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-rw-r--r--wqflask/wqflask/gsearch.py135
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html11
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",
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-27 13:33:48 +0000