You are missing two certmonger CA helpers, dogtag-ipa-ca-renew-agent and
dogtag-ipa-ca-renew-agent-reuse.

Re-add them as root with:

# getcert add-ca -c dogtag-ipa-ca-renew-agent -e
/usr/libexec/certmonger/dogtag-ipa-ca-renew-agent-submit
# getcert add-ca -c dogtag-ipa-ca-renew-agent-reuse -e
/usr/libexec/certmonger/dogtag-ipa-ca-renew-agent-submit --reuse-existing

Confirm with getcert list that every tracked request has a CA value.

That should do the trick, you can now run:

# ipa-server-upgrade

rob

David Carter via FreeIPA-users wrote:
> With some redactions:
> 
> # getcert list
> Number of certificates and requests being tracked: 9.
> Request ID '20190815160425':
> status: MONITORING
> stuck: no
> key pair storage: type=FILE,location='/var/lib/ipa/ra-agent.key'
> certificate: type=FILE,location='/var/lib/ipa/ra-agent.pem'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=IPA RA,O=XXXXXXXXXXXXX
> expires: 2021-08-04 16:04:27 UTC
> key usage: digitalSignature,keyEncipherment,dataEncipherment
> eku: id-kp-serverAuth,id-kp-clientAuth
> pre-save command: /usr/libexec/ipa/certmonger/renew_ra_cert_pre
> post-save command: /usr/libexec/ipa/certmonger/renew_ra_cert
> track: yes
> auto-renew: yes
> Request ID '20190815160528':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='auditSigningCert
> cert-pki-ca',token='NSS Certificate DB',pin set
> certificate:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='auditSigningCert
> cert-pki-ca',token='NSS Certificate DB'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=CA Audit,O=XXXXXXXXXXXXX
> expires: 2021-08-04 16:03:26 UTC
> key usage: digitalSignature,nonRepudiation
> pre-save command: /usr/libexec/ipa/certmonger/stop_pkicad
> post-save command: /usr/libexec/ipa/certmonger/renew_ca_cert
> "auditSigningCert cert-pki-ca"
> track: yes
> auto-renew: yes
> Request ID '20190815160529':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='ocspSigningCert 
> cert-pki-ca',token='NSS
> Certificate DB',pin set
> certificate:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='ocspSigningCert 
> cert-pki-ca',token='NSS
> Certificate DB'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=OCSP Subsystem,O=XXXXXXXXXXXXX
> expires: 2021-08-04 16:03:24 UTC
> eku: id-kp-OCSPSigning
> pre-save command: /usr/libexec/ipa/certmonger/stop_pkicad
> post-save command: /usr/libexec/ipa/certmonger/renew_ca_cert
> "ocspSigningCert cert-pki-ca"
> track: yes
> auto-renew: yes
> Request ID '20190815160530':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='subsystemCert
> cert-pki-ca',token='NSS Certificate DB',pin set
> certificate:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='subsystemCert
> cert-pki-ca',token='NSS Certificate DB'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=CA Subsystem,O=XXXXXXXXXXXXX
> expires: 2021-08-04 16:03:25 UTC
> key usage: digitalSignature,nonRepudiation,keyEncipherment,dataEncipherment
> eku: id-kp-clientAuth
> pre-save command: /usr/libexec/ipa/certmonger/stop_pkicad
> post-save command: /usr/libexec/ipa/certmonger/renew_ca_cert
> "subsystemCert cert-pki-ca"
> track: yes
> auto-renew: yes
> Request ID '20190815160531':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='caSigningCert
> cert-pki-ca',token='NSS Certificate DB',pin set
> certificate:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='caSigningCert
> cert-pki-ca',token='NSS Certificate DB'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=Certificate Authority,O=XXXXXXXXXXXXX
> expires: 2039-08-15 16:03:22 UTC
> key usage: digitalSignature,nonRepudiation,keyCertSign,cRLSign
> pre-save command: /usr/libexec/ipa/certmonger/stop_pkicad
> post-save command: /usr/libexec/ipa/certmonger/renew_ca_cert
> "caSigningCert cert-pki-ca"
> track: yes
> auto-renew: yes
> Request ID '20190815160532':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='Server-Cert
> cert-pki-ca',token='NSS Certificate DB',pin set
> certificate:
> type=NSSDB,location='/etc/pki/pki-tomcat/alias',nickname='Server-Cert
> cert-pki-ca',token='NSS Certificate DB'
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=XXXXXXXXXXXXX,O=XXXXXXXXXXXXX
> expires: 2021-08-04 16:03:24 UTC
> dns: XXXXXXXXXXXXX
> key usage: digitalSignature,keyEncipherment,dataEncipherment
> eku: id-kp-serverAuth
> pre-save command: /usr/libexec/ipa/certmonger/stop_pkicad
> post-save command: /usr/libexec/ipa/certmonger/renew_ca_cert
> "Server-Cert cert-pki-ca"
> track: yes
> auto-renew: yes
> Request ID '20190815160610':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/dirsrv/slapd-XXXXXXXXXXXXX',nickname='Server-Cert',token='NSS
> Certificate DB',pinfile='/etc/dirsrv/slapd-XXXXXXXXXXXXX/pwdfile.txt'
> certificate:
> type=NSSDB,location='/etc/dirsrv/slapd-XXXXXXXXXXXXX',nickname='Server-Cert',token='NSS
> Certificate DB'
> CA: IPA
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=XXXXXXXXXXXXX,O=XXXXXXXXXXXXX
> expires: 2021-08-15 16:06:11 UTC
> dns: XXXXXXXXXXXXX
> principal name: ldap/XXXXXXXXXXXXX@XXXXXXXXXXXXX
> key usage: digitalSignature,nonRepudiation,keyEncipherment,dataEncipherment
> eku: id-kp-serverAuth,id-kp-clientAuth
> pre-save command: 
> post-save command: /usr/libexec/ipa/certmonger/restart_dirsrv XXXXXXXXXXXXX
> track: yes
> auto-renew: yes
> Request ID '20190815160720':
> status: MONITORING
> stuck: no
> key pair storage:
> type=NSSDB,location='/etc/httpd/alias',nickname='Server-Cert',token='NSS
> Certificate DB',pinfile='/etc/httpd/alias/pwdfile.txt'
> certificate:
> type=NSSDB,location='/etc/httpd/alias',nickname='Server-Cert',token='NSS
> Certificate DB'
> CA: IPA
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=XXXXXXXXXXXXX,O=XXXXXXXXXXXXX
> expires: 2021-08-15 16:07:21 UTC
> dns: XXXXXXXXXXXXX
> principal name: HTTP/XXXXXXXXXXXXX@XXXXXXXXXXXXX
> key usage: digitalSignature,nonRepudiation,keyEncipherment,dataEncipherment
> eku: id-kp-serverAuth,id-kp-clientAuth
> pre-save command: 
> post-save command: /usr/libexec/ipa/certmonger/restart_httpd
> track: yes
> auto-renew: yes
> Request ID '20190815160739':
> status: MONITORING
> stuck: no
> key pair storage: type=FILE,location='/var/kerberos/krb5kdc/kdc.key'
> certificate: type=FILE,location='/var/kerberos/krb5kdc/kdc.crt'
> CA: IPA
> issuer: CN=Certificate Authority,O=XXXXXXXXXXXXX
> subject: CN=XXXXXXXXXXXXX,O=XXXXXXXXXXXXX
> expires: 2021-08-15 16:07:40 UTC
> principal name: krbtgt/XXXXXXXXXXXXX@XXXXXXXXXXXXX
> key usage: digitalSignature,nonRepudiation,keyEncipherment,dataEncipherment
> eku: id-kp-serverAuth,id-pkinit-KPKdc
> pre-save command: 
> post-save command: /usr/libexec/ipa/certmonger/renew_kdc_cert
> track: yes
> auto-renew: yes
> 
> 
>> On Mar 4, 2020, at 12:16 PM, Rob Crittenden <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> David Carter via FreeIPA-users wrote:
>>> Freeipa was running fine, then I guess it tried to update and now I
>>> have an unusable system and it's impacting other systems. I've seen
>>> this error in a few online postings but no fix that I can apply.
>>>
>>> When I run it manually:
>>>
>>> [root@kdc1 log]# ipa-server-upgrade
>>> Upgrading IPA:. Estimated time: 1 minute 30 seconds
>>>  [1/11]: stopping directory server
>>>  [2/11]: saving configuration
>>>  [3/11]: disabling listeners
>>>  [4/11]: enabling DS global lock
>>>  [5/11]: disabling Schema Compat
>>>  [6/11]: starting directory server
>>>  [7/11]: updating schema
>>>  [8/11]: upgrading server
>>>  [9/11]: stopping directory server
>>>  [10/11]: restoring configuration
>>>  [11/11]: starting directory server
>>> Done.
>>> Update complete
>>> Upgrading IPA services
>>> Upgrading the configuration of the IPA services
>>> [Verifying that root certificate is published]
>>> [Migrate CRL publish directory]
>>> CRL tree already moved
>>> [Verifying that CA proxy configuration is correct]
>>> [Verifying that KDC configuration is using ipa-kdb backend]
>>> [Fix DS schema file syntax]
>>> Syntax already fixed
>>> [Removing RA cert from DS NSS database]
>>> RA cert already removed
>>> [Enable sidgen and extdom plugins by default]
>>> [Updating HTTPD service IPA configuration]
>>> [Updating HTTPD service IPA WSGI configuration]
>>> Nothing to do for configure_httpd_wsgi_conf
>>> [Updating mod_nss protocol versions]
>>> Protocol versions already updated
>>> [Updating mod_nss cipher suite]
>>> [Updating mod_nss enabling OCSP]
>>> [Fixing trust flags in /etc/httpd/alias]
>>> Trust flags already processed
>>> [Moving HTTPD service keytab to gssproxy]
>>> [Removing self-signed CA]
>>> [Removing Dogtag 9 CA]
>>> [Checking for deprecated KDC configuration files]
>>> [Checking for deprecated backups of Samba configuration files]
>>> [Add missing CA DNS records]
>>> IPA CA DNS records already processed
>>> [Removing deprecated DNS configuration options]
>>> DNS is not configured
>>> [Ensuring minimal number of connections]
>>> DNS is not configured
>>> [Updating GSSAPI configuration in DNS]
>>> DNS is not configured
>>> [Updating pid-file configuration in DNS]
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> DNS is not configured
>>> [Upgrading CA schema]
>>> CA schema update complete (no changes)
>>> [Verifying that CA audit signing cert has 2 year validity]
>>> [Update certmonger certificate renewal configuration]
>>> Failed to get request: bus, object_path and dbus_interface must not
>>> be None.
>>> IPA server upgrade failed: Inspect /var/log/ipaupgrade.log and run
>>> command ipa-server-upgrade manually.
>>> bus, object_path and dbus_interface must not be None.
>>> The ipa-server-upgrade command failed. See /var/log/ipaupgrade.log
>>> for more information
>>> The tail of the log file (it is very long):
>>>
>>> 2020-03-03T03:51:44Z DEBUG stderr=
>>> 2020-03-03T03:51:44Z DEBUG Loading Index file from
>>> '/var/lib/ipa/sysrestore/sysrestore.index'
>>> 2020-03-03T03:51:44Z DEBUG Starting external process
>>> 2020-03-03T03:51:44Z DEBUG args=/usr/bin/certutil -d
>>> dbm:/etc/pki/pki-tomcat/alias -L -f /etc/pki/pki-tomcat/alias/pwdfile.txt
>>> 2020-03-03T03:51:44Z DEBUG Process finished, return code=0
>>> 2020-03-03T03:51:44Z DEBUG stdout=
>>> Certificate Nickname                                         Trust
>>> Attributes
>>>                                                             
>>> SSL,S/MIME,JAR/XPI
>>>
>>> caSigningCert cert-pki-ca                                    CTu,Cu,Cu
>>> auditSigningCert cert-pki-ca                                 u,u,Pu
>>> Server-Cert cert-pki-ca                                      u,u,u
>>> ocspSigningCert cert-pki-ca                                  u,u,u
>>> subsystemCert cert-pki-ca                                    u,u,u
>>>
>>> 2020-03-03T03:51:44Z DEBUG stderr=
>>> 2020-03-03T03:51:44Z ERROR Failed to get request: bus, object_path
>>> and dbus_interface must not be None.
>>> 2020-03-03T03:51:44Z ERROR IPA server upgrade failed: Inspect
>>> /var/log/ipaupgrade.log and run command ipa-server-upgrade manually.
>>> 2020-03-03T03:51:44Z DEBUG   File
>>> "/usr/lib/python2.7/site-packages/ipapython/admintool.py", line 178,
>>> in execute
>>>    return_value = self.run()
>>>  File
>>> "/usr/lib/python2.7/site-packages/ipaserver/install/ipa_server_upgrade.py",
>>> line 56, in run
>>>    raise admintool.ScriptError(str(e))
>>>
>>> 2020-03-03T03:51:44Z DEBUG The ipa-server-upgrade command failed,
>>> exception: ScriptError: bus, object_path and dbus_interface must not
>>> be None.
>>> 2020-03-03T03:51:44Z ERROR bus, object_path and dbus_interface must
>>> not be None.
>>> 2020-03-03T03:51:44Z ERROR The ipa-server-upgrade command failed. See
>>> /var/log/ipaupgrade.log for more information
>>> I can run the certutil command separately, so it doesn't seem to be
>>> that. I have no idea what the issue is, where to look, or how I can
>>> fix this. Suggestions?
>>>
>>> OS: CentOS 7
>>> IPA version: VERSION: 4.6.5, API_VERSION: 2.231
>>
>> What is the output of getcert list-cas
>>
>> One or more is missing.
>>
>> BTW this terrible error message is fixed upstream and will appear in
>> future versions of RHEL 8 with a much better description.
>>
>> rob
>>
> 
> 
> 
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