Merge branch 'master' into feat/GPE-1173

gen3/bin/kube-roll-all.sh

@@ -243,6 +243,12 @@ else
   gen3_log_info "not deploying dicom-viewer - no manifest entry for '.versions[\"dicom-viewer\"]'"
 fi
 
+if g3k_manifest_lookup '.versions["gen3-discovery-ai"]' 2> /dev/null; then
+  gen3 kube-setup-gen3-discovery-ai &
+else
+  gen3_log_info "not deploying gen3-discovery-ai - no manifest entry for '.versions[\"gen3-discovery-ai\"]'"
+fi
+
 if g3k_manifest_lookup '.versions["ohdsi-atlas"]' && g3k_manifest_lookup '.versions["ohdsi-webapi"]' 2> /dev/null; then
   gen3 kube-setup-ohdsi &
 else

gen3/bin/kube-setup-gen3-discovery-ai.sh

@@ -0,0 +1,154 @@
+#!/bin/bash
+#
+# Deploy the gen3-discovery-ai service
+#
+
+source "${GEN3_HOME}/gen3/lib/utils.sh"
+gen3_load "gen3/gen3setup"
+
+# NOTE: no db for this service yet, but we'll likely need it in the future
+setup_database() {
+  gen3_log_info "setting up gen3-discovery-ai service ..."
+
+  if g3kubectl describe secret gen3-discovery-ai-g3auto > /dev/null 2>&1; then
+    gen3_log_info "gen3-discovery-ai-g3auto secret already configured"
+    return 0
+  fi
+  if [[ -n "$JENKINS_HOME" || ! -f "$(gen3_secrets_folder)/creds.json" ]]; then
+    gen3_log_err "skipping db setup in non-adminvm environment"
+    return 0
+  fi
+  # Setup .env file that gen3-discovery-ai service consumes
+  if [[ ! -f "$secretsFolder/gen3-discovery-ai.env" || ! -f "$secretsFolder/base64Authz.txt" ]]; then
+    local secretsFolder="$(gen3_secrets_folder)/g3auto/gen3-discovery-ai"
+
+    if [[ ! -f "$secretsFolder/dbcreds.json" ]]; then
+      if ! gen3 db setup gen3-discovery-ai; then
+        gen3_log_err "Failed setting up database for gen3-discovery-ai service"
+        return 1
+      fi
+    fi
+    if [[ ! -f "$secretsFolder/dbcreds.json" ]]; then
+      gen3_log_err "dbcreds not present in Gen3Secrets/"
+      return 1
+    fi
+
+    # go ahead and rotate the password whenever we regen this file
+    local password="$(gen3 random)"
+    cat - > "$secretsFolder/gen3-discovery-ai.env" <<EOM
+DEBUG=0
+DB_HOST=$(jq -r .db_host < "$secretsFolder/dbcreds.json")
+DB_USER=$(jq -r .db_username < "$secretsFolder/dbcreds.json")
+DB_PASSWORD=$(jq -r .db_password < "$secretsFolder/dbcreds.json")
+DB_DATABASE=$(jq -r .db_database < "$secretsFolder/dbcreds.json")
+ADMIN_LOGINS=gateway:$password
+EOM
+    # make it easy for nginx to get the Authorization header ...
+    echo -n "gateway:$password" | base64 > "$secretsFolder/base64Authz.txt"
+  fi
+  gen3 secrets sync 'setup gen3-discovery-ai-g3auto secrets'
+}
+
+if ! g3k_manifest_lookup '.versions."gen3-discovery-ai"' 2> /dev/null; then
+  gen3_log_info "kube-setup-gen3-discovery-ai exiting - gen3-discovery-ai service not in manifest"
+  exit 0
+fi
+
+# There's no db for this service *yet* 
+#
+# if ! setup_database; then
+#   gen3_log_err "kube-setup-gen3-discovery-ai bailing out - database failed setup"
+#   exit 1
+# fi
+
+setup_storage() {
+  local saName="gen3-discovery-ai-sa"
+  g3kubectl create sa "$saName" > /dev/null 2>&1 || true
+
+  local secret
+  local secretsFolder="$(gen3_secrets_folder)/g3auto/gen3-discovery-ai"
+
+  secret="$(g3kubectl get secret gen3-discovery-ai-g3auto -o json 2> /dev/null)"
+  local hasStorageCfg
+  hasStorageCfg=$(jq -r '.data | has("storage_config.json")' <<< "$secret")
+
+  if [ "$hasStorageCfg" = "false" ]; then
+    gen3_log_info "setting up storage for gen3-discovery-ai service"
+    #
+    # gen3-discovery-ai-g3auto secret still does not exist
+    # we need to setup an S3 bucket and IAM creds
+    # let's avoid creating multiple buckets for different
+    # deployments to the same k8s cluster (dev, etc)
+    #
+    local bucketName
+    local accountNumber
+    local environment
+
+    if ! accountNumber="$(aws sts get-caller-identity --output text --query 'Account')"; then
+      gen3_log_err "could not determine account numer"
+      return 1
+    fi
+
+    gen3_log_info "accountNumber: ${accountNumber}"
+
+    if ! environment="$(g3kubectl get configmap manifest-global -o json | jq -r .data.environment)"; then
+      gen3_log_err "could not determine environment from manifest-global - bailing out of gen3-discovery-ai setup"
+      return 1
+    fi
+
+    gen3_log_info "environment: ${environment}"
+
+    # try to come up with a unique but composable bucket name
+    bucketName="gen3-discovery-ai-${accountNumber}-${environment//_/-}"
+
+    gen3_log_info "bucketName: ${bucketName}"
+
+    if aws s3 ls --page-size 1 "s3://${bucketName}" > /dev/null 2>&1; then
+      gen3_log_info "${bucketName} s3 bucket already exists - probably in use by another namespace - copy the creds from there to $(gen3_secrets_folder)/g3auto/gen3-discovery-ai"
+      # continue on ...
+    elif ! gen3 s3 create "${bucketName}"; then
+      gen3_log_err "maybe failed to create bucket ${bucketName}, but maybe not, because the terraform script is flaky"
+    fi
+
+    local hostname
+    hostname="$(gen3 api hostname)"
+    jq -r -n --arg bucket "${bucketName}" --arg hostname "${hostname}" '.bucket=$bucket | .prefix=$hostname' > "${secretsFolder}/storage_config.json"
+    gen3 secrets sync 'setup gen3-discovery-ai credentials'
+
+    local roleName
+    roleName="$(gen3 api safe-name gen3-discovery-ai)" || return 1
+
+    if ! gen3 awsrole info "$roleName" > /dev/null; then # setup role
+      bucketName="$( (gen3 secrets decode 'gen3-discovery-ai-g3auto' 'storage_config.json' || echo ERROR) | jq -r .bucket)" || return 1
+      gen3 awsrole create "$roleName" "$saName" || return 1
+      gen3 s3 attach-bucket-policy "$bucketName" --read-write --role-name "${roleName}"
+      # try to give the gitops role read/write permissions on the bucket
+      local gitopsRoleName
+      gitopsRoleName="$(gen3 api safe-name gitops)"
+      gen3 s3 attach-bucket-policy "$bucketName" --read-write --role-name "${gitopsRoleName}"
+    fi
+  fi
+
+  return 0
+}
+
+if ! setup_storage; then
+  gen3_log_err "kube-setup-gen3-discovery-ai bailing out - storage failed setup"
+  exit 1
+fi
+
+gen3_log_info "Setup complete, syncing configuration to bucket"
+
+bucketName="$( (gen3 secrets decode 'gen3-discovery-ai-g3auto' 'storage_config.json' || echo ERROR) | jq -r .bucket)" || exit 1
+aws s3 sync "$(dirname $(g3k_manifest_path))/gen3-discovery-ai/knowledge" "s3://$bucketName" --delete
+
+gen3 roll gen3-discovery-ai
+g3kubectl apply -f "${GEN3_HOME}/kube/services/gen3-discovery-ai/gen3-discovery-ai-service.yaml"
+
+if [[ -z "$GEN3_ROLL_ALL" ]]; then
+  gen3 kube-setup-networkpolicy
+  gen3 kube-setup-revproxy
+fi
+
+gen3_log_info "The gen3-discovery-ai service has been deployed onto the kubernetes cluster"
+gen3_log_info "test with: curl https://commons-host/ai"

kube/services/gen3-discovery-ai/README.md

@@ -0,0 +1,42 @@
+# Gen3 Discovery AI Configuration
+
+Expects data in a `gen3-discovery-ai` folder relative to 
+where the `manifest.json` is. 
+
+Basic setup:
+
+`{{dir where manifest.json is}}/gen3-discovery-ai/knowledge/`
+
+- `tsvs` folder
+    - tsvs with topic_name at beginning of file
+- `markdown` folder
+    - {{topic_name_1}}
+        - markdown file(s)
+    - {{topic_name_2}}
+        - markdown file(s)
+
+The `kube-setup-gen3-discovery-ai` script syncs the above `/knowledge` folder to
+an S3 bucket. The service configuration then pulls from the S3 bucket and runs load commands 
+to get the data into chromadb.
+
+> Note: See the `gen3-discovery-ai` service repo docs and README for more details on data load capabilities.
+
+Check the `gen3-discovery-ai-deploy.yaml` for what commands are being run in the automation.
+
+Expects secrets setup in `g3auto/gen3-discovery-ai` folder
+ - `credentials.json`: Google service account key if using a topic with Google Vertex AI
+ - `env`: .env file contents for service configuration (see service repo for a default one)
+
+## Populating Disk for In-Memory Vectordb Chromadb
+
+In order to setup pre-configured topics, we need to load a bunch of data 
+into Chromadb (which is an in-mem vectordb with an option to persist to disk).
+
+To load topics consistently, we setup an S3 bucket to house the persisted 
+data for the vectordb.
+
+### Getting data from S3 in mem
+
+We specify a path for Chromadb to use for persisted data and when it sees 
+data there, it loads it in. So the deployment automation: 1. aws syncs the bucket
+and then 2. calls a script to load the files into the in-mem vectorstore from there. 

kube/services/gen3-discovery-ai/gen3-discovery-ai-deploy.yaml

@@ -0,0 +1,181 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: gen3-discovery-ai-deployment
+spec:
+  selector:
+    # Only select pods based on the 'app' label
+    matchLabels:
+      app: gen3-discovery-ai
+      release: production
+  strategy:
+    type: RollingUpdate
+    rollingUpdate:
+      maxSurge: 1
+      maxUnavailable: 0
+  template:
+    metadata:
+      labels:
+        app: gen3-discovery-ai
+        release: production
+        GEN3_DATE_LABEL
+    spec:
+      serviceAccountName: gen3-discovery-ai-sa
+      volumes:
+        - name: gen3-discovery-ai-g3auto-volume
+          secret:
+            secretName: gen3-discovery-ai-g3auto
+        - name: gen3-discovery-ai-knowledge-library-volume
+          emptyDir: {}
+      initContainers:
+      # chromadb's persisted disk support requires the ability to write. We don't technically need this ability
+      # since we're populating the entirety of the database from configured files (no live updates).
+      #
+      # Solution: utilize emptyDir as a writable space.
+      #
+      # Procedure: in init containers, copy files from s3 to writable
+      #            temporary space in emptyDir, use files from writable space
+      #            to load into knowledge libary, move final knowledge library
+      #            files into top-level emptyDir and make available in final container
+      - name: gen3-discovery-ai-aws-init
+        GEN3_AWSHELPER_IMAGE|-image: quay.io/cdis/awshelper:master-|
+        imagePullPolicy: Always
+        ports:
+        - containerPort: 8080
+        env:
+          - name: GEN3_DEBUG
+            GEN3_DEBUG_FLAG|-value: "False"-|
+        volumeMounts:
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/.env
+            subPath: env
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/credentials.json
+            subPath: credentials.json
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/storage_config.json
+            subPath: storage_config.json
+          - name: gen3-discovery-ai-knowledge-library-volume
+            mountPath: /gen3discoveryai/knowledge
+        imagePullPolicy: Always
+        resources:
+          requests:
+            cpu: 1
+          limits:
+            cpu: 2
+            memory: 512Mi
+        command: ["/bin/bash"]
+        args:
+          - "-c"
+          - |
+            bucketName=$(grep -o "\"bucket\": *\"[^\"]*\"" /gen3discoveryai/storage_config.json | awk -F'"' '{print $4}')
+            echo BUCKET: "$bucketName"
+            echo
+            echo BEFORE /gen3discoveryai/knowledge  
+            ls -Ra /gen3discoveryai/knowledge 
+            echo
+            echo syncing from s3
+            aws s3 sync "s3://${bucketName}" "/gen3discoveryai/knowledge/tmp"
+            echo
+            echo AFTER /gen3discoveryai/knowledge 
+            ls -Ra /gen3discoveryai/knowledge
+      - name: gen3-discovery-ai-knowledge-init
+        GEN3_GEN3-DISCOVERY-AI_IMAGE
+        imagePullPolicy: Always
+        ports:
+        - containerPort: 8080
+        env:
+          - name: GEN3_DEBUG
+            GEN3_DEBUG_FLAG|-value: "False"-|
+          - name: ANONYMIZED_TELEMETRY
+            value: "False"
+          - name: GOOGLE_APPLICATION_CREDENTIALS
+            value: /gen3discoveryai/credentials.json
+        volumeMounts:
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/.env
+            subPath: env
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/credentials.json
+            subPath: credentials.json
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/storage_config.json
+            subPath: storage_config.json
+          - name: gen3-discovery-ai-knowledge-library-volume
+            mountPath: /gen3discoveryai/knowledge
+        imagePullPolicy: Always
+        resources:
+          requests:
+            cpu: 1
+          limits:
+            cpu: 2
+            memory: 512Mi
+        command: ["/bin/bash"]
+        args:
+          - "-c"
+          - |
+            echo
+            echo BEFORE /gen3discoveryai/knowledge  
+            ls -Ra /gen3discoveryai/knowledge 
+            echo running load_into_knowledge_store.py
+            poetry run python /gen3discoveryai/bin/load_into_knowledge_store.py tsvs /gen3discoveryai/knowledge/tmp/tsvs
+            
+            if [ -d "/gen3discoveryai/knowledge/tmp/markdown" ]; then
+                for dir in "/gen3discoveryai/knowledge/tmp/markdown"/*; do
+                    if [ -d "$dir" ]; then
+                        dir_name=$(basename "$dir")
+
+                        echo "Processing directory: $dir_name. Full path: $dir"
+                        poetry run python /gen3discoveryai/bin/load_into_knowledge_store.py markdown --topic $dir_name $dir
+                    fi
+                done
+            else
+                echo "Not syncing markdown, directory not found: /gen3discoveryai/knowledge/tmp/markdown"
+            fi
+
+            rm -r /gen3discoveryai/knowledge/tmp/
+            echo
+            echo AFTER /gen3discoveryai/knowledge 
+            ls -Ra /gen3discoveryai/knowledge
+      containers:
+      - name: gen3-discovery-ai
+        GEN3_GEN3-DISCOVERY-AI_IMAGE
+        imagePullPolicy: Always
+        ports:
+        - containerPort: 8080
+        env:
+          - name: GEN3_DEBUG
+            GEN3_DEBUG_FLAG|-value: "False"-|
+          - name: ANONYMIZED_TELEMETRY
+            value: "False"
+          - name: GOOGLE_APPLICATION_CREDENTIALS
+            value: /gen3discoveryai/credentials.json
+        volumeMounts:
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/.env
+            subPath: env
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/credentials.json
+            subPath: credentials.json
+          - name: gen3-discovery-ai-g3auto-volume
+            readOnly: true
+            mountPath: /gen3discoveryai/storage_config.json
+            subPath: storage_config.json
+          - name: gen3-discovery-ai-knowledge-library-volume
+            mountPath: /gen3discoveryai/knowledge
+        imagePullPolicy: Always
+        resources:
+          requests:
+            cpu: 1
+          limits:
+            cpu: 2
+            # NOTE: If the configured data for the knowledge library (vector database) is large, you may need to bump this
+            memory: 512Mi