From cef130716782cf5c06453705bee7ab6aed1dcce0 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 29 Jun 2020 12:19:23 -0500 Subject: Change that hopefully fixes some encoding stuff --- wqflask/base/trait.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7fc016f3..5903fb08 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -6,6 +6,7 @@ import resource import codecs import requests import random +import urllib from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData @@ -144,6 +145,7 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" + return formatted @property @@ -474,9 +476,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.haveinfo = True for i, field in enumerate(dataset.display_fields): - holder = trait_info[i] - #if isinstance(trait_info[i], basestring): - # holder = holder.encode('latin1') + holder = trait_info[i] + if isinstance(trait_info[i], basestring): + holder = holder.encode('latin1') setattr(trait, field, holder) if dataset.type == 'Publish': -- cgit v1.2.3 From f1a539098884eb99191809dac7fba823872270ae Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 29 Jun 2020 12:45:47 -0500 Subject: Loading screen should now show correct N when re-mapping or zooming into a map --- wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +- wqflask/wqflask/marker_regression/run_mapping.py | 5 ++++- wqflask/wqflask/templates/loading.html | 2 +- wqflask/wqflask/templates/mapping_results.html | 4 ++-- wqflask/wqflask/views.py | 12 ++++++------ 5 files changed, 14 insertions(+), 11 deletions(-) diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 74fa4329..89f56c30 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -147,7 +147,7 @@ class DisplayMappingResults(object): self.dataset = start_vars['dataset'] self.this_trait = start_vars['this_trait'] - self.n_samples = start_vars['num_vals'] + self.n_samples = start_vars['n_samples'] self.species = start_vars['species'] self.genofile_string = "" if 'genofile_string' in start_vars: diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c859fdaa..c9d10f7c 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -124,7 +124,10 @@ class RunMapping(object): self.samples.append(sample) self.vals.append(value) - self.num_vals = len(self.vals) + if 'n_samples' in start_vars: + self.n_samples = start_vars['n_samples'] + else: + self.n_samples = len([val for val in self.vals if val != "x"]) #ZS: Check if genotypes exist in the DB in order to create links for markers diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index 49bcbff7..15ab4080 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -11,7 +11,7 @@ {% if start_vars.tool_used == "Mapping" %}

Computing the Maps


- n = {{ start_vars.num_vals }} + n = {{ start_vars.n_samples }}
Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index c5d49168..132d5249 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -35,7 +35,7 @@ {% for sample in samples %} {% endfor %} - + @@ -435,7 +435,7 @@ 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', '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', 'num_vals'] + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples'] $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 80164a22..131345d3 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -630,7 +630,7 @@ def loading_page(): logger.info(request.url) initial_start_vars = request.form start_vars_container = {} - num_vals = 0 #ZS: So it can be displayed on loading page + n_samples = 0 #ZS: So it can be displayed on loading page if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} @@ -638,8 +638,8 @@ def loading_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - if 'num_vals' in start_vars: - num_vals = int(start_vars['num_vals']) + if 'n_samples' in start_vars: + n_samples = int(start_vars['n_samples']) else: if 'group' in start_vars: dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group']) @@ -658,9 +658,9 @@ def loading_page(): for sample in samples: value = start_vars.get('value:' + sample) if value != "x": - num_vals += 1 + n_samples += 1 - start_vars['num_vals'] = num_vals + start_vars['n_samples'] = n_samples start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs'] start_vars_container['start_vars'] = start_vars @@ -730,7 +730,7 @@ def mapping_results_page(): 'mapmodel_rqtl_geno', 'temp_trait', 'reaper_version', - 'num_vals', + 'n_samples', 'transform' ) start_vars = {} -- cgit v1.2.3 From b7d3b90bb9a074200e440eaeb22b782053efc819 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 29 Jun 2020 12:55:13 -0500 Subject: Fixed remaining issue with the logic for creating the type dropdown option groups for the home page search --- wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js index d5711f6d..d172907a 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -119,6 +119,9 @@ redo_dropdown = function(dropdown, items) { _results.push(dropdown.append(this_opt_group)) this_opt_group = $("") this_opt_group.append($("