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-rw-r--r--wqflask/base/data_set.py34
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py11
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/docs.py4
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html2
-rw-r--r--wqflask/wqflask/templates/correlation_page.html12
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html10
-rw-r--r--wqflask/wqflask/views.py4
8 files changed, 26 insertions, 53 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index afffe780..e0ef559c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1173,40 +1173,6 @@ class TempDataSet(DataSet):
self.fullname = 'Temporary Storage'
self.shortname = 'Temp'
- @staticmethod
- def handle_pca(desc):
- if 'PCA' in desc:
- # Todo: Modernize below lines
- desc = desc[desc.rindex(':')+1:].strip()
- else:
- desc = desc[:desc.index('entered')].strip()
- return desc
-
- def get_desc(self):
- query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
- logger.sql(query)
- g.db.execute(query)
- desc = g.db.fetchone()[0]
- desc = self.handle_pca(desc)
- return desc
-
- def retrieve_sample_data(self, trait):
- query = """
- SELECT
- Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
- FROM
- TempData, Temp, Strain
- WHERE
- TempData.StrainId = Strain.Id AND
- TempData.Id = Temp.DataId AND
- Temp.name = '%s'
- Order BY
- Strain.Name
- """ % escape(trait.name)
-
- logger.sql(query)
- results = g.db.execute(query).fetchall()
-
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..0f3d455c 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,8 +17,15 @@ class CorrScatterPlot(object):
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
- self.dataset_1 = data_set.create_dataset(params['dataset_1'])
- self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+ if "Temp" in params['dataset_1']:
+ self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+ else:
+ self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+ if "Temp" in params['dataset_2']:
+ self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+ else:
+ self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+
#self.dataset_3 = data_set.create_dataset(params['dataset_3'])
self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..3beee84f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -147,7 +147,7 @@ class CorrelationMatrix(object):
if num_overlap < self.lowest_overlap:
self.lowest_overlap = num_overlap
- if num_overlap == 0:
+ if num_overlap < 2:
corr_result_row.append([target_trait, 0, num_overlap])
pca_corr_result_row.append(0)
else:
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..9fad1cf1 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,7 +11,7 @@ class Docs(object):
def __init__(self, entry, start_vars={}):
sql = """
- SELECT Docs.title, Docs.content
+ SELECT Docs.title, CAST(Docs.content AS BINARY)
FROM Docs
WHERE Docs.entry LIKE %s
"""
@@ -22,7 +22,7 @@ class Docs(object):
self.content = ""
else:
self.title = result[0]
- self.content = result[1].encode("latin1")
+ self.content = result[1]
self.editable = "false"
# ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9b96de1c..d556f31a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -51,7 +51,7 @@
{% if result[0].name == trait.name and result[0].dataset == trait.dataset %}
<td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td>
{% else %}
- <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+ <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
{% endif %}
{% endfor %}
</tr>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index bb2a697f..fb218e29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -144,7 +144,7 @@
<td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
<td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
<td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
- <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+ <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
<td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
<td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
{% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -164,15 +164,15 @@
<td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
{% elif target_dataset.type == "Publish" %}
{% if trait.abbreviation %}
- <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
+ <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td>
{% else %}
- <TD data-export="N/A">N/A</TD>
+ <td data-export="N/A">N/A</td>
{% endif %}
<td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
{% if trait.authors %}
<td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
{% else %}
- <TD data-export="N/A">N/A</TD>
+ <td data-export="N/A">N/A</td>
{% endif %}
<td data-export="{{ trait.pubmed_text }}">
{% if trait.pubmed_text != "N/A" %}
@@ -183,7 +183,7 @@
{{ trait.pubmed_text }}
{% endif %}
</td>
- <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+ <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
<td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
<td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
<td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
@@ -191,7 +191,7 @@
<td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
{% elif target_dataset.type == "Geno" %}
<td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD>
- <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+ <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
<td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
<td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
{% endif %}
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 06b71f53..6b3bec9a 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -17,13 +17,13 @@
</header>
-->
- <div class="container-fluid" style="min-width: 1200px;">
+ <div class="container-fluid" style="min-width: 1210px;">
{{ flash_me() }}
<div class="row" style="width: 100%;">
- <div class="col-xs-5" style="min-width: 530px; max-width: 550px;">
+ <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
<section id="search">
<div>
<h1>Select and search</h1>
@@ -84,7 +84,7 @@
<label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
<div class="col-xs-10 controls" style="padding-left: 20px;">
<div class="col-8">
- <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+ <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
</div>
</div>
</div>
@@ -105,7 +105,7 @@
<label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
<div class="col-xs-10 controls" style="padding-left: 20px;">
<div class="col-8">
- <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+ <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
</div>
</div>
</div>
@@ -184,7 +184,7 @@
</section>
</div>
- <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;">
+ <div class="col-xs-4" style="width: 600px !important;">
<section id="affiliates">
<div class="page-header">
<h1>Affiliates</h1>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 42a10c7a..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -50,7 +50,7 @@ from wqflask.search_results import SearchResultPage
from wqflask.export_traits import export_search_results_csv
from wqflask.gsearch import GSearch
from wqflask.update_search_results import GSearch as UpdateGSearch
-from wqflask.docs import Docs
+from wqflask.docs import Docs, update_text
from wqflask.db_info import InfoPage
from utility import temp_data
@@ -350,7 +350,7 @@ def environments():
@app.route("/update_text", methods=('POST',))
def update_page():
- docs.update_text(request.form)
+ update_text(request.form)
doc = Docs(request.form['entry_type'], request.form)
return render_template("docs.html", **doc.__dict__)
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-13 06:49:33 +0000