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-rwxr-xr-xweb/webqtl/schema/ShowCommentPage.py123
-rwxr-xr-xweb/webqtl/schema/ShowSchemaPage.py194
-rwxr-xr-xweb/webqtl/schema/UpdateCommentPage.py101
-rwxr-xr-xweb/webqtl/schema/__init__.py0
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