diff options
| -rwxr-xr-x | scripts/maintenance/readProbeSetSE_v7.py | 6 | ||||
| -rw-r--r-- | wqflask/tests/utility/test_hmac.py | 13 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/test_user_session.py | 15 | ||||
| -rw-r--r-- | wqflask/utility/hmac.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/plink_mapping.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/export_trait_data.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/snp_browser/snp_browser.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 73 |
9 files changed, 110 insertions, 29 deletions
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index edd9e7b0..2cfe2e07 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -72,14 +72,14 @@ GeneList = [] isCont = 1 header = fp.readline() header = header.strip().split('\t') -header = list(map(string.strip, header)) +header = [item.strip() for item in header] nfield = len(header) line = fp.readline() kj = 0 while line: line2 = line.strip().split('\t') - line2 = list(map(string.strip, line2)) + line2 = [item.strip() for item in line2] if len(line2) != nfield: isCont = 0 print(("Error : " + line)) @@ -110,7 +110,7 @@ isCont = 1 fp.seek(0) header = fp.readline() header = header.strip().split('\t') -header = list(map(string.strip, header)) +header = [item.strip() for item in header] header = list(map(translateAlias, header)) header = header[dataStart:] Ids = [] diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py index 7c61c0a6..4e3652f8 100644 --- a/wqflask/tests/utility/test_hmac.py +++ b/wqflask/tests/utility/test_hmac.py @@ -17,6 +17,19 @@ class TestHmacUtil(unittest.TestCase): """Test hmac creation with a utf-8 string""" self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946") + @mock.patch("utility.hmac.app.config", + {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80' + '\xd9\\H@\\\x9f`\x98d^' + '\xb4a;\xc6OM\x946a\xbc' + '\xfc\x80:*\xebc')}) + def test_hmac_creation_with_cookie(self): + """Test hmac creation with a cookie""" + cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce" + uuid_, _, signature = cookie.partition(":") + self.assertEqual( + hmac_creation(uuid_), + "af4fcf5eace9e7c864ce") + @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"}) def test_data_hmac(self): """Test data_hmac fn with a utf-8 string""" diff --git a/wqflask/tests/wqflask/test_user_session.py b/wqflask/tests/wqflask/test_user_session.py new file mode 100644 index 00000000..ebb0334a --- /dev/null +++ b/wqflask/tests/wqflask/test_user_session.py @@ -0,0 +1,15 @@ +"""Test cases for some methods in user_session.py""" + +import unittest +from wqflask.user_session import verify_cookie + + +class TestUserSession(unittest.TestCase): + def test_verify_cookie(self): + """ + Test cookie verification + """ + self.assertEqual( + "3f4c1dbf-5b56-4260-87d6-f35445bda37e", + verify_cookie(("3f4c1dbf-5b56-4260-87d6-" + "f35445bda37e:af4fcf5eace9e7c864ce"))) diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py index 6623f69a..29891677 100644 --- a/wqflask/utility/hmac.py +++ b/wqflask/utility/hmac.py @@ -10,7 +10,7 @@ def hmac_creation(stringy): """Helper function to create the actual hmac""" secret = app.config['SECRET_HMAC_CODE'] - hmaced = hmac.new(bytearray(secret, "utf-8"), + hmaced = hmac.new(bytearray(secret, "latin-1"), bytearray(stringy, "utf-8"), hashlib.sha1) hm = hmaced.hexdigest() diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index aa3f8518..65eba7e3 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -2809,7 +2809,7 @@ class DisplayMappingResults(object): f"end={theGO['TxEnd']}&" f"geneName={theGO['GeneSymbol']}&" f"s1={self.diffCol[0]}&s2=%d"), - theGO["snpCount"] # The text to display + str(theGO["snpCount"]) # The text to display ) snpString.set_blank_target() snpString.set_attribute("class", "normalsize") diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 6c38c34f..fd91b6ca 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -84,7 +84,7 @@ def get_samples_from_ped_file(dataset): while line: lineList = line.strip().split('\t') - lineList = list(map(string.strip, lineList)) + lineList = [item.strip() for item in lineList] sample_name = lineList[0] sample_list.append(sample_name) @@ -157,6 +157,6 @@ def parse_plink_output(output_filename, species): def build_line_list(line=None): line_list = line.strip().split(' ')# irregular number of whitespaces between columns line_list = [item for item in line_list if item !=''] - line_list = list(map(string.strip, line_list)) + line_list = [item.strip() for item in line_list] return line_list 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/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py index 2df71b12..6c3fcf53 100644 --- a/wqflask/wqflask/snp_browser/snp_browser.py +++ b/wqflask/wqflask/snp_browser/snp_browser.py @@ -457,7 +457,7 @@ class SnpBrowser(object): function_list = [] if function_details: function_list = function_details.strip().split(",") - function_list = list(map(string.strip, function_list)) + function_list = [item.strip() for item in function_list] function_list[0] = function_list[0].title() function_details = ", ".join(item for item in function_list) function_details = function_details.replace("_", " ") @@ -723,11 +723,11 @@ def get_effect_details_by_category(effect_name = None, effect_value = None): codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous'] effect_detail_list = effect_value.strip().split('|') - effect_detail_list = list(map(string.strip, effect_detail_list)) + effect_detail_list = [item.strip() for item in effect_detail_list] for index, item in enumerate(effect_detail_list): item_list = item.strip().split(',') - item_list = list(map(string.strip, item_list)) + item_list = [item.strip() for item in item_list] gene_id = item_list[0] gene_name = item_list[1] 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() { |