From 0219ae481087e10b19176b90ae86b4ca6eabadc9 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Sun, 1 Sep 2024 22:28:02 +0200 Subject: [PATCH 1/2] fix:[coconut-app]-update values.yml --- charts/coconut-app/Chart.yaml | 2 +- charts/coconut-app/values.yaml | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/charts/coconut-app/Chart.yaml b/charts/coconut-app/Chart.yaml index 7791708..c55c957 100644 --- a/charts/coconut-app/Chart.yaml +++ b/charts/coconut-app/Chart.yaml @@ -15,7 +15,7 @@ type: application # This is the chart version. This version number should be incremented each time you make changes # to the chart and its templates, including the app version. # Versions are expected to follow Semantic Versioning (https://semver.org/) -version: 0.4.0 +version: 0.4.1 # This is the version number of the application being deployed. This version number should be # incremented each time you make changes to the application. Versions are not expected to diff --git a/charts/coconut-app/values.yaml b/charts/coconut-app/values.yaml index 2e7c6e0..50cc09e 100644 --- a/charts/coconut-app/values.yaml +++ b/charts/coconut-app/values.yaml @@ -8,9 +8,9 @@ replicaCount: 1 appProperties: name: coconut key: - env: development + env: production debug: true - url: https://coconut2.nmrxiv.org + url: https://coconut.naturalproducts.net/ queueConnection: sync schemaVersion: 1.0 description: | @@ -26,7 +26,7 @@ webservices: orcidIdSearchApi: https://pub.orcid.org/v2.1/search orcidIdEmploymentApi: https://pub.orcid.org/v3.0/{orcid_id}/employments orcidIdPersonApi: https://pub.orcid.org/v3.0/{orcid_id}/person - cmApi: https://dev.api.naturalproducts.net/v1/ + cmApi: https://api.naturalproducts.net/v1/ logProperties: logChannel: stack @@ -45,14 +45,14 @@ rdkitcatridgepostgres: appImage: name: php - repository: europe-west3-docker.pkg.dev/coconut-366808/coconut-dev/coconut-app + repository: nfdi4chem/coconut pullPolicy: Always # Overrides the image tag whose default is the chart appVersion. tag: latest nginxImage: name: nginx - repository: europe-west3-docker.pkg.dev/coconut-366808/coconut-dev/coconut-nginx + repository: nfdi4chem/coconut pullPolicy: Always # Overrides the image tag whose default is the chart appVersion. tag: latest @@ -136,7 +136,7 @@ mail: host: 'smtp.uni-jena.de' port: 587 from: info.coconut@uni-jena.de - fromName: "coconut-dev" + fromName: "coconut" user: test password: secret mailer: smtp @@ -145,7 +145,7 @@ cheminfo-microservice: enabled: false image: name: chem-py-microservice - repository: europe-west3-docker.pkg.dev/coconut-366808/cheminformatics-python-microservice/chem-py-microservice + repository: nfdi4chem/cheminformatics-microservice pullPolicy: Always tag: latest service: From d170f6484ea277b06975b953e923a4efd0f45e17 Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Thu, 28 Nov 2024 15:52:57 +0100 Subject: [PATCH 2/2] fix: linting issues fixed. various updates to the config map and secrets. --- charts/coconut-app/templates/configmap.yaml | 11 +++ charts/coconut-app/templates/secret.yml | 16 +++ charts/coconut-app/values.yaml | 104 +++++++++++--------- 3 files changed, 82 insertions(+), 49 deletions(-) diff --git a/charts/coconut-app/templates/configmap.yaml b/charts/coconut-app/templates/configmap.yaml index c8e6442..acc2d6d 100644 --- a/charts/coconut-app/templates/configmap.yaml +++ b/charts/coconut-app/templates/configmap.yaml @@ -66,3 +66,14 @@ data: DOI_HOST: {{ .Values.doi.doiHost }} DOI_PROVIDER: {{ .Values.doi.doiProvider }} +#Datacite Properties + DATACITE_PREFIX: "{{ .Values.datacite.prefix }}" + DATACITE_ENDPOINT: {{ .Values.datacite.endpoint }} + +#OAuth Properties + {{ if .Values.oauthProperties.github.enabled }} + GITHUB_REDIRECT_URL: {{ .Values.oauthProperties.github.redirectURL }} + {{ end }} + {{ if .Values.oauthProperties.google.enabled }} + GOOGLE_REDIRECT_URL: {{ .Values.oauthProperties.google.redirectURL }} + {{ end }} \ No newline at end of file diff --git a/charts/coconut-app/templates/secret.yml b/charts/coconut-app/templates/secret.yml index 3cfad29..c6a582d 100644 --- a/charts/coconut-app/templates/secret.yml +++ b/charts/coconut-app/templates/secret.yml @@ -34,4 +34,20 @@ data: {{- if .Values.larabug.enabled }} LB_KEY: {{ .Values.larabug.lbKey |b64enc | quote }} LB_PROJECT_KEY: {{ .Values.larabug.lbProjectKey |b64enc | quote }} + {{- end -}} + + #OAuth Properties Secrets + {{- if .Values.oauthProperties.github.enabled }} + GITHUB_CLIENT_ID: {{ .Values.oauthProperties.github.clientID |b64enc | quote }} + GITHUB_CLIENT_SECRET: {{ .Values.oauthProperties.github.clientSecret |b64enc | quote }} + {{- end -}} + {{- if .Values.oauthProperties.google.enabled }} + GOOGLE_CLIENT_ID: {{ .Values.oauthProperties.google.clientID |b64enc | quote }} + GOOGLE_CLIENT_SECRET: {{ .Values.oauthProperties.google.clientSecret |b64enc | quote }} + {{- end -}} + + {{- if .Values.datacite.enabled }} + #Datacite Secrets + DATACITE_USERNAME: {{ .Values.datacite.username |b64enc | quote }} + DATACITE_SECRET: {{ .Values.datacite.secret |b64enc | quote }} {{- end -}} \ No newline at end of file diff --git a/charts/coconut-app/values.yaml b/charts/coconut-app/values.yaml index 50cc09e..467b5ba 100644 --- a/charts/coconut-app/values.yaml +++ b/charts/coconut-app/values.yaml @@ -7,16 +7,16 @@ replicaCount: 1 # Default app properties for laravel. appProperties: name: coconut - key: + key: base64:88Td66VUaLDIea0DEgJQVdoXU1WolK+kdoEPBepQYH0= env: production debug: true url: https://coconut.naturalproducts.net/ queueConnection: sync schemaVersion: 1.0 description: | - COCONUT Online is an open-source project that stores, searches, and analyzes Natural Products (NPs). - The database contains over 50 open NP resources, and the data is accessible free of charge and without any restrictions. - Each entry corresponds to a "flat" NP structure and is associated with their known stereochemical forms, + COCONUT Online is an open-source project that stores, searches, and analyzes Natural Products (NPs). + The database contains over 50 open NP resources, and the data is accessible free of charge and without any restrictions. + Each entry corresponds to a "flat" NP structure and is associated with their known stereochemical forms, literature, organisms that produce them, natural geographic presence, and precomputed molecular properties if available. webservices: @@ -32,7 +32,7 @@ logProperties: logChannel: stack logLevel: debug -#DB Properties +# DB Properties rdkitcatridgepostgres: enabled: true auth: @@ -110,7 +110,7 @@ ingress: # hosts: # - chart-example.local -resources: +resources: # We usually recommend not to specify default resources and to leave this as a conscious # choice for the user. This also increases chances charts run on environments with little # resources, such as Minikube. If you do want to specify resources, uncomment the following @@ -152,37 +152,18 @@ cheminfo-microservice: type: ClusterIP port: 80 -# oauthProperties: -# enabled: false -# twitterClientID: -# twitterClientSecret: -# twitterRedirectUrl: -# githubClientID: -# githubClientSecret: -# githubRedirectUrl: -# orcidClientID: -# orcidClientSecret: -# orcidRedirectUrl: -# orcidEnvironment: - -#Enable this properties for Single Sign-On follow the documentation for more info https://docs.coconut.org/docs/developer-guides/configurations/oauth -# oauthProperties: -# twitter: -# enabled: false -# clientID: -# clientSecret: -# redirectURL: -# github: -# enabled: false -# clientID: -# clientSecret: -# redirectURL: -# orcid: -# enabled: false -# clientID: -# clientSecret: -# redirectURL: -# environment: +# Enable this properties for Single Sign-On follow the documentation for more info https://docs.coconut.org/docs/developer-guides/configurations/oauth +oauthProperties: + google: + enabled: false + clientID: + clientSecret: + redirectURL: + github: + enabled: false + clientID: + clientSecret: + redirectURL: # storage: # pvc: @@ -221,16 +202,14 @@ worker: redis: enabled: false - #architecture: standalone + # architecture: standalone auth: enabled: true password: secret global: storageClass: standard - #host: nmrxiv-redis-master + # host: nmrxiv-redis-master port: 6379 - replica: - replicaCount: 1 master: persistence: enabled: true @@ -238,6 +217,7 @@ redis: service: type: LoadBalancer replica: + replicaCount: 1 persistence: enabled: true size: 1Gi @@ -270,21 +250,47 @@ scheduler: larabug: enabled: false - lbKey: + lbKey: lbProjectKey: +datacite: + enabled: false + host: + username: + secret: + prefix: + endpoint: https://api.test.datacite.org + +rabbitmq: + enabled: false + queueConnection: sync + port: 5672 + # host: nmrxiv-rabbitmq + auth: + username: 'rabbitmq_user' + password: 'password' + # erlangCookie: 'erlangCookieerlangCookie' + global: + storageClass: 'standard' + metrics: + enabled: false + ingress: + enabled: false + path: '/' + hostname: '' + fileStorage: # Below values are for file storage configuration. # You can have desired S3 compatible driver of your choice. Follow to read more https://laravel.com/docs/9.x/filesystem enabled: false - fileSystemDriver: - fileSystemDriverPublic: - awsAccessKeyID: - awsSecretAccessKey: - awsDefaultRegion: - awsBucket: + fileSystemDriver: + fileSystemDriverPublic: + awsAccessKeyID: + awsSecretAccessKey: + awsDefaultRegion: + awsBucket: awsEndpoint: - awsURL: + awsURL: nodeSelector: {}