diff options
| -rw-r--r-- | wqflask/wqflask/search_results.py | 72 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 58 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 53 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 22 |
4 files changed, 149 insertions, 56 deletions
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index d393d0c1..a9972349 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -771,37 +771,40 @@ class SearchResultPage(templatePage): DescriptionText = self.ORDescriptionText itemCmd = item[0] - lowerLimit = float(item[1]) - upperLimit = float(item[2]) + lower_limit = float(item[1]) + upper_limit = float(item[2]) if itemCmd.upper() in ("TRANSLRS", "CISLRS"): if item[3]: mthresh = float(item[3]) clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \ - (self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit)) + (self.dbType, min(lower_limit, upper_limit), self.dbType, max(lower_limit, upper_limit)) if itemCmd.upper() == "CISLRS": clauseItem += """ and %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) < %2.7f """ % (self.dbType, self.speciesId, self.dbType, self.dbType, mthresh) - DescriptionText.append(HT.Span(' with a ', HT.U('cis-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit), mthresh))) + DescriptionText.append(HT.Span(' with a ', HT.U('cis-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer' % (min(lower_limit, upper_limit), max(lower_limit, upper_limit), mthresh))) else: clauseItem += """ and %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and (%s.Chr != Geno.Chr or (%s.Chr != Geno.Chr and ABS(%s.Mb-Geno.Mb) > %2.7f)) """ % (self.dbType, self.speciesId, self.dbType, self.dbType, self.dbType, mthresh) - DescriptionText.append(HT.Span(' with a ', HT.U('trans-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit), mthresh))) + DescriptionText.append(HT.Span(' with a ', HT.U('trans-QTL'), ' having an LRS between %g and %g using a %g Mb exclusion buffer' % (min(lower_limit, upper_limit), max(lower_limit, upper_limit), mthresh))) query.append(" (%s) " % clauseItem) self.orderByDefalut = "LRS" else: pass elif itemCmd.upper() in ("RANGE"): #XZ, 03/05/2009: Xiaodong changed Data to ProbeSetData - clauseItem = " (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) > %2.7f and (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) < %2.7f " % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)) + clauseItem = " (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) > %2.7f and (select Pow(2, max(value) -min(value)) from ProbeSetData where Id = ProbeSetXRef.dataId) < %2.7f " % (min(lower_limit, upper_limit), max(lower_limit, upper_limit)) query.append(" (%s) " % clauseItem) - DescriptionText.append(HT.Span(' with a range of expression that varied between %g and %g' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)), " (fold difference)")) + DescriptionText.append(HT.Span(' with a range of expression that varied between %g and %g' % (min(lower_limit, upper_limit), max(lower_limit, upper_limit)), " (fold difference)")) else: clauseItem = " %sXRef.%s > %2.7f and %sXRef.%s < %2.7f " % \ - (self.dbType, itemCmd, min(lowerLimit, upperLimit), self.dbType, itemCmd, max(lowerLimit, upperLimit)) + (self.dbType, itemCmd, min(lower_limit, upper_limit), self.dbType, itemCmd, max(lower_limit, upper_limit)) query.append(" (%s) " % clauseItem) self.orderByDefalut = itemCmd - DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)))) + DescriptionText.append(HT.Span(' with ', HT.U(itemCmd), ' between %g and %g' % (min(lower_limit, upper_limit), max(lower_limit, upper_limit)))) for k, item in enumerate(m3_OR+m3_AND): + print("enumerating m3_OR+m3_AND with k: %s - item %s" % (k, item)) + if self.dbType not in ("ProbeSet", "Geno"): + continue if k >=len(m3_OR): query = self.ANDQuery DescriptionText = self.ANDDescriptionText @@ -809,23 +812,32 @@ class SearchResultPage(templatePage): query = self.ORQuery DescriptionText = self.ORDescriptionText itemCmd = item[0] - chrsch = item[1] - lowerLimit = float(item[2]) - upperLimit = float(item[3]) - fname = 'target genes' + + + chr_number = item[1] # chromosome number + lower_limit = float(item[2]) + upper_limit = float(item[3]) + if self.dbType == "ProbeSet": - clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \ - (self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit)) + fname = 'target genes' elif self.dbType == "Geno": fname = 'loci' - clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % \ - (self.dbType, chrsch, self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit)) - else: - continue + + if lower_limit > upper_limit: + lower_limit, upper_limit = upper_limit, lower_limit + + + + clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % ( + self.dbType, chr_number, self.dbType, lower_limit, self.dbType, upper_limit) + + query.append(" (%s) " % clauseItem) self.orderByDefalut = itemCmd - DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \ - (chrsch, min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)))) + + self.results_desc = dict() + #DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \ + # (chr_number, min(lower_limit, upper_limit), max(lower_limit, upper_limit)))) for k, item in enumerate(m5_OR+m5_AND): if k >=len(m5_OR): @@ -835,22 +847,22 @@ class SearchResultPage(templatePage): query = self.ORQuery DescriptionText = self.ORDescriptionText itemCmd = item[0] - lowerLimit = float(item[1]) - upperLimit = float(item[2]) - chrsch = item[3] - MblowerLimit = float(item[4]) - MbupperLimit = float(item[5]) + lower_limit = float(item[1]) + upper_limit = float(item[2]) + chr_number = item[3] + mb_lower_limit = float(item[4]) + mb_upper_limit = float(item[5]) if self.dbType == "ProbeSet" or self.dbType == "Publish": clauseItem = " %sXRef.LRS > %2.7f and %sXRef.LRS < %2.7f " % \ - (self.dbType, min(lowerLimit, upperLimit), self.dbType, max(lowerLimit, upperLimit)) + (self.dbType, min(lower_limit, upper_limit), self.dbType, max(lower_limit, upper_limit)) clauseItem += " and %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and Geno.Chr = '%s' and Geno.Mb > %2.7f and Geno.Mb < %2.7f" \ - % (self.dbType, self.speciesId, chrsch, min(MblowerLimit, MbupperLimit), max(MblowerLimit, MbupperLimit)) + % (self.dbType, self.speciesId, chr_number, min(mb_lower_limit, mb_upper_limit), max(mb_lower_limit, mb_upper_limit)) query.append(" (%s) " % clauseItem) self.orderByDefalut = "MB" DescriptionText.append(HT.Span(' with ', HT.U('LRS'), ' between %g and %g' % \ - (min(lowerLimit, upperLimit), max(lowerLimit, upperLimit)), \ + (min(lower_limit, upper_limit), max(lower_limit, upper_limit)), \ ' on chromosome %s between %g and %g Mb' % \ - (chrsch, min(MblowerLimit, MbupperLimit), max(MblowerLimit, MbupperLimit)))) + (chr_number, min(mb_lower_limit, mb_upper_limit), max(mb_lower_limit, mb_upper_limit)))) pass return 1 diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 29489fb9..b89e15ce 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -196,28 +196,56 @@ $ -> exclude_by_value = $('#attribute_values').val() cell_class = ".column_name-#{attribute_name}" - $(cell_class).each (index, element)=> + $(cell_class).each (index, element) => if $.trim($(element).text()) == exclude_by_value row = $(element).parent('tr') $(row).find(".trait_value_input").val("x") - - #sample_lists = js_data['sample_lists'] - #console.log("sample_lists is:", sample_lists) - #for sample_list in sample_lists - # for sample in sample_list - # console.log("sample is:", sample) - # if sample.extra_attributes[attribute_name] == exclude_by_value - # console.log("is exclude_by_value") - # console.log("sample.name is:", sample.name) - # attr_cell = $('td:contains('+sample.name+')').parent().find('td.column_name-'+ attribute_name) - # console.log("attr_cell is:", attr_cell) - # value_cell = attr_cell.parent().find('td.column_name-Value') - # value_cell.children('input').val("x") - $('#exclude_group').click(block_by_attribute_value) ##End Block Samples By Attribute Value Code + + ##Block Samples By Index Code + block_by_index = -> + index_string = $('#remove_samples_field').val() + console.log("index_string is:", index_string) + index_list = [] + for index_set in index_string.split(",") + if index_set.indexOf('-') != -1 + try + start_index = parseInt(index_set.split("-")[0]) + console.log("start_index:", start_index) + end_index = parseInt(index_set.split("-")[1]) + console.log("end_index:", end_index) + index_list.push(index) for index in [start_index..end_index] + catch error + alert("Syntax error") + else + #try + index = parseInt(index_set) + console.log("index:", index) + index_list.push(index) + #catch(erro) + # alert("Syntax error") + console.log("index_list:", index_list) + for index in index_list + if $('#block_group').val() == "primary" + console.log("block_group:", $('#block_group').val()) + console.log("row:", $('#Primary_'+index.toString())) + $('#Primary_'+index.toString()).find('.trait_value_input').val("x") + else if $('#block_group').val() == "other" + $('#Other_'+index.toString()).find('.trait_value_input').val("x") + + $('#remove_samples_field').validate( + rules: + field: + required: true + number: true + ) + + $('#block_by_index').click(block_by_index) + + ##End Block Samples By Index Code console.log("before registering show_hide_outliers") $('#show_hide_outliers').click(show_hide_outliers) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index a5582519..6d3dee13 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -11,7 +11,7 @@ }; $(function() { - var block_by_attribute_value, change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values; + var block_by_attribute_value, block_by_index, change_stats_value, create_value_dropdown, edit_data_change, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, show_hide_outliers, stats_mdp_change, update_stat_values; hide_tabs = function(start) { var x, _i, _results; _results = []; @@ -238,6 +238,57 @@ }); }; $('#exclude_group').click(block_by_attribute_value); + block_by_index = function() { + var end_index, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results; + index_string = $('#remove_samples_field').val(); + console.log("index_string is:", index_string); + index_list = []; + _ref = index_string.split(","); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + index_set = _ref[_i]; + if (index_set.indexOf('-') !== -1) { + try { + start_index = parseInt(index_set.split("-")[0]); + console.log("start_index:", start_index); + end_index = parseInt(index_set.split("-")[1]); + console.log("end_index:", end_index); + for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) { + index_list.push(index); + } + } catch (error) { + alert("Syntax error"); + } + } else { + index = parseInt(index_set); + console.log("index:", index); + index_list.push(index); + } + } + console.log("index_list:", index_list); + _results = []; + for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { + index = index_list[_k]; + if ($('#block_group').val() === "primary") { + console.log("block_group:", $('#block_group').val()); + console.log("row:", $('#Primary_' + index.toString())); + _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x")); + } else if ($('#block_group').val() === "other") { + _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x")); + } else { + _results.push(void 0); + } + } + return _results; + }; + $('#remove_samples_field').validate({ + rules: { + field: { + required: true, + number: true + } + } + }); + $('#block_by_index').click(block_by_index); console.log("before registering show_hide_outliers"); $('#show_hide_outliers').click(show_hide_outliers); console.log("after registering show_hide_outliers"); diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index f85cf98e..5a364f8b 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -1214,18 +1214,19 @@ <div style= "border: 3px solid #EEEEEE; -moz-border-radius: 10px; -webkit-border-radius: 10px; width: 625px; padding: 5px 5px 10px 8px; font-size: 12px; background: #DDDDDD;"> <span id="showHideOptions" style="line-height:225%;"><strong> Block samples by index: </strong> - <input type="text" name="removeField" style= - "background-color:white;border: 1px solid black;font-size: 14px;"> <span id="blockMenuSpan"><select name= - "block_method" size="1"> - <option value="1"> - BXD Only + <input type="text" id="remove_samples_field" style= + "background-color:white;border: 1px solid black;font-size: 14px;"> + <span id="blockMenuSpan"> + <select id="block_group" size="1"> + <option value="primary"> + {{ sample_group_types['primary_only'] }} </option> - - <option value="0"> - Non-BXD Only + <option value="other"> + {{ sample_group_types['other_only'] }} </option> - </select></span> - <input type="button" name="blockSamples" class="button" value=" Block "> + </select> + </span> + <input type="button" id="block_by_index" class="button" value=" Block "> <br> {% if sample_groups[0].attributes %} @@ -1362,6 +1363,7 @@ <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>--> <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script> + <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script> <script type="text/javascript" src="/static/new/javascript/stats.js"></script> <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script> |