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author | Zachary Sloan | 2012-11-30 18:03:52 -0600 |
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committer | Zachary Sloan | 2012-11-30 18:03:52 -0600 |
commit | 43f69f26507d934a15d8e8d20f0ac3023fdb7691 (patch) | |
tree | 6f88f014447eed5533e4e8aa46f33a2843867203 /wqflask/base/webqtlTrait.py | |
parent | b8fa8728b7afebbada49f29b85fa5db40e137e1b (diff) | |
download | genenetwork2-43f69f26507d934a15d8e8d20f0ac3023fdb7691.tar.gz |
Started switching to using basic sqlalchemy to handle db connection/queries
Began fixing bugs related to this fix, still in progress
Diffstat (limited to 'wqflask/base/webqtlTrait.py')
-rwxr-xr-x | wqflask/base/webqtlTrait.py | 69 |
1 files changed, 39 insertions, 30 deletions
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py index cc0e2321..1dceba08 100755 --- a/wqflask/base/webqtlTrait.py +++ b/wqflask/base/webqtlTrait.py @@ -12,6 +12,7 @@ from utility import webqtlUtil from pprint import pformat as pf +from flask import Flask, g class webqtlTrait: """ @@ -20,38 +21,46 @@ class webqtlTrait: """ - def __init__(self, db_conn, **kw): + def __init__(self, **kw): print("in webqtlTrait") - self.db_conn = db_conn - self.cursor = self.db_conn.cursor() - self.dataset = None # database object - self.name = '' # Trait ID, ProbeSet ID, Published ID, etc. - self.cellid = '' - self.identification = 'un-named trait' - self.group = '' - self.haveinfo = 0 - self.sequence = '' # Blat sequence, available for ProbeSet - self.data = {} - 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.' + #self.db_conn = db_conn + #self.cursor = self.db_conn.cursor() + 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) + 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.data = kw.get(data, {}) + + if kw.get('fullname'): + name2 = value.split("::") + if len(name2) == 2: + self.dataset, self.name = name2 + 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.db_conn, self.dataset) + #assert self.cursor, "Don't have a cursor" + self.dataset = create_dataset(self.dataset) #if self.dataset == None, not from a database print("self.dataset is:", self.dataset, type(self.dataset)) @@ -432,7 +441,7 @@ class webqtlTrait: self.cursor.execute(query) traitInfo = self.cursor.fetchone() if traitInfo: - self.haveinfo = 1 + self.haveinfo = True #XZ: assign SQL query result to trait attributes. for i, field in enumerate(self.dataset.display_fields): |