geneid" + } + } + } + """ + results = get_ncbi_summary(trait) + self.assertEqual(results, None) + + def test_hash_num_cases_is_probeset(self): + """test for hash num_cases with dataset.type set to Probeset""" + create_dataset = TraitObject({"type": "ProbeSet"}) + create_trait = TraitObject({"dataset": create_dataset}) + self.assertFalse(has_num_cases(create_trait)) + + def test_hash_num_cases_no_probeset(self): + """test for hash num cases with dataset.type not Probeset""" + create_dataset = TraitObject({"type": "Temp"}) + construct_data = { + "nm1": TraitObject({"num_cases": False}), + "nm2": TraitObject({"num_cases": True}), + "nm3": TraitObject({"num_cases": False}) + } + construct_data2 = { + "nm1": TraitObject({"num_cases": False}), + "nm2": TraitObject({"num_cases": False}), + "nm3": TraitObject({"num_cases": False}) + } + create_trait = TraitObject( + {"dataset": create_dataset, "data": construct_data}) + create_trait2 = TraitObject( + {"dataset": create_dataset, "data": construct_data2}) + + results = has_num_cases(create_trait) + self.assertTrue(has_num_cases(create_trait)) + self.assertFalse(has_num_cases(create_trait2)) + + def test_get_table_widths(self): + """test for getting table widths""" + sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]} + ), TraitObject( + {"se_exists": False, "attributes": ["at1", "at2"] + })] + + results_with_numcase = get_table_widths(sample_groups, True) + result_no_numcase = get_table_widths(sample_groups, False) + + results_one_sample = get_table_widths( + [TraitObject({"se_exists": True, "attributes": []})], True) + expected_with_numcase = (450, "750px") + expected_no_numcase = (450, "670px") + expected_one_sample = (250, "540px") + self.assertEqual(results_with_numcase, expected_with_numcase) + self.assertEqual(result_no_numcase, expected_no_numcase) + self.assertEqual(results_one_sample, + expected_one_sample) + + def test_get_categorical_variables_no_sample_attributes(self): + """test for getting categorical variable names with no samples""" + trait = TraitObject({}) + sample_list = TraitObject({"se_exists": True, "attributes": []}) + self.assertEqual(get_categorical_variables(trait, sample_list), []) + + def test_get_categorical_variables_with_sample_attributes(self): + """test for getting categorical variable names with no samples""" + this_trait = TraitObject({"data": { + "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}), + "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}), + "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}}) + }}) + sample_list = TraitObject({"attributes": { + "sample_attribute_1": TraitObject({"name": "ex1"}), + "sample_attribute_2": TraitObject({"name": "ex2"}), + "sample_attribute_3": TraitObject({"name": "ex3"}), + "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"}) + }}) + results = get_categorical_variables(this_trait, sample_list) + self.assertEqual( + ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results) + + def test_get_trait_units(self): + """test for getting trait units""" + trait = TraitObject( + {"description_fmt": "[this is a description] another test [N/A]"}) + trait_no_unit_type = TraitObject({"description_fmt": ""}) + results = get_trait_units(trait) + results_no_unit = get_trait_units(trait_no_unit_type) + self.assertEqual(results, "this is a descriptionN/A") + self.assertEqual(results_no_unit, "Value") + + @mock.patch("wqflask.show_trait.show_trait.g") + def test_get_nearest_marker(self, mock_db): + """test for getting nearest marker with non-empty db""" + + mock_db.db.execute.return_value.fetchall.return_value = [ + ["Geno1", "Geno2"], ["Geno3"]] + + trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"}) + group_name = TraitObject({"name": "group_name"}) + this_db = TraitObject({"group": group_name}) + results_with_item_db = get_nearest_marker(trait, this_db) + called_with_value = """SELECT Geno.Name + FROM Geno, GenoXRef, GenoFreeze + WHERE Geno.Chr = 'test_chr' AND + GenoXRef.GenoId = Geno.Id AND + GenoFreeze.Id = GenoXRef.GenoFreezeId AND + GenoFreeze.Name = 'group_nameGeno' + ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1""" + + mock_db.db.execute.assert_called_with(called_with_value) + + self.assertEqual(results_with_item_db, "Geno1") + + @mock.patch("wqflask.show_trait.show_trait.g") + def test_get_nearest_marker_empty_db(self, mock_db): + """test for getting nearest marker with empty db""" + mock_db.db.execute.return_value.fetchall.return_value = [] + trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"}) + group_name = TraitObject({"name": "group_name"}) + this_db = TraitObject({"group": group_name}) + results_empty_db = get_nearest_marker(trait, this_db) + mock_db.db.execute.assert_called_once() + self.assertEqual(results_empty_db, "") + + @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile") + def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales): + """test for getting genotype scales with genofile as list """ + # where genofile is instance of list + genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"}, + {"filename": "file2", "location": "~/data/files/f2"}, + {"filename": "file3", "location": "~/data/files/f3"}] + + mock_get_scales.side_effect = [[["morgan", "cM"]], + [["morgan", "cM"]], + [["physic", "Mb"]]] + + results = get_genotype_scales(genofiles_list) + expected_results = { + "~/data/files/f1": [["morgan", "cM"]], + "~/data/files/f2": [["morgan", "cM"]], + "~/data/files/f3": [["physic", "Mb"]] + } + + multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'), + mock.call('~/data/files/f3')] + mock_get_scales.assert_has_calls(multiple_calls) + self.assertEqual(results, expected_results) + + @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile") + def test_genotype_scales_with_genofile_other(self, mock_get_scales): + """test for getting genotype scales with genofile as a string""" + file_location = "~/another_file_location" + mock_get_scales.return_value = [["physic", "Mb"]] + expected_results = {f"{file_location}": [["physic", "Mb"]]} + self.assertEqual(get_genotype_scales(file_location), expected_results) + mock_get_scales.assert_called_once_with(file_location) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 04d47624..6d6572ff 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1460,7 +1460,7 @@ class DisplayMappingResults(object): else: continue - smd.sort(lambda A, B: cmp(A.value, B.value)) + smd.sort(key = lambda A: A.value) smd.reverse() samplelist = list(self.genotype.prgy) diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 37c1d6d5..a535c493 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -34,13 +34,18 @@ class SampleList(object): # ZS: self.this_trait will be a list if it is a Temp trait if isinstance(self.this_trait, list): - if (counter <= len(self.this_trait) and - str(self.this_trait[counter-1]).upper() != 'X'): - sample = webqtlCaseData.webqtlCaseData( - name=sample_name, - value=float(self.this_trait[counter-1])) - else: - sample = webqtlCaseData.webqtlCaseData(name=sample_name) + sample = webqtlCaseData.webqtlCaseData(name=sample_name) + if counter <= len(self.this_trait): + if isinstance(self.this_trait[counter-1], (bytes, bytearray)): + if (self.this_trait[counter-1].decode("utf-8").lower() != 'x'): + sample = webqtlCaseData.webqtlCaseData( + name=sample_name, + value=float(self.this_trait[counter-1])) + else: + if (self.this_trait[counter-1].lower() != 'x'): + sample = webqtlCaseData.webqtlCaseData( + name=sample_name, + value=float(self.this_trait[counter-1])) else: # ZS - If there's no value for the sample/strain, # create the sample object (so samples with no value diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index edf9638c..0c6ae198 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 @@ -372,7 +372,7 @@ class ShowTrait(object): # We're checking a string here! assert isinstance(this_group, str), "We need a string type thing here" - if this_group[:3] == 'BXD' and this_group != "BXD-Harvested": + if this_group[:3] == 'BXD' and this_group != "BXD-Longevity": this_group = 'BXD' if this_group: diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index d8964f5d..5e1a279b 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -67,7 +67,7 @@ table.dataTable.cell-border tbody tr td:first-child { } .showtrait-main-div { - min-width: 700px; + min-width: 1100px; } table.dataTable tbody td.column_name-Checkbox { diff --git a/wqflask/wqflask/static/new/css/trait_list.css b/wqflask/wqflask/static/new/css/trait_list.css new file mode 100644 index 00000000..691dcb12 --- /dev/null +++ b/wqflask/wqflask/static/new/css/trait_list.css @@ -0,0 +1,12 @@ +div.tool-button-container {
+ min-width: 950px;
+}
+
+div.collection-table-options {
+ min-width: 1100px;
+}
+
+div.show-hide-container {
+ margin-bottom: 5px;
+ margin-top: 10px;
+}
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index c0f36eaa..34582f21 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -147,7 +147,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] -$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { +$(".rqtl-tab, #rqtl_geno_compute").on("click", (function(_this) { return function() { if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ var form_data, url; @@ -171,7 +171,7 @@ $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { }; })(this)); -$(".gemma_tab, #gemma_compute").on("click", (function(_this) { +$(".gemma-tab, #gemma_compute").on("click", (function(_this) { return function() { if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ var form_data, url; @@ -192,7 +192,7 @@ $(".gemma_tab, #gemma_compute").on("click", (function(_this) { }; })(this)); -$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) { +$(".reaper-tab, #interval_mapping_compute").on("click", (function(_this) { return function() { if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ var form_data, url; @@ -260,7 +260,7 @@ $("#mapmethod_rqtl_geno").change(function() { } }); -$("li.mapping_tab").click(function() { +$("li.mapping-tab").click(function() { if ($(this).hasClass("rqtl")){ $(".rqtl_description").css("display", "block"); } else { diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 873a6703..e37f8104 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -4,6 +4,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}"> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -16,7 +17,7 @@ </h1> <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3> - <div> + <div class="tool-button-container"> <form id="collection_form" action="/delete" method="post"> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" /> <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" /> @@ -68,20 +69,22 @@ <div> <br /> - <form id="export_form" method="POST" action="/export_traits_csv"> - <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button> - <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button> - <button class="btn btn-success" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button> - <input type="hidden" name="database_name" id="database_name" value="None"> - <input type="hidden" name="export_data" id="export_data" value=""> - <input type="hidden" name="file_name" id="file_name" value="collection_table"> - <button class="btn btn-default" id="export_traits">Download</button> - <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ..."> - <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> - <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> - <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button> - <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button> - </form> + <div class="collection-table-options"> + <form id="export_form" method="POST" action="/export_traits_csv"> + <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button> + <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button> + <button class="btn btn-success" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button> + <input type="hidden" name="database_name" id="database_name" value="None"> + <input type="hidden" name="export_data" id="export_data" value=""> + <input type="hidden" name="file_name" id="file_name" value="collection_table"> + <button class="btn btn-default" id="export_traits">Download</button> + <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ..."> + <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ..."> + <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> + <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button> + <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button> + </form> + </div> <div style="margin-top: 10px; margin-bottom: 5px;"> <b>Show/Hide Columns:</b> </div> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 134f15be..bc0b592c 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -367,8 +367,8 @@ { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] }, { "type": "natural" }, { "type": "scientific" }, - { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, - { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] }, + { "type": "natural-minus-na", 'orderSequence': [ "desc", "asc"] }, + { "type": "natural-minus-na", 'orderSequence': [ "desc", "asc"] }, { "type": "scientific" }, { "type": "natural-minus-na" }, { "type": "natural-minus-na" }, diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 6d9ea8fe..36f144c2 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -5,6 +5,7 @@ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}"> <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}"> <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> + <link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -40,10 +41,10 @@ {% elif word.search_term|length == 5 %} with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} {% endif %} - {% elif word.key|lower == "position" %} - with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} + {% elif word.key|lower == "position" or word.key|lower == "mb" %} + with <u>target genes</u> on chromosome <strong>{% if (word.search_term[0]|lower).split('chr')|length > 1 %}{{ (word.search_term[0]|lower).split('chr')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %} {% else %} - {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>"{{ word.search_term[0] }}"</b>{% if loop.last %}{% else %} and {% endif %}{% endif %} + {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>{{ word.search_term[0] }}</b>{% if loop.last %}{% else %} and {% endif %}{% endif %} {% endif %} {% endfor %} {% endif %} @@ -133,11 +134,29 @@ <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> </div> </form> - <br /> {% if dataset.type != 'Geno' %} - <br /> - <div style="margin-bottom: 5px;"> + <div class="show-hide-container"> <b>Show/Hide Columns:</b> + <br> + <button class="toggle-vis" data-column="1">Index</button> + <button class="toggle-vis" data-column="2">Record</button> + {% if dataset.type == 'ProbeSet' %} + <button class="toggle-vis" data-column="3">Symbol</button> + <button class="toggle-vis" data-column="4">Description</button> + <button class="toggle-vis" data-column="5">Location</button> + <button class="toggle-vis" data-column="6">Mean</button> + <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="8">Peak Location</button> + <button class="toggle-vis" data-column="9">Effect Size</button> + {% elif dataset.type == 'Publish' %} + <button class="toggle-vis" data-column="3">Description</button> + <button class="toggle-vis" data-column="4">Mean</button> + <button class="toggle-vis" data-column="5">Authors</button> + <button class="toggle-vis" data-column="6">Year</button> + <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="8">Peak Location</button> + <button class="toggle-vis" data-column="9">Effect Size</button> + {% endif %} </div> {% endif %} <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}> @@ -209,7 +228,7 @@ } //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters - $('#trait_table').DataTable( { + trait_table = $('#trait_table').DataTable( { 'drawCallback': function( settings ) { $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { @@ -381,7 +400,7 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "Max LRS<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", + 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>", 'type': "natural-minus-na", 'data': "lrs_score", 'width': "80px", @@ -408,24 +427,7 @@ }{% endif %} ], "order": [[1, "asc" ]], - {% if dataset.type != 'Geno' %} - buttons: [ - { - extend: 'columnsToggle', - columns: function( idx, data, node ) { - if (idx != 0) { - return true; - } else { - return false; - } - }, - postfixButtons: [ 'colvisRestore' ] - } - ], - 'sDom': "Bpitirp", - {% else %} - 'sDom': "pitirp", - {% endif %} + 'sDom': "itirp", 'iDisplayLength': 500, 'deferRender': true, 'paging': true, @@ -439,6 +441,23 @@ console.timeEnd("Creating table"); + $('.toggle-vis').on( 'click', function (e) { + e.preventDefault(); + + // Get the column API object + var column = trait_table.column( $(this).attr('data-column') ); + + // Toggle the visibility + column.visible( ! column.visible() ); + + if (column.visible()){ + $(this).removeClass("active"); + } else { + $(this).addClass("active"); + } + } ); + + $('#redraw').click(function() { var table = $('#trait_table').DataTable(); table.colReorder.reset() @@ -452,3 +471,4 @@ }); </script> {% endblock %} + |