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-rw-r--r--wqflask/base/trait.py17
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py83
-rw-r--r--wqflask/wqflask/static/new/javascript/plotly_probability_plot.js19
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js73
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js2
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html2
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html8
-rw-r--r--wqflask/wqflask/templates/loading.html20
-rw-r--r--wqflask/wqflask/templates/new_security/login_user.html83
-rw-r--r--wqflask/wqflask/templates/search_result_page.html11
-rw-r--r--wqflask/wqflask/views.py10
12 files changed, 194 insertions, 136 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 0527449b..39dd075e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -3,6 +3,7 @@ from __future__ import absolute_import, division, print_function
import string
import resource
import codecs
+import requests
import redis
Redis = redis.StrictRedis()
@@ -120,11 +121,17 @@ class GeneralTrait(object):
@property
def alias_fmt(self):
'''Return a text formatted alias'''
- if self.alias:
- alias = string.replace(self.alias, ";", " ")
- alias = string.join(string.split(alias), ", ")
- else:
- alias = 'Not available'
+
+ alias = 'Not available'
+ if self.symbol:
+ response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol)
+ alias_list = json.loads(response.content)
+ alias = "; ".join(alias_list)
+
+ if alias == 'Not available':
+ if self.alias:
+ alias = string.replace(self.alias, ";", " ")
+ alias = string.join(string.split(alias), ", ")
return alias
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 1dd80962..f1f5840f 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -142,40 +142,6 @@ class ShowTrait(object):
self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
self.z_scores = get_z_scores(self.sample_groups)
- # Todo: Add back in the ones we actually need from below, as we discover we need them
- hddn = OrderedDict()
-
- if self.dataset.group.allsamples:
- hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
-
- hddn['trait_id'] = self.trait_id
- hddn['dataset'] = self.dataset.name
- hddn['temp_trait'] = False
- if self.temp_trait:
- hddn['temp_trait'] = True
- hddn['group'] = self.temp_group
- hddn['species'] = self.temp_species
- hddn['use_outliers'] = False
- hddn['method'] = "gemma"
- hddn['selected_chr'] = -1
- hddn['mapping_display_all'] = True
- hddn['suggestive'] = 0
- hddn['num_perm'] = 0
- hddn['manhattan_plot'] = ""
- hddn['control_marker'] = ""
- if not self.temp_trait:
- if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
- hddn['control_marker'] = self.nearest_marker
- #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
- hddn['do_control'] = False
- hddn['maf'] = 0.05
- hddn['compare_traits'] = []
- hddn['export_data'] = ""
- hddn['export_format'] = "excel"
-
- # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
- self.hddn = hddn
-
self.temp_uuid = uuid.uuid4()
self.sample_group_types = OrderedDict()
@@ -216,18 +182,61 @@ class ShowTrait(object):
sample_column_width = max_samplename_width * 8
- if self.num_values >= 500:
+ if self.num_values >= 5000:
self.maf = 0.01
else:
self.maf = 0.05
trait_symbol = None
+ short_description = None
if not self.temp_trait:
if self.this_trait.symbol:
trait_symbol = self.this_trait.symbol
+ short_description = trait_symbol
+
+ elif self.this_trait.post_publication_abbreviation:
+ short_description = self.this_trait.post_publication_abbreviation
+
+ elif self.this_trait.pre_publication_abbreviation:
+ short_description = self.this_trait.pre_publication_abbreviation
+
+ # Todo: Add back in the ones we actually need from below, as we discover we need them
+ hddn = OrderedDict()
+
+ if self.dataset.group.allsamples:
+ hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
+ hddn['primary_samples'] = string.join(self.primary_sample_names, ',')
+ hddn['trait_id'] = self.trait_id
+ hddn['dataset'] = self.dataset.name
+ hddn['temp_trait'] = False
+ if self.temp_trait:
+ hddn['temp_trait'] = True
+ hddn['group'] = self.temp_group
+ hddn['species'] = self.temp_species
+ hddn['use_outliers'] = False
+ hddn['method'] = "gemma"
+ hddn['selected_chr'] = -1
+ hddn['mapping_display_all'] = True
+ hddn['suggestive'] = 0
+ hddn['num_perm'] = 0
+ hddn['manhattan_plot'] = ""
+ hddn['control_marker'] = ""
+ if not self.temp_trait:
+ if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+ hddn['control_marker'] = self.nearest_marker
+ #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
+ hddn['do_control'] = False
+ hddn['maf'] = 0.05
+ hddn['compare_traits'] = []
+ hddn['export_data'] = ""
+ hddn['export_format'] = "excel"
+
+ # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
+ self.hddn = hddn
js_data = dict(trait_id = self.trait_id,
trait_symbol = trait_symbol,
+ short_description = short_description,
unit_type = trait_units,
dataset_type = self.dataset.type,
data_scale = self.dataset.data_scale,
@@ -396,6 +405,8 @@ class ShowTrait(object):
sample_group_type='primary',
header="%s Only" % (self.dataset.group.name))
self.sample_groups = (primary_samples,)
+
+ self.primary_sample_names = primary_sample_names
self.dataset.group.allsamples = all_samples_ordered
def quantile_normalize_vals(sample_groups):
@@ -493,7 +504,7 @@ def get_genofiles(this_dataset):
return jsondata['genofile']
def get_table_widths(sample_groups, has_num_cases=False):
- stats_table_width = 200
+ stats_table_width = 250
if len(sample_groups) > 1:
stats_table_width = 450
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index a9c5676c..cc4195e4 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -171,22 +171,23 @@
}
var layout = {
- title: js_data.trait_id,
+ title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
margin: {
- l: 65,
+ l: 100,
r: 30,
t: 80,
- b: 80
+ b: 60
},
xaxis: {
- title: "Normal Theoretical Quantiles",
+ title: "<b>Normal Theoretical Quantiles</b>",
range: [first_x, last_x],
zeroline: false,
visible: true,
linecolor: 'black',
linewidth: 1,
titlefont: {
- size: 16
+ family: "arial",
+ size: 20
},
ticklen: 4,
tickfont: {
@@ -194,19 +195,21 @@
}
},
yaxis: {
- title: "Data Quantiles",
+ title: "<b>Data Quantiles</b>",
zeroline: false,
visible: true,
linecolor: 'black',
linewidth: 1,
titlefont: {
- size: 16
+ family: "arial",
+ size: 20
},
ticklen: 4,
tickfont: {
size: 16
},
- tickformat: tick_digits
+ tickformat: tick_digits,
+ automargin: true
},
hovermode: "closest"
}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8366ec0a..48b6da5e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -30,11 +30,11 @@ Stat_Table_Rows = [
}, {
vn: "min",
pretty: "Minimum",
- digits: 2
+ digits: 3
}, {
vn: "max",
pretty: "Maximum",
- digits: 2
+ digits: 3
}
]
@@ -67,7 +67,7 @@ Stat_Table_Rows.push(
digits: 3
}, {
vn: "interquartile",
- pretty: "<font color='blue'>Interquartile Range</font>",
+ pretty: "<font color='black'>Interquartile Range</font>",
url: "http://www.genenetwork.org/glossary.html#Interquartile",
digits: 3
}, {
@@ -334,9 +334,9 @@ update_prob_plot = function() {
make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
if (js_data.trait_symbol != null) {
- header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
} else {
- header = "<thead><tr><th style=\"text-align: center;\" colspan=\"100%\">Trait: " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
}
_ref = js_data.sample_group_types;
for (key in _ref) {
@@ -990,12 +990,13 @@ var hist_trace = {
root.histogram_data = [hist_trace];
root.histogram_layout = {
bargap: 0.05,
- title: js_data.trait_id,
+ title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
xaxis: {
autorange: true,
- title: "Value",
+ title: "<b>Value</b>",
titlefont: {
- size: 16
+ family: "arial",
+ size: 20
},
ticklen: 4,
tickfont: {
@@ -1004,23 +1005,25 @@ root.histogram_layout = {
},
yaxis: {
autorange: true,
- title: "Count",
+ title: "<b>Count</b>",
titlefont: {
- size: 16
+ family: "arial",
+ size: 20
},
showline: true,
ticklen: 4,
tickfont: {
size: 16
- }
+ },
+ automargin: true
},
width: 500,
height: 600,
margin: {
- l: 50,
+ l: 70,
r: 30,
t: 100,
- b: 60
+ b: 50
}
};
@@ -1036,25 +1039,34 @@ $('.histogram_samples_group').change(function() {
});
root.box_layout = {
- title: js_data.trait_id,
xaxis: {
showline: true,
+ titlefont: {
+ family: "arial",
+ size: 20
+ },
tickfont: {
size: 16
},
},
yaxis: {
- title: js_data.unit_type,
+ title: "<b>" + js_data.unit_type +"</b>",
autorange: true,
showline: true,
+ titlefont: {
+ family: "arial",
+ size: 20
+ },
ticklen: 4,
tickfont: {
size: 16
},
- tickformat: tick_digits
+ tickformat: tick_digits,
+ zeroline: false,
+ automargin: true
},
margin: {
- l: 50,
+ l: 90,
r: 30,
t: 30,
b: 80
@@ -1122,7 +1134,7 @@ if (full_sample_lists.length > 1) {
{
type: 'box',
y: get_sample_vals(full_sample_lists[0]),
- name: sample_group_list[0],
+ name: "<b>Trait " + js_data.trait_id + "</b>",
boxpoints: 'Outliers',
jitter: 0.5,
whiskerwidth: 0.2,
@@ -1150,28 +1162,36 @@ $('.box_plot_tab').click(function() {
// Violin Plot
root.violin_layout = {
- title: js_data.trait_id,
xaxis: {
showline: true,
+ titlefont: {
+ family: "arial",
+ size: 20
+ },
tickfont: {
size: 16
}
},
yaxis: {
- title: js_data.unit_type,
+ title: "<b>"+js_data.unit_type+"</b>",
autorange: true,
showline: true,
+ titlefont: {
+ family: "arial",
+ size: 20
+ },
ticklen: 4,
tickfont: {
size: 16
},
tickformat: tick_digits,
- zeroline: false
+ zeroline: false,
+ automargin: true
},
margin: {
- l: 50,
+ l: 90,
r: 30,
- t: 80,
+ t: 30,
b: 80
}
};
@@ -1239,14 +1259,11 @@ if (full_sample_lists.length > 1) {
box: {
visible: true
},
- line: {
- color: 'green',
- },
meanline: {
visible: true
},
- name: sample_group_list[0],
- x0: sample_group_list[0]
+ name: "<b>Trait " + js_data.trait_id + "</b>",
+ x0: "<b>Trait " + js_data.trait_id + "</b>"
}
]
}
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 8001dfc9..8db9522c 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -156,7 +156,7 @@
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', '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']
+ 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
$("#rqtl_geno_compute").on("click", (function(_this) {
return function() {
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 80bbd7f5..2366bdec 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -94,7 +94,7 @@
<form method="get" action="/gsearch">
<div class="row" style="width: 100%; position: absolute; bottom: 0; top: 30px;">
- <select style="width: 170px; margin-top: 15px; margin-left: 10px;" name="type">
+ <select style="width: 150px; margin-top: 15px; margin-left: 20px;" name="type">
<option value="gene">Genes / Molecules</option>
<option value="phenotype" {% if type=="phenotype" %}selected{% endif %}>Phenotypes</option>
</select>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 7e67ece2..34a15c6a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -10,7 +10,7 @@
<div class="container" width="100%">
<h1>Correlation Matrix</h1>
-<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from dark blue to white, while values ranging from -0.4 to -1.0 range from orange to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div>
+<div style="width: 100%; max-width: 850px;">Lower left cells list Pearson product-moment correlations; upper right cells list Spearman rank order correlations. Each cell also contains the n of cases. Values ranging from 0.4 to 1.0 range from orange to white, while values ranging from -0.4 to -1.0 range from dark blue to white. Select any cell to generate a scatter plot. Select trait labels for more information.</div>
<hr style="height: 1px; background-color: #A9A9A9;">
{% if lowest_overlap < 8 %}
<div style="margin-bottom: 10px;"><i><font style="color: red;">Caution</font>: This matrix of correlations contains some cells with small sample sizes of fewer than 8.</i></div>
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 286f6c1f..ed91a886 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -28,7 +28,7 @@
<div class="page-header">
<h1>Select and search</h1>
</div>
- <form method="get" action="/search" name="SEARCHFORM">
+ <form method="get" action="/search" target="_blank" name="SEARCHFORM">
<fieldset>
<div style="padding: 20px" class="form-horizontal">
@@ -199,9 +199,9 @@
<h1>Github</h1>
<ul>
<li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
- <li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>
- <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
<li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
+ <!--<li><a href="https://github.com/genenetwork/gn-docs/wiki">GN2 Document Wiki</a></li>-->
+ <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
</ul>
</div>
</section>
@@ -241,7 +241,7 @@
<h3>GeneNetwork v2:</h3>
<ul>
<li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li>
- <li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>
+ <!--<li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>-->
</ul>
<h3>GeneNetwork v1:</h3>
<ul>
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 25560249..3eb061e5 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -7,10 +7,24 @@
<div class="container">
<div>
<div style="min-height: 80vh; display: flex; align-items: center;">
- <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
+ <div style="margin-bottom: 5px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
+ {% if start_vars.tool_used == "Mapping" %}
+ <h1>Computing the Map</h1>
+ <br>
+ <i>n</i> = {{ start_vars.num_vals }}
+ <br>
+ Method = {{ start_vars.method }}
+ <br>
+ {% if start_vars.transform != "" %}
+ transform = {{ start_vars.transform }}
+ <br>
+ {% endif %}
+ MAF = {{ start_vars.maf }}
+ {% else %}
<h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
+ {% endif %}
</div>
- <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
+ <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>
@@ -22,5 +36,5 @@
<script type="text/javascript">
$("#loading_form").attr("action", "{{ start_vars.form_url }}");
-$("#loading_form").submit();
+setTimeout(function(){ $("#loading_form").submit()}, 350);
</script> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 27b20ebf..c9aaf028 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -2,53 +2,11 @@
{% block title %}Register{% endblock %}
{% block content %}
- <div class="container">
+ <div class="container" style="min-width: 1250px;">
{{ flash_me() }}
- <div class="page-header">
- <h1>&nbsp;&nbsp;&nbsp;&nbsp;Login</h1>
- </div>
-
-
- <div class="security_box">
-
- <h4>Don't have an account?</h4>
-
- {% if es_server: %}
- <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
- {% else: %}
- <div class="alert alert-warning">
- <p>You cannot create an account at this moment.<br />
- Please try again later.</p>
- </div>
- {% endif %}
-
- <hr />
- <h4>Login with external services</h4>
-
- {% if external_login: %}
- <div>
- {% if external_login["github"]: %}
- <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
- {% else %}
- <p>Github login is not available right now</p>
- {% endif %}
-
- {% if external_login["orcid"]: %}
- <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
- {% else %}
- <p>ORCID login is not available right now</p>
- {% endif %}
- </div>
- {% else: %}
- <div class="alert alert-warning">
- <p>Sorry, you cannot login with Github or ORCID at this time.</p>
- </div>
- {% endif %}
- <hr />
-
- <h4>Already have an account? Sign in here.</h4>
+ <h4>Already have an account? Sign in here.</h4>
{% if es_server: %}
<form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm">
@@ -69,7 +27,6 @@
</div>
</div>
-
<div class="form-group">
<label class="col-xs-1 control-label" for="remember"></label>
<div style="margin-left:20px;" class="col-xs-4 controls">
@@ -87,6 +44,42 @@
</div>
</fieldset>
+ <div class="security_box">
+
+ <h4>Don't have an account?</h4>
+
+ {% if es_server: %}
+ <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
+ {% else: %}
+ <div class="alert alert-warning">
+ <p>You cannot create an account at this moment.<br />
+ Please try again later.</p>
+ </div>
+ {% endif %}
+
+ <hr />
+ <h4>Login with external services</h4>
+
+ {% if external_login: %}
+ <div>
+ {% if external_login["github"]: %}
+ <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
+ {% else %}
+ <p>Github login is not available right now</p>
+ {% endif %}
+
+ {% if external_login["orcid"]: %}
+ <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
+ {% else %}
+ <p>ORCID login is not available right now</p>
+ {% endif %}
+ </div>
+ {% else: %}
+ <div class="alert alert-warning">
+ <p>Sorry, you cannot login with Github or ORCID at this time.</p>
+ </div>
+ {% endif %}
+
</form>
{% else: %}
<div class="alert alert-warning">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f5978196..2dded69f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -13,7 +13,7 @@
<div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
<!-- Need to customize text more for other types of searches -->
- <p>We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+ <p><b>Search Results:</b> We searched <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
to find all records
{% for word in search_terms %}
{% if word.key|lower == "rif" %}
@@ -249,6 +249,7 @@
'columns': [
{
'data': null,
+ 'width': "30px",
'orderDataType': "dom-checkbox",
'orderSequence': [ "desc", "asc"],
'render': function(data, type, row, meta) {
@@ -258,12 +259,14 @@
{
'title': "Index",
'type': "natural",
+ 'width': "30px",
'data': "index"
},
{
'title': "Record",
'type': "natural",
'data': null,
+ 'width': "60px",
'orderDataType': "dom-inner-text",
'render': function(data, type, row, meta) {
return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
@@ -277,7 +280,6 @@
{
'title': "Description",
'type': "natural",
- 'width': "300px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -290,12 +292,13 @@
{
'title': "Location",
'type': "natural",
- 'width': "140px",
+ 'width': "120px",
'data': "location"
},
{
'title': "Mean",
'type': "natural",
+ 'width': "40px",
'data': "mean",
'orderSequence': [ "desc", "asc"]
},
@@ -308,7 +311,7 @@
{
'title': "Max LRS Location",
'type': "natural",
- 'width': "140px",
+ 'width': "120px",
'data': "lrs_location"
},
{
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fe858d52..7b585b03 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -560,6 +560,7 @@ 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
if 'wanted_inputs' in initial_start_vars:
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
@@ -567,6 +568,15 @@ def loading_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
+ if 'primary_samples' in start_vars:
+ samples = start_vars['primary_samples'].split(",")
+ for sample in samples:
+ value = start_vars.get('value:' + sample)
+ if value != "x":
+ num_vals += 1
+
+ start_vars['num_vals'] = num_vals
+
start_vars_container['start_vars'] = start_vars
else:
start_vars_container['start_vars'] = initial_start_vars