diff options
| -rw-r--r-- | wqflask/wqflask/snp_browser/snp_browser.py | 39 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/snp_browser.html | 26 | ||||
| -rw-r--r-- | 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 @@ </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': ' ', @@ -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 |