diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 18 | ||||
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 166 |
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: |