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authorzsloan2016-04-13 21:16:22 +0000
committerzsloan2016-04-13 21:16:22 +0000
commit15b3a1543f59a097039ae964ba26775236022401 (patch)
treec63bcffbe06edb5d250c81623ee70cf36bc6b20a /wqflask/base/trait.py
parent2b47c104b3baeb2871f7669cef41ab5a112779ea (diff)
downloadgenenetwork2-15b3a1543f59a097039ae964ba26775236022401.tar.gz
Moved the code getting the description/location because it was throwing an error for phenotype traits
Diffstat (limited to 'wqflask/base/trait.py')
-rw-r--r--wqflask/base/trait.py75
1 files changed, 38 insertions, 37 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 51a4d986..6c5ca8b2 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -308,42 +308,6 @@ class GeneralTrait(object):
if isinstance(trait_info[i], basestring):
holder = unicode(trait_info[i], "utf8", "ignore")
setattr(self, field, holder)
-
- description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
- if len(description_string) > 1 and description_string != 'None':
- description_display = description_string
- else:
- description_display = self.symbol
-
- if (len(description_display) > 1 and description_display != 'N/A' and
- len(target_string) > 1 and target_string != 'None'):
- description_display = description_display + '; ' + target_string.strip()
-
- # Save it for the jinja2 template
- self.description_display = description_display
-
- #XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
- trait_location_value = 1000000
-
- if self.chr and self.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = convert_location_to_value(self.chr, self.mb)
- #try:
- # trait_location_value = int(self.chr)*1000 + self.mb
- #except ValueError:
- # if self.chr.upper() == 'X':
- # trait_location_value = 20*1000 + self.mb
- # else:
- # trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
- # self.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
- self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
- self.location_value = trait_location_value
if self.dataset.type == 'Publish':
self.confidential = 0
@@ -378,8 +342,8 @@ class GeneralTrait(object):
if self.pubmed_id:
self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
+
self.homologeneid = None
-
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.
@@ -407,6 +371,43 @@ class GeneralTrait(object):
if result:
self.homologeneid = result[0]
+
+ description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
+ target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+
+ if len(description_string) > 1 and description_string != 'None':
+ description_display = description_string
+ else:
+ description_display = self.symbol
+
+ if (len(description_display) > 1 and description_display != 'N/A' and
+ len(target_string) > 1 and target_string != 'None'):
+ description_display = description_display + '; ' + target_string.strip()
+
+ # Save it for the jinja2 template
+ self.description_display = description_display
+
+ #XZ: trait_location_value is used for sorting
+ trait_location_repr = 'N/A'
+ trait_location_value = 1000000
+
+ if self.chr and self.mb:
+ #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+ #This is so we can convert the location to a number used for sorting
+ trait_location_value = convert_location_to_value(self.chr, self.mb)
+ #try:
+ # trait_location_value = int(self.chr)*1000 + self.mb
+ #except ValueError:
+ # if self.chr.upper() == 'X':
+ # trait_location_value = 20*1000 + self.mb
+ # else:
+ # trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
+ # self.mb)
+
+ #ZS: Put this in function currently called "convert_location_to_value"
+ self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
+ self.location_value = trait_location_value
+
if get_qtl_info:
#LRS and its location