From 4a3c48c4b91c0cce9d7d0e9896be893d6e80a883 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Sat, 25 Jan 2014 00:29:35 -0600
Subject: On branch master
---
.../maintenance/dataset/phenotypes/phenotypes.py | 24 +++++++++++++++++-----
1 file changed, 19 insertions(+), 5 deletions(-)
(limited to 'wqflask/maintenance')
diff --git a/wqflask/maintenance/dataset/phenotypes/phenotypes.py b/wqflask/maintenance/dataset/phenotypes/phenotypes.py
index 08fc1432..821e5687 100644
--- a/wqflask/maintenance/dataset/phenotypes/phenotypes.py
+++ b/wqflask/maintenance/dataset/phenotypes/phenotypes.py
@@ -50,9 +50,9 @@ def fetch():
print "get %d phenotypes" % (len(results))
for phenotyperow in results:
publishxrefid = phenotyperow[0]
- original_description = phenotyperow[1]
- pre_publication_description = phenotyperow[2]
- post_publication_description = phenotyperow[3]
+ original_description = clearspaces(phenotyperow[1])
+ pre_publication_description = clearspaces(phenotyperow[2])
+ post_publication_description = clearspaces(phenotyperow[3])
phenotypesfile.write("%s\t%s\t%s\t%s\t" % (publishxrefid, original_description, pre_publication_description, post_publication_description))
sql = """
SELECT Strain.Name, PublishData.value
@@ -71,10 +71,24 @@ def fetch():
strainname = strainname.lower()
value = strainvalue[1]
strainvaluedic[strainname] = value
- print strainvaluedic
- break
+ for strain in strains:
+ if strain in strainvaluedic:
+ phenotypesfile.write(str(strainvaluedic[strain]))
+ else:
+ phenotypesfile.write('x')
+ phenotypesfile.write('\t')
+ phenotypesfile.write('\n')
+ phenotypesfile.flush()
# release
phenotypesfile.close()
+
+def clearspaces(s):
+ if s:
+ s = re.sub('\s+', ' ', s)
+ s = s.strip()
+ return s
+ else:
+ return None
# main
if __name__ == "__main__":
--
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