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-rw-r--r--wqflask/wqflask/show_trait/show_trait.py3
-rw-r--r--wqflask/wqflask/templates/loading.html98
-rw-r--r--wqflask/wqflask/templates/mapping_results.html3
3 files changed, 56 insertions, 48 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index fcebbc4d..b6fcbcb8 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -263,6 +263,9 @@ class ShowTrait:
hddn['temp_trait'] = True
hddn['group'] = self.temp_group
hddn['species'] = self.temp_species
+ else:
+ hddn['group'] = self.dataset.group.name
+ hddn['species'] = self.dataset.group.species
hddn['use_outliers'] = False
hddn['method'] = "gemma"
hddn['selected_chr'] = -1
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 124f0608..95cecf76 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -7,56 +7,60 @@
{% endfor %}
<div class="container">
<div>
- <div style="min-height: 80vh; display: flex; align-items: center; text-align: center;">
+ <div style="min-height: 80vh; display: flex; align-items: center; text-align: left;">
<div style="margin-bottom: 5px; left: 50%; margin-right: -50%; margin-top: 10%; transform: translate(-50%, -50%); position: absolute;">
- {% if start_vars.tool_used == "Mapping" %}
- <h1>Computing the Maps</h1>
- <br>
- <i>n</i> = {{ start_vars.n_samples }}
- <br>
- Method = {% if start_vars.method == "gemma" %}GEMMA {% if start_vars.use_loco == "True" %}using LOCO {% endif %}{% else %}{{ start_vars.method }}{% endif %}
- <br>
- {% set genofile_desc = start_vars.genofile.split(":")[1] %}
- Genotype File = {{ genofile_desc }}
- {% if start_vars.num_perm | int > 0 %}
- <br>
- # Permutations = {{ start_vars.num_perm }}
- {% endif %}
- {% if start_vars.num_bootstrap | int > 0 %}
- <br>
- # Bootstrap = {{ start_vars.num_bootstrap }}
- {% endif %}
- {% if start_vars.transform != "" %}
- <br>
- transform = {{ start_vars.transform }}
- {% endif %}
- {% if start_vars.maf != "" and start_vars.method != "reaper" %}
- <br>
- MAF >= {{ start_vars.maf }}
- {% endif %}
- {% if start_vars.covariates != "" and start_vars.method != "reaper" %}
- <br>
- {% set covariate_list = start_vars.covariates.split(",") %}
- Trait Covariates: {% for covariate in covariate_list %}{% set this_covariate = covariate.split(":")[0] %}{{ this_covariate }}{% if not loop.last %}, {% endif %}{% endfor %}
- {% endif %}
- {% if start_vars.control_marker != "" and start_vars.do_control == "true" and start_vars.method != "gemma" %}
- <br>
- Marker Covariate: {{ start_vars.control_marker }}
- {% endif %}
- {% else %}
- <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
- {% endif %}
- <br><br>
- <img align="center" src="/static/gif/89.gif">
- </div>
- <!--<div style="margin-left: auto; margin-right: auto; display: block; width: 50%; top:50%;">
+ {% if start_vars.tool_used == "Mapping" %}
+ <h1>Computing the Maps</h1>
+ <br>
+ <b>Trait Metadata</b>
+ <br>
+ species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b>
+ <br>
+ group = <b><i>{{ start_vars.group[0] | upper }}{{ start_vars.group[1:] }}</i></b>
+ <br>
+ trait identifier = <b><i>{{ start_vars.trait_id }}</i></b>
+ <br>
+ n of sample = <b><i>{{ start_vars.n_samples }}</i></b>
+ {% if start_vars.transform != "" %}
+ <br>
+ transformation = <b><i>{{ start_vars.transform }}</i></b>
+ {% endif %}
+ <br><br>
+ <b>Mapping Metadata</b>
+ <br>
+ mapping method = <b><i>{% if start_vars.method == "gemma" %}GEMMA {% if start_vars.use_loco == "True" %}using LOCO {% endif %}{% else %}{{ start_vars.method }}{% endif %}</i></b>
+ {% if start_vars.maf != "" and start_vars.method != "reaper" %}
+ <br>
+ minor allele frequency lower limit = <b><i>{{ start_vars.maf }}</i></b>
+ {% endif %}
+ {% if start_vars.covariates != "" and start_vars.method != "reaper" %}
+ <br>
+ {% set covariate_list = start_vars.covariates.split(",") %}
+ cofactors = <b><i>{% for covariate in covariate_list %}{% set this_covariate = covariate.split(":")[0] %}{{ this_covariate }}{% if not loop.last %}, {% endif %}{% endfor %}</i></b>
+ {% endif %}
+ {% if start_vars.control_marker != "" and start_vars.do_control == "true" and start_vars.method != "gemma" %}
+ <br>
+ marker covariate = <b><i>{{ start_vars.control_marker }}</i></b>
+ {% endif %}
+ {% set genofile_desc = start_vars.genofile.split(":")[1] %}
+ <br>
+ Genotype File = <b><i>{{ genofile_desc }}</i></b>
+ {% if start_vars.num_perm | int > 0 and start_vars.method != "gemma" %}
+ <br>
+ n of permutations = <b><i>{{ start_vars.num_perm }}</i></b>
+ {% endif %}
+ {% if start_vars.num_bootstrap | int > 0 and start_vars.method == "reaper" %}
+ <br>
+ n of bootstrap = <b><i>{{ start_vars.num_bootstrap }}</i></b>
+ {% endif %}
+ {% else %}
+ <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
+ {% endif %}
+ <br><br>
+ <div style="text-align: center;">
<img align="center" src="/static/gif/89.gif">
- </div>-->
- <!--
- <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
- <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+ </div>
</div>
- -->
</div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index f054506c..73d7501b 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -17,8 +17,9 @@
<input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
{% if temp_trait is defined %}
<input type="hidden" name="temp_trait" value="{{ temp_trait }}">
- <input type="hidden" name="group" value="{{ group }}">
{% endif %}
+ <input type="hidden" name="group" value="{{ dataset.group.name }}">
+ <input type="hidden" name="species" value="{{ dataset.group.species }}">
<input type="hidden" name="trait_id" value="{{ this_trait.name }}">
<input type="hidden" name="dataset" value="{{ dataset.name }}">
<input type="hidden" name="genofile" value="{{ genofile_string }}">