diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 23 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 16 |
8 files changed, 59 insertions, 85 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 298a3559..a36b947c 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -86,8 +86,6 @@ class CorrelationResults(object): else: helper_functions.get_species_dataset_trait(self, start_vars) - #self.dataset.group.read_genotype_file() - corr_samples_group = start_vars['corr_samples_group'] self.sample_data = {} @@ -453,13 +451,13 @@ class CorrelationResults(object): if not excluded_samples: excluded_samples = () + sample_val_dict = json.loads(start_vars['sample_vals']) for sample in sample_names: if sample not in excluded_samples: - # print("Looking for",sample,"in",start_vars) - value = start_vars.get('value:' + sample) - if value: - if not value.strip().lower() == 'x': - self.sample_data[str(sample)] = float(value) + value = sample_val_dict[sample] + if not value.strip().lower() == 'x': + self.sample_data[str(sample)] = float(value) + def do_bicor(this_trait_vals, target_trait_vals): r_library = ro.r["library"] # Map the library function diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 08c2d750..9f1b050d 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -270,8 +270,9 @@ class DisplayMappingResults(object): # Needing for form submission when doing single chr # mapping or remapping after changing options - self.samples = start_vars['samples'] - self.vals = start_vars['vals'] + self.sample_vals = start_vars['sample_vals'] + self.sample_vals_dict = json.loads(self.sample_vals) + self.transform = start_vars['transform'] self.mapping_method = start_vars['mapping_method'] self.mapping_results_path = start_vars['mapping_results_path'] @@ -492,11 +493,10 @@ class DisplayMappingResults(object): ## count the amount of individuals to be plotted, and increase self.graphHeight if self.haplotypeAnalystChecked and self.selectedChr > -1: thisTrait = self.this_trait - _strains, _vals, _vars, _aliases = thisTrait.export_informative() smd=[] - for ii, _val in enumerate(self.vals): - if _val != "x": - temp = GeneralObject(name=self.samples[ii], value=float(_val)) + for sample in self.sample_vals_dict.keys(): + if self.sample_vals_dict[sample] != "x": + temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) smd.append(temp) else: continue @@ -1464,12 +1464,11 @@ class DisplayMappingResults(object): yPaddingTop = yTopOffset thisTrait = self.this_trait - _strains, _vals, _vars, _aliases = thisTrait.export_informative() smd=[] - for ii, _val in enumerate(self.vals): - if _val != "x": - temp = GeneralObject(name=self.samples[ii], value=float(_val)) + for sample in self.sample_vals_dict.keys(): + if self.sample_vals_dict[sample] != "x": + temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample])) smd.append(temp) else: continue diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 891fcc66..a1f87b61 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -71,56 +71,22 @@ class RunMapping(object): all_samples_ordered = self.dataset.group.all_samples_ordered() self.vals = [] - if 'samples' in start_vars: - self.samples = start_vars['samples'].split(",") - if (len(genofile_samplelist) != 0): - for sample in genofile_samplelist: - if sample in self.samples: - value = start_vars.get('value:' + sample) - if value: - self.vals.append(value) - else: - self.vals.append("x") - else: - for sample in self.samples: - value = start_vars.get('value:' + sample) - if value: - self.vals.append(value) + self.samples = [] + self.sample_vals = start_vars['sample_vals'] + sample_val_dict = json.loads(self.sample_vals) + samples = sample_val_dict.keys() + if (len(genofile_samplelist) != 0): + for sample in genofile_samplelist: + self.samples.append(sample) + if sample in samples: + self.vals.append(sample_val_dict[sample]) + else: + self.vals.append("x") else: - self.samples = [] - if (len(genofile_samplelist) != 0): - for sample in genofile_samplelist: - if sample in self.dataset.group.samplelist: - in_trait_data = False - for item in self.this_trait.data: - if self.this_trait.data[item].name == sample: - value = start_vars['value:' + self.this_trait.data[item].name] - self.samples.append(self.this_trait.data[item].name) - self.vals.append(value) - in_trait_data = True - break - if not in_trait_data: - value = start_vars.get('value:' + sample) - if value: - self.samples.append(sample) - self.vals.append(value) - else: - self.vals.append("x") - else: - for sample in self.dataset.group.samplelist: # sample is actually the name of an individual - in_trait_data = False - for item in self.this_trait.data: - if self.this_trait.data[item].name == sample: - value = start_vars['value:' + self.this_trait.data[item].name] - self.samples.append(self.this_trait.data[item].name) - self.vals.append(value) - in_trait_data = True - break - if not in_trait_data: - value = start_vars.get('value:' + sample) - if value: - self.samples.append(sample) - self.vals.append(value) + for sample in self.dataset.group.samplelist: + if sample in samples: + self.vals.append(sample_val_dict[sample]) + self.samples.append(sample) if 'n_samples' in start_vars: self.n_samples = start_vars['n_samples'] diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 765f2f2d..b8ffa8e8 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -409,6 +409,25 @@ process_id = function() { } return processed; }; + +fetch_sample_values = function() { + // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster) + sample_val_dict = {}; + + table = 'samples_primary'; + if ($('#' + table).length){ + table_api = $('#' + table).DataTable(); + val_nodes = table_api.column(3).nodes().to$(); + for (_j = 0; _j < val_nodes.length; _j++){ + sample_name = val_nodes[_j].childNodes[0].name.split(":")[1] + sample_val = val_nodes[_j].childNodes[0].value + sample_val_dict[sample_name] = sample_val + } + } + + return sample_val_dict; +} + edit_data_change = function() { var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; already_seen = {}; @@ -526,7 +545,7 @@ on_dataset_change = function() { $('select[name=corr_dataset]').change(on_dataset_change); submit_special = function(url) { - get_table_contents_for_form_submit("trait_data_form"); + $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values())) $("#trait_data_form").attr("action", url); $("#trait_data_form").submit(); }; @@ -550,7 +569,7 @@ get_table_contents_for_form_submit = function(form_id) { }); } -var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr', +var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr', 'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper'] $(".corr_compute").on("click", (function(_this) { diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 34582f21..3ae52975 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -141,7 +141,7 @@ $('input[name=display_all]').change((function(_this) { })(this)); //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping -var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 985d542c..c2256e47 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -31,10 +31,7 @@ {% endif %} <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> - <input type="hidden" name="samples" value="{{ samples|join(",") }}"> - {% for sample in samples %} - <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}"> - {% endfor %} + <input type="hidden" name="sample_vals" value="{{ sample_vals }}"> <input type="hidden" name="n_samples" value="{{ n_samples }}"> <input type="hidden" name="maf" value="{{ maf }}"> <input type="hidden" name="use_loco" value="{{ use_loco }}"> @@ -464,7 +461,7 @@ }); - var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index c881eb76..77fc9342 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -35,6 +35,7 @@ <input type="hidden" name="genofile" value=""> <input type="hidden" name="covariates" value=""> <input type="hidden" name="transform" value=""> + <input type="hidden" name="sample_vals" value=""> <div class="container showtrait-main-div"> <div class="panel-group" id="accordion"> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 632e0d2d..2b3e2a37 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -650,12 +650,13 @@ def loading_page(): wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} for key, value in list(initial_start_vars.items()): - if key in wanted or key.startswith(('value:')): + if key in wanted: start_vars[key] = value if 'n_samples' in start_vars: n_samples = int(start_vars['n_samples']) else: + sample_vals_dict = json.loads(start_vars['sample_vals']) if 'group' in start_vars: dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group']) else: @@ -671,8 +672,7 @@ def loading_page(): samples = genofile_samples for sample in samples: - value = start_vars.get('value:' + sample) - if value != "x": + if sample_vals_dict[sample] != "x": n_samples += 1 start_vars['n_samples'] = n_samples @@ -689,7 +689,6 @@ def loading_page(): @app.route("/run_mapping", methods=('POST',)) def mapping_results_page(): initial_start_vars = request.form - #logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items()) logger.info(request.url) temp_uuid = initial_start_vars['temp_uuid'] wanted = ( @@ -699,6 +698,7 @@ def mapping_results_page(): 'species', 'samples', 'vals', + 'sample_vals', 'first_run', 'output_files', 'geno_db_exists', @@ -752,13 +752,11 @@ def mapping_results_page(): ) start_vars = {} for key, value in list(initial_start_vars.items()): - if key in wanted or key.startswith(('value:')): + if key in wanted: start_vars[key] = value - #logger.debug("Mapping called with start_vars:", start_vars) version = "v3" key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True) - #logger.info("key is:", pf(key)) with Bench("Loading cache"): result = None # Just for testing #result = Redis.get(key) @@ -804,10 +802,6 @@ def mapping_results_page(): rendered_template = render_template("pair_scan_results.html", **result) else: gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ - #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - #logger.info("pickled result length:", len(pickled_result)) - #Redis.set(key, pickled_result) - #Redis.expire(key, 1*60) with Bench("Rendering template"): #if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): |