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-rw-r--r--scripts/add_missing_columns.sh24
-rw-r--r--wqflask/utility/tools.py2
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py81
-rw-r--r--wqflask/wqflask/templates/admin/group_manager.html3
-rw-r--r--wqflask/wqflask/templates/collections/list.html4
-rw-r--r--wqflask/wqflask/templates/collections/view.html4
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html2
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html4
-rw-r--r--wqflask/wqflask/templates/correlation_page.html4
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html4
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html4
-rw-r--r--wqflask/wqflask/templates/mapping_results.html4
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html4
-rw-r--r--wqflask/wqflask/templates/search_error.html2
-rw-r--r--wqflask/wqflask/templates/search_result_page.html4
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
-rw-r--r--wqflask/wqflask/templates/snp_browser.html2
17 files changed, 121 insertions, 33 deletions
diff --git a/scripts/add_missing_columns.sh b/scripts/add_missing_columns.sh
new file mode 100644
index 00000000..70d5fdeb
--- /dev/null
+++ b/scripts/add_missing_columns.sh
@@ -0,0 +1,24 @@
+ #! /bin/bash
+ #
+ # Add missing columns to test db downloaded from:
+ # https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip
+
+ QUERY="
+ ALTER TABLE InbredSet
+ ADD Family varchar(20) AFTER FullName,
+ ADD FamilyOrder varchar(20) AFTER Family,
+ ADD MenuOrderId smallint(6) AFTER FamilyOrder,
+ ADD InbredSetCode varchar(5) AFTER MenuOrderId;
+
+ ALTER TABLE PublishXRef
+ ADD mean double AFTER DataId;
+
+ -- This takes some time
+ ALTER TABLE ProbeSet
+ ADD UniProtID varchar(20) AFTER ProteinName;
+ "
+
+ USER=gn2
+ DBNAME=db_webqtl_s
+ PASS=mysql_password
+ mysql -u"$USER" -p"$PASS" -h localhost -D "$DBNAME" -e "$QUERY"
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 2914d354..89d88516 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -292,7 +292,7 @@ JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
assert_dir(JS_GUIX_PATH)
assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
-CSS_PATH = "UNKNOWN"
+CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
# assert_dir(JS_PATH)
JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index ecce9a07..e4a4d127 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -10,10 +10,29 @@ from base.trait import GeneralTrait
from base.data_set import create_dataset
from utility import webqtlUtil
from utility.tools import locate, TEMPDIR
+from flask import g
import utility.logger
logger = utility.logger.getLogger(__name__ )
+# Get a trait's type (numeric, categorical, etc) from the DB
+def get_trait_data_type(trait_db_string):
+ logger.info("get_trait_data_type");
+ the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
+ logger.info("the_query done");
+ results_json = g.db.execute(the_query).fetchone()
+ logger.info("the_query executed");
+ results_ob = json.loads(results_json[0])
+ logger.info("json results loaded");
+ if trait_db_string in results_ob:
+ logger.info("found");
+ return results_ob[trait_db_string]
+ else:
+ logger.info("not found");
+ return "numeric"
+
+
+# Run qtl mapping using R/qtl
def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
logger.info("Start run_rqtl_geno");
## Get pointers to some common R functions
@@ -71,7 +90,8 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
logger.info("Marker covars done");
if cofactors != "":
- cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
+ logger.info("Cofactors: " + cofactors);
+ cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
@@ -80,7 +100,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
#logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
- #ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
if pair_scan:
if do_control == "true":
logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
@@ -225,6 +244,34 @@ def add_phenotype(cross, pheno_as_string, col_name):
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
return ro.r["the_cross"]
+def add_categorical_covar(cross, covar_as_string, i):
+ ro.globalenv["the_cross"] = cross
+ logger.info("cross set");
+ ro.r('covar <- as.factor(' + covar_as_string + ')')
+ logger.info("covar set");
+ ro.r('newcovar <- model.matrix(~covar-1)')
+ logger.info("model.matrix finished");
+ ro.r('cat("new covar columns", ncol(newcovar), "\n")')
+ nCol = ro.r('ncol(newcovar)')
+ logger.info("ncol covar done: " + str(nCol[0]));
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ logger.info("pheno pulled from cross");
+ nCol = int(nCol[0])
+ logger.info("nCol python int:" + str(nCol));
+ col_names = []
+ #logger.info("loop")
+ for x in range(1, (nCol+1)):
+ #logger.info("loop" + str(x));
+ col_name = "covar_" + str(i) + "_" + str(x)
+ #logger.info("col_name" + col_name);
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])')
+ col_names.append(col_name)
+ #logger.info("loop" + str(x) + "done");
+
+ logger.info("returning from add_categorical_covar");
+ return ro.r["the_cross"], col_names
+
+
def add_names(cross, names_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
@@ -243,6 +290,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covariate_list = covariates.split(",")
covar_name_string = "c("
for i, covariate in enumerate(covariate_list):
+ logger.info("Covariate: " + covariate);
this_covar_data = []
covar_as_string = "c("
trait_name = covariate.split(":")[0]
@@ -270,18 +318,33 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_as_string += ")"
- col_name = "covar_" + str(i)
- cross = add_phenotype(cross, covar_as_string, col_name)
+ datatype = get_trait_data_type(covariate)
+ logger.info("Covariate: " + covariate + " is of type: " + datatype);
+ if(datatype == "categorical"): # Cat variable
+ logger.info("call of add_categorical_covar");
+ cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
+ logger.info("add_categorical_covar returned");
+ for z, col_name in enumerate(col_names): # Go through the additional covar names
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ if(z < (len(col_names) -1)):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
- if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
+ logger.info("covar_name_string:" + covar_name_string);
else:
+ col_name = "covar_" + str(i)
+ cross = add_phenotype(cross, covar_as_string, col_name)
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
covar_name_string += '"' + col_name + '"'
covar_name_string += ")"
-
+ logger.info("covar_name_string:" + covar_name_string);
covars_ob = pull_var("trait_covars", cross, covar_name_string)
-
return cross, covars_ob
def create_marker_covariates(control_marker, cross):
@@ -294,7 +357,7 @@ def create_marker_covariates(control_marker, cross):
ro.r('covnames <- covnames[covInGeno]')
ro.r("cat('covnames (purged): ', covnames,'\n')")
ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
-
+ # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
def process_pair_scan_results(result):
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index 50c2a42c..ac5c1350 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -77,7 +77,8 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 3829b950..c8705c7d 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Your Collections{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
@@ -66,7 +66,7 @@
{% block js %}
<script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 1a622bb4..60a1a081 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}View Collection{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
@@ -166,7 +166,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index ffc8244d..5877e367 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
<link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9af52021..cb9fb815 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
@@ -135,7 +135,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index b73a6981..23136257 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
{% endblock %}
@@ -198,7 +198,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 556d46d3..8c261eec 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index f6ffff47..05b2f988 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 94ac0350..b4429b46 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Mapping Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
<link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" />
@@ -337,7 +337,7 @@
<script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 1ccb2b27..b13b393f 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Pair Scan{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
@@ -65,7 +65,7 @@
<script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
diff --git a/wqflask/wqflask/templates/search_error.html b/wqflask/wqflask/templates/search_error.html
index 7399b377..df8d9dff 100644
--- a/wqflask/wqflask/templates/search_error.html
+++ b/wqflask/wqflask/templates/search_error.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
{% endblock %}
{% block content %}
<!-- Start of body -->
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 0f5c39b0..767e3487 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -152,7 +152,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 27c3e398..d29be30b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 4422ba73..88cb4d31 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/typeahead-bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/snp_browser.css" />
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-21 22:56:49 +0000