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-rw-r--r--wqflask/utility/tools.py2
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py71
-rw-r--r--wqflask/wqflask/templates/admin/group_manager.html2
-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
16 files changed, 81 insertions, 38 deletions
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 e1aa290b..152bb5be 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -12,6 +12,7 @@ import utility.logger
logger = utility.logger.getLogger(__name__ )
def run_rqtl_geno(vals, samples, dataset, 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
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -21,6 +22,8 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
print(r_library("qtl")) # Load R/qtl
+ logger.info("QTL library loaded");
+
## Get pointers to some R/qtl functions
scanone = ro.r["scanone"] # Map the scanone function
scantwo = ro.r["scantwo"] # Map the scantwo function
@@ -40,28 +43,35 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
genofilelocation = locate(dataset.group.genofile, "genotype")
else:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
+ logger.info("Going to create a cross from geno");
cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
-
+ logger.info("before calc_genoprob");
if manhattan_plot:
cross_object = calc_genoprob(cross_object)
else:
- cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
-
+ cross_object = calc_genoprob(cross_object, step=5, stepwidth="max")
+ logger.info("after calc_genoprob");
pheno_string = sanitize_rqtl_phenotype(vals)
-
+ logger.info("phenostring done");
+ names_string = sanitize_rqtl_names(samples)
+ logger.info("sanitized pheno and names");
cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
-
+ cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype
+ logger.info("Added pheno and names");
# Scan for QTLs
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
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
-
+ #logger.info("Saving");
+ #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
+ #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)
@@ -128,7 +138,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(type == '4-way'){
genocodes <- c('1','2','3','4')
} else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
@@ -139,8 +149,17 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
- cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
- if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ if(type == '4-way'){
+ cat('Loading in as 4-WAY\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else{
+ cat('Loading in as normal\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ }
+ if(type == 'riset'){
+ cat('Converting to RISELF\n')
+ cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ }
return(cross)
}
""" % (dataset.group.genofile))
@@ -176,9 +195,33 @@ def sanitize_rqtl_phenotype(vals):
return pheno_as_string
+def sanitize_rqtl_names(vals):
+ pheno_as_string = "c("
+ for i, val in enumerate(vals):
+ if val == "x":
+ if i < (len(vals) - 1):
+ pheno_as_string += "NA,"
+ else:
+ pheno_as_string += "NA"
+ else:
+ if i < (len(vals) - 1):
+ pheno_as_string += "'" + str(val) + "',"
+ else:
+ pheno_as_string += "'" + str(val) + "'"
+ pheno_as_string += ")"
+
+ return pheno_as_string
+
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
- ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
+ return ro.r["the_cross"]
+
+def add_names(cross, names_as_string, col_name):
+ ro.globalenv["the_cross"] = cross
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = '+ names_as_string +')')
return ro.r["the_cross"]
def pull_var(var_name, cross, var_string):
@@ -204,8 +247,8 @@ def add_cofactors(cross, this_dataset, covariates, samples):
this_dataset.group.get_samplelist()
trait_samples = this_dataset.group.samplelist
trait_sample_data = trait_ob.data
- for index, sample in enumerate(trait_samples):
- if sample in samples:
+ for index, sample in enumerate(samples):
+ if sample in trait_samples:
if sample in trait_sample_data:
sample_value = trait_sample_data[sample].value
this_covar_data.append(sample_value)
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index ea9026a6..1c536cb2 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -46,7 +46,7 @@
{% 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/DT_bootstrap/DT_bootstrap.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 6639f46a..34734a01 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 03b03aa7..b696a3fa 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 %}
@@ -193,7 +193,7 @@
<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 7e05be18..8699343f 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" />
@@ -333,7 +333,7 @@
<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 21:43:51 +0000