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-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py39
-rw-r--r--wqflask/wqflask/templates/snp_browser.html26
-rw-r--r--wqflask/wqflask/views.py10
3 files changed, 59 insertions, 16 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index a2fb7195..9ae8892b 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
from PIL import (Image)
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
from base import species
from base import webqtlConfig
@@ -14,16 +14,16 @@ class SnpBrowser(object):
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
self.initialize_parameters(start_vars)
- self.limit_number = 10000
if self.first_run == "false":
self.filtered_results = self.get_browser_results()
+ self.table_rows = self.get_table_rows()
+ self.rows_count = len(self.table_rows)
- if len(self.filtered_results) <= self.limit_number:
- self.table_rows = self.get_table_rows()
- else:
- self.empty_columns = None
- self.table_rows = []
+ del self.filtered_results
+
+ if 'sEcho' not in start_vars:
+ self.table_rows = self.table_rows[:500]
if self.limit_strains == "true":
self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
@@ -380,7 +380,7 @@ class SnpBrowser(object):
the_rows = []
for i, result in enumerate(self.filtered_results):
- this_row = []
+ this_row = {}
if self.variant_type == "SNP":
snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
allele_value_list = result[14:]
@@ -520,8 +520,6 @@ class SnpBrowser(object):
"source_name": str(source_name)
}
#this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
- else:
- this_row = {}
the_rows.append(this_row)
@@ -643,6 +641,27 @@ class SnpBrowser(object):
#for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+class SnpPage(object):
+
+ def __init__(self, start_vars):
+ self.snp_browser = SnpBrowser(start_vars)
+ # self.table_rows = self.filter_rows()
+ self.rows_count = self.snp_browser.rows_count
+ self.sEcho = start_vars['sEcho']
+
+ def filter_rows(self):
+ pass
+
+ def get_page(self):
+ output = {}
+ output['sEcho'] = str(self.sEcho)
+ output['iTotalRecords'] = str(self.rows_count)
+ output['iTotalDisplayRecords'] = str(100)
+ # logger.info(len(self.table_rows), type(self.table_rows), self.table_rows[0])
+ logger.info(self.snp_browser.rows_count, len(self.snp_browser.table_rows))
+ output['data'] = self.snp_browser.table_rows[:100]
+ return output
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 83606804..f3e928af 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -188,10 +188,7 @@
</div>
<div style="margin-top: 20px;">
- {% if filtered_results is defined %}
- {% if filtered_results|length > limit_number %}
- There are more than 10000 results. Consider limiting your search to a smaller range.
- {% else %}
+ {% if table_rows is defined %}
<table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
<thead>
<tr>
@@ -214,7 +211,6 @@
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
</table>
- {% endif %}
{% endif %}
</div>
</div>
@@ -229,11 +225,23 @@
<script type='text/javascript'>
var json_rows = {{ table_rows|safe }};
+ var json_rows_count = {{ rows_count|safe }};
var empty_columns = {{ empty_columns|safe }};
</script>
<script language="javascript">
+ var getParams = function(url) {
+ var parser = document.createElement('a');
+ parser.href = url;
+ var params = parser.search.substring(1);
+ console.log(params);
+ if(params.length > 0) {
+ return ('?'+params);
+ }
+ return params;
+ };
+
var substringMatcher = function(strs) {
return function findMatches(q, cb) {
var matches, substringRegex;
@@ -266,7 +274,7 @@
source: substringMatcher(rat_genes)
});
- {% if filtered_results is defined %}
+ {% if table_rows is defined %}
$("#results_table").DataTable( {
'data': json_rows,
{% if variant_type == "SNP" %}
@@ -423,6 +431,10 @@
'order': [[1, "asc" ]],
'sDom': "rtip",
'iDisplayLength': 500,
+ 'bServerSide': true,
+ 'bProcessing': true,
+ 'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
+ 'deferLoading': json_rows_count,
'processing': true,
'language': {
'loadingRecords': '&nbsp;',
@@ -525,6 +537,8 @@
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+
$("input[name=export_csv]").click(function() {
var csv = [];
var rows = document.querySelectorAll("table tr");
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 08673f79..a2c66d53 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -897,6 +897,7 @@ def corr_scatter_plot_page():
def snp_browser_page():
logger.info(request.url)
template_vars = snp_browser.SnpBrowser(request.args)
+ logger.info(template_vars.__dict__.keys())
return render_template("snp_browser.html", **template_vars.__dict__)
@@ -906,6 +907,15 @@ def db_info_page():
return render_template("info_page.html", **template_vars.__dict__)
+@app.route("/snp_browser_table", methods=('GET',))
+def snp_browser_table():
+ logger.info(request.url)
+ logger.info(request.args)
+
+ current_page = snp_browser.SnpPage(request.args).get_page()
+
+ return flask.jsonify(current_page)
+
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
#ZS: Currently just links to GN1