diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 33 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfigLocal.py | 4 | ||||
| -rwxr-xr-x | wqflask/base/webqtlTrait.py | 69 |
3 files changed, 60 insertions, 46 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 633f7545..015b2623 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -22,6 +22,8 @@ from __future__ import print_function, division +from flask import Flask, g + from htmlgen import HTMLgen2 as HT import webqtlConfig @@ -31,25 +33,28 @@ from pprint import pformat as pf # Used by create_database to instantiate objects DS_NAME_MAP = {} -def create_dataset(db_conn, dataset_name): - cursor = db_conn.cursor() - cursor.execute(""" +def create_dataset(dataset_name): + #cursor = db_conn.cursor() + print("dataset_name:", dataset_name) + + dataset_type = g.db.execute(""" SELECT DBType.Name FROM DBList, DBType WHERE DBList.Name = %s and DBType.Id = DBList.DBTypeId - """, (dataset_name)) - print("dataset_name:", dataset_name) - dataset_type = cursor.fetchone()[0] - print("dataset_type:", pf(dataset_type)) + """, (dataset_name)).fetchone().Name + + #dataset_type = cursor.fetchone()[0] + print("[blubber] dataset_type:", pf(dataset_type)) dataset_ob = DS_NAME_MAP[dataset_type] #dataset_class = getattr(data_set, dataset_ob) - + print("dataset_ob:", dataset_ob) print("DS_NAME_MAP:", pf(DS_NAME_MAP)) dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, db_conn) + return dataset_class(dataset_name) + class DataSet(object): """ @@ -58,12 +63,12 @@ class DataSet(object): """ - def __init__(self, name, db_conn): + def __init__(self, name): assert name self.name = name - self.db_conn = db_conn - self.cursor = self.db_conn.cursor() + #self.db_conn = db_conn + #self.cursor = self.db_conn.cursor() self.id = None self.type = None self.group = None @@ -271,7 +276,7 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - def get_trait_info(self, trait_list): + def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: if not this_trait.haveinfo: this_trait.retrieveInfo() @@ -355,7 +360,7 @@ class MrnaAssayDataSet(DataSet): ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = "%s" - ''' % self.db_conn.escape_string(self.name) + ''' % g.db.escape_string(self.name) def check_confidentiality(self): diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py index 5aab48ac..84686234 100755 --- a/wqflask/base/webqtlConfigLocal.py +++ b/wqflask/base/webqtlConfigLocal.py @@ -4,12 +4,12 @@ MYSQL_SERVER = 'localhost' DB_NAME = 'db_webqtl_zas1024' -DB_USER = 'webqtlupd' +DB_USER = 'webqtl' DB_PASSWD = 'webqtl' MYSQL_UPDSERVER = 'localhost' DB_UPDNAME = 'db_webqtl_zas1024' -DB_UPDUSER = 'webqtlupd' +DB_UPDUSER = 'webqtl' DB_UPDPASSWD = 'webqtl' GNROOT = '/home/zas1024/gn/' 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): |