{% endfor %}
{% for strain in header_fields[1] %}
-
{{ strain }}
+
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
{% endfor %}
{% else %}
{% for header in header_fields %}
--
cgit v1.2.3
From 7a4068d6d46d923c30316887e1d20f2fa6caa859 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:15:22 -0500
Subject: add export to CSV button to export current page
---
wqflask/wqflask/templates/snp_browser.html | 43 +++++++++++++++++++++++++++---
1 file changed, 40 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 36f893bc..284b55c5 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -107,6 +107,12 @@
+
+
+
+
+
+
@@ -192,14 +198,14 @@
{% if header_fields|length == 2 %}
{% for header in header_fields[0] %}
-
{{ header }}
+
{{ header }}
{% endfor %}
{% for strain in header_fields[1] %}
-
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
+
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
{% endfor %}
{% else %}
{% for header in header_fields %}
-
{{ header }}
+
{{ header }}
{% endfor %}
{% endif %}
@@ -518,6 +524,37 @@
});
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+ $("input[name=export_csv]").click(function() {
+ var csv = [];
+ var rows = document.querySelectorAll("table tr");
+
+ var headers = [];
+ var col_header = rows[0].querySelectorAll("th");
+ console.log(col_header.length);
+ for(var i = 1; i < col_header.length; i++) {
+ console.log(col_header[i].getAttribute("name"));
+ headers.push(col_header[i].getAttribute("name"));
+ }
+ csv.push(headers.join(","));
+
+ for (var i = 1; i < rows.length; i++) {
+ var row = [], cols = rows[i].querySelectorAll("td");
+
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
+
+ csv.push(row.join(","));
+ }
+
+ var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+ var downloadLink = document.createElement("a");
+ downloadLink.download = "hello.csv";
+ downloadLink.href = window.URL.createObjectURL(csvFile);
+ downloadLink.style.display = "none";
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ });
{% endblock %}
--
cgit v1.2.3
From f99b69155d35900a75c000fbb79f6bcfb3fa6ff1 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:30:04 -0500
Subject: export only checked rows to csv; update csv file name
---
wqflask/wqflask/templates/snp_browser.html | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 284b55c5..83606804 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -531,25 +531,27 @@
var headers = [];
var col_header = rows[0].querySelectorAll("th");
- console.log(col_header.length);
for(var i = 1; i < col_header.length; i++) {
- console.log(col_header[i].getAttribute("name"));
headers.push(col_header[i].getAttribute("name"));
}
csv.push(headers.join(","));
for (var i = 1; i < rows.length; i++) {
var row = [], cols = rows[i].querySelectorAll("td");
+ var checkBox = rows[i].querySelector("input");
+ console.log(checkBox);
- for (var j = 1; j < cols.length; j++)
- row.push(cols[j].innerText);
+ if(checkBox.checked == true) {
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
- csv.push(row.join(","));
+ csv.push(row.join(","));
+ }
}
var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
var downloadLink = document.createElement("a");
- downloadLink.download = "hello.csv";
+ downloadLink.download = "variant_data.csv";
downloadLink.href = window.URL.createObjectURL(csvFile);
downloadLink.style.display = "none";
document.body.appendChild(downloadLink);
--
cgit v1.2.3
From 349b395375703e727465a1f05f4a5e2d4fc64d2a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 19 Jul 2020 17:21:15 -0500
Subject: add server side processing due to large tables in DataTables; work on
server-side processing API pending for sorting, paging etc
---
wqflask/wqflask/snp_browser/snp_browser.py | 39 ++++++++++++++++++++++--------
wqflask/wqflask/templates/snp_browser.html | 26 +++++++++++++++-----
wqflask/wqflask/views.py | 10 ++++++++
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 @@
- {% 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 %}