pki-server cert-fix operation shows no output except deprecation warnings

[taherrin]

Summary:

When using pki-server cert-fix command, the output no longer shows the status of the cert fix operation

Build:

OS: fedora-41
Build: dogtag-pki-11.6.0-0.3.alpha3.20250131152214UTC.0a88a9be.fc41.x86_64
COPR: @pki/master

Steps to reproduce:

1. Install dogtag-pki packages
2. Install DS & CA
3. Run pki-server cert-fix command:

# pki-server cert-fix --ldap-url ldap://pki1.example.com:389 --agent-uid caadmin -i topology-00-CA -p 20443

Expected Result:

The output should show the status of the cert-fix operation

# pki-server --help
INFO: Loading instance type: pki-tomcatd
INFO: Loading instance: topology-00-CA
INFO: Loading global Tomcat config: /etc/tomcat/tomcat.conf
INFO: Loading PKI Tomcat config: /usr/share/pki/etc/tomcat.conf
INFO: Loading instance Tomcat config: /var/lib/pki/topology-00-CA/conf/tomcat.conf
INFO: Loading password config: /var/lib/pki/topology-00-CA/conf/password.conf
INFO: Loading subsystem config: /var/lib/pki/topology-00-CA/conf/ca/CS.cfg
INFO: Loading subsystem registry: /var/lib/pki/topology-00-CA/conf/ca/registry.cfg
INFO: Loading instance registry: /etc/sysconfig/pki/tomcat/topology-00-CA/topology-00-CA
INFO: Fixing the following system certs: ['ca_ocsp_signing', 'sslserver', 'subsystem', 'ca_audit_signing']
INFO: Renewing the following additional certs: []
Enter Directory Manager password: 
INFO: Stopping the instance to proceed with system cert renewal
INFO: Configuring LDAP connection for CA
INFO: Storing subsystem config: /var/lib/pki/topology-00-CA/conf/ca/CS.cfg
INFO: Storing registry config: /var/lib/pki/topology-00-CA/conf/ca/registry.cfg
INFO: Setting selftests.container.order.startup to CAPresence, SystemCertsVerification
INFO: Storing subsystem config: /var/lib/pki/topology-00-CA/conf/ca/CS.cfg
INFO: Storing registry config: /var/lib/pki/topology-00-CA/conf/ca/registry.cfg
INFO: Selftests disabled for subsystems: ca
INFO: Resetting password for uid=caadmin,ou=people,o=topology-00-CA-CA
INFO: Creating a temporary sslserver cert
INFO: Trying to create a new temp cert for sslserver.
INFO: Generate temp SSL certificate
INFO: SKI: 0x6777E55975A58250971D0A91DCC88408F85C5097
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: Creating AKID extension:
INFO: - keyid
INFO: - AKID: 0x6777e55975a58250971d0a91dcc88408f85c5097
INFO: Creating key usage extension:
INFO: - critical
INFO: - digitalSignature
INFO: - nonRepudiation
INFO: - keyEncipherment
INFO: - dataEncipherment
INFO: Creating extended key usage extension:
INFO: - serverAuth
INFO: Temp cert for sslserver is available at /var/lib/pki/topology-00-CA/conf/certs/sslserver.crt.
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: NSSDatabase: Importing cert Server-Cert cert-topology-00-CA into Internal Key Storage Token
INFO: Starting the instance
INFO: Sleeping for 10 seconds to allow server time to start...
INFO: Requesting new cert for ca_ocsp_signing
INFO: Trying to setup a secure connection to CA subsystem.
INFO: Secure connection with CA is established.
INFO: Placing cert creation request for serial: 278373290198096421295102290526709575295
INFO: Request ID: 84086684423735707200951288362975952505
INFO: Request Status: complete
INFO: Serial Number: 0xf6c12eafc64ff089c6bfccdab12f9527
INFO: Issuer: CN=CA Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: Subject: CN=CA OCSP Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: New cert is available at: /var/lib/pki/topology-00-CA/conf/certs/ca_ocsp_signing.crt
INFO: Requesting new cert for sslserver
INFO: Trying to setup a secure connection to CA subsystem.
INFO: Secure connection with CA is established.
INFO: Placing cert creation request for serial: 281408239077615326066274605522303057409
INFO: Request ID: 206077800539468764439139295278403649870
INFO: Request Status: complete
INFO: Serial Number: 0x27da67338993f5e105fe1a0696523515
INFO: Issuer: CN=CA Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: Subject: CN=pki1.example.com,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: New cert is available at: /var/lib/pki/topology-00-CA/conf/certs/sslserver.crt
INFO: Requesting new cert for subsystem
INFO: Trying to setup a secure connection to CA subsystem.
INFO: Secure connection with CA is established.
INFO: Placing cert creation request for serial: 105547520523090159906889705393629022693
INFO: Request ID: 168601289268192895280018314915886530806
INFO: Request Status: complete
INFO: Serial Number: 0xea0eab582303d224c73e8295d770936a
INFO: Issuer: CN=CA Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: Subject: CN=Subsystem Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: New cert is available at: /var/lib/pki/topology-00-CA/conf/certs/subsystem.crt
INFO: Requesting new cert for ca_audit_signing
INFO: Trying to setup a secure connection to CA subsystem.
INFO: Secure connection with CA is established.
INFO: Placing cert creation request for serial: 10597335687972365775415769547024874632
INFO: Request ID: 71453930562412349778579347789824850258
INFO: Request Status: complete
INFO: Serial Number: 0xab90f43dd6eade3edd2e4603b80e2745
INFO: Issuer: CN=CA Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: Subject: CN=CA Audit Signing Certificate,OU=topology-00-CA,O=topology-00_Foobarmaster.org
INFO: New cert is available at: /var/lib/pki/topology-00-CA/conf/certs/ca_audit_signing.crt
INFO: Stopping the instance
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: NSSDatabase: Importing cert ocspSigningCert cert-topology-00-CA CA into Internal Key Storage Token
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: NSSDatabase: Importing cert Server-Cert cert-topology-00-CA into Internal Key Storage Token
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: NSSDatabase: Importing cert subsystemCert cert-topology-00-CA into Internal Key Storage Token
INFO: Initializing NSS
INFO: Logging into internal token
INFO: Using internal token
INFO: NSSDatabase: Importing cert auditSigningCert cert-topology-00-CA CA into Internal Key Storage Token
INFO: Importing new subsystem cert into uid=pkidbuser,ou=people,o=topology-00-CA-CA
modifying entry "uid=pkidbuser,ou=people,o=topology-00-CA-CA"

INFO: Setting selftests.container.order.startup to CAPresence:critical, SystemCertsVerification:critical
INFO: Storing subsystem config: /var/lib/pki/topology-00-CA/conf/ca/CS.cfg
INFO: Storing registry config: /var/lib/pki/topology-00-CA/conf/ca/registry.cfg
INFO: Selftests enabled for subsystems: ca
INFO: Restoring LDAP connection for CA
INFO: Storing subsystem config: /var/lib/pki/topology-00-CA/conf/ca/CS.cfg
INFO: Storing registry config: /var/lib/pki/topology-00-CA/conf/ca/registry.cfg
INFO: Starting the instance with renewed certs

Actual Result:

Cert-fix output displays mostly deprecation warnings. even with --debug option:

# pki-server -v --debug cert-fix --ldap-url ldap://pki1.example.com:389 --agent-uid caadmin -i topology-00-CA -p 20443
Enter Directory Manager password: 
WARNING: No selftests configured in /var/lib/pki/topology-00-CA/conf/ca/CS.cfg (selftests.container.order.startup).
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1649: The PKIConnection parameter in AccountClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1789: The PKIConnection parameter in CertClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1649: The PKIConnection parameter in AccountClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1789: The PKIConnection parameter in CertClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1649: The PKIConnection parameter in AccountClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1789: The PKIConnection parameter in CertClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1649: The PKIConnection parameter in AccountClient.__init__() has been deprecated. Provide PKIClient instead.
WARNING: /usr/lib/python3.13/site-packages/pki/server/__init__.py:1789: The PKIConnection parameter in CertClient.__init__() has been deprecated. Provide PKIClient instead.
modifying entry "uid=pkidbuser,ou=people,o=topology-00-CA-CA"