aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorZachary Sloan2012-09-28 16:56:42 -0500
committerZachary Sloan2012-09-28 16:56:42 -0500
commit8bd404246b83f46f34c9b162c39c2dfc6ab39049 (patch)
tree46f0b0428fa4d064c8597bca2235986b1e8c9ba3
parente3da0943461b8f5c498c374d58cfcdf65b98c1ba (diff)
downloadgenenetwork2-8bd404246b83f46f34c9b162c39c2dfc6ab39049.tar.gz
Removed show_trait_page.py and moved relevant code over to DataEditingPage.py (though the user security stuff still needs to be moved over)
-rwxr-xr-xwqflask/base/webqtlFormData.py1
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py44
-rw-r--r--wqflask/wqflask/views.py6
3 files changed, 46 insertions, 5 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 63263895..710c9f53 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -43,6 +43,7 @@ from utility import webqtlUtil
+
class webqtlFormData:
'Represents data from a WebQTL form page, needed to generate the next page'
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 92d0feaf..12e816f8 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -20,13 +20,29 @@ from basicStatistics import BasicStatisticsFunctions
from pprint import pformat as pf
+###############################################
+#
+# Todo: Put in security to ensure that user has permission to access confidential data sets
+# And add i.p.limiting as necessary
+#
+##############################################
+
+
+
class DataEditingPage(templatePage):
- def __init__(self, fd, this_trait=None):
+ def __init__(self, fd):
+ self.fd = fd
templatePage.__init__(self, fd)
assert self.openMysql(), "No datbase!"
+ this_trait = self.get_this_trait()
+
+ ##read genotype file
+ fd.RISet = this_trait.riset
+ fd.readGenotype()
+
if not fd.genotype:
fd.readData(incf1=1)
@@ -43,7 +59,6 @@ class DataEditingPage(templatePage):
else:
fmID='dataEditing'
-
# Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery
hddn = OrderedDict(
FormID = fmID,
@@ -149,6 +164,31 @@ class DataEditingPage(templatePage):
self.js_data = dict(sample_groups = self.sample_group_types)
+ def get_this_trait(self):
+ # When is traitInfos used?
+ #if traitInfos:
+ # database, ProbeSetID, CellID = traitInfos
+ #else:
+ database = self.fd['database']
+ probe_set_id = self.fd['ProbeSetID']
+ cell_id = self.fd.get('CellID')
+
+ this_trait = webqtlTrait(db=database, name=probe_set_id, cellid=cell_id, cursor=self.cursor)
+
+ ##identification, etc.
+ self.fd.identification = '%s : %s' % (this_trait.db.shortname, probe_set_id)
+ this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
+ &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, probe_set_id, self.fd['RISet'])
+
+ if cell_id:
+ self.fd.identification = '%s/%s'%(self.fd.identification, cell_id)
+ this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, cell_id)
+
+ this_trait.retrieveInfo()
+ this_trait.retrieveData()
+ return this_trait
+
+
def dispTraitInformation(self, fd, title1Body, hddn, this_trait):
_Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 0befb74a..bc80a1e6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -10,7 +10,7 @@ from wqflask import app
from flask import render_template, request
from wqflask import search_results
-from wqflask.show_trait import show_trait_page
+from wqflask.show_trait import DataEditingPage
from wqflask.correlation import CorrelationPage
from wqflask.dataSharing import SharingInfo, SharingInfoPage
@@ -75,8 +75,8 @@ def whats_new():
def show_trait():
# Here it's currently too complicated not to use an fd that is a webqtlFormData
fd = webqtlFormData.webqtlFormData(request.args)
- template_vars = show_trait_page.ShowTraitPage(fd)
-
+ #template_vars = show_trait_page.ShowTraitPage(fd)
+ template_vars = DataEditingPage.DataEditingPage(fd)
template_vars.js_data = json.dumps(template_vars.js_data)
print("show_trait template_vars:", pf(template_vars.__dict__))