diff options
| -rw-r--r-- | wqflask/wqflask/snp_browser/snp_browser.py | 92 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/snp_browser.html | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 4 |
3 files changed, 80 insertions, 23 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 9ae8892b..116da149 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -23,12 +23,12 @@ class SnpBrowser(object): del self.filtered_results if 'sEcho' not in start_vars: - self.table_rows = self.table_rows[:500] + self.table_rows = [] 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) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns) else: - self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) + self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns) def initialize_parameters(self, start_vars): if 'first_run' in start_vars: @@ -643,23 +643,75 @@ class SnpBrowser(object): 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 __init__(self, request): + self.request_values = request + self.sEcho = self.request_values['sEcho'] - def filter_rows(self): - pass + self.snp_browser = SnpBrowser(request) + self.rows_count = self.snp_browser.rows_count + self.table_rows = self.snp_browser.table_rows + self.header_data_names = self.snp_browser.header_data_names + + logger.info(self.table_rows[0]) + + self.sort_rows() + self.paginate_rows() + + def sort_rows(self): + ''' + Sorts the rows taking in to account the column (or columns) that the + user has selected. + ''' + def is_reverse(str_direction): + ''' Maps the 'desc' and 'asc' words to True or False. ''' + return True if str_direction == 'desc' else False + + if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0): + for i in range(0, int(self.request_values['iSortingCols'])): + column_number = int(self.request_values['iSortCol_' + str(i)]) + column_name = self.header_data_names[column_number - 1] + sort_direction = self.request_values['sSortDir_' + str(i)] + self.table_rows = sorted(self.table_rows, + key=lambda x: x[column_name], + reverse=is_reverse(sort_direction)) + + def paginate_rows(self): + ''' + Selects a subset of the filtered and sorted data based on if the table + has pagination, the current page and the size of each page. + ''' + def requires_pagination(): + ''' Check if the table is going to be paginated ''' + if self.request_values['iDisplayStart'] != "": + if int(self.request_values['iDisplayLength']) != -1: + return True + return False + + if not requires_pagination(): + return + + start = int(self.request_values['iDisplayStart']) + length = int(self.request_values['iDisplayLength']) + + # if search returns only one page + if len(self.table_rows) <= length: + # display only one page + self.table_rows = self.table_rows[start:] + else: + limit = -len(self.table_rows) + start + length + if limit < 0: + # display pagination + self.table_rows = self.table_rows[start:limit] + else: + # display last page of pagination + self.table_rows = self.table_rows[start:] 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] + output['iTotalRecords'] = str(float('Nan')) + output['iTotalDisplayRecords'] = str(self.rows_count) + output['data'] = self.table_rows return output def get_browser_sample_lists(species_id=1): @@ -692,9 +744,13 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None) empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this header_fields = [] + header_data_names = [] if variant_type == "SNP": header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details']) + header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details'] + header_fields.append(strain_list) + header_data_names += strain_list if empty_columns != None: if empty_columns['snp_source'] == "false": @@ -721,11 +777,15 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None) if empty_columns['function_details'] == "false": empty_field_count += 1 header_fields[0].remove('Details') + + for col in empty_columns: + header_data_names.remove(col) elif variant_type == "InDel": header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'] + header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'] - return header_fields, empty_field_count + return header_fields, empty_field_count, header_data_names def get_effect_details_by_category(effect_name = None, effect_value = None): gene_list = [] diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html index f3e928af..cbc12e06 100644 --- a/wqflask/wqflask/templates/snp_browser.html +++ b/wqflask/wqflask/templates/snp_browser.html @@ -276,7 +276,6 @@ {% if table_rows is defined %} $("#results_table").DataTable( { - 'data': json_rows, {% if variant_type == "SNP" %} 'columns': [ { @@ -432,10 +431,10 @@ 'sDom': "rtip", 'iDisplayLength': 500, 'bServerSide': true, - 'bProcessing': true, 'sAjaxSource': '/snp_browser_table'+getParams(window.location.href), - 'deferLoading': json_rows_count, - 'processing': true, + 'infoCallback': function(settings, start, end, max, total, pre) { + return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries"; + }, 'language': { 'loadingRecords': ' ', 'processing': 'Loading...' diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index a2c66d53..8e7f6ec3 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -909,9 +909,7 @@ def db_info_page(): @app.route("/snp_browser_table", methods=('GET',)) def snp_browser_table(): - logger.info(request.url) - logger.info(request.args) - + logger.info(request.url) current_page = snp_browser.SnpPage(request.args).get_page() return flask.jsonify(current_page) |