rnacentral.yaml 14 KB
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apiVersion: v1
kind: Service
metadata:
  name: rnacentral
  labels:
    app: rnacentral
spec:
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  type: NodePort  # EBI asked to expose the service using NodePort
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  ports:
  - port: {{ .Values.rnacentralPort }}
    targetPort: {{ .Values.rnacentralPort }}
    protocol: TCP
  selector:
    app: rnacentral
---
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apiVersion: v1
kind: ConfigMap
metadata:
  name: openssl-config
data:
  openssl.cnf: |-
    #
    # Using this file to avoid DH KEY TOO SMALL error
    # This is a security issue, as described here: https://weakdh.org/
    # I also raised a ticket to see if it can be fixed on the server side [vac #497561]
    #

    #
    # OpenSSL example configuration file.
    # This is mostly being used for generation of certificate requests.
    #

    # Note that you can include other files from the main configuration
    # file using the .include directive.
    #.include filename

    # This definition stops the following lines choking if HOME isn't
    # defined.
    HOME			= .

    # Extra OBJECT IDENTIFIER info:
    #oid_file		= $ENV::HOME/.oid
    oid_section		= new_oids

    # System default
    openssl_conf = default_conf

    # To use this configuration file with the "-extfile" option of the
    # "openssl x509" utility, name here the section containing the
    # X.509v3 extensions to use:
    # extensions		=
    # (Alternatively, use a configuration file that has only
    # X.509v3 extensions in its main [= default] section.)

    [ new_oids ]

    # We can add new OIDs in here for use by 'ca', 'req' and 'ts'.
    # Add a simple OID like this:
    # testoid1=1.2.3.4
    # Or use config file substitution like this:
    # testoid2=${testoid1}.5.6

    # Policies used by the TSA examples.
    tsa_policy1 = 1.2.3.4.1
    tsa_policy2 = 1.2.3.4.5.6
    tsa_policy3 = 1.2.3.4.5.7

    ####################################################################
    [ ca ]
    default_ca	= CA_default		# The default ca section

    ####################################################################
    [ CA_default ]

    dir		= ./demoCA		# Where everything is kept
    certs		= $dir/certs		# Where the issued certs are kept
    crl_dir		= $dir/crl		# Where the issued crl are kept
    database	= $dir/index.txt	# database index file.
    #unique_subject	= no			# Set to 'no' to allow creation of
    					# several certs with same subject.
    new_certs_dir	= $dir/newcerts		# default place for new certs.

    certificate	= $dir/cacert.pem 	# The CA certificate
    serial		= $dir/serial 		# The current serial number
    crlnumber	= $dir/crlnumber	# the current crl number
    					# must be commented out to leave a V1 CRL
    crl		= $dir/crl.pem 		# The current CRL
    private_key	= $dir/private/cakey.pem# The private key

    x509_extensions	= usr_cert		# The extensions to add to the cert

    # Comment out the following two lines for the "traditional"
    # (and highly broken) format.
    name_opt 	= ca_default		# Subject Name options
    cert_opt 	= ca_default		# Certificate field options

    # Extension copying option: use with caution.
    # copy_extensions = copy

    # Extensions to add to a CRL. Note: Netscape communicator chokes on V2 CRLs
    # so this is commented out by default to leave a V1 CRL.
    # crlnumber must also be commented out to leave a V1 CRL.
    # crl_extensions	= crl_ext

    default_days	= 365			# how long to certify for
    default_crl_days= 30			# how long before next CRL
    default_md	= default		# use public key default MD
    preserve	= no			# keep passed DN ordering

    # A few difference way of specifying how similar the request should look
    # For type CA, the listed attributes must be the same, and the optional
    # and supplied fields are just that :-)
    policy		= policy_match

    # For the CA policy
    [ policy_match ]
    countryName		= match
    stateOrProvinceName	= match
    organizationName	= match
    organizationalUnitName	= optional
    commonName		= supplied
    emailAddress		= optional

    # For the 'anything' policy
    # At this point in time, you must list all acceptable 'object'
    # types.
    [ policy_anything ]
    countryName		= optional
    stateOrProvinceName	= optional
    localityName		= optional
    organizationName	= optional
    organizationalUnitName	= optional
    commonName		= supplied
    emailAddress		= optional

    ####################################################################
    [ req ]
    default_bits		= 2048
    default_keyfile 	= privkey.pem
    distinguished_name	= req_distinguished_name
    attributes		= req_attributes
    x509_extensions	= v3_ca	# The extensions to add to the self signed cert

    # Passwords for private keys if not present they will be prompted for
    # input_password = secret
    # output_password = secret

    # This sets a mask for permitted string types. There are several options.
    # default: PrintableString, T61String, BMPString.
    # pkix	 : PrintableString, BMPString (PKIX recommendation before 2004)
    # utf8only: only UTF8Strings (PKIX recommendation after 2004).
    # nombstr : PrintableString, T61String (no BMPStrings or UTF8Strings).
    # MASK:XXXX a literal mask value.
    # WARNING: ancient versions of Netscape crash on BMPStrings or UTF8Strings.
    string_mask = utf8only

    # req_extensions = v3_req # The extensions to add to a certificate request

    [ req_distinguished_name ]
    countryName			= Country Name (2 letter code)
    countryName_default		= AU
    countryName_min			= 2
    countryName_max			= 2

    stateOrProvinceName		= State or Province Name (full name)
    stateOrProvinceName_default	= Some-State

    localityName			= Locality Name (eg, city)

    0.organizationName		= Organization Name (eg, company)
    0.organizationName_default	= Internet Widgits Pty Ltd

    # we can do this but it is not needed normally :-)
    #1.organizationName		= Second Organization Name (eg, company)
    #1.organizationName_default	= World Wide Web Pty Ltd

    organizationalUnitName		= Organizational Unit Name (eg, section)
    #organizationalUnitName_default	=

    commonName			= Common Name (e.g. server FQDN or YOUR name)
    commonName_max			= 64

    emailAddress			= Email Address
    emailAddress_max		= 64

    # SET-ex3			= SET extension number 3

    [ req_attributes ]
    challengePassword		= A challenge password
    challengePassword_min		= 4
    challengePassword_max		= 20

    unstructuredName		= An optional company name

    [ usr_cert ]

    # These extensions are added when 'ca' signs a request.

    # This goes against PKIX guidelines but some CAs do it and some software
    # requires this to avoid interpreting an end user certificate as a CA.

    basicConstraints=CA:FALSE

    # Here are some examples of the usage of nsCertType. If it is omitted
    # the certificate can be used for anything *except* object signing.

    # This is OK for an SSL server.
    # nsCertType			= server

    # For an object signing certificate this would be used.
    # nsCertType = objsign

    # For normal client use this is typical
    # nsCertType = client, email

    # and for everything including object signing:
    # nsCertType = client, email, objsign

    # This is typical in keyUsage for a client certificate.
    # keyUsage = nonRepudiation, digitalSignature, keyEncipherment

    # This will be displayed in Netscape's comment listbox.
    nsComment			= "OpenSSL Generated Certificate"

    # PKIX recommendations harmless if included in all certificates.
    subjectKeyIdentifier=hash
    authorityKeyIdentifier=keyid,issuer

    # This stuff is for subjectAltName and issuerAltname.
    # Import the email address.
    # subjectAltName=email:copy
    # An alternative to produce certificates that aren't
    # deprecated according to PKIX.
    # subjectAltName=email:move

    # Copy subject details
    # issuerAltName=issuer:copy

    #nsCaRevocationUrl		= http://www.domain.dom/ca-crl.pem
    #nsBaseUrl
    #nsRevocationUrl
    #nsRenewalUrl
    #nsCaPolicyUrl
    #nsSslServerName

    # This is required for TSA certificates.
    # extendedKeyUsage = critical,timeStamping

    [ v3_req ]

    # Extensions to add to a certificate request

    basicConstraints = CA:FALSE
    keyUsage = nonRepudiation, digitalSignature, keyEncipherment

    [ v3_ca ]


    # Extensions for a typical CA


    # PKIX recommendation.

    subjectKeyIdentifier=hash

    authorityKeyIdentifier=keyid:always,issuer

    basicConstraints = critical,CA:true

    # Key usage: this is typical for a CA certificate. However since it will
    # prevent it being used as an test self-signed certificate it is best
    # left out by default.
    # keyUsage = cRLSign, keyCertSign

    # Some might want this also
    # nsCertType = sslCA, emailCA

    # Include email address in subject alt name: another PKIX recommendation
    # subjectAltName=email:copy
    # Copy issuer details
    # issuerAltName=issuer:copy

    # DER hex encoding of an extension: beware experts only!
    # obj=DER:02:03
    # Where 'obj' is a standard or added object
    # You can even override a supported extension:
    # basicConstraints= critical, DER:30:03:01:01:FF

    [ crl_ext ]

    # CRL extensions.
    # Only issuerAltName and authorityKeyIdentifier make any sense in a CRL.

    # issuerAltName=issuer:copy
    authorityKeyIdentifier=keyid:always

    [ proxy_cert_ext ]
    # These extensions should be added when creating a proxy certificate

    # This goes against PKIX guidelines but some CAs do it and some software
    # requires this to avoid interpreting an end user certificate as a CA.

    basicConstraints=CA:FALSE

    # Here are some examples of the usage of nsCertType. If it is omitted
    # the certificate can be used for anything *except* object signing.

    # This is OK for an SSL server.
    # nsCertType			= server

    # For an object signing certificate this would be used.
    # nsCertType = objsign

    # For normal client use this is typical
    # nsCertType = client, email

    # and for everything including object signing:
    # nsCertType = client, email, objsign

    # This is typical in keyUsage for a client certificate.
    # keyUsage = nonRepudiation, digitalSignature, keyEncipherment

    # This will be displayed in Netscape's comment listbox.
    nsComment			= "OpenSSL Generated Certificate"

    # PKIX recommendations harmless if included in all certificates.
    subjectKeyIdentifier=hash
    authorityKeyIdentifier=keyid,issuer

    # This stuff is for subjectAltName and issuerAltname.
    # Import the email address.
    # subjectAltName=email:copy
    # An alternative to produce certificates that aren't
    # deprecated according to PKIX.
    # subjectAltName=email:move

    # Copy subject details
    # issuerAltName=issuer:copy

    #nsCaRevocationUrl		= http://www.domain.dom/ca-crl.pem
    #nsBaseUrl
    #nsRevocationUrl
    #nsRenewalUrl
    #nsCaPolicyUrl
    #nsSslServerName

    # This really needs to be in place for it to be a proxy certificate.
    proxyCertInfo=critical,language:id-ppl-anyLanguage,pathlen:3,policy:foo

    ####################################################################
    [ tsa ]

    default_tsa = tsa_config1	# the default TSA section

    [ tsa_config1 ]

    # These are used by the TSA reply generation only.
    dir		= ./demoCA		# TSA root directory
    serial		= $dir/tsaserial	# The current serial number (mandatory)
    crypto_device	= builtin		# OpenSSL engine to use for signing
    signer_cert	= $dir/tsacert.pem 	# The TSA signing certificate
    					# (optional)
    certs		= $dir/cacert.pem	# Certificate chain to include in reply
    					# (optional)
    signer_key	= $dir/private/tsakey.pem # The TSA private key (optional)
    signer_digest  = sha256			# Signing digest to use. (Optional)
    default_policy	= tsa_policy1		# Policy if request did not specify it
    					# (optional)
    other_policies	= tsa_policy2, tsa_policy3	# acceptable policies (optional)
    digests     = sha1, sha256, sha384, sha512  # Acceptable message digests (mandatory)
    accuracy	= secs:1, millisecs:500, microsecs:100	# (optional)
    clock_precision_digits  = 0	# number of digits after dot. (optional)
    ordering		= yes	# Is ordering defined for timestamps?
    				# (optional, default: no)
    tsa_name		= yes	# Must the TSA name be included in the reply?
    				# (optional, default: no)
    ess_cert_id_chain	= no	# Must the ESS cert id chain be included?
    				# (optional, default: no)
    ess_cert_id_alg		= sha1	# algorithm to compute certificate
    				# identifier (optional, default: sha1)
    [default_conf]
    ssl_conf = ssl_sect

    [ssl_sect]
    system_default = system_default_sect

    [system_default_sect]
    MinProtocol = TLSv1.2
    CipherString = DEFAULT@SECLEVEL=1
---
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apiVersion: apps/v1
kind: Deployment
metadata:
  name: rnacentral
spec:
  replicas: {{ .Values.rnacentralReplicas }}
  selector:
    matchLabels:
      app: rnacentral
  template:
    metadata:
      labels:
        app: rnacentral
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      annotations:
        rollme: {{ randAlphaNum 5 | quote }}
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    spec:
      containers:
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        - image: rnacentral/rnacentral-webcode:{{ .Values.rnacentralBranch }}
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          name: rnacentral
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          imagePullPolicy: Always
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          ports:
          - containerPort: {{ .Values.rnacentralPort }}
          resources:
            requests:
              memory: {{ .Values.rnacentralRequestsMemory }}
              cpu: {{ .Values.rnacentralRequestsCPU }}
            limits:
              memory: {{ .Values.rnacentralLimitssMemory }}
              cpu: {{ .Values.rnacentralLimitsCPU }}
          volumeMounts:
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            - name: openssl-config
              mountPath: /etc/ssl/openssl.cnf
              subPath: openssl.cnf
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            - name: static-volume
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              mountPath: /srv/static
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          envFrom:
          - secretRef:
              name: {{ .Values.database }}
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          - secretRef:
              name: s3
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          - configMapRef:
              name: {{ .Values.proxy }}
      restartPolicy: Always
      volumes:
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        - name: openssl-config
          configMap:
            name: openssl-config
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        - name: static-volume
          persistentVolumeClaim:
            claimName: static-volume