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authorzsloan2019-03-07 17:14:56 -0600
committerzsloan2019-03-07 17:14:56 -0600
commit9769245cf3595273055d686a689cdcecb4b3645a (patch)
treecedc6d91e4c366fee5357d94db248d55e234bbfb /wqflask
parent44f1f0d9ce426d7241356b6e6b17223854e4f10c (diff)
downloadgenenetwork2-9769245cf3595273055d686a689cdcecb4b3645a.tar.gz
Changed the way covariates are displayed when selected for mapping
Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/trait.py4
-rw-r--r--wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js17
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js2
-rw-r--r--wqflask/wqflask/templates/show_trait_transform_and_filter.html1
4 files changed, 19 insertions, 5 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 9f76306f..79aa196f 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -220,6 +220,7 @@ def jsonable(trait):
dataset=dataset.name,
dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
@@ -232,6 +233,7 @@ def jsonable(trait):
dataset=dataset.name,
dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
lrs_score=trait.LRS_score_repr,
@@ -397,6 +399,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if trait.confidential:
+ trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
#if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -406,6 +409,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#
# description = self.pre_publication_description
else:
+ trait.abbreviation = trait.post_publication_abbreviation
if description:
trait.description_display = description.strip()
else:
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index fc6e5a78..8cd6dac3 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -81,17 +81,22 @@ submit_click = function() {
$('#collections_holder').find('input[type=checkbox]:checked').each(function() {
var this_dataset, this_trait;
this_trait = $(this).parents('tr').find('.trait').text();
+ this_trait_display = $(this).parents('tr').find('.trait').data("display_name");
this_description = $(this).parents('tr').find('.description').text();
- console.log("this_trait is:", this_trait);
+ console.log("this_trait is:", this_trait_display);
this_dataset = $(this).parents('tr').find('.dataset').data("dataset");
console.log("this_dataset is:", this_dataset);
covariates_string += this_trait + ":" + this_dataset + ","
- this_covariate_display_string = this_trait + ": " + this_description
+ //this_covariate_display_string = this_trait + ": " + this_description
+ this_covariate_display_string = this_trait_display
if (this_covariate_display_string.length > 50) {
this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..."
}
covariates_display_string += this_covariate_display_string + "\n"
});
+ // Trim the last newline from display_string
+ covariates_display_string = covariates_display_string.replace(/\n$/, "")
+
// Trim the last comma
covariates_string = covariates_string.substring(0, covariates_string.length - 1)
//covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
@@ -189,7 +194,13 @@ process_traits = function(trait_data, textStatus, jqXHR) {
trait = trait_data[_i];
the_html += "<tr class='trait_line'>";
the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>";
- the_html += "<td class='trait'>" + trait.name + "</td>";
+ if ("abbreviation" in trait) {
+ the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>";
+ } else if ("symbol" in trait) {
+ the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>";
+ } else {
+ the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>";
+ }
the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>";
the_html += "<td class='description'>" + trait.description + "</td>";
}
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 2ab87d03..28af232d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -225,7 +225,7 @@
};
})(this));
- $("#interval_mapping_compute").on("mouseover", (function(_this) {
+ $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
return function() {
if ($(".outlier").length && $(".outlier-alert").length < 1) {
return showalert(outlier_text, "alert-success outlier-alert");
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 6803da58..94b3fda3 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,6 +1,5 @@
<div>
<div class="form-horizontal">
- <legend>Block samples</legend>
<p>Edit or delete values in the Trait Data boxes, and use the
<strong>Reset</strong> option as
needed.