Add all the source codes into the github.

1 files changed, 159 insertions, 0 deletions

diff --git a/web/webqtl/management/assignUserToDatasetPage.py b/web/webqtl/management/assignUserToDatasetPage.py
new file mode 100755
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+++ b/web/webqtl/management/assignUserToDatasetPage.py
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+# 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'
+