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Cookies are lost in the http request headers

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One of the applications that i am working on is having a very strange issue. What is happening is that when a user logs into the application and navigates through the application, some of the requests are losing cookies in the http request headers, as a result weblogic thinks that this is a new request. This issue happens on all the requests within the application and is intermittent for some users and consistent for other users. Note that this issue happens in all of our environments and we have seen that it is happening only on IE as almost all users use IE browser. 

After looking at the IIS Web Server logs and Fiddler sessions, we see that the request is able to parse the cookies from the Cookie header, but in the next few lines when it tries to read all the headers from Client, there is "Found no = in key/value pair in the request header, continue ... " in the logs instead of getting " Header from client:[Cookie]=[s_cc=value; s_sq=value; CSISESSION=value; WL_Cookie_Name=value;]". (See the underlined statements from the logs for difference between the 2 requests).

Good Request (some URI) - 

Found cookie from cookie header: WL_Cookie_Name=SessionId_Value!Primary_JVM_Id_Value!NONE
Parsing cookie WL_Cookie_Name=SessionId_Value!Primary_JVM_Id_Value!NONE

........ some other lines related to resolving the request to primary/secondary JVM Id........

Entering method BaseProxy::parse_headers
 No of headers =55
 Header from client:[Connection]=[Keep-Alive]
 Header from client:[Content-Length]=[0]
 Header from client:[Accept]=[application/x-ms-application, image/jpeg, application/xaml+xml, image/gif, image/pjpeg, application/x-ms-xbap, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, */*]
 Header from client:[Accept-Encoding]=[gzip, deflate]
 Header from client:[Accept-Language]=[en-US]
 Header from client:[Authorization]=[SiteMinder]
 Header from client:[Cookie]=[s_cc=value; s_sq=value; CSISESSION=value; WL_Cookie_Name=value;]
 Header from client:[Host]=[host_name]

Request where cookies are lost in http request headers (same URI as above) - 

Found cookie from cookie header: WL_Cookie_Name=SessionId_Value!Primary_JVM_Id_Value!NONE
Parsing cookie WL_Cookie_Name=SessionId_Value!Primary_JVM_Id_Value!NONE

........ some other lines related to resolving the request to primary/secondary JVM Id........

Entering method BaseProxy::parse_headers
 No of headers =55
 Header from client:[Connection]=[Keep-Alive]
 Header from client:[Content-Length]=[0]
 Header from client:[Accept]=[application/x-ms-application, image/jpeg, application/xaml+xml, image/gif, image/pjpeg, application/x-ms-xbap, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, */*]
 Header from client:[Accept-Encoding]=[gzip, deflate]
 Header from client:[Accept-Language]=[en-US]
 Header from client:[Authorization]=[SiteMinder]
 Found no = in key/value pair in the request header, continue ...
 Header from client:[Host]=[host_name]

Please assist on any pointers that would help us resolve the issue. It has almost one year since we have this issue.

Set up is that we have 1 or 2 Web Servers, 1 or more than 1 Weblogic Application Servers in a clustered environment. Application uses Site minder for authentication.


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