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

4 files changed, 0 insertions, 418 deletions

diff --git a/web/webqtl/schema/ShowCommentPage.py b/web/webqtl/schema/ShowCommentPage.py
deleted file mode 100755
index 449fd56a..00000000
--- a/web/webqtl/schema/ShowCommentPage.py
+++ /dev/null
@@ -1,123 +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 sys
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-
-
-
-class ShowCommentPage(templatePage):
-    def __init__(self,fd):
-        sys.stderr = sys.stdout
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-        #{
-            print 'Content-type: text/html\n'
-            print 'Can not update the comment of %s' %(TableName)
-            return
-        #}
-
-        Cursor_Comment = self.cursor
-        TableName = fd.formdata.getfirst('TableName')
-
-        SqlCmd = 'select Comment from TableComments where TableName=\'%s\'' %(TableName)
-        Cursor_Comment.execute(SqlCmd)
-        Comment = Cursor_Comment.fetchall()
-        if Comment:
-           Comment = Comment[0][0]
-           if str(Comment)=='None':
-              Comment=''
-        else:
-           Comment = ''
-
-        ##########setup HtmlForm Comment##########
-        HtmlInputHidden_TableName = HT.Input(type='hidden', name='TableName', value=TableName)
-        HtmlInputHidden_ActionID = HT.Input(type='hidden', name='ActionID', value='UpdateComment')
-        HtmlTextarea_Comment = HT.Textarea(name='Comment', text=Comment, rows=8, cols=100)
-
-        HtmlForm_Comment = HT.Form(cgi=webqtlConfig.CGIDIR+'main.py?FormID=schemaUpdateComment')
-        HtmlForm_Comment.append('<B>%s</B><BR><BR>' %(TableName))  #show table's name
-        HtmlForm_Comment.append('<B><I>Comment:</I></B><BR>')           #show table's comment
-        HtmlForm_Comment.append(HtmlTextarea_Comment)
-        HtmlForm_Comment.append('<BR>')
-        HtmlForm_Comment.append(HtmlInputHidden_TableName)
-        HtmlForm_Comment.append(HtmlInputHidden_ActionID)
-
-        ###########################
-        #update fields' annotation#
-        ###########################
-        HtmlForm_Comment.append('<BR><BR>')
-
-        try:
-        #{
-            HtmlTR_Annotation = []
-            Cursor_Comment.execute('desc %s' %(TableName))
-            TableDesc = Cursor_Comment.fetchall()
-            for i in range(0, len(TableDesc)):
-            #{
-                TableField = TableName+'.'+str(TableDesc[i][0])
-                TableFieldForeignKey = TableField+'ForeignKey'
-                TableFieldAnnotation = TableField+'Annotation'
-                HtmlText_ForeignKey = HT.Input(type='text', name=TableFieldForeignKey, size=20)
-                HtmlText_Annotation = HT.Input(type='text', name=TableFieldAnnotation, size=80)
-
-
-                Cursor_Comment.execute('select Annotation, Foreign_Key from TableFieldAnnotation where TableField=%s', (TableField))
-                Annotation = Cursor_Comment.fetchone()
-                if Annotation:
-                #{
-                    if str(Annotation[1]) != 'None':
-                        HtmlText_ForeignKey.value=Annotation[1]
-                    if str(Annotation[0]) != 'None':
-                        HtmlText_Annotation.value=Annotation[0].replace('"', '&quot;')
-                #}
-                HtmlTD_Annotation = []
-                HtmlTD_Annotation.append(TableField)
-                HtmlTD_Annotation.append(HtmlText_ForeignKey)
-                HtmlTD_Annotation.append(HtmlText_Annotation)
-   
-                HtmlTR_Annotation.append(HtmlTD_Annotation)
-            #}
-
-            HtmlTable_Annotation= HT.Table(border=0, width='0%', heading=['Field', 'Foreign_Key', 'Annotation'], body = HtmlTR_Annotation)
-            HtmlForm_Comment.append(HtmlTable_Annotation)
-        #}
-        except:
-            pass
-
-        HtmlForm_Comment.submit.value='submit'
-        HtmlForm_Comment.reset = HT.Input(type='reset', name='reset', value='reset')
-        ##########end of HtmlForm##########
-
-        self.dict['body'] = HtmlForm_Comment
-
-
diff --git a/web/webqtl/schema/ShowSchemaPage.py b/web/webqtl/schema/ShowSchemaPage.py
deleted file mode 100755
index e9ced5a1..00000000
--- a/web/webqtl/schema/ShowSchemaPage.py
+++ /dev/null
@@ -1,194 +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 sys
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-from utility import webqtlUtil
-
-
-
-###################################################
-#Description: show the schema of webqtl's database#
-#Author: Hongqiang Li                             #
-#Version: 1.0                                     #
-###################################################
-
-class ShowSchemaPage(templatePage):
-    def __init__(self,fd):
-	cookies = fd.cookies
-        sys.stderr = sys.stdout
-        templatePage.__init__(self, fd)
-        body = HT.SimpleDocument()
-
-        ###############################################################################
-        #get user's privilege from cookie, if the user doesn't have enough privilege, #
-        #he won't see the update comment icon                                         #
-        ###############################################################################
-        ShowUpdateIcon = False 
-
-        if not self.openMysql():
-           return
-
-        Cursor_WebQtl = Cursor_Comment = self.cursor
-
-        if webqtlConfig.USERDICT[self.privilege] >= webqtlConfig.USERDICT['user']:
-			ShowUpdateIcon = True
-
-        ##################
-        #show description#
-        ##################
-        body.append('<BR>')
-        body.append('<H1>')
-        body.append('Description of Schema')
-        if ShowUpdateIcon:
-        #{
-            # Modified by Hongqiang Li
-            # Image_Update = HT.Image('http://web2qtl.utmem.edu/images/modify.gif')
-            Image_Update = HT.Image('/images/modify.gif')
-            #
-            Href_Update = HT.Href(webqtlConfig.CGIDIR+'main.py?FormID=schemaShowComment&TableName=Description_of_Schema', Image_Update)
-            body.append(Href_Update)
-        #}
-        body.append('</H1>')
-         
-        Cursor_WebQtl.execute('select Comment from TableComments where TableName=\'Description_of_Schema\'')
-        Comment = Cursor_WebQtl.fetchone();
-        if Comment:
-            if str(Comment[0])!='None':
-                body.append(Comment[0])
-
-        body.append('<HR WIDTH=100%>')
-        body.append('<H2>Tables</H2>')
-
-        ##################
-        #show table names#
-        ##################
-        Cursor_WebQtl.execute('show tables')
-        Tables=Cursor_WebQtl.fetchall()
-        BlockedTables = ['User', 'TableComments', 'TableFieldAnnotation', 'ProbeSetXRef_TEMP', 'DBList', 'DBType', 'HumanGene', 'LCorr', 'Temp', 'TempData']
-        for i in range(0, len(Tables)):
-        #{
-            TableName = Tables[i][0]
-            if TableName in BlockedTables: #skip the table who is blocked
-                continue
-
-            HrefTable_Schema = HT.Href(webqtlConfig.CGIDIR+'main.py?FormID=schemaShowPage#'+TableName, TableName)
-            body.append(str(HrefTable_Schema)+'<BR>')
-        #}
-        body.append('<hr width=100%>')
-    
-        for i in range(0, len(Tables)):
-        #{
-            TableName = Tables[i][0]
-            if TableName in BlockedTables: #skip the table who is blocked
-                continue
-
-            #####################
-            #get table's comment#
-            #####################
-            SqlCmd = 'select Comment from TableComments where TableName=\'%s\'' %(TableName)
-            Cursor_WebQtl.execute(SqlCmd)
-            Comment = Cursor_WebQtl.fetchall()
-
-            ####################################
-            #get the content of a table's schma#
-            ####################################
-            Cursor_WebQtl.execute('desc %s' %(TableName))
-            TableDesc = Cursor_WebQtl.fetchall();
-
-            HtmlTR_Schema = []
-            for row in range(0, len(TableDesc)):
-            #{
-                HtmlTD_Schema = []
-                for col in range(0, len(TableDesc[row])):
-                    if str(TableDesc[row][col])=='None' or str(TableDesc[row][col])=='': #just means I don't want show 'None' *_^
-                       HtmlTD_Schema.append('&nbsp;')
-                    else:
-                       HtmlTD_Schema.append(TableDesc[row][col])
-
-                ##############################
-                #get table fileds' annotation#
-                ##############################
-                TableField = TableName+'.'+TableDesc[row][0]
-                Cursor_WebQtl.execute('select Annotation, Foreign_Key from TableFieldAnnotation where TableField=%s', (TableField))
-                Annotation = Cursor_WebQtl.fetchone();
-                if Annotation:
-                #{
-                    if str(Annotation[1])=='None' or str(Annotation[1])=='':
-                        HtmlTD_Schema.append('&nbsp;')
-                    else:
-                        HtmlTD_Schema.append(Annotation[1])
-                    if str(Annotation[0])=='None' or str(Annotation[0])=='':
-                        HtmlTD_Schema.append('&nbsp;')
-                    else:
-                        HtmlTD_Schema.append(Annotation[0])
-                #}
-                else:
-                #{
-                    HtmlTD_Schema.append('&nbsp;')
-                    HtmlTD_Schema.append('&nbsp;')
-                #}
-
-            	HtmlTR_Schema.append(HtmlTD_Schema)
-            #}
-
-            ###############################
-            #Html code of a table's schema#
-            ###############################
-            body.append(HT.NAME(TableName, TableName))
-            if ShowUpdateIcon:
-            #{
-                # Modified by Hongqiang Li
-                #Image_Update = HT.Image('http://web2qtl.utmem.edu/images/modify.gif')
-                Image_Update = HT.Image('/images/modify.gif')
-                #
-                Href_Update = HT.Href(webqtlConfig.CGIDIR+'main.py?FormID=schemaShowComment&TableName=%s' %(TableName), Image_Update)
-                body.append(Href_Update)
-            #}
-            body.append('<BR><BR>')
-
-            body.append('<B>Comment:</B><BR>')
-            #body.append("<I>")
-            if Comment:
-                if str(Comment[0][0])!='None':
-                    for content in Comment[0][0].split('\n'):
-                        body.append(content)
-                        body.append('<BR>')
-            #body.append("</I>")
-
-            HtmlTable_Schema = HT.Table(width='0%', heading=['Field', 'Type', 'Null', 'Key', 'Default', 'Extra', 'Foreign_Key', 'Annotation'], body = HtmlTR_Schema)
-            body.append(HtmlTable_Schema)
-            body.append('<hr width=100%>')
-        #}
-
-        self.dict['body'] = body
-
-
-
diff --git a/web/webqtl/schema/UpdateCommentPage.py b/web/webqtl/schema/UpdateCommentPage.py
deleted file mode 100755
index eb1dbb67..00000000
--- a/web/webqtl/schema/UpdateCommentPage.py
+++ /dev/null
@@ -1,101 +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 sys
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-from base import webqtlConfig
-
-
-class UpdateCommentPage(templatePage):
-    def __init__(self,fd):
-        sys.stderr = sys.stdout
-        templatePage.__init__(self, fd)
-        body = HT.SimpleDocument()        
-
-        if not self.updMysql():
-        #{
-            print 'Content-type: text/html\n'
-            print 'Can not update the comment of %s' %(TableName)
-            return
-        #}
-
-
-        Cursor_Comment=self.cursor
-        TableName = fd.formdata.getfirst('TableName')
-        Comment = fd.formdata.getfirst('Comment')
-
-        ########################
-        #update table's comment#
-        ########################
-        Cursor_Comment.execute('select * from TableComments where TableName=%s', (TableName))
-        if Cursor_Comment.fetchall():
-            Cursor_Comment.execute('update TableComments set Comment=%s where TableName=%s', (Comment, TableName))
-        else:
-            Cursor_Comment.execute('insert into TableComments values(%s,%s)', (TableName, Comment))
-
-
-        #################################
-        #update table fields' annotation#
-        #################################
-        try:
-        #{
-            Cursor_Comment.execute('desc %s' %(TableName))
-            TableDesc = Cursor_Comment.fetchall()
-            for i in range(0, len(TableDesc)):
-            #{
-                TableField = TableName+'.'+str(TableDesc[i][0])
-                TableFieldForeignKey = TableField+'ForeignKey'
-                TableFieldAnnotation = TableField+'Annotation'
-
-                ForeignKey = fd.formdata.getfirst(TableFieldForeignKey)
-                if ForeignKey == 'None':
-                    ForeignKey=''
-                Annotation = fd.formdata.getfirst(TableFieldAnnotation)
-                if Annotation == 'None':
-                    Annotation='&nbsp;'
-
-                Cursor_Comment.execute('select * from TableFieldAnnotation where TableField=%s', (TableField))
-                if Cursor_Comment.fetchall():
-                    Cursor_Comment.execute('update TableFieldAnnotation set Foreign_Key=%s, Annotation=%s where TableField=%s', (ForeignKey, Annotation, TableField))
-                else:
-                    Cursor_Comment.execute('insert into TableFieldAnnotation values(%s,%s,%s)', (TableField, ForeignKey, Annotation))
-            #}
-        #}
-        except:
-            pass
-
-        HtmlHref = HT.Href(webqtlConfig.CGIDIR+'main.py?FormID=schemaShowPage#%s' %(TableName), 'table')
-        HtmlBlock = HT.Blockquote();
-        HtmlBlock.append('This ')
-        HtmlBlock.append(HtmlHref)
-        HtmlBlock.append('\'s comment has been succesfully updated')
-
-        body.append(HtmlBlock)
-        self.dict['body'] = body
-
diff --git a/web/webqtl/schema/__init__.py b/web/webqtl/schema/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/schema/__init__.py
+++ /dev/null