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authorroot2014-02-20 14:33:26 -0600
committerroot2014-02-20 14:33:26 -0600
commit22d6fcf01a61581b8c2a5ed478a01787afbaeabd (patch)
tree4cd9b7001663ef6143caf07573898c3018d7bf2b /wqflask/maintenance
parent19e66ab781c7b0725b8739ecb1b5dc77d2537ec0 (diff)
downloadgenenetwork2-22d6fcf01a61581b8c2a5ed478a01787afbaeabd.tar.gz
Committer: root <root@alexandria.uthsc.edu>
On branch master
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/dataset/datastructure.py25
-rw-r--r--wqflask/maintenance/dataset/load_phenotypes.py14
2 files changed, 30 insertions, 9 deletions
diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
index ce588c78..b2af5777 100644
--- a/wqflask/maintenance/dataset/datastructure.py
+++ b/wqflask/maintenance/dataset/datastructure.py
@@ -1,7 +1,7 @@
import utilities
def get_probesetfreezes(inbredsetid):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
FROM ProbeSetFreeze, ProbeFreeze
@@ -12,7 +12,7 @@ def get_probesetfreezes(inbredsetid):
return cursor.fetchall()
def get_probesetfreeze(probesetfreezeid):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
FROM ProbeSetFreeze
@@ -22,7 +22,7 @@ def get_probesetfreeze(probesetfreezeid):
return cursor.fetchone()
def get_strains(inbredsetid):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT Strain.`Id`, Strain.`Name`
FROM StrainXRef, Strain
@@ -34,7 +34,7 @@ def get_strains(inbredsetid):
return cursor.fetchall()
def get_inbredset(probesetfreezeid):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT InbredSet.`Id`, InbredSet.`Name`, InbredSet.`FullName`
FROM InbredSet, ProbeFreeze, ProbeSetFreeze
@@ -44,9 +44,20 @@ def get_inbredset(probesetfreezeid):
"""
cursor.execute(sql, (probesetfreezeid))
return cursor.fetchone()
+
+def get_species(inbredsetid):
+ cursor, con = utilities.get_cursor()
+ sql = """
+ SELECT Species.`Id`, Species.`Name`, Species.`MenuName`, Species.`FullName`
+ FROM InbredSet, Species
+ WHERE InbredSet.`Id`=%s
+ AND InbredSet.`SpeciesId`=Species.`Id`
+ """
+ cursor.execute(sql, (inbredsetid))
+ return cursor.fetchone()
def get_nextdataid_phenotype():
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT PublishData.`Id`
FROM PublishData
@@ -60,7 +71,7 @@ def get_nextdataid_phenotype():
return dataid
def insert_strain(speciesid, strainname):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
INSERT INTO Strain
SET
@@ -71,7 +82,7 @@ def insert_strain(speciesid, strainname):
cursor.execute(sql, (strainname, strainname, speciesid))
def get_strain(speciesid, strainname):
- cursor = utilities.get_cursor()
+ cursor, con = utilities.get_cursor()
sql = """
SELECT Strain.`Id`, Strain.`Name`
FROM Strain
diff --git a/wqflask/maintenance/dataset/load_phenotypes.py b/wqflask/maintenance/dataset/load_phenotypes.py
index 77133d0c..e74f8725 100644
--- a/wqflask/maintenance/dataset/load_phenotypes.py
+++ b/wqflask/maintenance/dataset/load_phenotypes.py
@@ -2,6 +2,7 @@ import sys
import csv
import utilities
+import datastructure
def main(argv):
# config
@@ -11,14 +12,21 @@ def main(argv):
print "\t%s" % (str(item))
# var
inbredsetid = config.get('config', 'inbredsetid')
- dataid = utilities.get_nextdataid_phenotype()
- cursor, con = utilities.get_cursor()
print "inbredsetid: %s" % inbredsetid
+ species = datastructure.get_species(inbredsetid)
+ speciesid = species[0]
+ print "speciesid: %s" % speciesid
+ dataid = datastructure.get_nextdataid_phenotype()
+ print "next data id: %s" % dataid
+ cursor, con = utilities.get_cursor()
# datafile
datafile = open(config.get('config', 'datafile'), 'r')
phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
phenotypedata_head = phenotypedata.next()
print "phenotypedata head:\n\t%s" % phenotypedata_head
+ strainnames = phenotypedata_head[1:]
+ strains = datastructure.get_strains_bynames(speciesid, strainnames)
+ print "%s" % strains
# metafile
metafile = open(config.get('config', 'metafile'), 'r')
phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
@@ -102,6 +110,8 @@ def main(argv):
rowcount = cursor.rowcount
publicationid = con.insert_id()
print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)
+ # data
+
if __name__ == "__main__":
print "command line arguments:\n\t%s" % sys.argv