Set ConfigMap values directly from values.yaml in helm

You are missing indentation in your values.yaml file, check YAML Multiline

myconfiguration: |-
  key1: >
    { "Project" : "This is config1 test"
    }
  key2 : >
    {
      "Project" : "This is config2 test"
    }

Also, the suggested syntax for YAML files is to use 2 spaces for indentation, so you may want to change your configmap to {{.Values.myconfiguration | indent 2}}