From ba2909f7dd931688f344536c422bb4ac27a3a183 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 11 Apr 2016 17:15:18 +0000
Subject: Changed the way trait data is retrieved for the global search page
(it now gets the LRS location repr and other variables needed to display in
table during the retrieve_info function in trait.py instead of
retrieve_trait_info in dataset.py) This change increases the speed by a bit
(85 seconds to 66 seconds for example)
Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
---
wqflask/base/trait.py | 78 ++++++++++++++++++++++++++++++++++++++++++---------
1 file changed, 64 insertions(+), 14 deletions(-)
mode change 100755 => 100644 wqflask/base/trait.py
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
old mode 100755
new mode 100644
index acff38d9..ce3a7608
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -256,10 +256,10 @@ class GeneralTrait(object):
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
-
- #print("query is:", query)
trait_info = g.db.execute(query).fetchone()
+
+
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif self.dataset.type == 'ProbeSet':
@@ -294,7 +294,6 @@ class GeneralTrait(object):
escape(self.dataset.name),
escape(self.name))
trait_info = g.db.execute(query).fetchone()
- #print("trait_info is: ", pf(trait_info))
else: #Temp type
query = """SELECT %s FROM %s WHERE Name = %s"""
trait_info = g.db.execute(query,
@@ -305,7 +304,6 @@ class GeneralTrait(object):
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(self.dataset.display_fields):
- #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
holder = trait_info[i]
if isinstance(trait_info[i], basestring):
holder = unicode(trait_info[i], "utf8", "ignore")
@@ -315,12 +313,37 @@ class GeneralTrait(object):
self.confidential = 0
if self.pre_publication_description and not self.pubmed_id:
self.confidential = 1
+
+ description = self.post_publication_description
+
+ #If the dataset is confidential and the user has access to confidential
+ #phenotype traits, then display the pre-publication description instead
+ #of the post-publication description
+ if self.confidential:
+ self.description_display = ""
+
+ #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
+ # privilege=self.dataset.privilege,
+ # userName=self.dataset.userName,
+ # authorized_users=self.authorized_users):
+ #
+ # description = self.pre_publication_description
+
+ if len(description) > 0:
+ self.description_display = description.strip()
+ else:
+ self.description_display = ""
+ if not self.year.isdigit():
+ self.pubmed_text = "N/A"
+ else:
+ self.pubmed_text = self.year
+
+ if self.pubmed_id:
+ self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
+
self.homologeneid = None
- #print("self.geneid is:", self.geneid)
- #print(" type:", type(self.geneid))
- #print("self.dataset.group.name is:", self.dataset.group.name)
if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid:
#XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
#XZ: So I have to test if geneid is number before execute the query.
@@ -330,10 +353,7 @@ class GeneralTrait(object):
# geneidIsNumber = True
#except ValueError:
# geneidIsNumber = False
-
#if geneidIsNumber:
-
-
query = """
SELECT
HomologeneId
@@ -353,6 +373,11 @@ class GeneralTrait(object):
self.homologeneid = result[0]
if get_qtl_info:
+ #LRS and its location
+ self.LRS_score_repr = "N/A"
+ self.LRS_score_value = 0
+ self.LRS_location_repr = "N/A"
+ self.LRS_location_value = 1000000
if self.dataset.type == 'ProbeSet' and not self.cellid:
query = """
SELECT
@@ -365,12 +390,8 @@ class GeneralTrait(object):
ProbeSetXRef.ProbeSetFreezeId ={}
""".format(self.name, self.dataset.id)
trait_qtl = g.db.execute(query).fetchone()
- #self.cursor.execute(query)
- #trait_qtl = self.cursor.fetchone()
if trait_qtl:
- #print("trait_qtl:", trait_qtl)
self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl
- #print("self.locus:", self.locus)
if self.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
@@ -403,8 +424,37 @@ class GeneralTrait(object):
""", (self.name, self.dataset.id)).fetchone()
if trait_qtl:
self.locus, self.lrs, self.additive = trait_qtl
+ if self.locus:
+ query = """
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = '{}' and
+ Geno.Name = '{}' and
+ Geno.SpeciesId = Species.Id
+ """.format(self.dataset.group.species, self.locus)
+ result = g.db.execute(query).fetchone()
+ if result:
+ self.locus_chr = result[0]
+ self.locus_mb = result[1]
+ else:
+ self.locus = self.locus_chr = self.locus_mb = ""
+ else:
+ self.locus = self.locus_chr = self.locus_mb = ""
else:
self.locus = self.lrs = self.additive = ""
+
+ if self.locus_chr != "" and self.locus_mb != "":
+ #XZ: LRS_location_value is used for sorting
+ try:
+ LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb)
+ except:
+ if self.locus_chr.upper() == 'X':
+ LRS_location_value = 20*1000 + float(self.locus_mb)
+ else:
+ LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb)
+
+ self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb))
+ self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs
+ self.LRS_score_value = LRS_score_value = self.lrs
else:
raise KeyError, `self.name`+' information is not found in the database.'
--
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