I have added an ssl cert secret in rancher and configured the ingress file in the helm chart as follows:

{{- $fullName := include "api-chart.fullname" . -}}
{{- $ingressPath := .Values.ingress.path -}}
{{- $apiIngressPath := .Values.ingress.apiPath -}}
apiVersion: extensions/v1beta1
kind: Ingress
metadata:
  name: {{ $fullName }}
  labels:
    app.kubernetes.io/name: {{ include "api-chart.name" . }}
    helm.sh/chart: {{ include "api-chart.chart" . }}
    app.kubernetes.io/instance: {{ .Release.Name }}
    app.kubernetes.io/managed-by: {{ .Release.Service }}
  annotations:
    kubernetes.io/ingress.class: nginx
{{- with .Values.ingress.annotations }}
{{ toYaml . | indent 4 }}
{{- end }}
spec:
  tls:
    - hosts:
        - {{ .Values.ingress.host }}
      secretName: {{ .Values.ssl.certSecretName }}
  rules:
    - host: {{ .Values.ingress.host }}
      http:
        paths:
          - path: {{ $ingressPath }}
            backend:
              serviceName: {{ $fullName }}
              servicePort: 80
          - path: {{ $apiIngressPath }}
            backend:
              serviceName: {{ $fullName }}
              servicePort: 8080

The default, fake, Nginx certificate is however still received when visiting the https site. Does the Nginx server also need to be changed? If so seems strange that it is a requirement to add the certificate info in two places. If not, what else could be wrong?

kubectl describe ingress gives the following response:

Name:             my-test-install-app72-project-jupyter-labs
Namespace:        default
Address:          10.240.0.4
Default backend:  default-http-backend:80 (<none>)
Rules:
  Host                                    Path  Backends
  ----                                    ----  --------
  project-jupyter-labs-2.company.com  
                                          /test72-new-user   my-test-install-app72-project-jupyter-labs:80 (10.244.4.20:8888)
                                          /base-url          my-test-install-app72-project-jupyter-labs:8080 (10.244.4.20:8080)
Annotations:
  field.cattle.io/publicEndpoints:              [{"addresses":["10.240.0.4"],
                                                  "port":80,
                                                  "protocol":"HTTP",
                                                  "serviceName":"default:my-test-install-app72-project-jupyter-labs",
                                                  "ingressName":"default:my-test-install-app72-project-jupyter-labs",
                                                  "hostname":"project-jupyter-labs-2.company.com",
                                                  "path":"/test72-new-user",
                                                  "allNodes":false},
                                                 {"addresses":["10.240.0.4"],
                                                  "port":80,
                                                  "protocol":"HTTP",
                                                  "serviceName":"default:my-test-install-app72-project-jupyter-labs",
                                                  "ingressName":"default:my-test-install-app72-project-jupyter-labs",
                                                  "hostname":"project-jupyter-labs-2.company.com",
                                                  "path":"/base-url",
                                                  "allNodes":false}]
  kubernetes.io/ingress.class:                  nginx
  meta.helm.sh/release-name:                    my-test-install-app72
  meta.helm.sh/release-namespace:               default
  nginx.ingress.kubernetes.io/proxy-body-size:  2G
Events:
  Type    Reason  Age                From                      Message
  ----    ------  ----               ----                      -------
  Normal  CREATE  81s                nginx-ingress-controller  Ingress default/my-test-install-app72-project-jupyter-labs
  Normal  CREATE  81s                nginx-ingress-controller  Ingress default/my-test-install-app72-project-jupyter-labs
  Normal  UPDATE  23s (x2 over 23s)  nginx-ingress-controller  Ingress default/my-test-install-app72-project-jupyter-labs
  Normal  UPDATE  23s (x2 over 23s)  nginx-ingress-controller  Ingress default/my-test-install-app72-project-jupyter-labs

UPDATE: I am having trouble accessing the error logs. It seems like you need to exec into the container as root to be able to see these. What I did find however is that the server section of the nginx.conf file contains the following:

ssl_certificate_by_lua_block {                                                                                                                   
                        certificate.call()                                                                                                                       
                }

If I change this to ssl_certifacte and ssl_certifacte_key paths to the cert and key files that I manually added to the container, then it works. Does the above ssl_certificate_by_lua_block look normal for the ingress.yaml file? If so, what else could be the problem? If not, what could be causing this to not be probably configured?

Applying the following patch seems to allow the correct SSL certificate to be made available for https:

kubectl patch ingress <app-instance-name> -p '{"spec":{"tls":[{"hosts":["project-jupyter-labs-2.company.com"], "secretName": "tls-secret-name"}]}}'

Why this solves the problem is still unclear to me. I would appreciate any possible explanations.