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-rw-r--r--wqflask/wqflask/gsearch.py76
1 files changed, 40 insertions, 36 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 8f66f7e9..e541b705 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -92,19 +92,30 @@ class GSearch:
if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
this_trait['location_repr'] = 'Chr%s: %.6f' % (
line[8], float(line[9]))
- try:
- this_trait['mean'] = '%.3f' % line[10]
- except:
- this_trait['mean'] = "N/A"
+
this_trait['LRS_score_repr'] = "N/A"
+ this_trait['additive'] = "N/A"
+ this_trait['mean'] = "N/A"
+
if line[11] != "" and line[11] != None:
- this_trait['LRS_score_repr'] = '%3.1f' % line[11]
+ this_trait['LRS_score_repr'] = f"{line[11]:.3f}"
+ if line[14] != "" and line[14] != None:
+ this_trait['additive'] = f"{line[14]:.3f}"
+ if line[10] != "" and line[10] != None:
+ this_trait['mean'] = f"{line[10]:.3f}"
+
+ locus_chr = line[16]
+ locus_mb = line[17]
+
+ 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['additive'] = "N/A"
if line[14] != "" and line[14] != None:
this_trait['additive'] = '%.3f' % line[14]
this_trait['dataset_id'] = line[15]
- this_trait['locus_chr'] = line[16]
- this_trait['locus_mb'] = line[17]
dataset_ob = SimpleNamespace(
id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"])
@@ -120,11 +131,6 @@ class GSearch:
if permissions['data'] == 'no-access':
continue
- max_lrs_text = "N/A"
- if this_trait['locus_chr'] and this_trait['locus_mb']:
- max_lrs_text = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}"
- this_trait['max_lrs_text'] = max_lrs_text
-
trait_list.append(this_trait)
self.trait_count = len(trait_list)
@@ -230,32 +236,38 @@ class GSearch:
'utf-8', 'replace')
else:
this_trait['description'] = "N/A"
- if line[13] != None and line[13] != "":
- this_trait['mean'] = f"{line[13]:.3f}"
- else:
- this_trait['mean'] = "N/A"
this_trait['dataset_id'] = line[14]
- this_trait['locus_chr'] = line[15]
- this_trait['locus_mb'] = line[16]
+
+ this_trait['LRS_score_repr'] = "N/A"
+ this_trait['additive'] = "N/A"
+ this_trait['mean'] = "N/A"
+
+ if line[10] != "" and line[10] != None:
+ this_trait['LRS_score_repr'] = f"{line[10]:.3f}"
+ if line[11] != "" and line[11] != None:
+ this_trait['additive'] = f"{line[11]:.3f}"
+ if line[13] != "" and line[13] != None:
+ this_trait['mean'] = f"{line[13]:.3f}"
+
+ locus_chr = line[16]
+ locus_mb = line[17]
+
+ 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']
- else:
- this_trait['pubmed_text'] = "N/A"
if line[9] != "" and line[9] != None:
this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
- else:
- this_trait['pubmed_link'] = "N/A"
if line[12]:
this_trait['display_name'] = line[12] + \
"_" + str(this_trait['name'])
- this_trait['LRS_score_repr'] = "N/A"
- if line[10] != "" and line[10] != None:
- this_trait['LRS_score_repr'] = '%3.1f' % line[10]
- this_trait['additive'] = "N/A"
- if line[11] != "" and line[11] != None:
- this_trait['additive'] = '%.3f' % line[11]
dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"])
permissions = check_resource_availability(dataset_ob, this_trait['name'])
@@ -266,14 +278,6 @@ class GSearch:
if permissions['data'] == 'no-access':
continue
- this_trait['max_lrs_text'] = "N/A"
- if this_trait['dataset'] == this_trait['group'] + "Publish":
- try:
- if this_trait['locus_chr'] and this_trait['locus_mb']:
- this_trait['max_lrs_text'] = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}"
- except:
- this_trait['max_lrs_text'] = "N/A"
-
trait_list.append(this_trait)
self.trait_count = len(trait_list)