Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 159 deletions

diff --git a/web/webqtl/management/assignUserToDatasetPage.py b/web/webqtl/management/assignUserToDatasetPage.py
deleted file mode 100755
index 8e089526..00000000
--- a/web/webqtl/management/assignUserToDatasetPage.py
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import os
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-
-#XZ, 02/06/2009: Xiaodong created this class
-class assignUserToDatasetPage(templatePage):
-
-    def __init__(self, fd):
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-
-
-        ifVerified = fd.formdata.getvalue('ifVerified')
-
-        if ifVerified != 'GN@UTHSC':
-            heading = "Error page"
-            detail = ["You are NoT verified as administrator."]
-            self.error(heading=heading,detail=detail)
-            return
-        else:
-
-            ProbeSetFreeze_FullName = fd.formdata.getvalue('ProbeSetFreeze_FullName')
-            User_name = fd.formdata.getvalue('User_name')
-
-            if ProbeSetFreeze_FullName and User_name:
-                ProbeSetFreeze_FullName = string.strip(ProbeSetFreeze_FullName)
-                User_name = string.strip(User_name)
-
-                #XZ, check if the input dataset name exists.
-                self.cursor.execute( 'select count(FullName) from ProbeSetFreeze where FullName="%s"' % ProbeSetFreeze_FullName )
-                result = self.cursor.fetchone()
-                if result:
-                    row_count = result[0]
-                    if row_count:
-                        pass
-                    else:
-                        heading = "Error page"
-                        detail = ["The dataset name %s does NOT exist in database." % ProbeSetFreeze_FullName]
-                        self.error(heading=heading,detail=detail)
-                        return
-                else:
-                    heading = "Error page"
-                    detail = ["No sql result returned when check dataset name."]
-                    self.error(heading=heading,detail=detail)
-                    return
-
-                #XZ, check if the input user name exists.
-                self.cursor.execute( 'select count(name) from User where name="%s"' % User_name )
-                result = self.cursor.fetchone()
-                if result:
-                    row_count = result[0]
-                    if row_count:
-                        pass
-                    else:
-                        heading = "Error page"
-                        detail = ["The user name %s does NOT exist in database." % User_name]
-                        self.error(heading=heading,detail=detail)
-                        return
-                else:
-                    heading = "Error page"
-                    detail = ["No sql result returned when check user name."]
-                    self.error(heading=heading,detail=detail)
-                    return
-
-                self.cursor.execute( 'select AuthorisedUsers from ProbeSetFreeze where FullName="%s"' % ProbeSetFreeze_FullName )
-                result = self.cursor.fetchone() # The FullName is unique.
-                if result:
-                    AuthorisedUsers = result[0]
-                    if not AuthorisedUsers:
-                        self.cursor.execute('update ProbeSetFreeze set AuthorisedUsers="%s" where FullName="%s"' %(User_name, ProbeSetFreeze_FullName) )
-                    else:
-                        AuthorisedUsersList=AuthorisedUsers.split(',')
-                        if not AuthorisedUsersList.__contains__(User_name):
-                            AuthorisedUsers = AuthorisedUsers + ',%s' % User_name
-                            self.cursor.execute('update ProbeSetFreeze set AuthorisedUsers="%s" where FullName="%s"' %(AuthorisedUsers, ProbeSetFreeze_FullName) )
-                else:
-                    heading = "Error page"
-                    detail = ["No sql result returned when query AuthorisedUsers."]
-                    self.error(heading=heading,detail=detail)
-                    return
-
-
-            TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
-
-            dataHeading = HT.Paragraph('Confidential Dataset Table', Class="title")
-
-            dataTable = HT.TableLite(border=1, cellpadding=0, cellspacing=0, Class="collap", width="100%")
-
-            dataHeaderRow = HT.TR()
-            dataHeaderRow.append(HT.TD("Dataset Id", Class='fs14 fwb ffl b1 cw cbrb'))
-            dataHeaderRow.append(HT.TD("Dataset Full Name", Class='fs14 fwb ffl b1 cw cbrb'))
-            dataHeaderRow.append(HT.TD("Authorised User", Class='fs14 fwb ffl b1 cw cbrb'))
-            dataTable.append(dataHeaderRow)
-
-            self.cursor.execute('select Id, FullName, AuthorisedUsers from ProbeSetFreeze where confidentiality=1 order by FullName,Id')
-
-            result = self.cursor.fetchall()
-
-            dataInfo = HT.Blockquote( 'There are %d confidential datasets.' % len(result) )
-
-
-            for one_row in result:
-                ProbeSetFreeze_Id, ProbeSetFreeze_FullName, ProbeSetFreeze_AuthorisedUsers = one_row
-                dataRow = HT.TR()
-                dataRow.append(HT.TD("%s" % ProbeSetFreeze_Id, Class='fs12 fwn ffl b1 c222'))
-                dataRow.append(HT.TD("%s" % ProbeSetFreeze_FullName, Class='fs12 fwn ffl b1 c222'))
-                dataRow.append(HT.TD("%s" % ProbeSetFreeze_AuthorisedUsers, Class='fs12 fwn ffl b1 c222'))
-                dataTable.append(dataRow)
-
-            assignUserForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name='assignUserForm', submit=HT.Input(type='hidden'))
-            assignUserForm.append(
-                HT.Blockquote(
-                              HT.Font('Dataset Full Name ', color='red'),
-                              HT.Input(type='text' ,name='ProbeSetFreeze_FullName',value='', size=50,maxlength=200),
-                              HT.Font('   User name ', color='red'),
-                              HT.Input(type='text' ,name='User_name',value='', size=20,maxlength=20),
-                              HT.Input(type='Submit', value='Submit', Class="button")),
-                HT.Input(type='hidden',name='FormID',value='assignUserToDataset'),
-                HT.Input(type='hidden',name='ifVerified',value='GN@UTHSC')
-            )
-
-            TD_LR.append(dataHeading, dataInfo, assignUserForm, dataTable, assignUserForm)
-
-            self.dict['body'] =  str(TD_LR)
-            self.dict['title'] =  'Confidential datasets'
-