Merging Danny's changes and Bonface's changes to js imports

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" />