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| author | Lei Yan | 2014-02-03 12:48:37 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-03 12:48:37 -0600 |
| commit | 818797d2fd7e425da47cf12ddab6001e3234c2e5 (patch) | |
| tree | 0e62f3f1cacbafa6a75528d2a39eb6acd46b0b2e | |
| parent | b462fae9df948dbf35232a764d61fbf10c930e82 (diff) | |
| download | genenetwork2-818797d2fd7e425da47cf12ddab6001e3234c2e5.tar.gz | |
On branch master
| -rw-r--r-- | wqflask/maintenance/dataset/phenotypes.py | 27 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/utilities.py (renamed from wqflask/maintenance/dataset/db.py) | 0 |
2 files changed, 13 insertions, 14 deletions
diff --git a/wqflask/maintenance/dataset/phenotypes.py b/wqflask/maintenance/dataset/phenotypes.py index 821e5687..ae1e82cc 100644 --- a/wqflask/maintenance/dataset/phenotypes.py +++ b/wqflask/maintenance/dataset/phenotypes.py @@ -6,6 +6,8 @@ import os import re import MySQLdb +import utilities + def fetch(): # parameters inbredsetid = 1 @@ -13,12 +15,7 @@ def fetch(): # phenotypesfile.write("id\tOriginal_description\tPre_publication_description\tPost_publication_description\t") # open db - host = 'localhost' - user = 'webqtl' - passwd = 'webqtl' - db = 'db_webqtl' - con = MySQLdb.Connect(db=db, user=user, passwd=passwd, host=host) - cursor = con.cursor() + cursor = utilities.get_cursor() # get strain list strains = [] sql = """ @@ -40,20 +37,22 @@ def fetch(): phenotypesfile.flush() # phenotypes sql = """ - SELECT PublishXRef.`Id`, Phenotype.`Original_description`, Phenotype.`Pre_publication_description`, Phenotype.`Post_publication_description` - FROM (PublishXRef, Phenotype) - WHERE PublishXRef.`PhenotypeId`=Phenotype.`Id` - AND PublishXRef.`InbredSetId`=%s + SELECT PublishXRef.`Id`, Publication.`Authors`, Phenotype.`Original_description`, Phenotype.`Pre_publication_description`, Phenotype.`Post_publication_description` + FROM (PublishXRef, Phenotype, Publication) + WHERE PublishXRef.`InbredSetId`=%s + AND PublishXRef.`PhenotypeId`=Phenotype.`Id` + AND PublishXRef.`PublicationId`=Publication.`Id` """ cursor.execute(sql, (inbredsetid)) results = cursor.fetchall() print "get %d phenotypes" % (len(results)) for phenotyperow in results: publishxrefid = phenotyperow[0] - 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)) + authors = clearspaces(phenotyperow[1]) + original_description = clearspaces(phenotyperow[2]) + pre_publication_description = clearspaces(phenotyperow[3]) + post_publication_description = clearspaces(phenotyperow[4]) + phenotypesfile.write("%s\t%s\t%s\t%s\t" % (publishxrefid, authors, original_description, pre_publication_description, post_publication_description)) sql = """ SELECT Strain.Name, PublishData.value FROM (PublishXRef, PublishData, Strain) diff --git a/wqflask/maintenance/dataset/db.py b/wqflask/maintenance/dataset/utilities.py index 453ee707..453ee707 100644 --- a/wqflask/maintenance/dataset/db.py +++ b/wqflask/maintenance/dataset/utilities.py |