diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py | 51 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 33 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 26 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_calculate_correlations.html | 152 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/user_login.py | 8 |
9 files changed, 154 insertions, 153 deletions
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index b8c13ab4..fe2569b8 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -5,7 +5,6 @@ from unittest import mock from wqflask.marker_regression.gemma_mapping import run_gemma from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file from wqflask.marker_regression.gemma_mapping import gen_covariates_file -from wqflask.marker_regression.gemma_mapping import parse_gemma_output from wqflask.marker_regression.gemma_mapping import parse_loco_output @@ -69,11 +68,9 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), - mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] - mock_os.system.assert_has_calls(system_calls) + self.assertEqual(mock_os.system.call_count,2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -138,31 +135,6 @@ class TestGemmaMapping(unittest.TestCase): filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output(self): - """add test for generating gemma output with obj returned""" - file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 -X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 -125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 -""" - with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, - {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( - "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_with_empty_return(self): - """add tests for parse gemma output where nothing returned""" - output_file_results = """chr\t today""" - with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - self.assertEqual(results, []) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") @@ -172,21 +144,26 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 "files": [["file_name", "user", "~/file1"], ["file_name", "user", "~/file2"]] } - return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t +chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5 +Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7 +X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" + + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" with mock.patch("builtins.open") as mock_open: handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( - read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value) mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { - 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + expected_results= [ + {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, + {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] self.assertEqual(expected_results, results) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 68ef0f04..65df59c3 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \ - ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2" ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index be983c87..a36b947c 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -71,7 +71,6 @@ class CorrelationResults(object): assert('corr_sample_method' in start_vars) assert('corr_samples_group' in start_vars) assert('corr_dataset' in start_vars) - #assert('min_expr' in start_vars) assert('corr_return_results' in start_vars) if 'loc_chr' in start_vars: assert('min_loc_mb' in start_vars) @@ -195,15 +194,15 @@ class CorrelationResults(object): if (float(self.correlation_data[trait][0]) >= self.p_range_lower and float(self.correlation_data[trait][0]) <= self.p_range_upper): - if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": - + if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean): if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr): continue - elif range_chr_as_int != None and (chr_as_int != range_chr_as_int): + if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": + if range_chr_as_int != None and (chr_as_int != range_chr_as_int): continue - elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)): + if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)): continue - elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)): + if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)): continue (trait_object.sample_r, @@ -517,6 +516,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap elif target_dataset.type == "Publish": results_dict['abbreviation_display'] = "N/A" results_dict['description'] = "N/A" + results_dict['mean'] = "N/A" results_dict['authors_display'] = "N/A" results_dict['additive'] = "N/A" if for_api: @@ -530,6 +530,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['abbreviation_display'] = trait.abbreviation if bool(trait.description_display): results_dict['description'] = trait.description_display + if bool(trait.mean): + results_dict['mean'] = f"{float(trait.mean):.3f}" if bool(trait.authors): authors_list = trait.authors.split(',') if len(authors_list) > 6: @@ -603,6 +605,7 @@ def get_header_fields(data_type, corr_method): 'Record', 'Abbreviation', 'Description', + 'Mean', 'Authors', 'Year', 'Sample rho', @@ -616,6 +619,7 @@ def get_header_fields(data_type, corr_method): 'Record', 'Abbreviation', 'Description', + 'Mean', 'Authors', 'Year', 'Sample r', diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 630a3afa..ab3a7278 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -54,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf TEMPDIR, trait_filename) if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'), + gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'), this_dataset.group.name, flat_files('genotype/bimbam'), genofile_name, @@ -62,7 +62,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf TEMPDIR, gwa_output_filename) else: - gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + gemma_command += ' -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), genofile_name, maf, TEMPDIR, @@ -184,11 +184,8 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): else: marker['chr'] = line.split("\t")[0] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - if loco == "True": - marker['p_value'] = float(line.split("\t")[9]) - else: - marker['p_value'] = float(line.split("\t")[10]) - marker['additive'] = float(line.split("\t")[7]) + marker['p_value'] = float(line.split("\t")[10]) + marker['additive'] = float(line.split("\t")[7]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index b71a9dd8..2b8a4d30 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -100,15 +100,7 @@ d3.select("#select_compare_trait").on("click", (function(_this) { return open_trait_selection(); }; })(this)); -d3.select("#select_covariates").on("click", (function(_this) { - return function() { - return open_covariate_selection(); - }; -})(this)); -$("#remove_covariates").click(function () { - $("input[name=covariates]").val("") - $(".selected-covariates").val("") -}); + $(".select_covariates").click(function () { open_covariate_selection(); }); @@ -475,7 +467,7 @@ edit_data_change = function() { if (is_number(sample_val) && sample_val !== "") { sample_val = parseFloat(sample_val); sample_sets[table].add_value(sample_val); - if (typeof var_nodes !== 'undefined'){ + if (typeof var_nodes === 'undefined'){ sample_var = null; } else { sample_var = var_nodes[_j].childNodes[0].value @@ -498,6 +490,7 @@ edit_data_change = function() { } } } + } update_stat_values(sample_sets); @@ -543,6 +536,24 @@ on_corr_method_change = function() { }; $('select[name=corr_type]').change(on_corr_method_change); +on_dataset_change = function() { + let dataset_type = $('select[name=corr_dataset] option:selected').data('type'); + + if (dataset_type == "mrna_assay"){ + $('#min_expr_filter').show(); + $('#location_filter').show(); + } + else if (dataset_type == "pheno"){ + $('#min_expr_filter').show(); + $('#location_filter').hide(); + } + else { + $('#min_expr_filter').hide(); + $('#location_filter').show(); + } +} +$('select[name=corr_dataset]').change(on_dataset_change); + submit_special = function(url) { $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values())) $("#trait_data_form").attr("action", url); @@ -650,6 +661,8 @@ block_by_attribute_value = function() { this_val_node.value = "x"; } } + + edit_data_change(); }; $('#exclude_by_attr').click(block_by_attribute_value); diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 8e2a23fd..6188c0e7 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -95,14 +95,15 @@ {% elif target_dataset.type == 'Publish' %} <button class="toggle-vis" data-column="3">Abbreviation</button> <button class="toggle-vis" data-column="4">Description</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">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button> - <button class="toggle-vis" data-column="8">N</button> - <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button> - <button class="toggle-vis" data-column="10">Peak LOD</button> - <button class="toggle-vis" data-column="11">Peak Location</button> - <button class="toggle-vis" data-column="12">Effect Size</button> + <button class="toggle-vis" data-column="5">Mean</button> + <button class="toggle-vis" data-column="6">Authors</button> + <button class="toggle-vis" data-column="7">Year</button> + <button class="toggle-vis" data-column="8">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button> + <button class="toggle-vis" data-column="9">N</button> + <button class="toggle-vis" data-column="10">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button> + <button class="toggle-vis" data-column="11">Peak LOD</button> + <button class="toggle-vis" data-column="12">Peak Location</button> + <button class="toggle-vis" data-column="13">Effect Size</button> {% else %} <button class="toggle-vis" data-column="3">Location</button> <button class="toggle-vis" data-column="4">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button> @@ -399,6 +400,13 @@ } }, { + 'title': "Mean", + 'type': "natural-minus-na", + 'width': "40px", + 'data': "mean", + 'orderSequence': [ "desc", "asc"] + }, + { 'title': "Authors", 'type': "natural", 'width': "400px", @@ -514,6 +522,8 @@ } ], {% if target_dataset.type == 'Geno' %} "order": [[6, "asc" ]], + {% elif target_dataset.type == 'Publish' %} + "order": [[10, "asc" ]], {% else %} "order": [[9, "asc" ]], {% endif %} diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index ba72ff27..eaa0c308 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -2,86 +2,85 @@ <div class="col-xs-3 correlation-options"> <div class="form-horizontal section-form-div"> - <div class="form-group"> - <label for="corr_type" class="col-xs-2 control-label">Method</label> - <div class="col-xs-3 controls"> - <select name="corr_type" class="form-control"> - <option value="sample">Sample r</option> - <option value="lit">Literature r</option> - <option value="tissue">Tissue r</option> - </select> - </div> - </div> + <div class="form-group"> + <label for="corr_type" class="col-xs-2 control-label">Method</label> + <div class="col-xs-3 controls"> + <select name="corr_type" class="form-control"> + <option value="sample">Sample r</option> + <option value="lit">Literature r</option> + <option value="tissue">Tissue r</option> + </select> + </div> + </div> - <div class="form-group"> - <label for="corr_dataset" class="col-xs-2 control-label">Database</label> - <div class="col-xs-10 controls"> - <select name="corr_dataset" class="form-control"> - {% for tissue in corr_tools.dataset_menu %} - {% if tissue.tissue %} - <optgroup label="{{ tissue.tissue }} ------"> - {% endif %} - {% for dataset in tissue.datasets %} - <option value="{{ dataset[1] }}" - {% if corr_tools.dataset_menu_selected == dataset[1] %} - selected - {% endif %}> - {{ dataset[0] }} - </option> - {% endfor %} - {% if tissue.tissue %} - </optgroup> - {% endif %} - {% endfor %} - </select> - </div> - </div> + <div class="form-group"> + <label for="corr_dataset" class="col-xs-2 control-label">Database</label> + <div class="col-xs-10 controls"> + <select name="corr_dataset" class="form-control"> + {% for tissue in corr_tools.dataset_menu %} + {% if tissue.tissue %} + <optgroup label="{{ tissue.tissue }} ------"> + {% endif %} + {% for dataset in tissue.datasets %} + <option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}" + {% if corr_tools.dataset_menu_selected == dataset[1] %} + selected + {% endif %}> + {{ dataset[0] }} + </option> + {% endfor %} + {% if tissue.tissue %} + </optgroup> + {% endif %} + {% endfor %} + </select> + </div> + </div> - <div class="form-group"> - <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label> - <div class="col-xs-4 controls"> - <select name="corr_return_results" class="form-control"> - {% for return_result in corr_tools.return_results_menu %} - <option value="{{ return_result }}" - {% if corr_tools.return_results_menu_selected == return_result %} - selected - {% endif %}> - Top {{ return_result }} - </option> - {% endfor %} - </select> - </div> - </div> + <div class="form-group"> + <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label> + <div class="col-xs-4 controls"> + <select name="corr_return_results" class="form-control"> + {% for return_result in corr_tools.return_results_menu %} + <option value="{{ return_result }}" + {% if corr_tools.return_results_menu_selected == return_result %} + selected + {% endif %}> + Top {{ return_result }} + </option> + {% endfor %} + </select> + </div> + </div> - <div class="form-group"> - <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label> - <div class="col-xs-4 controls"> - <select name="corr_samples_group" class="form-control"> - {% for group, pretty_group in sample_group_types.items() %} - <option value="{{ group }}">{{ pretty_group }}</option> - {% endfor %} - </select> - </div> - </div> + <div class="form-group"> + <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label> + <div class="col-xs-4 controls"> + <select name="corr_samples_group" class="form-control"> + {% for group, pretty_group in sample_group_types.items() %} + <option value="{{ group }}">{{ pretty_group }}</option> + {% endfor %} + </select> + </div> + </div> - <div id="corr_sample_method" class="form-group"> - <label for="corr_sample_method" class="col-xs-2 control-label">Type</label> - <div class="col-xs-4 controls"> - <select name="corr_sample_method" class="form-control"> - <option value="pearson">Pearson</option> - <option value="spearman">Spearman Rank</option> - <option value="bicor">Biweight Midcorrelation</option> - </select> - </div> - </div> - {% if dataset.type != "Publish" %} - <div class="form-group"> - <label class="col-xs-2 control-label">Min Expr</label> - <div class="col-xs-4 controls"> - <input name="min_expr" value="" type="text" class="form-control min-expr-field"> - </div> - </div> - <div class="form-group"> + <div id="corr_sample_method" class="form-group"> + <label for="corr_sample_method" class="col-xs-2 control-label">Type</label> + <div class="col-xs-4 controls"> + <select name="corr_sample_method" class="form-control"> + <option value="pearson">Pearson</option> + <option value="spearman">Spearman Rank</option> + <option value="bicor">Biweight Midcorrelation</option> + </select> + </div> + </div> + <div id="min_expr_filter" class="form-group" style="display: {% if dataset.type != 'Geno' %}block{% else %}none{% endif %};"> + <label class="col-xs-2 control-label">Min Expr</label> + <div class="col-xs-4 controls"> + <input name="min_expr" value="" type="text" class="form-control min-expr-field"> + </div> + </div> + <div id="location_filter" class="form-group" style="display: {% if dataset.type != 'Publish' %}block{% else %}none{% endif %};"> <label class="col-xs-2 control-label">Location</label> <div class="col-xs-6 controls"> <span> @@ -91,7 +90,6 @@ <br> </div> </div> - {% endif %} <div class="form-group"> <label class="col-xs-2 control-label">Range</label> <div class="col-xs-5 controls"> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index eca436c6..c42fe4aa 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -74,8 +74,8 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button> - <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button> + <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> </div> <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> {% endif %} @@ -317,8 +317,8 @@ No collections available. Please add traits to a collection to use them as covariates. {% else %} <div class="select-covar-div"> - <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button> - <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button> + <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button> + <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button> </div> <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea> {% endif %} diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py index f25ebc32..bc608e84 100644 --- a/wqflask/wqflask/user_login.py +++ b/wqflask/wqflask/user_login.py @@ -25,7 +25,7 @@ from utility.logger import getLogger logger = getLogger(__name__) from smtplib import SMTP -from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY +from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL THREE_DAYS = 60 * 60 * 24 * 3 @@ -239,7 +239,7 @@ def github_oauth2(): } result = requests.post("https://github.com/login/oauth/access_token", json=data) - result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]} + result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]} github_user = get_github_user_details(result_dict["access_token"]) @@ -277,9 +277,11 @@ def orcid_oauth2(): data = { "client_id": ORCID_CLIENT_ID, "client_secret": ORCID_CLIENT_SECRET, - "grant_type": "authorization_code", + "grant_type": "authorization_code", + "redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2", "code": code } + result = requests.post(ORCID_TOKEN_URL, data=data) result_dict = json.loads(result.text.encode("utf-8")) |