diff options
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/export_trait_data.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 73 |
3 files changed, 73 insertions, 20 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 5b26e372..9e46c0c5 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -35,7 +35,7 @@ class GSearch(object): ProbeSetFreeze.FullName AS probesetfreeze_fullname, ProbeSet.Name AS probeset_name, ProbeSet.Symbol AS probeset_symbol, - ProbeSet.`description` AS probeset_description, + CAST(ProbeSet.`description` AS BINARY) AS probeset_description, ProbeSet.Chr AS chr, ProbeSet.Mb AS mb, ProbeSetXRef.Mean AS mean, diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py index 48feb492..379b746c 100644 --- a/wqflask/wqflask/show_trait/export_trait_data.py +++ b/wqflask/wqflask/show_trait/export_trait_data.py @@ -14,10 +14,16 @@ def export_sample_table(targs): final_sample_data = meta_data + column_headers = ["Name", "Value"] + if any(sample["se"] for sample in sample_data['primary_samples']): + column_headers.append("SE") + if any(sample["num_cases"] for sample in sample_data['primary_samples']): + column_headers.append("N") + + final_sample_data.append(column_headers) for sample_group in ['primary_samples', 'other_samples']: for row in sample_data[sample_group]: sorted_row = dict_to_sorted_list(row) - print("sorted_row is:", pf(sorted_row)) final_sample_data.append(sorted_row) return trait_name, final_sample_data @@ -39,7 +45,15 @@ def get_export_metadata(trait_id, dataset_name): metadata.append(["Title: " + (this_trait.title if this_trait.title else "N/A")]) metadata.append(["Journal: " + (this_trait.journal if this_trait.journal else "N/A")]) metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name]) - metadata.append([]) + else: + metadata.append(["Record ID: " + trait_id]) + metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name]) + if this_trait.symbol: + metadata.append(["Symbol: " + this_trait.symbol]) + metadata.append(["Dataset: " + dataset.name]) + metadata.append(["Group: " + dataset.group.name]) + + metadata.append([]) return metadata diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 397adb52..a34811f8 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -885,26 +885,65 @@ $('#qnorm').click(switch_qnorm_data); get_sample_table_data = function(table_name) { var samples; samples = []; - $('#' + table_name).find('.value_se').each((function(_this) { - return function(_index, element) { - var attribute_info, key, row_data, _ref; - row_data = {}; - row_data.name = $.trim($(element).find('.column_name-Sample').text()); - row_data.value = $(element).find('.edit-sample-value:eq(0)').val(); - if ($(element).find('.edit-sample-se').length > 0) { - row_data.se = $(element).find('.edit-sample-se').val(); + + var se_exists = false; + var n_exists = false; + + if ($('#' + table_name).length){ + table_api = $('#' + table).DataTable(); + sample_vals = []; + + name_nodes = table_api.column(2).nodes().to$(); + val_nodes = table_api.column(3).nodes().to$(); + if (js_data.se_exists){ + var_nodes = table_api.column(5).nodes().to$(); + if (js_data.has_num_cases) { + n_nodes = table_api.column(6).nodes().to$(); } - if ($(element).find('.edit_sample_num_cases').length > 0) { - row_data.num_cases = $(element).find('.edit_sample_num_cases').val(); + } else { + if (js_data.has_num_cases){ + n_nodes = table_api.column(4).nodes().to$(); } - attr_keys = Object.keys(js_data.attributes).sort() - for (i=0; i < attr_keys.length; i++) { - attribute_info = js_data.attributes[attr_keys[i]]; - row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_").replace("/", "\\/")).text()); + } + + for (_j = 0; _j < val_nodes.length; _j++){ + sample_val = val_nodes[_j].childNodes[0].value + sample_name = $.trim(name_nodes[_j].childNodes[0].textContent) + if (is_number(sample_val) && sample_val !== "") { + sample_val = parseFloat(sample_val); + if (typeof var_nodes == 'undefined'){ + sample_var = null; + } else { + sample_var = var_nodes[_j].childNodes[0].value; + if (is_number(sample_var)) { + sample_var = parseFloat(sample_var); + se_exists = true; + } else { + sample_var = null; + } + } + if (typeof n_nodes == 'undefined'){ + sample_n = null; + } else { + sample_n = n_nodes[_j].childNodes[0].value; + if (is_number(sample_n)) { + n_exists = true; + sample_n = parseInt(sample_n); + } else { + sample_n = null; + } + } + row_dict = { + name: sample_name, + value: sample_val, + se: sample_var, + num_cases: sample_n + } + samples.push(row_dict) } - return samples.push(row_data); - }; - })(this)); + } + } + return samples; }; export_sample_table_data = function() { |