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authorZachary Sloan2013-10-15 15:06:36 -0500
committerZachary Sloan2013-10-15 15:06:36 -0500
commita823e66f8dc742e1608b3e0db6d521d5f63b641a (patch)
tree7e6a52af9b5c78a290329d33ce8df4777a603f26 /wqflask
parent34c6c908ac072609a2f923946d474504d3fa0331 (diff)
downloadgenenetwork2-a823e66f8dc742e1608b3e0db6d521d5f63b641a.tar.gz
Changed templates to call the header macro
Correlation page now works with Non-BXD (or whatever group) or All Samples options
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py14
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py4
-rw-r--r--wqflask/wqflask/templates/base.html4
-rw-r--r--wqflask/wqflask/templates/correlation_page.html8
-rw-r--r--wqflask/wqflask/templates/index_page.html2
-rw-r--r--wqflask/wqflask/templates/marker_regression.html10
-rw-r--r--wqflask/wqflask/templates/quick_search.html11
-rw-r--r--wqflask/wqflask/templates/search_result_page.html10
-rw-r--r--wqflask/wqflask/templates/show_trait.html11
9 files changed, 24 insertions, 50 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 9fa7beb3..f25e7974 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -322,7 +322,7 @@ class DatasetGroup(object):
self.incparentsf1 = 0
self.genotype = genotype_1
- self.samplelist = list(genotype.prgy)
+ self.samplelist = list(self.genotype.prgy)
#class DataSets(object):
@@ -440,10 +440,12 @@ class DataSet(object):
def get_trait_data(self, sample_list=None):
if sample_list:
- self.samplelist = sample_list + self.group.parlist + self.group.f1list
+ self.samplelist = sample_list
else:
- self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
-
+ self.samplelist = self.group.samplelist
+
+ if (self.group.parlist + self.group.f1list) in self.samplelist:
+ self.samplelist += self.group.parlist + self.group.f1list
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
@@ -503,8 +505,8 @@ class DataSet(object):
and {}Freeze.Name = '{}'
and {}.Id = {}XRef.{}Id
order by {}.Id
- """.format(*mescape(self.type, self.type, self.type, self.type,
- self.name, dataset_type, self.type, self.type, dataset_type))
+ """.format(*mescape(self.type, self.type, self.type, self.name,
+ dataset_type, self.type, dataset_type, dataset_type))
else:
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index a5c80674..8f23165c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -178,10 +178,10 @@ class CorrelationResults(object):
trait_object.lit_corr = lit_corr_data[trait][1]
self.correlation_results.append(trait_object)
- if self.corr_type != "lit":
+ if self.corr_type != "lit" and self.dataset.type == "ProbeSet":
self.do_lit_correlation_for_trait_list()
- if self.corr_type != "tissue":
+ if self.corr_type != "tissue" and self.dataset.type == "ProbeSet":
self.do_tissue_correlation_for_trait_list()
#print("self.correlation_results: ", pf(self.correlation_results))
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 8efba6a7..a14eeb44 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -29,9 +29,9 @@
{% macro header(main, second) %}
<header class="jumbotron subhead" id="overview">
<div class="container">
- <h1>Login</h1>
+ <h1>{{ main }}</h1>
<p class="lead">
- Gain access to GeneNetwork.
+ {{ second }}
</p>
</div>
</header>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 4d09cf20..7e149506 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -6,12 +6,8 @@
<link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
{% endblock %}
{% block content %}
-
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>Correlation</h1>
- </div>
- </header>
+
+ {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }}
<table id="corr_results" class="table table-hover table-striped table-bordered">
<thead>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 98682e57..d177a7bd 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -3,8 +3,6 @@
{% block content %}
<!-- Start of body -->
-
-
<header class="jumbotron subhead" id="overview">
<div class="container">
<h1>GeneNetwork</h1>
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 9260acab..64d2e9b7 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -9,14 +9,8 @@
{% endblock %}
{% block content %} <!-- Start of body -->
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>Marker Regression</h1>
- <p class="lead">
- {{ this_trait.name }}: {{ this_trait.description_fmt }}
- </p>
- </div>
- </header>
+ {{ header("Marker Regression",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
<div class="container">
<div>
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index b0e38708..2f268c5a 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -2,14 +2,9 @@
{% block title %}QuickSearch Results{% endblock %}
{% block content %}
<!-- Start of body -->
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>QuickSearch Results</h1>
- <p class="lead">
- GeneNetwork found {{ numify(results|count, "record", "records") }}.
- </p>
- </div>
- </header>
+
+ {{ header("QuickSearch Results",
+ 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
<div class="container">
<div class="page-header">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 11f68bba..1fe7cce9 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,14 +2,8 @@
{% block title %}Search Results{% endblock %}
{% block content %}
<!-- Start of body -->
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>Search Results</h1>
- <p class="lead">
- GeneNetwork found {{ numify(results|count, "record", "records") }}.
- </p>
- </div>
- </header>
+ {{ header("Search Results",
+ 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
<div class="container">
<div class="page-header">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 799245c3..e3c84de7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -7,14 +7,9 @@
{% endblock %}
{% block content %} <!-- Start of body -->
- <header class="jumbotron subhead" id="overview">
- <div class="container">
- <h1>{{ this_trait.symbol}}</h1>
- <p class="lead">
- {{ this_trait.name }}: {{ this_trait.description_fmt }}
- </p>
- </div>
- </header>
+ {{ header("{}".format(this_trait.symbol),
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
<form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
class="form-horizontal">