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-rwxr-xr-xwqflask/base/data_set.py18
-rwxr-xr-xwqflask/base/webqtlTrait.py166
2 files changed, 85 insertions, 99 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cd9e810e..7833f5c1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -68,13 +68,10 @@ class DataSet(object):
assert name
self.name = name
- #self.db_conn = db_conn
- #self.cursor = self.db_conn.cursor()
self.id = None
self.type = None
self.group = None
- #if self.cursor and self.id == 0:
self.setup()
self.check_confidentiality()
@@ -200,6 +197,7 @@ class PhenotypeDataSet(DataSet):
description = this_trait.post_publication_description
if this_trait.confidential:
+ continue # for now
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
description = this_trait.pre_publication_description
this_trait.description_display = description
@@ -217,13 +215,13 @@ class PhenotypeDataSet(DataSet):
this_trait.LRS_location_value = 1000000
if this_trait.lrs:
- self.cursor.execute("""
+ result = g.db.execute("""
select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = '%s' and
- Geno.Name = '%s' and
+ where Species.Name = %s and
+ Geno.Name = %s and
Geno.SpeciesId = Species.Id
- """ % (species, this_trait.locus))
- result = self.cursor.fetchone()
+ """, (species, this_trait.locus)).fetchone()
+ #result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
@@ -509,13 +507,13 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table)
- ob.cursor.execute(query, ob.name)
+ result = g.db.execute(query, ob.name)
(dataset_id,
name,
full_name,
confidential,
- authorized_users) = ob.cursor.fetchall()[0]
+ authorized_users) = result.fetchall()[0]
if confidential:
# Allow confidential data later
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 9763e441..dec5fa00 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -14,7 +14,7 @@ from pprint import pformat as pf
from flask import Flask, g
-class webqtlTrait:
+class GeneralTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
@@ -22,9 +22,7 @@ class webqtlTrait:
"""
def __init__(self, **kw):
- print("in webqtlTrait")
- #self.db_conn = db_conn
- #self.cursor = self.db_conn.cursor()
+ print("in GeneralTrait")
self.dataset = kw.get('dataset', None) # database object
self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc.
self.cellid = kw.get('cellid', None)
@@ -41,45 +39,31 @@ class webqtlTrait:
elif len(name2) == 3:
self.dataset, self.name, self.cellid = name2
- #print("foo")
- #print("kw in webqtlTrait are:", pf(kw))
- #print("printed\n\n")
- #for name, value in kw.items():
- # if self.__dict__.has_key(name):
- # setattr(self, name, value)
- # elif name == 'fullname':
- # name2 = value.split("::")
- # if len(name2) == 2:
- # self.dataset, self.name = name2
- # elif len(name2) == 3:
- # self.dataset, self.name, self.cellid = name2
- # else:
- # raise KeyError, repr(value) + ' parameter format error.'
- # else:
- # raise KeyError, repr(name) + ' not a valid parameter for this class.'
-
- if self.dataset and isinstance(self.dataset, basestring):
- #assert self.cursor, "Don't have a cursor"
- self.dataset = create_dataset(self.dataset)
+ #if self.dataset and isinstance(self.dataset, basestring):
+ self.dataset = create_dataset(self.dataset)
+
+
- #if self.dataset == None, not from a database
print("self.dataset is:", self.dataset, type(self.dataset))
- if self.dataset:
- if self.dataset.type == "Temp":
- self.cursor.execute('''
- SELECT
- InbredSet.Name
- FROM
- InbredSet, Temp
- WHERE
- Temp.InbredSetId = InbredSet.Id AND
- Temp.Name = "%s"
- ''', self.name)
- self.group = self.cursor.fetchone()[0]
- else:
- self.group = self.dataset.get_group()
+ #if self.dataset:
+
+ self.dataset.get_group()
+
+ if self.dataset.type == "Temp":
+ self.cursor.execute('''
+ SELECT
+ InbredSet.Name
+ FROM
+ InbredSet, Temp
+ WHERE
+ Temp.InbredSetId = InbredSet.Id AND
+ Temp.Name = "%s"
+ ''', self.name)
+ self.group = self.cursor.fetchone()[0]
+ else:
+ self.group = self.dataset.get_group()
- print("trinity, self.group is:", self.group)
+ print("trinity, self.group is:", self.group)
#
# In ProbeSet, there are maybe several annotations match one sequence
@@ -93,24 +77,24 @@ class webqtlTrait:
# The variable self.sequence should be changed to self.BlatSeq
# It also should be changed in other places where it are used.
- if self.dataset:
- if self.dataset.type == 'ProbeSet':
- print("Doing ProbeSet Query")
- query = '''
- SELECT
- ProbeSet.BlatSeq
- FROM
- ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSet.Id=ProbeSetXRef.ProbeSetId and
- ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
- ProbeSet.Name = %s and
- ProbeSetFreeze.Name = %s
- ''', (self.name, self.dataset.name)
- print("query is:", query)
- self.cursor.execute(*query)
- self.sequence = self.cursor.fetchone()[0]
- print("self.sequence is:", self.sequence)
+ #if self.dataset:
+ if self.dataset.type == 'ProbeSet':
+ print("Doing ProbeSet Query")
+ query = '''
+ SELECT
+ ProbeSet.BlatSeq
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSet.Id=ProbeSetXRef.ProbeSetId and
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
+ ProbeSet.Name = %s and
+ ProbeSetFreeze.Name = %s
+ ''', (self.name, self.dataset.name)
+ print("query is:", query)
+ self.sequence = g.db.execute(*query).fetchone()[0]
+ #self.sequence = self.cursor.fetchone()[0]
+ print("self.sequence is:", self.sequence)
def getName(self):
@@ -380,13 +364,10 @@ class webqtlTrait:
#def items(self):
# return self.__dict__.items()
- def retrieveInfo(self, QTL = None):
- assert self.dataset
+ def retrieve_info(self, QTL=False):
+ assert self.dataset, "Dataset doesn't exist"
if self.dataset.type == 'Publish':
- #self.dataset.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
- # 'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
- # 'Units', 'comments']
- query = '''
+ traitInfo = g.db.execute("""
SELECT
PublishXRef.Id, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
@@ -404,43 +385,50 @@ class webqtlTrait:
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id =%s
- ''' % (self.name, self.dataset.id)
+ """, (self.name, self.dataset.id)).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':
display_fields_string = ',ProbeSet.'.join(self.dataset.display_fields)
display_fields_string = 'ProbeSet.' + display_fields_string
- query = """
+ traitInfo = g.db.execute("""
SELECT %s
FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
WHERE
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s'
- """ % (display_fields_string, self.dataset.name, self.name)
+ ProbeSetFreeze.Name = %s AND
+ ProbeSet.Name = %s
+ """, (display_fields_string, self.dataset.name, self.name)).fetchone()
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif self.dataset.type == 'Geno':
display_fields_string = string.join(self.dataset.display_fields,',Geno.')
display_fields_string = 'Geno.' + display_fields_string
- query = """
+ traitInfo = g.db.execute("""
SELECT %s
FROM Geno, GenoFreeze, GenoXRef
WHERE
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoXRef.GenoId = Geno.Id AND
- GenoFreeze.Name = '%s' AND
- Geno.Name = '%s'
- """ % (display_fields_string, self.dataset.name, self.name)
+ GenoFreeze.Name = %s AND
+ Geno.Name = %s
+ """, (display_fields_string, self.dataset.name, self.name)).fetchone()
else: #Temp type
- traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = '%s'
+ traitInfo = g.db.execute("""SELECT %s FROM %s WHERE Name = %s
""", (string.join(self.dataset.display_fields,','),
self.dataset.type, self.name)).fetchone()
+
+ query = """SELECT %s FROM %s WHERE Name = %s
+ """ % (string.join(self.dataset.display_fields,','),
+ self.dataset.type, self.name)
+
+ print("query is:", pf(query))
+ print("traitInfo is: ", pf(traitInfo))
-
- self.cursor.execute(query)
- traitInfo = self.cursor.fetchone()
+
+ #self.cursor.execute(query)
+ #traitInfo = self.cursor.fetchone()
if traitInfo:
self.haveinfo = True
@@ -465,7 +453,7 @@ class webqtlTrait:
geneidIsNumber = 0
if geneidIsNumber:
- query = """
+ result = g.db.execute("""
SELECT
HomologeneId
FROM
@@ -475,9 +463,9 @@ class webqtlTrait:
InbredSet.Name = '%s' AND
InbredSet.SpeciesId = Species.Id AND
Species.TaxonomyId = Homologene.TaxonomyId
- """ % (self.geneid, self.group)
- self.cursor.execute(query)
- result = self.cursor.fetchone()
+ """, (self.geneid, self.group)).fetchone()
+ #self.cursor.execute(query)
+ #result = self.cursor.fetchone()
else:
result = None
@@ -486,7 +474,7 @@ class webqtlTrait:
if QTL:
if self.dataset.type == 'ProbeSet' and not self.cellid:
- query = '''
+ traitQTL = g.db.execute("""
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean
FROM
@@ -495,15 +483,15 @@ class webqtlTrait:
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSet.Name = "%s" AND
ProbeSetXRef.ProbeSetFreezeId =%s
- ''' % (self.name, self.dataset.id)
- self.cursor.execute(query)
- traitQTL = self.cursor.fetchone()
+ """, (self.name, self.dataset.id)).fetchone()
+ #self.cursor.execute(query)
+ #traitQTL = self.cursor.fetchone()
if traitQTL:
self.locus, self.lrs, self.pvalue, self.mean = traitQTL
else:
self.locus = self.lrs = self.pvalue = self.mean = ""
if self.dataset.type == 'Publish':
- query = '''
+ traitQTL = g.db.execute("""
SELECT
PublishXRef.Locus, PublishXRef.LRS
FROM
@@ -512,9 +500,9 @@ class webqtlTrait:
PublishXRef.Id = %s AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id =%s
- ''' % (self.name, self.dataset.id)
- self.cursor.execute(query)
- traitQTL = self.cursor.fetchone()
+ """, (self.name, self.dataset.id)).fetchone()
+ #self.cursor.execute(query)
+ #traitQTL = self.cursor.fetchone()
if traitQTL:
self.locus, self.lrs = traitQTL
else:
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:19:52 +0000