[InterMine Dev] set limited permission to user account

Pengcheng Yang yangpc at biols.ac.cn
Fri Aug 7 22:36:51 BST 2015


Hi Justin,

Thank you for your reply and the helpful information.

Yes, the URL passed to JBrowse was blocked by the login page. I think 
maybe the cookies could resolve this problem, because the cookie has 
stored the login information. I will check how to implement and let you 
know in this thread if any progress has been made.

Thank you very much!

Best,
Pengcheng


On 2015/8/7 22:48, Justin Clark-Casey wrote:
> Hi Pengcheng.  I'm afraid I'm not very familiar with JBrowse yet, 
> though as it happens I need to look at it pretty soon to work out why 
> it stopped working properly on http://synbiomine.org (the mine I work 
> on).
>
> However, I believe the mechanism (as you may have already seen) is 
> that InterMine passes a service URL to the JBrowse installation which 
> it then uses to get the data from an InterMine web service. I'm 
> guessing it's this last part that's failing now you've put in the 
> login requirement.
>
> I'm afraid I don't know at the moment how you would let JBrowse bypass 
> this J2EE mechanism.
>
> On 06/08/15 01:53, Pengcheng Yang wrote:
>> Hi Justin,
>>
>> Thank you for your help. Another question derived from this 
>> implementation.
>>
>> After implement this function. It is required to login. However, it also
>> prevent the JBrowse to acquire the content of the Mine. The embedded
>> JBrowse also don't work. Is there a method to let JBrowse skip the login
>> page?
>>
>> Best,
>> Pengcheng Yang
>>
>>
>> On 2015/8/6 7:23, Pengcheng Yang wrote:
>>>
>>> Hi Justin,
>>>
>>> Thank you for your help. It has been done follow your suggestion.
>>>
>>> Best,
>>> Pengcheng Yang
>>>
>>>
>>> On 2015/8/5 23:13, Justin Clark-Casey wrote:
>>>> Hi Pengcheng,
>>>>
>>>> Perhaps change
>>>>
>>>> intermine/webapp/main/resources/webapp/WEB-INF/web.xml
>>>>
>>>> and add your login2.jsp to
>>>>
>>>> intermine/webapp/main/resources/webapp/login2.jsp
>>>>
>>>> before rebuilding the webapp?
>>>>
>>>> -- Justin
>>>>
>>>> On 05/08/15 01:01, Pengcheng Yang wrote:
>>>>> Hi,
>>>>>
>>>>> Currently I implement this through [1], however, I found I have to 
>>>>> redo
>>>>> this after every time I redeploy the Mine Project. Is there any 
>>>>> way to
>>>>> embed this two scripts into the Mine before deploying.
>>>>>
>>>>> Thanks for any suggestions!
>>>>>
>>>>> Best,
>>>>> Pengcheng Yang
>>>>>
>>>>>
>>>>> [1] implement the user permission limitation
>>>>>
>>>>> after every time redeploy the database
>>>>>
>>>>> ###############################
>>>>>
>>>>> ##add the following line to
>>>>> apache-tomcat/webapps/PROJECT/WEB-INF/web.xml in the
>>>>>
>>>>> ###############################
>>>>>
>>>>> <security-constraint>
>>>>>
>>>>> <web-resource-collection>
>>>>>
>>>>> <display-name>Example Security Constraint</display-name>
>>>>>
>>>>> <web-resource-name>My Test</web-resource-name>
>>>>>
>>>>> <url-pattern>/*</url-pattern>
>>>>>
>>>>> </web-resource-collection>
>>>>>
>>>>> <auth-constraint>
>>>>>
>>>>> <role-name>tomcat</role-name>
>>>>>
>>>>> </auth-constraint>
>>>>>
>>>>> </security-constraint>
>>>>>
>>>>> <login-config>
>>>>>
>>>>> <auth-method>FORM</auth-method>
>>>>>
>>>>> <realm-name>Example Form-Based Authentication Area</realm-name>
>>>>>
>>>>> <form-login-config>
>>>>>
>>>>> <form-login-page>/login2.jsp</form-login-page>
>>>>>
>>>>> <form-error-page>/error2.jsp</form-error-page>
>>>>>
>>>>> </form-login-config>
>>>>>
>>>>> </login-config>
>>>>>
>>>>> ####################
>>>>>
>>>>> ##the file apache-tomcat/webapps/PROJECT/login2.jsp
>>>>>
>>>>> ###################
>>>>>
>>>>> <%@ page contentType="text/html; charset=UTF-8" 
>>>>> pageEncoding="UTF-8" %>
>>>>>
>>>>> <%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
>>>>>
>>>>> <%@ taglib uri="http://java.sun.com/jsp/jstl/functions" 
>>>>> prefix="fn" %>
>>>>>
>>>>> <%@ taglib uri="/WEB-INF/struts-html.tld" prefix="html" %>
>>>>>
>>>>> <%@ taglib tagdir="/WEB-INF/tags" prefix="im"%>
>>>>>
>>>>> <%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
>>>>>
>>>>> <!-- login.jsp -->
>>>>>
>>>>> <html:xhtml/>
>>>>>
>>>>> <form method="POST" action='<%=
>>>>> response.encodeURL("j_security_check") %>' >
>>>>>
>>>>> <table border="0" cellspacing="5">
>>>>>
>>>>> <tr>
>>>>>
>>>>> <th align="right">Username:</th>
>>>>>
>>>>> <td align="left"><input type="text" name="j_username"></td>
>>>>>
>>>>> </tr>
>>>>>
>>>>> <tr>
>>>>>
>>>>> <th align="right">Password:</th>
>>>>>
>>>>> <td align="left"><input type="password" name="j_password"></td>
>>>>>
>>>>> </tr>
>>>>>
>>>>> <tr>
>>>>>
>>>>> <td align="right"><input type="submit" value="Log In"></td>
>>>>>
>>>>> <td align="left"><input type="reset"></td>
>>>>>
>>>>> </tr>
>>>>>
>>>>> </table>
>>>>>
>>>>> </form>
>>>>>
>>>>>
>>>>> ======================================
>>>>>
>>>>>
>>>>>
>>>>> On 2015/7/23 16:16, Pengcheng Yang wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I have implemented the function using the role-name and the
>>>>>> url-pattern, following the [1,2,3] direction.
>>>>>>
>>>>>>
>>>>>> http://stackoverflow.com/questions/1089600/tomcat-security-constraint-for-valid-user 
>>>>>>
>>>>>>
>>>>>>
>>>>>> http://stackoverflow.com/questions/11382159/tomcat-7-form-based-authentification 
>>>>>>
>>>>>>
>>>>>>
>>>>>> https://tomcat.apache.org/tomcat-7.0-doc/realm-howto.html
>>>>>>
>>>>>> Is this feature possible be integrated into InterMine in the future?
>>>>>>
>>>>>> Best,
>>>>>> Pengcheng Yang
>>>>>>
>>>>>>
>>>>>> On 2015/7/23 9:13, Pengcheng Yang wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> The solution here:
>>>>>>> https://tomcat.apache.org/tomcat-7.0-doc/realm-howto.html
>>>>>>>
>>>>>>> Has anyone configured through Tomcat Realm to manage user
>>>>>>> authentication? Is it possible to implement this feature on
>>>>>>> InterMine?
>>>>>>>
>>>>>>> Thanks a lot!
>>>>>>>
>>>>>>> Best,
>>>>>>> Pengcheng Yang
>>>>>>>
>>>>>>> On 2015/7/22 21:06, Pengcheng Yang wrote:
>>>>>>>> Dear InterMine developers,
>>>>>>>>
>>>>>>>> I want to set the authority to users with limited permission to
>>>>>>>> visit specific data set. Two years ago, the same question has been
>>>>>>>> initialized at:
>>>>>>>> http://gmod.827538.n3.nabble.com/user-accounts-pages-td4036801.html. 
>>>>>>>>
>>>>>>>> However, it seems that this function has not yet been implemented.
>>>>>>>>
>>>>>>>> I found it can be implemented through the
>>>>>>>> apache-tomcat-7.0.63/webapps/mine/WEB-INF/web.xml file. Has anyone
>>>>>>>> implemented this function?
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Pengcheng Yang
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
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>





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