diff options
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 135 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_pheno.html | 11 |
2 files changed, 72 insertions, 74 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 53a124d0..9df7b2e1 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -72,38 +72,38 @@ class GSearch: dataset_to_permissions = {} with Bench("Creating trait objects"): for i, line in enumerate(re): - this_trait = {} - this_trait['index'] = i + 1 - this_trait['name'] = line[5] - this_trait['dataset'] = line[3] - this_trait['dataset_fullname'] = line[4] - this_trait['hmac'] = hmac.data_hmac( + trait_dict = {} + trait_dict['index'] = i + 1 + trait_dict['name'] = line[5] + trait_dict['dataset'] = line[3] + trait_dict['dataset_fullname'] = line[4] + trait_dict['hmac'] = hmac.data_hmac( '{}:{}'.format(line[5], line[3])) - this_trait['species'] = line[0] - this_trait['group'] = line[1] - this_trait['tissue'] = line[2] - this_trait['symbol'] = "N/A" + trait_dict['species'] = line[0] + trait_dict['group'] = line[1] + trait_dict['tissue'] = line[2] + trait_dict['symbol'] = "N/A" if line[6]: - this_trait['symbol'] = line[6] - this_trait['description'] = "N/A" + trait_dict['symbol'] = line[6] + trait_dict['description'] = "N/A" if line[7]: - this_trait['description'] = line[7].decode( + trait_dict['description'] = line[7].decode( 'utf-8', 'replace') - this_trait['location_repr'] = "N/A" + trait_dict['location_repr'] = "N/A" if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): - this_trait['location_repr'] = 'Chr%s: %.6f' % ( + trait_dict['location_repr'] = 'Chr%s: %.6f' % ( line[8], float(line[9])) - this_trait['LRS_score_repr'] = "N/A" - this_trait['additive'] = "N/A" - this_trait['mean'] = "N/A" + trait_dict['LRS_score_repr'] = "N/A" + trait_dict['additive'] = "N/A" + trait_dict['mean'] = "N/A" if line[11] != "" and line[11] != None: - this_trait['LRS_score_repr'] = f"{line[11]:.3f}" + trait_dict['LRS_score_repr'] = f"{line[11]:.3f}" if line[14] != "" and line[14] != None: - this_trait['additive'] = f"{line[14]:.3f}" + trait_dict['additive'] = f"{line[14]:.3f}" if line[10] != "" and line[10] != None: - this_trait['mean'] = f"{line[10]:.3f}" + trait_dict['mean'] = f"{line[10]:.3f}" locus_chr = line[16] locus_mb = line[17] @@ -111,15 +111,15 @@ class GSearch: max_lrs_text = "N/A" if locus_chr and locus_mb: max_lrs_text = f"Chr{locus_chr}: {locus_mb}" - this_trait['max_lrs_text'] = max_lrs_text + trait_dict['max_lrs_text'] = max_lrs_text - this_trait['additive'] = "N/A" + trait_dict['additive'] = "N/A" if line[14] != "" and line[14] != None: - this_trait['additive'] = '%.3f' % line[14] - this_trait['dataset_id'] = line[15] + trait_dict['additive'] = '%.3f' % line[14] + trait_dict['dataset_id'] = line[15] dataset_ob = SimpleNamespace( - id=this_trait["dataset_id"], type="ProbeSet", name=this_trait["dataset"], species=this_trait["species"]) + id=trait_dict["dataset_id"], type="ProbeSet", name=trait_dict["dataset"], species=trait_dict["species"]) if dataset_ob.id not in dataset_to_permissions: permissions = check_resource_availability(dataset_ob) dataset_to_permissions[dataset_ob.id] = permissions @@ -132,7 +132,7 @@ class GSearch: if permissions['data'] == 'no-access': continue - trait_list.append(this_trait) + trait_list.append(trait_dict) self.trait_count = len(trait_list) self.trait_list = trait_list @@ -215,43 +215,43 @@ class GSearch: trait_list = [] with Bench("Creating trait objects"): for i, line in enumerate(re): - this_trait = {} - this_trait['index'] = i + 1 - this_trait['name'] = str(line[4]) + trait_dict = {} + trait_dict['index'] = i + 1 + trait_dict['name'] = str(line[4]) if len(str(line[12])) == 3: - this_trait['display_name'] = str( - line[12]) + "_" + this_trait['name'] + trait_dict['display_name'] = str( + line[12]) + "_" + trait_dict['name'] else: - this_trait['display_name'] = this_trait['name'] - this_trait['dataset'] = line[2] - this_trait['dataset_fullname'] = line[3] - this_trait['hmac'] = hmac.data_hmac( + trait_dict['display_name'] = trait_dict['name'] + trait_dict['dataset'] = line[2] + trait_dict['dataset_fullname'] = line[3] + trait_dict['hmac'] = hmac.data_hmac( '{}:{}'.format(line[4], line[2])) - this_trait['species'] = line[0] - this_trait['group'] = line[1] + trait_dict['species'] = line[0] + trait_dict['group'] = line[1] if line[9] != None and line[6] != None: - this_trait['description'] = line[6].decode( + trait_dict['description'] = line[6].decode( 'utf-8', 'replace') elif line[5] != None: - this_trait['description'] = line[5].decode( + trait_dict['description'] = line[5].decode( 'utf-8', 'replace') else: - this_trait['description'] = "N/A" - this_trait['dataset_id'] = line[14] + trait_dict['description'] = "N/A" + trait_dict['dataset_id'] = line[14] - this_trait['LRS_score_repr'] = "N/A" - this_trait['additive'] = "N/A" - this_trait['mean'] = "N/A" + trait_dict['LRS_score_repr'] = "N/A" + trait_dict['additive'] = "N/A" + trait_dict['mean'] = "N/A" if line[10] != "" and line[10] != None: - this_trait['LRS_score_repr'] = f"{line[10]:.3f}" + trait_dict['LRS_score_repr'] = f"{line[10]:.3f}" # Some Max LRS values in the DB are wrongly listed as 0.000, but shouldn't be displayed - if this_trait['LRS_score_repr'] == "0.000": - this_trait['LRS_score_repr'] = "N/A" + if trait_dict['LRS_score_repr'] == "0.000": + trait_dict['LRS_score_repr'] = "N/A" if line[11] != "" and line[11] != None: - this_trait['additive'] = f"{line[11]:.3f}" + trait_dict['additive'] = f"{line[11]:.3f}" if line[13] != "" and line[13] != None: - this_trait['mean'] = f"{line[13]:.3f}" + trait_dict['mean'] = f"{line[13]:.3f}" locus_chr = line[15] locus_mb = line[16] @@ -259,22 +259,29 @@ class GSearch: max_lrs_text = "N/A" if locus_chr and locus_mb: max_lrs_text = f"Chr{locus_chr}: {locus_mb}" - this_trait['max_lrs_text'] = max_lrs_text - - this_trait['authors'] = line[7] - this_trait['year'] = line[8] - this_trait['pubmed_text'] = "N/A" - this_trait['pubmed_link'] = "N/A" - if this_trait['year'].isdigit(): - this_trait['pubmed_text'] = this_trait['year'] + trait_dict['max_lrs_text'] = max_lrs_text + + trait_dict['authors'] = line[7] + + trait_dict['authors'] = line[7] + trait_dict['authors_display'] = trait_dict['authors'] + author_list = trait_dict['authors'].split(",") + if len(author_list) >= 2: + trait_dict['authors_display'] = (",").join(author_list[:2]) + ", et al." + + trait_dict['year'] = line[8] + trait_dict['pubmed_text'] = "N/A" + trait_dict['pubmed_link'] = "N/A" + if trait_dict['year'].isdigit(): + trait_dict['pubmed_text'] = trait_dict['year'] if line[9] != "" and line[9] != None: - this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8] + trait_dict['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8] if line[12]: - this_trait['display_name'] = line[12] + \ - "_" + str(this_trait['name']) + trait_dict['display_name'] = line[12] + \ + "_" + str(trait_dict['name']) - dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"]) - permissions = check_resource_availability(dataset_ob, this_trait['name']) + dataset_ob = SimpleNamespace(id=trait_dict["dataset_id"], type="Publish", species=trait_dict["species"]) + permissions = check_resource_availability(dataset_ob, trait_dict['name']) if type(permissions['data']) is list: if "view" not in permissions['data']: continue @@ -282,7 +289,7 @@ class GSearch: if permissions['data'] == 'no-access': continue - trait_list.append(this_trait) + trait_list.append(trait_dict) self.trait_count = len(trait_list) self.trait_list = trait_list diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index a7357b03..0d18a0bf 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -146,16 +146,7 @@ 'type': "natural", 'width': "300px", 'targets': 7, - 'data': null, - 'render': function(data) { - author_list = data.authors.split(",") - if (author_list.length >= 6) { - author_string = author_list.slice(0, 6).join(",") + ", et al." - } else{ - author_string = data.authors - } - return author_string - } + 'data': "authors_display" }, { 'title': "Year", |