aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorZachary Sloan2012-11-30 18:03:52 -0600
committerZachary Sloan2012-11-30 18:03:52 -0600
commit43f69f26507d934a15d8e8d20f0ac3023fdb7691 (patch)
tree6f88f014447eed5533e4e8aa46f33a2843867203 /wqflask
parentb8fa8728b7afebbada49f29b85fa5db40e137e1b (diff)
downloadgenenetwork2-43f69f26507d934a15d8e8d20f0ac3023fdb7691.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')
-rwxr-xr-xwqflask/base/data_set.py33
-rwxr-xr-xwqflask/base/webqtlConfigLocal.py4
-rwxr-xr-xwqflask/base/webqtlTrait.py69
-rw-r--r--wqflask/cfg/zach_settings.py3
-rw-r--r--wqflask/wqflask/do_search.py24
-rw-r--r--wqflask/wqflask/search_results.py3
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py25
-rw-r--r--wqflask/wqflask/views.py14
8 files changed, 106 insertions, 69 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):
diff --git a/wqflask/cfg/zach_settings.py b/wqflask/cfg/zach_settings.py
index ed97f222..8d3bf4ab 100644
--- a/wqflask/cfg/zach_settings.py
+++ b/wqflask/cfg/zach_settings.py
@@ -1,2 +1,5 @@
LOGFILE = """/tmp/flask_gn_log"""
+
TRAP_BAD_REQUEST_ERRORS = True
+
+DB_URI = """mysql://webqtl:webqtl@localhost/db_webqtl_zas1024""" \ No newline at end of file
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 17078802..bae3df08 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -144,14 +144,22 @@ class PhenotypeSearch(DoSearch):
'Publication.Title',
'Publication.Authors',
'PublishXRef.Id')
+
+ header_fields = ['',
+ 'Record ID',
+ 'Description',
+ 'Authors',
+ 'Year',
+ 'Max LRS',
+ 'Max LRS Location']
def get_where_clause(self):
"""Generate clause for WHERE portion of query"""
#Todo: Zach will figure out exactly what both these lines mean
#and comment here
- if "'" not in self.search_term:
- search_term = "[[:<:]]" + self.search_term + "[[:>:]]"
+ if "'" not in self.search_term[0]:
+ search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]"
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
@@ -195,6 +203,10 @@ class GenotypeSearch(DoSearch):
FROM GenoXRef, GenoFreeze, Geno """
search_fields = ('Name', 'Chr')
+
+ header_fields = ['',
+ 'Record ID',
+ 'Location']
def get_fields_clause(self):
"""Generate clause for part of the WHERE portion of query"""
@@ -203,13 +215,13 @@ class GenotypeSearch(DoSearch):
# against each field in search_fields (above)
fields_clause = []
- if "'" not in self.search_term:
- self.search_term = "[[:<:]]" + self.search_term + "[[:>:]]"
+ if "'" not in self.search_term[0]:
+ self.search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]"
for field in self.search_fields:
fields_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
- field,
- self.search_term)))
+ field),
+ self.search_term))
print("hello ;where_clause is:", pf(fields_clause))
fields_clause = "(%s)" % ' OR '.join(fields_clause)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c7bbdaf2..04b14e8f 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -83,7 +83,8 @@ class SearchResultPage(templatePage):
self.dataset_group_ids = map(lambda x: x[2], results)
else:
print("self.dataset is:", pf(self.dataset))
- self.dataset = create_dataset(self.db_conn, self.dataset)
+ # Replaces a string with an object
+ self.dataset = create_dataset(self.dataset)
print("self.dataset is now:", pf(self.dataset))
self.search()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e8ad0b1d..7060f2ea 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -31,16 +31,15 @@ from pprint import pformat as pf
class ShowTrait(templatePage):
- def __init__(self, fd):
- self.fd = fd
+ def __init__(self, args):
+ print("in ShowTrait, args are:", args)
+ self.group = args.group
+ self.trait_id = trait_id
+ self.dataset = dataset
- print("red1 fd.group:", fd.group)
- templatePage.__init__(self, fd)
+ #assert self.openMysql(), "No database!"
- print("red2 fd.group:", fd.group)
- assert self.openMysql(), "No database!"
-
- print("red3 fd.group:", fd.group)
+ #print("red3 fd.group:", fd.group)
this_trait = self.get_this_trait()
print("red4 fd.group:", fd.group)
@@ -183,11 +182,13 @@ class ShowTrait(templatePage):
#if traitInfos:
# database, ProbeSetID, CellID = traitInfos
#else:
- dataset = self.fd['dataset']
- trait_id = self.fd['trait_id']
- cell_id = self.fd.get('CellID')
+ #dataset = self.fd['dataset']
+ #trait_id = self.fd['trait_id']
+ #cell_id = self.fd.get('CellID')
- this_trait = webqtlTrait(self.db_conn, dataset=dataset, name=trait_id, cellid=cell_id)
+ this_trait = webqtlTrait(dataset=dataset,
+ name=trait_id,
+ cellid=cell_id)
##identification, etc.
self.fd.identification = '%s : %s' % (this_trait.dataset.shortname, trait_id)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index cdc3379f..17dc42fb 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -7,10 +7,12 @@ import simplejson as json
import yaml
import flask
+import sqlalchemy
+#import config
from wqflask import app
-from flask import render_template, request, make_response, Response
+from flask import render_template, request, make_response, Response, Flask, g, config
from wqflask import search_results
from wqflask.show_trait import show_trait
@@ -27,6 +29,10 @@ from pprint import pformat as pf
#logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
#_log = logging.getLogger("correlation")
+@app.before_request
+def connect_db():
+ print("blue app.config:", app.config, pf(vars(app.config)))
+ g.db = sqlalchemy.create_engine(app.config['DB_URI'])
@app.route("/")
def index_page():
@@ -86,9 +92,9 @@ def whats_new_page():
@app.route("/show_trait")
def show_trait_page():
# Here it's currently too complicated not to use an fd that is a webqtlFormData
- fd = webqtlFormData.webqtlFormData(request.args)
- print("stp y1:", pf(vars(fd)))
- template_vars = show_trait.ShowTrait(fd)
+ #fd = webqtlFormData.webqtlFormData(request.args)
+ #print("stp y1:", pf(vars(fd)))
+ template_vars = show_trait.ShowTrait(request.args)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ",