diff options
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 192 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 1 | ||||
| -rwxr-xr-x | wqflask/wqflask/search_results.py | 77 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/scatter-matrix.js | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait.coffee | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait.js | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_statistics_new.html | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 2 |
9 files changed, 230 insertions, 58 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 29f3de98..31dc11b5 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -38,7 +38,6 @@ class DoSearch(object): query = self.normalize_spaces(query) print("in do_search query is:", pf(query)) results = g.db.execute(query, no_parameters=True).fetchall() - #results = self.cursor.fetchall() return results #def escape(self, stringy): @@ -139,11 +138,8 @@ class MrnaAssaySearch(DoSearch): return query - def run(self): - """Generates and runs a simple search of an mRNA expression dataset""" - - print("Running ProbeSetSearch") - query = self.base_query + """WHERE (MATCH (ProbeSet.Name, + def get_where_clause(self): + where_clause = """(MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, @@ -156,6 +152,37 @@ class MrnaAssaySearch(DoSearch): """ % (escape(self.search_term[0]), escape(str(self.dataset.id))) + return where_clause + + def run_combined(self, from_clause, where_clause): + """Generates and runs a combined search of an mRNA expression dataset""" + + print("Running ProbeSetSearch") + #query = self.base_query + from_clause + " WHERE " + where_clause + + from_clause = self.normalize_spaces(from_clause) + + query = (self.base_query + + """%s + WHERE %s + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = %s + """ % (escape(from_clause), + where_clause, + escape(str(self.dataset.id)))) + + print("final query is:", pf(query)) + + + return self.execute(query) + + def run(self): + """Generates and runs a simple search of an mRNA expression dataset""" + + print("Running ProbeSetSearch") + where_clause = self.get_where_clause() + query = self.base_query + "WHERE " + where_clause + #print("final query is:", pf(query)) return self.execute(query) @@ -433,12 +460,15 @@ class LrsSearch(MrnaAssaySearch): DoSearch.search_types['LRS'] = 'LrsSearch' - def run(self): + def get_from_clause(self): + if self.search_operator == "=": + return ", Geno" + else: + return "" + def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] - self.from_clause = ", Geno" - if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.lrs_min, self.lrs_max = self.search_term[:2] @@ -451,7 +481,7 @@ class LrsSearch(MrnaAssaySearch): if len(self.search_term) > 2: self.chr_num = self.search_term[2] - self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num)) + self.sub_clause += """ Geno.Chr = %s and """ % (self.chr_num) if len(self.search_term) == 5: self.mb_low, self.mb_high = self.search_term[3:] self.sub_clause += """ Geno.Mb > %s and @@ -459,21 +489,71 @@ class LrsSearch(MrnaAssaySearch): """ % self.mescape(min(self.mb_low, self.mb_high), max(self.mb_low, self.mb_high)) print("self.sub_clause is:", pf(self.sub_clause)) + + #%s.Chr = Geno.Chr + where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s + """ % self.mescape(self.dataset.type, + self.species_id) else: # Deal with >, <, >=, and <= print("self.search_term is:", self.search_term) - self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, + self.sub_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) + where_clause = self.sub_clause + - self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and - Geno.SpeciesId = %s and - %s.Chr = Geno.Chr - """ % self.mescape(self.dataset.type, - self.species_id, - self.dataset.type) + return where_clause - print("where_clause is:", pf(self.where_clause)) + def get_final_query(self): + self.from_clause = self.get_from_clause() + self.where_clause = self.get_where_clause() + self.query = self.compile_final_query(self.from_clause, self.where_clause) + + return self.query + + def run(self): + + self.from_clause = self.get_from_clause() + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.lrs_min, self.lrs_max = self.search_term[:2] + # + # self.sub_clause = """ %sXRef.LRS > %s and + # %sXRef.LRS < %s and """ % self.mescape(self.dataset.type, + # min(self.lrs_min, self.lrs_max), + # self.dataset.type, + # max(self.lrs_min, self.lrs_max)) + # + # if len(self.search_term) > 2: + # self.chr_num = self.search_term[2] + # self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num)) + # if len(self.search_term) == 5: + # self.mb_low, self.mb_high = self.search_term[3:] + # self.sub_clause += """ Geno.Mb > %s and + # Geno.Mb < %s and + # """ % self.mescape(min(self.mb_low, self.mb_high), + # max(self.mb_low, self.mb_high)) + # print("self.sub_clause is:", pf(self.sub_clause)) + #else: + # # Deal with >, <, >=, and <= + # print("self.search_term is:", self.search_term) + # self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, + # self.search_operator, + # self.search_term[0]) + # + #self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and + # Geno.SpeciesId = %s and + # %s.Chr = Geno.Chr + # """ % self.mescape(self.dataset.type, + # self.species_id, + # self.dataset.type) + + self.where_clause = self.get_where_clause() self.query = self.compile_final_query(self.from_clause, self.where_clause) @@ -586,25 +666,54 @@ class MeanSearch(MrnaAssaySearch): DoSearch.search_types['MEAN'] = "MeanSearch" - def run(self): - + def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.mean_min, self.mean_max = self.search_term[:2] - self.where_clause = """ %sXRef.mean > %s and + where_clause = """ %sXRef.mean > %s and %sXRef.mean < %s """ % self.mescape(self.dataset.type, min(self.mean_min, self.mean_max), self.dataset.type, max(self.mean_min, self.mean_max)) else: # Deal with >, <, >=, and <= - self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, + where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, self.search_operator, - self.search_term[0]) + self.search_term[0]) + + return where_clause + def get_final_query(self): + self.where_clause = self.get_where_clause() + print("where_clause is:", pf(self.where_clause)) + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.query + + def run(self): + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.mean_min, self.mean_max = self.search_term[:2] + # + # self.where_clause = """ %sXRef.mean > %s and + # %sXRef.mean < %s """ % self.mescape(self.dataset.type, + # min(self.mean_min, self.mean_max), + # self.dataset.type, + # max(self.mean_min, self.mean_max)) + #else: + # # Deal with >, <, >=, and <= + # self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, + # self.search_operator, + # self.search_term[0]) + + self.where_clause = self.get_where_clause() print("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -616,14 +725,11 @@ class RangeSearch(MrnaAssaySearch): DoSearch.search_types['RANGE'] = "RangeSearch" - def run(self): - - self.search_term = [float(value) for value in self.search_term] - + def get_where_clause(self): if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.range_min, self.range_max = self.search_term[:2] - self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + where_clause = """ (SELECT Pow(2, max(value) -min(value)) FROM ProbeSetData WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND (SELECT Pow(2, max(value) -min(value)) @@ -633,12 +739,38 @@ class RangeSearch(MrnaAssaySearch): max(self.range_min, self.range_max)) else: # Deal with >, <, >=, and <= - self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + where_clause = """ (SELECT Pow(2, max(value) -min(value)) FROM ProbeSetData WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s """ % (escape(self.search_term[0])) - print("where_clause is:", pf(self.where_clause)) + print("where_clause is:", pf(where_clause)) + + return where_clause + + def run(self): + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.range_min, self.range_max = self.search_term[:2] + # self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND + # (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s + # """ % self.mescape(min(self.range_min, self.range_max), + # max(self.range_min, self.range_max)) + #else: + # # Deal with >, <, >=, and <= + # self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s + # """ % (escape(self.search_term[0])) + + self.where_clause = self.get_where_clause() self.query = self.compile_final_query(where_clause = self.where_clause) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 60221c05..fa680f5f 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -720,6 +720,7 @@ class MarkerRegression(object): #def gen_human_results(self, pheno_vector, tempdata): def gen_human_results(self, pheno_vector, key, temp_uuid): file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name) + print("file_base:", file_base) plink_input = input.plink(file_base, type='b') input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz") diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index c6521106..a2958108 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -221,26 +221,63 @@ class SearchResultPage(object): self.search_terms = parser.parse(self.search_terms) print("After parsing:", self.search_terms) - for a_search in self.search_terms: - print("[kodak] item is:", pf(a_search)) - search_term = a_search['search_term'] - search_operator = a_search['separator'] - if a_search['key']: - search_type = a_search['key'].upper() - else: - # We fall back to the dataset type as the key to get the right object - search_type = self.dataset.type + if len(self.search_terms) > 1: + combined_from_clause = "" + combined_where_clause = "" + for i, a_search in enumerate(self.search_terms): + print("[kodak] item is:", pf(a_search)) + search_term = a_search['search_term'] + search_operator = a_search['separator'] + if a_search['key']: + search_type = a_search['key'].upper() + else: + # We fall back to the dataset type as the key to get the right object + search_type = self.dataset.type + + print("search_type is:", pf(search_type)) + + search_ob = do_search.DoSearch.get_search(search_type) + search_class = getattr(do_search, search_ob) + the_search = search_class(search_term, + search_operator, + self.dataset, + ) + + #search_query = the_search.get_final_query() + + get_from_clause = getattr(the_search, "get_from_clause", None) + if callable(get_from_clause): + from_clause = the_search.get_from_clause() + combined_from_clause += from_clause + where_clause = the_search.get_where_clause() + combined_where_clause += "(" + where_clause + ")" + if (i+1) < len(self.search_terms): + combined_where_clause += "AND" + + results = the_search.run_combined(combined_from_clause, combined_where_clause) + self.results.extend(results) + + else: + for a_search in self.search_terms: + print("[kodak] item is:", pf(a_search)) + search_term = a_search['search_term'] + search_operator = a_search['separator'] + if a_search['key']: + search_type = a_search['key'].upper() + else: + # We fall back to the dataset type as the key to get the right object + search_type = self.dataset.type - print("search_type is:", pf(search_type)) - - search_ob = do_search.DoSearch.get_search(search_type) - search_class = getattr(do_search, search_ob) - print("search_class is: ", pf(search_class)) - the_search = search_class(search_term, - search_operator, - self.dataset, - ) - self.results.extend(the_search.run()) - #print("in the search results are:", self.results) + print("search_type is:", pf(search_type)) + + search_ob = do_search.DoSearch.get_search(search_type) + search_class = getattr(do_search, search_ob) + print("search_class is: ", pf(search_class)) + the_search = search_class(search_term, + search_operator, + self.dataset, + ) + self.results.extend(the_search.run()) + #print("in the search results are:", self.results) self.header_fields = the_search.header_fields diff --git a/wqflask/wqflask/static/new/javascript/scatter-matrix.js b/wqflask/wqflask/static/new/javascript/scatter-matrix.js index 38fd276e..38cdc75b 100644 --- a/wqflask/wqflask/static/new/javascript/scatter-matrix.js +++ b/wqflask/wqflask/static/new/javascript/scatter-matrix.js @@ -56,9 +56,11 @@ ScatterMatrix.prototype.render = function () { var container = d3.select('#scatterplot_container').append('div') .attr('class', 'scatter-matrix-container'); var control = container.append('div') - .attr('class', 'scatter-matrix-control'); + .attr('class', 'scatter-matrix-control') + .style({'float':'left'}) var svg = container.append('div') .attr('class', 'scatter-matrix-svg') + .style({'float':'right'}) .html('<em>Loading data...</em>'); this.onData(function() { diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 2cdad5ee..d05ccbf7 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -95,12 +95,12 @@ $ -> new Box_Plot(all_samples) d3.select("#select_compare_trait").on("click", => - $('.qtlcharts').empty() + $('.scatter-matrix-container').remove() open_trait_selection() ) d3.select("#clear_compare_trait").on("click", => - $('.qtlcharts').empty() + $('.scatter-matrix-container').remove() ) open_trait_selection = () -> diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 40bc3d0a..159dafcb 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -91,13 +91,13 @@ $(function() { }); d3.select("#select_compare_trait").on("click", (function(_this) { return function() { - $('.qtlcharts').empty(); + $('.scatter-matrix-container').remove(); return open_trait_selection(); }; })(this)); d3.select("#clear_compare_trait").on("click", (function(_this) { return function() { - return $('.qtlcharts').empty(); + return $('.scatter-matrix-container').remove(); }; })(this)); open_trait_selection = function() { diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 6f5fe237..d6c7b18e 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -84,7 +84,7 @@ <div class="mapping_method_fields form-group"> <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label> <div style="margin-left: 20px;" class="col-xs-2 controls"> - <input name="num_perm_pylmm" value="2000" type="text" class="form-control"> + <input name="num_perm_pylmm" value="0" type="text" class="form-control"> </div> </div> <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;"> diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html index 9ce60c0b..f2ebbbef 100755 --- a/wqflask/wqflask/templates/show_trait_statistics_new.html +++ b/wqflask/wqflask/templates/show_trait_statistics_new.html @@ -121,7 +121,7 @@ </div>--> <div class="tab-pane" id="scatterplot_matrix"> - <div class="btn-group"> + <div style="margin-bottom:40px;" class="btn-group"> <button type="button" class="btn btn-default" id="select_compare_trait"> <i class="icon-th-large"></i> Select Traits </button> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index cdf93147..9110c5a1 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -293,7 +293,7 @@ def marker_regression_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - version = "v4" + version = "v3" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): |