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After importing the signed certificates in addition to the Hub CA and HTTPS certificate, configure your Tomcat server.xml file to use the correct certificate to serve SHRINE https requests. Tomcat normally uses port 6443 to serve SHRINE. 

To serve SSL find this section and change it to use the right keystore password and key alias to serve https from tomcat. Although you can use the same keyAlias to sign shrine queries and to support TLS for https most sites choose to use their own cert signed by a CA in a public cert tree. This prevents dire warnings from browsers. Follow standard procedures for serving https via TLS from tomcat. Find the example in shrine-setup/server.xml .

    <!-- Define a SSL/TLS HTTP/1.1 Connector on port 8443
         This connector uses the NIO implementation that requires the JSSE
         style configuration. When using the APR/native implementation, the
         OpenSSL style configuration is required as described in the APR/native
         documentation -->

    <Connector port="6443" protocol="org.apache.coyote.http11.Http11NioProtocol"
               maxThreads="150" SSLEnabled="true" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS"
               keystoreFile="/opt/shrine/shrine.keystore"
               keystorePass="password"
               keyAlias="<name_of_keystore_PrivateKeyEntry>" />


The URLs to the SHRINE webclient, steward, and changed in SHRINE 2.0.0. If you would like to add redirects to the old URLs, add a RewriteValve to the server.xml file and copy the shrine-setup/rewrite.config file to /opt/shrine/tomcat/conf/Catalina/localhost.    


server.xml
<Host name="localhost"  appBase="webapps" unpackWARs="true" autoDeploy="true">

    <Valve className="org.apache.catalina.valves.rewrite.RewriteValve" />
........


Here's a sample server.xml file (note the 'Connector port = "6443"' section):

server.xml
<?xml version='1.0' encoding='utf-8'?>
<!--
  Licensed to the Apache Software Foundation (ASF) under one or more
  contributor license agreements.  See the NOTICE file distributed with
  this work for additional information regarding copyright ownership.
  The ASF licenses this file to You under the Apache License, Version 2.0
  (the "License"); you may not use this file except in compliance with
  the License.  You may obtain a copy of the License at
 
      http://www.apache.org/licenses/LICENSE-2.0
 
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
-->


<!-- Note:  A "Server" is not itself a "Container", so you may not
     define subcomponents such as "Valves" at this level.
     Documentation at /docs/config/server.html
 -->

<Server port="8005" shutdown="SHUTDOWN">
  <Listener className="org.apache.catalina.startup.VersionLoggerListener" />
  <!-- Security listener. Documentation at /docs/config/listeners.html
  <Listener className="org.apache.catalina.security.SecurityListener" />
  -->

  <!--APR library loader. Documentation at /docs/apr.html -->
  <Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />
  <!-- Prevent memory leaks due to use of particular java/javax APIs-->
  <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
  <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
  <Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />

  <!-- Global JNDI resources
       Documentation at /docs/jndi-resources-howto.html
  -->

  <GlobalNamingResources>
    <!-- Editable user database that can also be used by
         UserDatabaseRealm to authenticate users
    -->

    <Resource name="UserDatabase" auth="Container"
              type="org.apache.catalina.UserDatabase"
              description="User database that can be updated and saved"
              factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
              pathname="conf/tomcat-users.xml" />
  </GlobalNamingResources>

  <!-- A "Service" is a collection of one or more "Connectors" that share
       a single "Container" Note:  A "Service" is not itself a "Container",
       so you may not define subcomponents such as "Valves" at this level.
       Documentation at /docs/config/service.html
   -->

  <Service name="Catalina">
    <!--The connectors can use a shared executor, you can define one or more named thread pools-->
    <!--
    <Executor name="tomcatThreadPool" namePrefix="catalina-exec-"
        maxThreads="150" minSpareThreads="4"/>
    -->

    <!-- A "Connector" represents an endpoint by which requests are received
         and responses are returned. Documentation at :
         Java HTTP Connector: /docs/config/http.html (blocking & non-blocking)
         Java AJP  Connector: /docs/config/ajp.html
         APR (HTTP/AJP) Connector: /docs/apr.html
         Define a non-SSL/TLS HTTP/1.1 Connector on port 8080
    -->

    <Connector port="6060" protocol="HTTP/1.1"
               connectionTimeout="20000"
               redirectPort="6443" />


    <!-- A "Connector" using the shared thread pool-->
    <!--
    <Connector executor="tomcatThreadPool"
               port="8080" protocol="HTTP/1.1"
               connectionTimeout="20000"
               redirectPort="8443" />
    -->

    <!-- Define a SSL/TLS HTTP/1.1 Connector on port 8443
         This connector uses the NIO implementation that requires the JSSE
         style configuration. When using the APR/native implementation, the
         OpenSSL style configuration is required as described in the APR/native
         documentation -->

    <Connector port="6443" protocol="org.apache.coyote.http11.Http11NioProtocol"
               maxThreads="150" SSLEnabled="true" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS"
               keystoreFile="/opt/shrine/shrine.keystore"
               keystorePass="password"
               keyAlias="<name_of_keystore_PrivateKeyEntry>" 
/>
 
    <!-- Define an AJP 1.3 Connector on port 8009 -->
    <Connector port="6009" protocol="AJP/1.3" redirectPort="8443" />
 

    <!-- An Engine represents the entry point (within Catalina) that processes
         every request.  The Engine implementation for Tomcat stand alone
         analyzes the HTTP headers included with the request, and passes them
         on to the appropriate Host (virtual host).
         Documentation at /docs/config/engine.html -->

    <!-- You should set jvmRoute to support load-balancing via AJP ie :
    <Engine name="Catalina" defaultHost="localhost" jvmRoute="jvm1">
    -->

    <Engine name="Catalina" defaultHost="localhost">


      <!--For clustering, please take a look at documentation at:
          /docs/cluster-howto.html  (simple how to)
          /docs/config/cluster.html (reference documentation) -->
      <!--
      <Cluster className="org.apache.catalina.ha.tcp.SimpleTcpCluster"/>
      -->

      <!-- Use the LockOutRealm to prevent attempts to guess user passwords
           via a brute-force attack -->


      <Realm className="org.apache.catalina.realm.LockOutRealm">
        <!-- This Realm uses the UserDatabase configured in the global JNDI
             resources under the key "UserDatabase".  Any edits
             that are performed against this UserDatabase are immediately
             available for use by the Realm.  -->


        <Realm className="org.apache.catalina.realm.UserDatabaseRealm"
               resourceName="UserDatabase"/>
      </Realm>

      <Host name="localhost"  appBase="webapps"
            unpackWARs="true" autoDeploy="true">


      <Valve className="org.apache.catalina.valves.rewrite.RewriteValve" />

        <!-- SingleSignOn valve, share authentication between web applications
             Documentation at: /docs/config/valve.html -->
        <!--
        <Valve className="org.apache.catalina.authenticator.SingleSignOn" />
        -->

        <!-- Access log processes all example.
             Documentation at: /docs/config/valve.html
             Note: The pattern used is equivalent to using pattern="common" -->


        <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
               prefix="localhost_access_log" suffix=".txt"
               pattern="%h %l %u %t &quot;%r&quot; %s %b" />


      </Host>
    </Engine>
  </Service>
</Server>

Optional Step

This step is optional for remote sites.

By default, our recommendation for a typical remote site is to have it submit a Certificate Signing Request (CSR) to the certificate authority (CA) of the SHRINE network to which they are joining. The CA will in turn generate a new certificate for the downstream site, and we will return that certificate, the hub certificate, and the CA certificate of the tier back to the downstream site. The site will then import the certificates into their shrine keystore file, and configure their shrine.conf and server.xml to point to the alias entry in the keystore that corresponds to the site.

A typical keystore after importing all the certs in would look like this (assuming that the downstream site is called "shrine.example.edu"):

Keystore type: jks
Keystore provider: SUN

Your keystore contains 3 entries

shrine.example.edu, Oct 31, 2018, PrivateKeyEntry, 
Certificate fingerprint (SHA1): 26:0B:FE:98:21:BA:C8:5A:A5:F5:35:79:8E:81:1A:E9:F4:3B:FF:56

shrine-act-test-ca, Jul 31, 2019, trustedCertEntry, 
Certificate fingerprint (SHA1): 13:4D:B5:5C:E3:48:A0:7B:9B:20:22:8B:0B:C1:BE:DD:B9:E4:1B:AD

shrine-act-test.hms.harvard.edu, Jul 31, 2019, trustedCertEntry, 
Certificate fingerprint (SHA1): 52:82:A0:6D:D1:48:B2:EA:BB:2C:58:BD:E5:C7:3B:21:75:2B:46:F6

shrine.conf contains a block like this:

keystore {
    file = "/opt/shrine/shrine.keystore"
    password = "xxxxxx"
    privateKeyAlias = "shrine.example.edu"
    keyStoreType = "JKS"
    caCertAliases = ["shrine-act-test-ca"]
  }

And server.xml will contain a block like this:

<Connector port="6443" protocol="org.apache.coyote.http11.Http11NioProtocol"
               maxThreads="150" SSLEnabled="true" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS"
               keystoreFile="/opt/shrine/shrine.keystore"
               keystorePass="xxxxxx"
               keyAlias="shrine.example.edu"/> 


When using the above approach a web browser attempting to access a shrine host configured in this way will generate a warning. The browser will not trust the CA because none of the CAs are public. Consequently, any certificate that the CA signs is not trusted by the browser. While the browser can be configured to ignore the warning and the CA can be manually imported into the browser's trust store, some downstream sites may opt for a more elegant approach. Using a third-party-signed certificate eliminates the warnings from the web browser; the root and intermediate CAs are already trusted by the browser.

Using a Third-Party-Signed Certificate for Serving https Requests in Tomcat.

A third-party certificate does not replace the network CA-signed certificate; the network CA-signed certificate is still required for signing all application-specific messages. This wiki does not attempt to cover any vendor-specific processes or output files, because those can vary over time and across industry. It is up to each remote site that chooses this option to work with its vendor on any necessary technical details.

This guide also assumes the possibility that a site may initially opt for network CA-signed certificate, but later switch over to a third-party certificate. For all examples used in our illustration below this guide uses a fictitious remote site called shrine.example.edu.

The first step for the remote site is to generate a certificate signing request (CSR) using a private key, and to send that CSR to an SSL/TLS vendor such as InCommon and Symantec. This step can be performed using either openssl or keytool. The vendor will in turn generate a certificate for the requested fully-qualified domain name (FQDN), and it may provide additional certificates for its root and intermediate CAs. The remote site should work with the vendor to concatenate all certificates together into one file, so that it would be possible to trace the chain of trust from the endpoint certificate all the way back to the root CA.

The next step is to ensure that the private key that was used to generate the CSR is in a separate file. If a utility such as openssl was used to generate the CSR, then a file containing the private key should already be present and this step is unnecessary. If, however, the site used keytool to generate the CSR, then the following commands should be run to extract the private key from the keystore into a separate file. Execute the following commands to extract the private key into a file called private_key.pem (the command below assumes that the keystore is called shrine.keystore):

$ keytool -importkeystore -srckeystore shrine.keystore -srcstorepass <source_keystore_password> -srcalias shrine.example.edu -destalias shrine.example.edu -destkeystore shrine.keystore.p12 -deststoretype PKCS12 -deststorepass <destination_keystore_password>
$ openssl pkcs12 -in shrine.keystore.p12 -nodes -nocerts -out private_key.pem

This private key should be guarded carefully. Ideal places include an encrypted disk volume and non-persistent, RAM-based disk (such as /dev/shm in CentOS or Debian). The key can also be stored in an offline and physically secure location.

Next, upon receiving the signed certificate from the third-party CA, the remote site should then bundle the private key with the chained certificates into a PKCS12 file (.pfx or .p12 suffix) so that SHRINE can verify the chain of trust from the endpoint certificate all the way back to the root CA. Without this trust verification, SHRINE will be unable to use the certificates as intended. For our purpose, the PKCS#12 file format is ideal because it can combine a private key with all corresponding chained certificates into a single entry in the file, and because the format is accessible by both openssl and keytool. In the following command (again, assuming that the private key file is called private_key.pem), the certificates_file contains the new endpoint certificate plus all intermediate certificates plus the root certificate, and the ca_file contains only the intermediate certificates plus the root certificate. Run this command to bundle the private key, the endpoint certificate, and all intermediate and root certificates into one single entry within the PKCS12 store:

$ openssl pkcs12 -export -in <certificates_file> -inkey private_key.pem -out shrine.keystore.p12.temp -name shrine.example.edu-https -CAfile <ca_file> -chain -password pass:<your_pkcs12_file_password>

Note here that the value of the -name field is "shrine.example.edu-https". The reason is that we will eventually be importing this entire entry back into the main Java keystore where another entry called shrine.example.edu already exists. Recalling our earlier discussion about the purposes of certificates, we note that shrine.example.edu entry is responsible for application message signing, while shrine.example.edu-https entry is responsible for web browser encryption. Therefore two distinct keystore entries are necessary.

The newly constructed PKCS12 file should now be imported into the original shrine.keystore. Execute the following command, and if prompted to overwrite existing entry, answer "yes":

$ keytool -importkeystore -srckeystore shrine.keystore.p12.temp -srcstoretype pkcs12 -srcstorepass <your_pkcs12_file_password> -srcalias shrine.example.edu-https -destkeystore shrine.keystore -deststoretype jks -deststorepass <your_destination_keystore_password> -destalias shrine.example.edu-https

Once the import is completed, your shrine.keystore should now look like this:

Keystore type: jks
Keystore provider: SUN

Your keystore contains 4 entries
shrine.example.edu, Oct 31, 2018, PrivateKeyEntry, 
Certificate fingerprint (SHA1): 26:0B:FE:98:21:BA:C8:5A:A5:F5:35:79:8E:81:1A:E9:F4:3B:FF:56

shrine.example.edu-https, Jul 31, 2019, PrivateKeyEntry, 
Certificate fingerprint (SHA1): EF:AF:5E:D3:1A:97:AA:F2:6D:50:B8:9A:23:98:B5:2C:0C:18:C3:4B

shrine-act-test-ca, Jul 31, 2019, trustedCertEntry, 
Certificate fingerprint (SHA1): 13:4D:B5:5C:E3:48:A0:7B:9B:20:22:8B:0B:C1:BE:DD:B9:E4:1B:AD

shrine-act-test.hms.harvard.edu, Jul 31, 2019, trustedCertEntry, 
Certificate fingerprint (SHA1): 52:82:A0:6D:D1:48:B2:EA:BB:2C:58:BD:E5:C7:3B:21:75:2B:46:F6

Notice that there are now two (2) entries associated with shrine.example.edu: the original one continues to be used for application signing, and we will configure the "-https" entry for use by Tomcat to encrypt web browser traffic.

Next, configure the alias entry in Tomcat's server.xml to point to the newly imported, third-party-generated certificate:

<Connector port="6443" protocol="org.apache.coyote.http11.Http11NioProtocol"
               maxThreads="150" SSLEnabled="true" scheme="https" secure="true"
               clientAuth="false" sslProtocol="TLS"
               keystoreFile="/opt/shrine/shrine.keystore"
               keystorePass="xxxxxxxxxx"
               keyAlias="shrine.example.edu-https"/>


Once all configuration files have been updated, restart Tomcat. If everything has been configured properly, you should no longer see any warning messages from your browser regarding untrusted certificates when accessing your SHRINE host.


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