diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 7 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 78 |
2 files changed, 19 insertions, 66 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 612b9209..36d4acaf 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -16,11 +16,11 @@ # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # -# +#we # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division +from __future__ import absolute_import, print_function, division import os from flask import Flask, g @@ -29,7 +29,7 @@ from htmlgen import HTMLgen2 as HT import reaper -import webqtlConfig +from base import webqtlConfig from base import species from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil @@ -50,6 +50,7 @@ def create_dataset(dataset_name): WHERE DBList.Name = '%s' and DBType.Id = DBList.DBTypeId """ % (escape(dataset_name)) + print("query is: ", pf(query)) dataset_type = g.db.execute(query).fetchone().Name #dataset_type = cursor.fetchone()[0] diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 8c9e3b10..241bf2ab 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,12 +1,12 @@ -from __future__ import division, print_function +from __future__ import absolute_import, division, print_function import string from htmlgen import HTMLgen2 as HT -import webqtlConfig -from webqtlCaseData import webqtlCaseData -from data_set import create_dataset +from base import webqtlConfig +from base.webqtlCaseData import webqtlCaseData +from base.data_set import create_dataset from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil @@ -24,76 +24,28 @@ class GeneralTrait: def __init__(self, **kw): print("in GeneralTrait") - self.dataset = kw.get('dataset', None) # database name - self.name = kw.get('name', None) # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = kw.get('cellid', None) + self.dataset = kw.get('dataset') # database name + self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. + self.cellid = kw.get('cellid') self.identification = kw.get('identification', 'un-named trait') - #self.group = kw.get('group', None) self.haveinfo = kw.get('haveinfo', False) - self.sequence = kw.get('sequence', None) # Blat sequence, available for ProbeSet + self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet self.data = kw.get('data', {}) - + if kw.get('fullname'): name2 = value.split("::") if len(name2) == 2: self.dataset, self.name = name2 + # self.cellid is set to None above elif len(name2) == 3: self.dataset, self.name, self.cellid = name2 - - #if self.dataset and isinstance(self.dataset, basestring): - self.dataset = create_dataset(self.dataset) - print("self.dataset is:", self.dataset, type(self.dataset)) - #if self.dataset: - - #self.dataset.get_group() + self.dataset = create_dataset(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() - - #print("trinity, self.group is:", self.group) - - # - # In ProbeSet, there are maybe several annotations match one sequence - # so we need use sequence(BlatSeq) as the identification, when we update - # one annotation, we update the others who match the sequence also. - # - # Hongqiang Li, 3/3/2008 - # - - #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield. - # 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.sequence = g.db.execute(*query).fetchone()[0] - # #self.sequence = self.cursor.fetchone()[0] - # print("self.sequence is:", self.sequence) + # Todo: These two lines are necessary most of the time, but perhaps not all of the time + # So we could add a simple if statement to short-circuit this if necessary + self.retrieve_info() + self.retrieve_sample_data() def get_name(self): |