From 13fb2397dfaac8165c7a71e1fce769bda08ee760 Mon Sep 17 00:00:00 2001 From: Aidan Hilt <11202897+AidanHilt@users.noreply.github.com> Date: Tue, 27 Feb 2024 11:51:18 -0500 Subject: [PATCH 01/21] Fix/argo wrapper default url (#2486) * Adding a secret to contain all values for any workflow templates * Adding an override namespace argument to kube-setup-argo * Fixing a typo * You'd think I'd never written Bash before * Adding the last part of the namespace override logic * Debug prints * Trying to figure out why the override namespace logic doesn't work * Just checking * Desperate * I think we can't use echo in gen3 scripts * Sanity check * Just a commit * Checking if we get the argo_namespace correctly * Making the print clearer * It's debug print time * Fixing references * Adding some stuff * Removing debugs, and adding --overwrite * Adding double quotes * Fixing kube-setup-argo-wrapper to have default values for argo-service URL and argo namespace * Fixing /tmp/config.ini collisions * Turns out that wasn't the way to go, instead we'll just delete /tmp/config.ini to account for multiple environments * Removed some extra stuff that snuck in --- .secrets.baseline | 2 +- gen3/bin/kube-setup-argo-wrapper.sh | 23 ++++++++++++++++------- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 0a8fe9cc99..936e306e55 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2023-10-26T21:32:44Z", + "generated_at": "2024-02-23T20:30:41Z", "plugins_used": [ { "name": "AWSKeyDetector" diff --git a/gen3/bin/kube-setup-argo-wrapper.sh b/gen3/bin/kube-setup-argo-wrapper.sh index 306050b124..9f7cc52ce4 100644 --- a/gen3/bin/kube-setup-argo-wrapper.sh +++ b/gen3/bin/kube-setup-argo-wrapper.sh @@ -18,17 +18,26 @@ if [[ -z "$GEN3_SOURCE_ONLY" ]]; then gen3 roll argo-wrapper g3kubectl apply -f "${GEN3_HOME}/kube/services/argo-wrapper/argo-wrapper-service.yaml" + if g3k_manifest_lookup .argo.argo_server_service_url 2> /dev/null; then - argo_server_service_url=$(g3k_manifest_lookup .argo.argo_server_service_url) + export ARGO_HOST=$(g3k_manifest_lookup .argo.argo_server_service_url) + else + export ARGO_HOST="http://argo-argo-workflows-server.argo.svc.cluster.local:2746" + fi + + if g3k_config_lookup '.argo_namespace' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json 2> /dev/null; then + export ARGO_NAMESPACE=$(g3k_config_lookup '.argo_namespace' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) + else + export ARGO_NAMESPACE="argo" + fi - export ARGO_HOST=${argo_server_service_url} - export ARGO_NAMESPACE=argo-$(gen3 db namespace) - envsubst <"${GEN3_HOME}/kube/services/argo-wrapper/config.ini" > /tmp/config.ini + envsubst <"${GEN3_HOME}/kube/services/argo-wrapper/config.ini" > /tmp/config.ini - g3kubectl delete configmap argo-wrapper-namespace-config - g3kubectl create configmap argo-wrapper-namespace-config --from-file /tmp/config.ini - fi + g3kubectl delete configmap argo-wrapper-namespace-config + g3kubectl create configmap argo-wrapper-namespace-config --from-file /tmp/config.ini + + rm /tmp/config.ini gen3_log_info "the argo-wrapper service has been deployed onto the kubernetes cluster" fi From 1a44bef0712ca5ffb4262615999787ef536644be Mon Sep 17 00:00:00 2001 From: emalinowski Date: Wed, 28 Feb 2024 06:20:07 -0600 Subject: [PATCH 02/21] fix(jenkins-zone): Added zone (#2487) Co-authored-by: Edward Malinowski Co-authored-by: Ajo Augustine --- kube/services/jenkins/jenkins-deploy.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/kube/services/jenkins/jenkins-deploy.yaml b/kube/services/jenkins/jenkins-deploy.yaml index c0eae2040b..954e996f21 100644 --- a/kube/services/jenkins/jenkins-deploy.yaml +++ b/kube/services/jenkins/jenkins-deploy.yaml @@ -38,6 +38,10 @@ spec: operator: In values: - on-demand + - key: topology.kubernetes.io/zone + operator: In + values: + - us-east-1a serviceAccountName: jenkins-service securityContext: runAsUser: 1000 From 6c27fc9a7fe6cd3affd7a108db3c80b51c664ad1 Mon Sep 17 00:00:00 2001 From: Michael Lukowski Date: Thu, 29 Feb 2024 09:59:10 -0600 Subject: [PATCH 03/21] updating the cedar data ingest (#2472) * updating the cedar data ingest * fix unsanitized request * address some comments --- .../healdata/heal-cedar-data-ingest.py | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index 71575e3c56..d3ff246c34 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -35,6 +35,16 @@ "Buisness Development": "Business Development" } +# repository links +REPOSITORY_STUDY_ID_LINK_TEMPLATE = { + "NIDDK Central": "https://repository.niddk.nih.gov/studies//", + "NIDA Data Share": "https://datashare.nida.nih.gov/study/", + "NICHD DASH": "https://dash.nichd.nih.gov/study/", + "ICPSR": "https://www.icpsr.umich.edu/web/ICPSR/studies/", + "BioSystics-AP": "https://biosystics-ap.com/assays/assaystudy//", +} + + # Defines field that we don't want to include in the filters OMITTED_VALUES_MAPPING = { "study_metadata.human_subject_applicability.gender_applicability": "Not applicable" @@ -114,6 +124,31 @@ def get_client_token(client_id: str, client_secret: str): return token +def get_related_studies(serial_num, hostname): + related_study_result = [] + + if serial_num: + mds = requests.get(f"https://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") + if mds.status_code == 200: + related_study_metadata = mds.json() + + for ( + related_study_metadata_key, + related_study_metadata_value, + ) in related_study_metadata.items(): + title = ( + related_study_metadata_value.get( + "gen3_discovery", {} + ) + .get("study_metadata", {}) + .get("minimal_info", {}) + .get("study_name", "") + ) + link = f"https://{hostname}/portal/discovery/{related_study_metadata_key}/" + related_study_result.append({"title": title, "link": link}) + return related_study_result + + parser = argparse.ArgumentParser() parser.add_argument("--directory", help="CEDAR Directory ID for registering ") @@ -214,6 +249,67 @@ def get_client_token(client_id: str, client_secret: str): mds_res["gen3_discovery"]["study_metadata"].update(cedar_record) mds_res["gen3_discovery"]["study_metadata"]["metadata_location"]["other_study_websites"] = cedar_record_other_study_websites + # setup citations + doi_citation = mds_res["gen3_discovery"]["study_metadata"].get("doi_citation", "") + mds_res["gen3_discovery"]["study_metadata"]["citation"]["heal_platform_citation"] = doi_citation + + + # setup repository_study_link + data_repositories = ( + mds_res.get("study_metadata", {}) + .get("metadata_location", {}) + .get("data_repositories", []) + ) + repository_citation = "Users must also include a citation to the data as specified by the local repository." + repository_citation_additional_text = ' The link to the study page at the local repository can be found in the "Data" tab.' + for repository in data_repositories: + if ( + repository["repository_name"] + and repository["repository_name"] + in REPOSITORY_STUDY_ID_LINK_TEMPLATE + and repository["repository_study_ID"] + ): + repository_study_link = REPOSITORY_STUDY_ID_LINK_TEMPLATE[ + repository["repository_name"] + ].replace("", repository["repository_study_ID"]) + repository.update({"repository_study_link": repository_study_link}) + if repository_citation_additional_text not in repository_citation: + repository_citation += repository_citation_additional_text + if len(data_repositories): + data_repositories[0] = { + **data_repositories[0], + "repository_citation": repository_citation, + } + mds_res["gen3_discovery"]["study_metadata"][ + "metadata_location" + ]["data_repositories"] = data_repositories + + + + # set up related studies + serial_num = None + try: + serial_num = ( + mds_res + .get("nih_reporter", {}) + .get("project_num_split", {}) + .get("serial_num", None) + ) + except Exception: + print(f"Unable to get serial number for study") + + if serial_num == None: + print(f"Unable to get serial number for study") + + related_study_result = get_related_studies(serial_num, hostname) + existing_related_study_result = mds_res.get("related_studies", []) + for related_study in related_study_result: + if related_study not in existing_related_study_result: + existing_related_study_result.append(copy.deepcopy(related_study)) + mds_res["gen3_discovery"][ + "related_studies" + ] = copy.deepcopy(existing_related_study_result) + # merge data from cedar that is not study level metadata into a level higher deleted_keys = [] for key, value in mds_res["gen3_discovery"]["study_metadata"].items(): From 072279d59732ff0109e9ca18bb05479b3bdcd577 Mon Sep 17 00:00:00 2001 From: Aidan Hilt <11202897+AidanHilt@users.noreply.github.com> Date: Thu, 29 Feb 2024 11:16:29 -0500 Subject: [PATCH 04/21] Feat/s3 bucket template (#2485) * Adding a secret to contain all values for any workflow templates * Adding an override namespace argument to kube-setup-argo * Fixing a typo * You'd think I'd never written Bash before * Adding the last part of the namespace override logic * Debug prints * Trying to figure out why the override namespace logic doesn't work * Just checking * Desperate * I think we can't use echo in gen3 scripts * Sanity check * Just a commit * Checking if we get the argo_namespace correctly * Making the print clearer * It's debug print time * Fixing references * Adding some stuff * Removing debugs, and adding --overwrite * Adding double quotes --- .secrets.baseline | 4 +-- gen3/bin/kube-setup-argo.sh | 66 ++++++++++++++++++++++++++----------- 2 files changed, 49 insertions(+), 21 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 936e306e55..b7e06622d6 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2024-02-23T20:30:41Z", + "generated_at": "2024-02-23T20:30:41Z" "plugins_used": [ { "name": "AWSKeyDetector" @@ -342,7 +342,7 @@ "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", "is_secret": false, "is_verified": false, - "line_number": 191, + "line_number": 206, "type": "Secret Keyword" } ], diff --git a/gen3/bin/kube-setup-argo.sh b/gen3/bin/kube-setup-argo.sh index ff2438833c..20676145b9 100644 --- a/gen3/bin/kube-setup-argo.sh +++ b/gen3/bin/kube-setup-argo.sh @@ -5,10 +5,25 @@ source "${GEN3_HOME}/gen3/lib/utils.sh" gen3_load "gen3/gen3setup" gen3_load "gen3/lib/kube-setup-init" +override_namespace=false +force=false + +for arg in "${@}"; do + if [ "$arg" == "--override-namespace" ]; then + override_namespace=true + elif [ "$arg" == "--force" ]; then + force=true + else + #Print usage info and exit + gen3_log_info "Usage: gen3 kube-setup-argo [--override-namespace] [--force]" + exit 1 + fi +done ctx="$(g3kubectl config current-context)" ctxNamespace="$(g3kubectl config view -ojson | jq -r ".contexts | map(select(.name==\"$ctx\")) | .[0] | .context.namespace")" +argo_namespace=$(g3k_config_lookup '.argo_namespace' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) function setup_argo_buckets { local accountNumber @@ -32,13 +47,13 @@ function setup_argo_buckets { roleName="gen3-argo-${environment//_/-}-role" bucketPolicy="argo-bucket-policy-${nameSpace}" internalBucketPolicy="argo-internal-bucket-policy-${nameSpace}" - if [[ ! -z $(g3k_config_lookup '."s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) || ! -z $(g3k_config_lookup '.argo."s3-bucket"') ]]; then - if [[ ! -z $(g3k_config_lookup '."s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) ]]; then + if [[ ! -z $(g3k_config_lookup '."downloadable-s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) || ! -z $(g3k_config_lookup '.argo."downloadable-s3-bucket"') ]]; then + if [[ ! -z $(g3k_config_lookup '."downloadable-s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) ]]; then gen3_log_info "Using S3 bucket found in manifest: ${bucketName}" - bucketName=$(g3k_config_lookup '."s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) + bucketName=$(g3k_config_lookup '."downloadable-s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) else gen3_log_info "Using S3 bucket found in manifest: ${bucketName}" - bucketName=$(g3k_config_lookup '.argo."s3-bucket"') + bucketName=$(g3k_config_lookup '.argo."downloadable-s3-bucket"') fi fi if [[ ! -z $(g3k_config_lookup '."internal-s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) || ! -z $(g3k_config_lookup '.argo."internal-s3-bucket"') ]]; then @@ -131,19 +146,19 @@ EOF g3kubectl create namespace argo || true g3kubectl label namespace argo app=argo || true # Grant admin access within the argo namespace to the default SA in the argo namespace - g3kubectl create rolebinding argo-admin --clusterrole=admin --serviceaccount=argo:default -n argo || true + g3kubectl create rolebinding argo-admin --clusterrole=admin --serviceaccount=argo:default -n $argo_namespace || true fi gen3_log_info "Creating IAM role ${roleName}" if aws iam get-role --role-name "${roleName}" > /dev/null 2>&1; then gen3_log_info "IAM role ${roleName} already exists.." roleArn=$(aws iam get-role --role-name "${roleName}" --query 'Role.Arn' --output text) gen3_log_info "Role annotate" - g3kubectl annotate serviceaccount default eks.amazonaws.com/role-arn=${roleArn} -n argo - g3kubectl annotate serviceaccount argo eks.amazonaws.com/role-arn=${roleArn} -n $nameSpace + g3kubectl annotate serviceaccount default eks.amazonaws.com/role-arn=${roleArn} --overwrite -n $argo_namespace + g3kubectl annotate serviceaccount argo eks.amazonaws.com/role-arn=${roleArn} --overwrite -n $nameSpace else gen3 awsrole create $roleName argo $nameSpace -f all_namespaces roleArn=$(aws iam get-role --role-name "${roleName}" --query 'Role.Arn' --output text) - g3kubectl annotate serviceaccount default eks.amazonaws.com/role-arn=${roleArn} -n argo + g3kubectl annotate serviceaccount default eks.amazonaws.com/role-arn=${roleArn} -n $argo_namespace fi # Grant admin access within the current namespace to the argo SA in the current namespace @@ -177,34 +192,47 @@ EOF for serviceName in indexd; do secretName="${serviceName}-creds" # Only delete if secret is found to prevent early exits - if [[ ! -z $(g3kubectl get secrets -n argo | grep $secretName) ]]; then - g3kubectl delete secret "$secretName" -n argo > /dev/null 2>&1 + if [[ ! -z $(g3kubectl get secrets -n $argo_namespace | grep $secretName) ]]; then + g3kubectl delete secret "$secretName" -n $argo_namespace > /dev/null 2>&1 fi done sleep 1 # I think delete is async - give backend a second to finish indexdFencePassword=$(cat $(gen3_secrets_folder)/creds.json | jq -r .indexd.user_db.$indexd_admin_user) - g3kubectl create secret generic "indexd-creds" --from-literal=user=$indexd_admin_user --from-literal=password=$indexdFencePassword -n argo + g3kubectl create secret generic "indexd-creds" --from-literal=user=$indexd_admin_user --from-literal=password=$indexdFencePassword -n $argo_namespace fi } function setup_argo_db() { - if ! secret="$(g3kubectl get secret argo-db-creds -n argo 2> /dev/null)"; then + if ! secret="$(g3kubectl get secret argo-db-creds -n $argo_namespace 2> /dev/null)"; then gen3_log_info "Setting up argo db persistence" gen3 db setup argo || true dbCreds=$(gen3 secrets decode argo-g3auto dbcreds.json) - g3kubectl create secret -n argo generic argo-db-creds --from-literal=db_host=$(echo $dbCreds | jq -r .db_host) --from-literal=db_username=$(echo $dbCreds | jq -r .db_username) --from-literal=db_password=$(echo $dbCreds | jq -r .db_password) --from-literal=db_database=$(echo $dbCreds | jq -r .db_database) + g3kubectl create secret -n $argo_namespace generic argo-db-creds --from-literal=db_host=$(echo $dbCreds | jq -r .db_host) --from-literal=db_username=$(echo $dbCreds | jq -r .db_username) --from-literal=db_password=$(echo $dbCreds | jq -r .db_password) --from-literal=db_database=$(echo $dbCreds | jq -r .db_database) else gen3_log_info "Argo DB setup already completed" fi } - setup_argo_buckets +function setup_argo_template_secret() { + gen3_log_info "Started the template secret process" + downloadable_bucket_name=$(g3k_config_lookup '."downloadable-s3-bucket"' $(g3k_manifest_init)/$(g3k_hostname)/manifests/argo/argo.json) + # Check if the secret already exists + if [[ ! -z $(g3kubectl get secret argo-template-values-secret -n $argo_namespace) ]]; then + gen3_log_info "Argo template values secret already exists, assuming it's stale and deleting" + g3kubectl delete secret argo-template-values-secret -n $argo_namespace + fi + gen3_log_info "Creating argo template values secret" + g3kubectl create secret generic argo-template-values-secret --from-literal=DOWNLOADABLE_BUCKET=$downloadable_bucket_name -n $argo_namespace +} + +setup_argo_buckets # only do this if we are running in the default namespace -if [[ "$ctxNamespace" == "default" || "$ctxNamespace" == "null" ]]; then +if [[ "$ctxNamespace" == "default" || "$ctxNamespace" == "null" || "$override_namespace" == true ]]; then setup_argo_db - if (! helm status argo -n argo > /dev/null 2>&1 ) || [[ "$1" == "--force" ]]; then - DBHOST=$(kubectl get secrets -n argo argo-db-creds -o json | jq -r .data.db_host | base64 -d) - DBNAME=$(kubectl get secrets -n argo argo-db-creds -o json | jq -r .data.db_database | base64 -d) + setup_argo_template_secret + if (! helm status argo -n $argo_namespace > /dev/null 2>&1 ) || [[ "$force" == true ]]; then + DBHOST=$(kubectl get secrets -n $argo_namespace argo-db-creds -o json | jq -r .data.db_host | base64 -d) + DBNAME=$(kubectl get secrets -n $argo_namespace argo-db-creds -o json | jq -r .data.db_database | base64 -d) if [[ -z $internalBucketName ]]; then BUCKET=$bucketName else @@ -218,7 +246,7 @@ if [[ "$ctxNamespace" == "default" || "$ctxNamespace" == "null" ]]; then helm repo add argo https://argoproj.github.io/argo-helm --force-update 2> >(grep -v 'This is insecure' >&2) helm repo update 2> >(grep -v 'This is insecure' >&2) - helm upgrade --install argo argo/argo-workflows -n argo -f ${valuesFile} --version 0.29.1 + helm upgrade --install argo argo/argo-workflows -n $argo_namespace -f ${valuesFile} --version 0.29.1 else gen3_log_info "kube-setup-argo exiting - argo already deployed, use --force to redeploy" fi From 90b66091c0d1d8b89e7182ad84201e99903d8e44 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Thu, 29 Feb 2024 13:29:05 -0600 Subject: [PATCH 05/21] Update heal-cedar-data-ingest.py (#2490) --- files/scripts/healdata/heal-cedar-data-ingest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index d3ff246c34..1da4ac2d52 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -128,7 +128,7 @@ def get_related_studies(serial_num, hostname): related_study_result = [] if serial_num: - mds = requests.get(f"https://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") + mds = requests.get(f"http://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") if mds.status_code == 200: related_study_metadata = mds.json() From bd6bc767c0461f8fc1f1d90fa8a755be1e7fc381 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Thu, 29 Feb 2024 13:49:47 -0600 Subject: [PATCH 06/21] fix missed import (#2491) --- .secrets.baseline | 346 ++++-------------- .../healdata/heal-cedar-data-ingest.py | 2 +- 2 files changed, 73 insertions(+), 275 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index b7e06622d6..2583e269f8 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,9 +1,9 @@ { "exclude": { - "files": "^.secrets.baseline$", + "files": null, "lines": null }, - "generated_at": "2024-02-23T20:30:41Z" + "generated_at": "2024-02-29T19:38:46Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -61,14 +61,12 @@ "Chef/repo/data_bags/README.md": [ { "hashed_secret": "8a9250639e092d90f164792e35073a9395bff366", - "is_secret": false, "is_verified": false, "line_number": 45, "type": "Secret Keyword" }, { "hashed_secret": "6367c48dd193d56ea7b0baad25b19455e529f5ee", - "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -77,25 +75,22 @@ "Docker/jenkins/Jenkins-CI-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, - "line_number": 121, + "line_number": 124, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, - "line_number": 143, + "line_number": 139, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, "line_number": 107, "type": "Secret Keyword" @@ -104,7 +99,6 @@ "Docker/jenkins/Jenkins2/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, "line_number": 108, "type": "Secret Keyword" @@ -113,7 +107,6 @@ "Docker/sidecar/service.key": [ { "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", - "is_secret": false, "is_verified": false, "line_number": 1, "type": "Private Key" @@ -122,7 +115,6 @@ "Jenkins/Stacks/Jenkins/jenkins.env.sample": [ { "hashed_secret": "eecee33686ac5861c2a7edc8b46bd0e5432bfddd", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -131,7 +123,6 @@ "ansible/roles/awslogs/defaults/main.yaml": [ { "hashed_secret": "9d4e1e23bd5b727046a9e3b4b7db57bd8d6ee684", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Basic Auth Credentials" @@ -140,14 +131,12 @@ "ansible/roles/slurm/README.md": [ { "hashed_secret": "4acfde1ff9c353ba2ef0dbe0df73bda2743cba42", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Base64 High Entropy String" }, { "hashed_secret": "579649582303921502d9e6d3f8755f13fdd2b476", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" @@ -156,7 +145,6 @@ "apis_configs/config_helper.py": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", - "is_secret": false, "is_verified": false, "line_number": 66, "type": "Basic Auth Credentials" @@ -165,7 +153,6 @@ "apis_configs/fence_credentials.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -174,21 +161,18 @@ "apis_configs/fence_settings.py": [ { "hashed_secret": "3ef0fb8a603abdc0b6caac44a23fdc6792f77ddf", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Basic Auth Credentials" }, { "hashed_secret": "b60d121b438a380c343d5ec3c2037564b82ffef3", - "is_secret": false, "is_verified": false, "line_number": 58, "type": "Secret Keyword" }, { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 80, "type": "Basic Auth Credentials" @@ -197,7 +181,6 @@ "apis_configs/indexd_settings.py": [ { "hashed_secret": "0a0d18c85e096611b5685b62bc60ec534d19bacc", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Basic Auth Credentials" @@ -206,7 +189,6 @@ "apis_configs/peregrine_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -215,7 +197,6 @@ "apis_configs/sheepdog_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -224,7 +205,6 @@ "doc/Gen3-data-upload.md": [ { "hashed_secret": "b8bd20d4a2701dc3aba0efbbf325f1359392d93e", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -233,7 +213,6 @@ "doc/api.md": [ { "hashed_secret": "625de83a7517422051911680cc803921ff99db90", - "is_secret": false, "is_verified": false, "line_number": 47, "type": "Hex High Entropy String" @@ -242,28 +221,24 @@ "doc/gen3OnK8s.md": [ { "hashed_secret": "2db6d21d365f544f7ca3bcfb443ac96898a7a069", - "is_secret": false, "is_verified": false, "line_number": 113, "type": "Secret Keyword" }, { "hashed_secret": "ff9ee043d85595eb255c05dfe32ece02a53efbb2", - "is_secret": false, "is_verified": false, "line_number": 143, "type": "Secret Keyword" }, { "hashed_secret": "70374248fd7129088fef42b8f568443f6dce3a48", - "is_secret": false, "is_verified": false, "line_number": 170, "type": "Secret Keyword" }, { "hashed_secret": "bcf22dfc6fb76b7366b1f1675baf2332a0e6a7ce", - "is_secret": false, "is_verified": false, "line_number": 189, "type": "Secret Keyword" @@ -272,7 +247,6 @@ "doc/kube-setup-data-ingestion-job.md": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Secret Keyword" @@ -281,7 +255,6 @@ "doc/logs.md": [ { "hashed_secret": "9addbf544119efa4a64223b649750a510f0d463f", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Secret Keyword" @@ -290,7 +263,6 @@ "doc/slurm_cluster.md": [ { "hashed_secret": "2ace62c1befa19e3ea37dd52be9f6d508c5163e6", - "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" @@ -299,14 +271,12 @@ "files/dashboard/usage-reports/package-lock.json": [ { "hashed_secret": "e095101882f706c4de95e0f75c5bcb9666e3f448", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "5422e4f96964d5739998b25ac214520c1b113e5b", - "is_secret": false, "is_verified": false, "line_number": 15, "type": "Base64 High Entropy String" @@ -315,14 +285,12 @@ "gen3/bin/api.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 407, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 477, "type": "Secret Keyword" @@ -331,7 +299,6 @@ "gen3/bin/kube-dev-namespace.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 135, "type": "Secret Keyword" @@ -340,7 +307,6 @@ "gen3/bin/kube-setup-argo.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 206, "type": "Secret Keyword" @@ -349,7 +315,6 @@ "gen3/bin/kube-setup-aurora-monitoring.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Secret Keyword" @@ -358,7 +323,6 @@ "gen3/bin/kube-setup-certs.sh": [ { "hashed_secret": "2e9ee120fd25e31048598693aca91d5473898a99", - "is_secret": false, "is_verified": false, "line_number": 50, "type": "Secret Keyword" @@ -367,14 +331,12 @@ "gen3/bin/kube-setup-dashboard.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 40, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 41, "type": "Secret Keyword" @@ -383,14 +345,12 @@ "gen3/bin/kube-setup-data-ingestion-job.sh": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" }, { "hashed_secret": "8695a632956b1b0ea7b66993dcc98732da39148c", - "is_secret": false, "is_verified": false, "line_number": 102, "type": "Secret Keyword" @@ -399,7 +359,6 @@ "gen3/bin/kube-setup-dicom-server.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 43, "type": "Secret Keyword" @@ -408,7 +367,6 @@ "gen3/bin/kube-setup-dicom.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -417,14 +375,26 @@ "gen3/bin/kube-setup-jenkins.sh": [ { "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, + "is_verified": false, + "line_number": 22, + "type": "Secret Keyword" + } + ], + "gen3/bin/kube-setup-jenkins2.sh": [ + { + "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", + "is_verified": false, + "line_number": 18, + "type": "Secret Keyword" + }, + { + "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", "is_verified": false, "line_number": 22, "type": "Secret Keyword" @@ -433,7 +403,6 @@ "gen3/bin/kube-setup-metadata.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 35, "type": "Secret Keyword" @@ -442,21 +411,18 @@ "gen3/bin/kube-setup-revproxy.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 55, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 57, "type": "Secret Keyword" @@ -465,21 +431,18 @@ "gen3/bin/kube-setup-secrets.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 79, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 82, "type": "Secret Keyword" }, { "hashed_secret": "6f7531b95bbc99ac25a5cc82edb825f319c5dee8", - "is_secret": false, "is_verified": false, "line_number": 95, "type": "Secret Keyword" @@ -488,14 +451,12 @@ "gen3/bin/kube-setup-sftp.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 36, "type": "Secret Keyword" }, { "hashed_secret": "83d11e3aec005a3b9a2077c6800683e202a95af4", - "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -504,7 +465,6 @@ "gen3/bin/kube-setup-sheepdog.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Secret Keyword" @@ -513,28 +473,24 @@ "gen3/bin/kube-setup-sower-jobs.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 120, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 122, "type": "Secret Keyword" @@ -543,21 +499,18 @@ "gen3/bin/kube-setup-ssjdispatcher.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 117, "type": "Secret Keyword" }, { "hashed_secret": "7992309146efaa8da936e34b0bd33242cd0e9f93", - "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 197, "type": "Secret Keyword" @@ -566,14 +519,12 @@ "gen3/lib/aws.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 640, "type": "Secret Keyword" }, { "hashed_secret": "5b4b6c62d3d99d202f095c38c664eded8f640ce8", - "is_secret": false, "is_verified": false, "line_number": 660, "type": "Secret Keyword" @@ -582,14 +533,12 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/apis_configs/fence-config.yaml": [ { "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Basic Auth Credentials" }, { "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db", - "is_secret": false, "is_verified": false, "line_number": 286, "type": "Secret Keyword" @@ -598,7 +547,6 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/creds.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -607,7 +555,6 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/g3auto/dbfarm/servers.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -616,7 +563,6 @@ "gen3/lib/logs/utils.sh": [ { "hashed_secret": "76143b4ffc8aa2a53f9700ce229f904e69f1e8b5", - "is_secret": false, "is_verified": false, "line_number": 3, "type": "Secret Keyword" @@ -625,7 +571,6 @@ "gen3/lib/manifestDefaults/hatchery/hatchery.json": [ { "hashed_secret": "0da0e0005ca04acb407af2681d0bede6d9406039", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -634,14 +579,12 @@ "gen3/lib/onprem.sh": [ { "hashed_secret": "29e52a9bac8f274fa41c51fce9c98eba0dd99cb3", - "is_secret": false, "is_verified": false, "line_number": 68, "type": "Secret Keyword" }, { "hashed_secret": "50f013532a9770a2c2cfdc38b7581dd01df69b70", - "is_secret": false, "is_verified": false, "line_number": 84, "type": "Secret Keyword" @@ -650,14 +593,12 @@ "gen3/lib/secrets/rotate-postgres.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 250, "type": "Secret Keyword" @@ -666,49 +607,42 @@ "gen3/lib/testData/etlconvert/expected2.yaml": [ { "hashed_secret": "fe54e5e937d642307ec155b47ac8a214cb40d474", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "cea0e701e53c42bede2212b22f58f9ff8324da55", - "is_secret": false, "is_verified": false, "line_number": 13, "type": "Base64 High Entropy String" }, { "hashed_secret": "d98d72830f08c9a8b96ed11d3d96ae9e71b72a26", - "is_secret": false, "is_verified": false, "line_number": 16, "type": "Base64 High Entropy String" }, { "hashed_secret": "667fd45d415f73f4132cf0ed11452beb51117b12", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "c2599d515ba3be74ed58821485ba769fc565e424", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Base64 High Entropy String" }, { "hashed_secret": "6ec5eb29e2884f0c9731493b38902e37c2d672ba", - "is_secret": false, "is_verified": false, "line_number": 35, "type": "Base64 High Entropy String" }, { "hashed_secret": "99126b74731670a59b663d5320712564ec7b5f22", - "is_secret": false, "is_verified": false, "line_number": 36, "type": "Base64 High Entropy String" @@ -717,7 +651,6 @@ "gen3/test/secretsTest.sh": [ { "hashed_secret": "c2c715092ef59cba22520f109f041efca84b8938", - "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" @@ -726,28 +659,24 @@ "gen3/test/terraformTest.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 156, "type": "Secret Keyword" }, { "hashed_secret": "1cc07dccfdf640eb0e403e490a873a5536759009", - "is_secret": false, "is_verified": false, "line_number": 172, "type": "Base64 High Entropy String" }, { "hashed_secret": "185a71a740ef6b9b21c84e6eaa47b89c7de181ef", - "is_secret": false, "is_verified": false, "line_number": 175, "type": "Base64 High Entropy String" }, { "hashed_secret": "329b7cd8191942bedd337107934d365c43a86e6c", - "is_secret": false, "is_verified": false, "line_number": 175, "type": "Secret Keyword" @@ -756,21 +685,18 @@ "kube/services/argocd/values.yaml": [ { "hashed_secret": "27c6929aef41ae2bcadac15ca6abcaff72cda9cd", - "is_secret": false, "is_verified": false, "line_number": 360, "type": "Private Key" }, { "hashed_secret": "edbd5e119f94badb9f99a67ac6ff4c7a5204ad61", - "is_secret": false, "is_verified": false, "line_number": 379, "type": "Secret Keyword" }, { "hashed_secret": "91dfd9ddb4198affc5c194cd8ce6d338fde470e2", - "is_secret": false, "is_verified": false, "line_number": 412, "type": "Secret Keyword" @@ -779,7 +705,6 @@ "kube/services/datadog/values.yaml": [ { "hashed_secret": "4a8ce7ae6a8a7f2624e232b61b18c2ac9789c44b", - "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -788,401 +713,362 @@ "kube/services/fenceshib/fenceshib-configmap.yaml": [ { "hashed_secret": "a985e14b9d6744a2d04f29347693b55c116e478c", - "is_secret": false, "is_verified": false, "line_number": 375, "type": "Base64 High Entropy String" }, { "hashed_secret": "adc747bc5eb82ef4b017f5c3759dcee5aa28c36f", - "is_secret": false, "is_verified": false, "line_number": 376, "type": "Base64 High Entropy String" }, { "hashed_secret": "59b1702ff0eaf92c9271cbd12f587de97df7e13b", - "is_secret": false, "is_verified": false, "line_number": 377, "type": "Base64 High Entropy String" }, { "hashed_secret": "b4a748bbfbbca8925d932a47ab3dcb970d34caf5", - "is_secret": false, "is_verified": false, "line_number": 378, "type": "Base64 High Entropy String" }, { "hashed_secret": "af646701a84f7dd9f0e87753f54def881326e78a", - "is_secret": false, "is_verified": false, "line_number": 379, "type": "Base64 High Entropy String" }, { "hashed_secret": "20c15ad9742124dc06e1612282c49bb443ebcbd9", - "is_secret": false, "is_verified": false, "line_number": 380, "type": "Base64 High Entropy String" }, { "hashed_secret": "9caded71b967a11b7a6cd0f20db91f06f3517d12", - "is_secret": false, "is_verified": false, "line_number": 381, "type": "Base64 High Entropy String" }, { "hashed_secret": "8f19501bc9241b71f7b6db929fb35ab12635dcd7", - "is_secret": false, "is_verified": false, "line_number": 382, "type": "Base64 High Entropy String" }, { "hashed_secret": "d6220f6a55df1ed11c4250f42ab07bb9da20541a", - "is_secret": false, "is_verified": false, "line_number": 383, "type": "Base64 High Entropy String" }, { "hashed_secret": "dadd9b96636f9529f2547d05d754dc310ceba0c3", - "is_secret": false, "is_verified": false, "line_number": 384, "type": "Base64 High Entropy String" }, { "hashed_secret": "3074bc66584550e20c3697a28f67a0762394943c", - "is_secret": false, "is_verified": false, "line_number": 385, "type": "Base64 High Entropy String" }, { "hashed_secret": "823131319b4c4b4688f44d3e832bfa9696f16b52", - "is_secret": false, "is_verified": 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String" }, { - "hashed_secret": "6681c1d7e1d327642a32cb8864ad51e4b8f981e5", - "is_secret": false, + "hashed_secret": "d29d7044f0944eb30e02cf445f6998e3343dd811", "is_verified": false, "line_number": 437, "type": "Base64 High Entropy String" }, { - "hashed_secret": "7f7b1f316ece195e5f584fe2faf6f9edc6942c6f", - "is_secret": false, + "hashed_secret": "80a869460f33722387d8d58e7d9d2e1bbd5d1fe1", + "is_verified": false, + "line_number": 438, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "4a06e2a02cbc665adccb4162dc57836895da65b8", "is_verified": false, "line_number": 439, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bb908c7bc655057f2edc42815c5dff82e9dea529", - "is_secret": false, + "hashed_secret": "ba2549f35835dfa101d3f660f7604dc78e3e226f", "is_verified": false, "line_number": 440, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bc2a0d18e3dd142df7b34e95342d47bf8aadabcb", - "is_secret": false, + "hashed_secret": "f354d4ee5fdb94ad29c7b3600264467f45b80eaa", "is_verified": false, "line_number": 441, "type": "Base64 High Entropy String" }, { - "hashed_secret": "d60f0bcea109bb6edb6e45fd387f5f2c86e49e1a", - "is_secret": false, + "hashed_secret": "bf17b587868ba7c3db9865b114261b5b8f1df870", "is_verified": false, "line_number": 442, "type": "Base64 High Entropy String" }, { - "hashed_secret": "e549dd40a741557cc1c4e377df0a141354e22688", - "is_secret": false, + "hashed_secret": "de1fd7a0d32cba528b4d80818c6601f2588d5383", "is_verified": false, "line_number": 443, "type": "Base64 High Entropy String" }, { - "hashed_secret": "2dd2486dae84cad50387c20bf687b6fbc6162b58", - "is_secret": false, + "hashed_secret": "bcad65055f6de654541db2bf27d4e27bd54d94c7", "is_verified": false, "line_number": 444, "type": "Base64 High Entropy String" }, { - "hashed_secret": "71622010fc7eb09d9273f59c548bde6a5da5dc0e", - "is_secret": false, + "hashed_secret": "f2e16f2dd532f65f79341342fdf57a093fc408d8", "is_verified": false, "line_number": 445, "type": "Base64 High Entropy String" }, { - "hashed_secret": "6f0115cf53bd49ec990c562ac6cbfc452c83cd46", - "is_secret": false, + "hashed_secret": "bb036a679a7d2df9fd2ca57068a446bf7f7dd106", "is_verified": false, "line_number": 446, "type": "Base64 High Entropy String" }, { - "hashed_secret": "70dddd534b2f9bb70871fefe0845b79c3b69363f", - "is_secret": false, + "hashed_secret": "5aa6568b1e8185578a6e964f5c322783ad349554", + "is_verified": false, + "line_number": 447, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "4d14835ff0b0bf5aad480296cb705c74ac65f413", "is_verified": false, "line_number": 448, "type": "Base64 High Entropy String" }, { - "hashed_secret": "acf3536b0416aa99608b0be17e87655370ece829", - "is_secret": false, + "hashed_secret": "3f23f77dcf454ad73c4d61c44fd9aa584ef946c1", + "is_verified": false, + "line_number": 451, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "1739fe5e5dfcf851b64f8b7b11538f1de29ce0b5", "is_verified": false, - "line_number": 449, + "line_number": 452, "type": "Base64 High Entropy String" }, { - "hashed_secret": "1d13ee35c7279c1fae1c6474ed47611994273e41", - "is_secret": false, + "hashed_secret": "8129db302110714fc735e3494bd82a65690e0963", "is_verified": false, - "line_number": 450, + "line_number": 453, "type": "Base64 High Entropy String" }, { - "hashed_secret": "d38cf89b25bd7378cdb4e00b4b59293001dd500b", - "is_secret": false, + "hashed_secret": "b48bfc62091164086a703115a0e68bdb09212591", "is_verified": false, - "line_number": 451, + "line_number": 454, "type": "Base64 High Entropy String" }, { - "hashed_secret": "1648f34ce2f1b563a8ed1c6d5d55b5e76a395903", - "is_secret": false, + "hashed_secret": "a10284feaf27f84081073a3267e3dce24ca7b911", "is_verified": false, - "line_number": 452, + "line_number": 455, "type": "Base64 High Entropy String" }, { - "hashed_secret": "9bf63f6f49fb01ff80959bc5a60c8688df92cc02", - "is_secret": false, + "hashed_secret": "3fd80f31de4be8dde9d2b421e832c7d4043fd49a", "is_verified": false, - "line_number": 453, + "line_number": 456, "type": "Base64 High Entropy String" } ], "kube/services/jobs/indexd-authz-job.yaml": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", - "is_secret": false, "is_verified": false, "line_number": 87, "type": "Basic Auth Credentials" @@ -1191,14 +1077,12 @@ "kube/services/monitoring/grafana-values.yaml": [ { "hashed_secret": "2ae868079d293e0a185c671c7bcdac51df36e385", - "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "7a64ff8446b06d38dc271019994f13823a2cbcf4", - "is_secret": false, "is_verified": false, "line_number": 166, "type": "Secret Keyword" @@ -1207,7 +1091,6 @@ "kube/services/revproxy/helpers.js": [ { "hashed_secret": "1d278d3c888d1a2fa7eed622bfc02927ce4049af", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" @@ -1216,7 +1099,6 @@ "kube/services/revproxy/helpersTest.js": [ { "hashed_secret": "e029d4904cc728879d70030572bf37d4510367cb", - "is_secret": false, "is_verified": false, "line_number": 22, "type": "JSON Web Token" @@ -1225,7 +1107,6 @@ "kube/services/superset/superset-deploy.yaml": [ { "hashed_secret": "96e4aceb7cf284be363aa248a32a7cc89785a9f7", - "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" @@ -1234,14 +1115,12 @@ "kube/services/superset/superset-redis.yaml": [ { "hashed_secret": "4af3596275edcb7cd5cc6c3c38bc10479902a08f", - "is_secret": false, "is_verified": false, "line_number": 165, "type": "Secret Keyword" }, { "hashed_secret": "9fe1c31809da38c55b2b64bfab47b92bc5f6b7b9", - "is_secret": false, "is_verified": false, "line_number": 265, "type": "Secret Keyword" @@ -1250,35 +1129,30 @@ "kube/services/superset/values.yaml": [ { "hashed_secret": "6f803b24314c39062efe38d0c1da8c472f47eab3", - "is_secret": false, "is_verified": false, "line_number": 54, "type": "Secret Keyword" }, { "hashed_secret": "6eae3a5b062c6d0d79f070c26e6d62486b40cb46", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" }, { "hashed_secret": "3eb416223e9e69e6bb8ee19793911ad1ad2027d8", - "is_secret": false, "is_verified": false, "line_number": 212, "type": "Secret Keyword" }, { "hashed_secret": "ff55435345834a3fe224936776c2aa15f6ed5358", - "is_secret": false, "is_verified": false, "line_number": 396, "type": "Secret Keyword" }, { "hashed_secret": "98a84a63e5633d17e3b27b69695f87aa7189e9dc", - "is_secret": false, "is_verified": false, "line_number": 503, "type": "Secret Keyword" @@ -1287,280 +1161,240 @@ "package-lock.json": [ { "hashed_secret": "0656ad0df3af4633dc369f13d5e8806973c5fd9d", - "is_secret": false, "is_verified": false, "line_number": 1481, "type": "Base64 High Entropy String" }, { "hashed_secret": "00091d875d922437c5fc9e6067a08e78c2482e87", - "is_secret": false, "is_verified": false, "line_number": 1489, "type": "Base64 High Entropy String" }, { "hashed_secret": "c4e5cc37e115bf7d86e76e3d799705bf691e4d00", - "is_secret": false, "is_verified": false, "line_number": 1521, "type": "Base64 High Entropy String" }, { "hashed_secret": "0512e37fbedf1d16828680a038a241b4780a5c04", - "is_secret": false, "is_verified": false, "line_number": 1547, "type": "Base64 High Entropy String" }, { "hashed_secret": "01868fd50edbfe6eb91e5b01209b543adc6857af", - "is_secret": false, "is_verified": false, "line_number": 1611, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6f48bf1e398deffc7fd31da17c3506b46c97a93", - "is_secret": false, "is_verified": false, "line_number": 1640, "type": "Base64 High Entropy String" }, { "hashed_secret": "85ce358dbdec0996cf3ccd2bf1c6602af68c181e", - "is_secret": false, "is_verified": false, "line_number": 1648, "type": "Base64 High Entropy String" }, { "hashed_secret": "6f9bfb49cb818d2fe07592515e4c3f7a0bbd7e0e", - "is_secret": false, "is_verified": false, "line_number": 1664, "type": "Base64 High Entropy String" }, { "hashed_secret": "7098a3e6d6d2ec0a40f04fe12509c5c6f4c49c0e", - "is_secret": false, "is_verified": false, "line_number": 1683, "type": "Base64 High Entropy String" }, { "hashed_secret": "1664ad175bba1795a7ecad572bae7e0740b94f56", - "is_secret": false, "is_verified": false, "line_number": 1733, "type": "Base64 High Entropy String" }, { "hashed_secret": "1ec4ce2eb945ce2f816dcb6ebdd1e10247f439a3", - "is_secret": false, "is_verified": false, "line_number": 1742, "type": "Base64 High Entropy String" }, { "hashed_secret": "a7af5768a6d936e36f28e1030d7f894d7aaf555e", - "is_secret": false, "is_verified": false, "line_number": 1755, "type": "Base64 High Entropy String" }, { "hashed_secret": "6fbc7dd864586173160874f2a86ca7d2d552cb85", - "is_secret": false, "is_verified": false, "line_number": 1769, "type": "Base64 High Entropy String" }, { "hashed_secret": "81a961f2c89c6209328b74a8768e30fd76c3ac72", - "is_secret": false, "is_verified": false, "line_number": 1855, "type": "Base64 High Entropy String" }, { "hashed_secret": "797d4751c536c421cb82b9f62e0a804af30d78f5", - "is_secret": false, "is_verified": false, "line_number": 1889, "type": "Base64 High Entropy String" }, { "hashed_secret": "0d55babfa89f240142c0adfc7b560500a1d3ae7c", - "is_secret": false, "is_verified": false, "line_number": 1894, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9fdc3025cd10bd8aa4508611e6b7b7a9d650a2c", - "is_secret": false, "is_verified": false, "line_number": 1921, "type": "Base64 High Entropy String" }, { "hashed_secret": "4cf9419259c0ce8eee84b468af3c72db8b001620", - "is_secret": false, "is_verified": false, "line_number": 1950, "type": "Base64 High Entropy String" }, { "hashed_secret": "24816e3eb4308e247bde7c1d09ffb7b79c519b71", - "is_secret": false, "is_verified": false, "line_number": 1983, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9adfe8a333d45f4776fe0eab31608be5d7b6a7d", - "is_secret": false, "is_verified": false, "line_number": 2004, "type": "Base64 High Entropy String" }, { "hashed_secret": "03d6fb388dd1b185129b14221f7127715822ece6", - "is_secret": false, "is_verified": false, "line_number": 2013, "type": "Base64 High Entropy String" }, { "hashed_secret": "ee161bb3f899720f95cee50a5f9ef9c9ed96278b", - "is_secret": false, "is_verified": false, "line_number": 2046, "type": "Base64 High Entropy String" }, { "hashed_secret": "ebeb5b574fa1ed24a40248275e6136759e766466", - "is_secret": false, "is_verified": false, "line_number": 2078, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6a555a428522ccf439fd516ce7c7e269274363f", - "is_secret": false, "is_verified": false, "line_number": 2083, "type": "Base64 High Entropy String" }, { "hashed_secret": "f7f85d9f7c87f1e576dcaf4cf50f35728f9a3265", - "is_secret": false, "is_verified": false, "line_number": 2111, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f1646b60abe74297d2f37a1eee5dc771ad834fc", - "is_secret": false, "is_verified": false, "line_number": 2138, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd933c71e82d5519ae0cb0779b370d02f6935759", - "is_secret": false, "is_verified": false, "line_number": 2143, "type": "Base64 High Entropy String" }, { "hashed_secret": "7090aa59cb52ad1f1810b08c4ac1ddf5c8fce523", - "is_secret": false, "is_verified": false, "line_number": 2150, "type": "Base64 High Entropy String" }, { "hashed_secret": "756444bea4ea3d67844d8ddf58ad32356e9c2430", - "is_secret": false, "is_verified": false, "line_number": 2188, "type": "Base64 High Entropy String" }, { "hashed_secret": "f74135fdd6b8dafdfb01ebbc61c5e5c24ee27cf8", - "is_secret": false, "is_verified": false, "line_number": 2291, "type": "Base64 High Entropy String" }, { "hashed_secret": "56fbae787f4aed7d0632e95840d71bd378d3a36f", - "is_secret": false, "is_verified": false, "line_number": 2303, "type": "Base64 High Entropy String" }, { "hashed_secret": "81cb6be182eb79444202c4563080aee75296a672", - "is_secret": false, "is_verified": false, "line_number": 2308, "type": "Base64 High Entropy String" }, { "hashed_secret": "f0f3f7bce32184893046ac5f8cc80da56c3ca539", - "is_secret": false, "is_verified": false, "line_number": 2317, "type": "Base64 High Entropy String" }, { "hashed_secret": "097893233346336f4003acfb6eb173ee59e648f0", - "is_secret": false, "is_verified": false, "line_number": 2327, "type": "Base64 High Entropy String" }, { "hashed_secret": "bb14c3b4ef4a9f2e86ffdd44b88d9b6729419671", - "is_secret": false, "is_verified": false, "line_number": 2332, "type": "Base64 High Entropy String" }, { "hashed_secret": "71344a35cff67ef081920095d1406601fb5e9b97", - "is_secret": false, "is_verified": false, "line_number": 2340, "type": "Base64 High Entropy String" }, { "hashed_secret": "eb3db6990fd43477a35dfeffc90b3f1ffa83c7bd", - "is_secret": false, "is_verified": false, "line_number": 2349, "type": "Base64 High Entropy String" }, { "hashed_secret": "266288bdc14807b538d1e48a5891e361fa9b4a14", - "is_secret": false, "is_verified": false, "line_number": 2357, "type": "Base64 High Entropy String" }, { "hashed_secret": "800477261175fd21f23e7321923e1fba6ae55471", - "is_secret": false, "is_verified": false, "line_number": 2369, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f0c251b9c2c21454445a98fde6915ceacde2136", - "is_secret": false, "is_verified": false, "line_number": 2387, "type": "Base64 High Entropy String" @@ -1569,7 +1403,6 @@ "tf_files/aws/cognito/README.md": [ { "hashed_secret": "f6920f370a30262b7dd70e97293c73ec89739b70", - "is_secret": false, "is_verified": false, "line_number": 106, "type": "Secret Keyword" @@ -1578,14 +1411,12 @@ "tf_files/aws/commons/README.md": [ { "hashed_secret": "d02e53411e8cb4cd709778f173f7bc9a3455f8ed", - "is_secret": false, "is_verified": false, "line_number": 60, "type": "Secret Keyword" }, { "hashed_secret": "9dc0da3613af850c5a018b0a88a5626fb8888e4e", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -1594,7 +1425,6 @@ "tf_files/aws/eks/sample.tfvars": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 107, "type": "Hex High Entropy String" @@ -1603,7 +1433,6 @@ "tf_files/aws/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 133, "type": "Hex High Entropy String" @@ -1612,14 +1441,12 @@ "tf_files/aws/modules/common-logging/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", - "is_secret": false, "is_verified": false, "line_number": 57, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Hex High Entropy String" @@ -1628,28 +1455,24 @@ "tf_files/aws/modules/common-logging/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1658,21 +1481,18 @@ "tf_files/aws/modules/common-logging/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" @@ -1681,7 +1501,6 @@ "tf_files/aws/modules/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 113, "type": "Hex High Entropy String" @@ -1690,14 +1509,12 @@ "tf_files/aws/modules/management-logs/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", - "is_secret": false, "is_verified": false, "line_number": 54, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", - "is_secret": false, "is_verified": false, "line_number": 56, "type": "Hex High Entropy String" @@ -1706,28 +1523,24 @@ "tf_files/aws/modules/management-logs/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1736,42 +1549,36 @@ "tf_files/aws/modules/management-logs/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "3cf8eb4e9254e1d6cc523da01f8b798b9a83101a", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Base64 High Entropy String" }, { "hashed_secret": "51118900cd675df1b44f254057398f3e52902a5d", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" }, { "hashed_secret": "60a6dfc8d43cd2f5c6292899fc2f94f2d4fc32c4", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" @@ -1780,7 +1587,6 @@ "tf_files/aws/slurm/README.md": [ { "hashed_secret": "fd85d792fa56981cf6a8d2a5c0857c74af86e99d", - "is_secret": false, "is_verified": false, "line_number": 83, "type": "Secret Keyword" @@ -1789,7 +1595,6 @@ "tf_files/azure/cloud.tf": [ { "hashed_secret": "7c1a4b52b64e4106041971c345a1f3eab58fb2a4", - "is_secret": false, "is_verified": false, "line_number": 424, "type": "Secret Keyword" @@ -1798,7 +1603,6 @@ "tf_files/gcp-bwg/roots/commons_setup/variables/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1807,7 +1611,6 @@ "tf_files/gcp-bwg/roots/templates/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1816,7 +1619,6 @@ "tf_files/gcp-bwg/roots/templates/answerfile-env-tenant.user.tfvars_NO_APP_SETUP": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 262, "type": "Secret Keyword" @@ -1825,21 +1627,18 @@ "tf_files/gcp/commons/sample.tfvars": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 11, "type": "Secret Keyword" }, { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "253c7b5e7c83a86346fc4501495b130813f08105", - "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" @@ -1848,7 +1647,6 @@ "tf_files/shared/modules/k8s_configs/creds.tpl": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 8, "type": "Secret Keyword" diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index 1da4ac2d52..730a3b36e8 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -1,5 +1,5 @@ import argparse -import json +import copy import sys import requests import pydash From 8103e82b1044daca4290831db63653b40b24b97c Mon Sep 17 00:00:00 2001 From: Hara Prasad Date: Thu, 29 Feb 2024 12:58:32 -0800 Subject: [PATCH 07/21] Add jenkins-dcp to the env pool reset script (#2489) --- files/scripts/ci-env-pool-reset.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/files/scripts/ci-env-pool-reset.sh b/files/scripts/ci-env-pool-reset.sh index c0c1f67c6d..362cfbfd57 100644 --- a/files/scripts/ci-env-pool-reset.sh +++ b/files/scripts/ci-env-pool-reset.sh @@ -29,6 +29,7 @@ source "${GEN3_HOME}/gen3/gen3setup.sh" cat - > jenkins-envs-services.txt < Date: Thu, 29 Feb 2024 15:20:15 -0800 Subject: [PATCH 08/21] (HP-572) create dynamodb table for gen3-license workspace (#2441) * (HP-572) create dynamodb table for gen3-license workspace * (HP-572) get GSI from hatchery config * (HP-572) remove extra quotes from 'GSI' * (HP-572) move distribute-license for backwards compatibility --------- Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com> --- gen3/bin/kube-setup-hatchery.sh | 57 ++++++++++++++++++++++++++++++--- 1 file changed, 53 insertions(+), 4 deletions(-) diff --git a/gen3/bin/kube-setup-hatchery.sh b/gen3/bin/kube-setup-hatchery.sh index 691fb354ab..5454d1e248 100644 --- a/gen3/bin/kube-setup-hatchery.sh +++ b/gen3/bin/kube-setup-hatchery.sh @@ -20,11 +20,60 @@ gen3 jupyter j-namespace setup # (g3k_kv_filter ${GEN3_HOME}/kube/services/hatchery/serviceaccount.yaml BINDING_ONE "name: hatchery-binding1-$namespace" BINDING_TWO "name: hatchery-binding2-$namespace" CURRENT_NAMESPACE "namespace: $namespace" | g3kubectl apply -f -) || true +function exists_or_create_gen3_license_table() { + # Create dynamodb table for gen3-license if it does not exist. + TARGET_TABLE="$1" + echo "Checking for dynamoDB table: ${TARGET_TABLE}" -# cron job to distribute licenses if using Stata workspaces -if [ "$(g3kubectl get configmaps/manifest-hatchery -o yaml | grep "\"image\": .*stata.*")" ]; -then - gen3 job cron distribute-licenses '* * * * *' + FOUND_TABLE=`aws dynamodb list-tables | jq -r .TableNames | jq -c -r '.[]' | grep $TARGET_TABLE` + if [ -n "$FOUND_TABLE" ]; then + echo "Target table already exists in dynamoDB: $FOUND_TABLE" + else + echo "Creating table ${TARGET_TABLE}" + GSI=`g3kubectl get configmaps/manifest-hatchery -o json | jq -r '.data."license-user-maps-global-secondary-index"'` + if [[ -z "$GSI" || "$GSI" == "null" ]]; then + echo "Error: No global-secondary-index in configuration" + return 0 + fi + aws dynamodb create-table \ + --no-cli-pager \ + --table-name "$TARGET_TABLE" \ + --attribute-definitions AttributeName=itemId,AttributeType=S \ + AttributeName=environment,AttributeType=S \ + AttributeName=isActive,AttributeType=S \ + --key-schema AttributeName=itemId,KeyType=HASH \ + AttributeName=environment,KeyType=RANGE \ + --provisioned-throughput ReadCapacityUnits=5,WriteCapacityUnits=5 \ + --global-secondary-indexes \ + "[ + { + \"IndexName\": \"$GSI\", + \"KeySchema\": [{\"AttributeName\":\"environment\",\"KeyType\":\"HASH\"}, + {\"AttributeName\":\"isActive\",\"KeyType\":\"RANGE\"}], + \"Projection\":{ + \"ProjectionType\":\"INCLUDE\", + \"NonKeyAttributes\":[\"itemId\",\"userId\",\"licenseId\",\"licenseType\"] + }, + \"ProvisionedThroughput\": { + \"ReadCapacityUnits\": 5, + \"WriteCapacityUnits\": 3 + } + } + ]" + fi +} + +TARGET_TABLE=`g3kubectl get configmaps/manifest-hatchery -o json | jq -r '.data."license-user-maps-dynamodb-table"'` +if [[ -z "$TARGET_TABLE" || "$TARGET_TABLE" == "null" ]]; then + echo "No gen3-license table in configuration" + # cron job to distribute licenses if using Stata workspaces but not using dynamoDB + if [ "$(g3kubectl get configmaps/manifest-hatchery -o yaml | grep "\"image\": .*stata.*")" ]; + then + gen3 job cron distribute-licenses '* * * * *' + fi +else + echo "Found gen3-license table in configuration: $TARGET_TABLE" + exists_or_create_gen3_license_table "$TARGET_TABLE" fi policy=$( cat < Date: Fri, 1 Mar 2024 15:46:10 -0600 Subject: [PATCH 09/21] Fix/revert (#2493) * Revert "fix missed import (#2491)" This reverts commit bd6bc767c0461f8fc1f1d90fa8a755be1e7fc381. * Revert "Update heal-cedar-data-ingest.py (#2490)" This reverts commit 90b66091c0d1d8b89e7182ad84201e99903d8e44. * Revert "updating the cedar data ingest (#2472)" This reverts commit 6c27fc9a7fe6cd3affd7a108db3c80b51c664ad1. --- .secrets.baseline | 346 ++++++++++++++---- .../healdata/heal-cedar-data-ingest.py | 98 +---- 2 files changed, 275 insertions(+), 169 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 2583e269f8..b7e06622d6 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,9 +1,9 @@ { "exclude": { - "files": null, + "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2024-02-29T19:38:46Z", + "generated_at": "2024-02-23T20:30:41Z" "plugins_used": [ { "name": "AWSKeyDetector" @@ -61,12 +61,14 @@ "Chef/repo/data_bags/README.md": [ { "hashed_secret": "8a9250639e092d90f164792e35073a9395bff366", + "is_secret": false, "is_verified": false, "line_number": 45, "type": "Secret Keyword" }, { "hashed_secret": "6367c48dd193d56ea7b0baad25b19455e529f5ee", + "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -75,22 +77,25 @@ "Docker/jenkins/Jenkins-CI-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "is_secret": false, "is_verified": false, - "line_number": 124, + "line_number": 121, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "is_secret": false, "is_verified": false, - "line_number": 139, + "line_number": 143, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "is_secret": false, "is_verified": false, "line_number": 107, "type": "Secret Keyword" @@ -99,6 +104,7 @@ "Docker/jenkins/Jenkins2/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "is_secret": false, "is_verified": false, "line_number": 108, "type": "Secret Keyword" @@ -107,6 +113,7 @@ "Docker/sidecar/service.key": [ { "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", + "is_secret": false, "is_verified": false, "line_number": 1, "type": "Private Key" @@ -115,6 +122,7 @@ "Jenkins/Stacks/Jenkins/jenkins.env.sample": [ { "hashed_secret": "eecee33686ac5861c2a7edc8b46bd0e5432bfddd", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -123,6 +131,7 @@ "ansible/roles/awslogs/defaults/main.yaml": [ { "hashed_secret": "9d4e1e23bd5b727046a9e3b4b7db57bd8d6ee684", + "is_secret": false, "is_verified": false, "line_number": 30, "type": "Basic Auth Credentials" @@ -131,12 +140,14 @@ "ansible/roles/slurm/README.md": [ { "hashed_secret": "4acfde1ff9c353ba2ef0dbe0df73bda2743cba42", + "is_secret": false, "is_verified": false, "line_number": 86, "type": "Base64 High Entropy String" }, { "hashed_secret": "579649582303921502d9e6d3f8755f13fdd2b476", + "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" @@ -145,6 +156,7 @@ "apis_configs/config_helper.py": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", + "is_secret": false, "is_verified": false, "line_number": 66, "type": "Basic Auth Credentials" @@ -153,6 +165,7 @@ "apis_configs/fence_credentials.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -161,18 +174,21 @@ "apis_configs/fence_settings.py": [ { "hashed_secret": "3ef0fb8a603abdc0b6caac44a23fdc6792f77ddf", + "is_secret": false, "is_verified": false, "line_number": 6, "type": "Basic Auth Credentials" }, { "hashed_secret": "b60d121b438a380c343d5ec3c2037564b82ffef3", + "is_secret": false, "is_verified": false, "line_number": 58, "type": "Secret Keyword" }, { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", + "is_secret": false, "is_verified": false, "line_number": 80, "type": "Basic Auth Credentials" @@ -181,6 +197,7 @@ "apis_configs/indexd_settings.py": [ { "hashed_secret": "0a0d18c85e096611b5685b62bc60ec534d19bacc", + "is_secret": false, "is_verified": false, "line_number": 59, "type": "Basic Auth Credentials" @@ -189,6 +206,7 @@ "apis_configs/peregrine_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", + "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -197,6 +215,7 @@ "apis_configs/sheepdog_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", + "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -205,6 +224,7 @@ "doc/Gen3-data-upload.md": [ { "hashed_secret": "b8bd20d4a2701dc3aba0efbbf325f1359392d93e", + "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -213,6 +233,7 @@ "doc/api.md": [ { "hashed_secret": "625de83a7517422051911680cc803921ff99db90", + "is_secret": false, "is_verified": false, "line_number": 47, "type": "Hex High Entropy String" @@ -221,24 +242,28 @@ "doc/gen3OnK8s.md": [ { "hashed_secret": "2db6d21d365f544f7ca3bcfb443ac96898a7a069", + "is_secret": false, "is_verified": false, "line_number": 113, "type": "Secret Keyword" }, { "hashed_secret": "ff9ee043d85595eb255c05dfe32ece02a53efbb2", + "is_secret": false, "is_verified": false, "line_number": 143, "type": "Secret Keyword" }, { "hashed_secret": "70374248fd7129088fef42b8f568443f6dce3a48", + "is_secret": false, "is_verified": false, "line_number": 170, "type": "Secret Keyword" }, { "hashed_secret": "bcf22dfc6fb76b7366b1f1675baf2332a0e6a7ce", + "is_secret": false, "is_verified": false, "line_number": 189, "type": "Secret Keyword" @@ -247,6 +272,7 @@ "doc/kube-setup-data-ingestion-job.md": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 30, "type": "Secret Keyword" @@ -255,6 +281,7 @@ "doc/logs.md": [ { "hashed_secret": "9addbf544119efa4a64223b649750a510f0d463f", + "is_secret": false, "is_verified": false, "line_number": 6, "type": "Secret Keyword" @@ -263,6 +290,7 @@ "doc/slurm_cluster.md": [ { "hashed_secret": "2ace62c1befa19e3ea37dd52be9f6d508c5163e6", + "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" @@ -271,12 +299,14 @@ "files/dashboard/usage-reports/package-lock.json": [ { "hashed_secret": "e095101882f706c4de95e0f75c5bcb9666e3f448", + "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "5422e4f96964d5739998b25ac214520c1b113e5b", + "is_secret": false, "is_verified": false, "line_number": 15, "type": "Base64 High Entropy String" @@ -285,12 +315,14 @@ "gen3/bin/api.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 407, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", + "is_secret": false, "is_verified": false, "line_number": 477, "type": "Secret Keyword" @@ -299,6 +331,7 @@ "gen3/bin/kube-dev-namespace.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 135, "type": "Secret Keyword" @@ -307,6 +340,7 @@ "gen3/bin/kube-setup-argo.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", + "is_secret": false, "is_verified": false, "line_number": 206, "type": "Secret Keyword" @@ -315,6 +349,7 @@ "gen3/bin/kube-setup-aurora-monitoring.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 59, "type": "Secret Keyword" @@ -323,6 +358,7 @@ "gen3/bin/kube-setup-certs.sh": [ { "hashed_secret": "2e9ee120fd25e31048598693aca91d5473898a99", + "is_secret": false, "is_verified": false, "line_number": 50, "type": "Secret Keyword" @@ -331,12 +367,14 @@ "gen3/bin/kube-setup-dashboard.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", + "is_secret": false, "is_verified": false, "line_number": 40, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", + "is_secret": false, "is_verified": false, "line_number": 41, "type": "Secret Keyword" @@ -345,12 +383,14 @@ "gen3/bin/kube-setup-data-ingestion-job.sh": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" }, { "hashed_secret": "8695a632956b1b0ea7b66993dcc98732da39148c", + "is_secret": false, "is_verified": false, "line_number": 102, "type": "Secret Keyword" @@ -359,6 +399,7 @@ "gen3/bin/kube-setup-dicom-server.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 43, "type": "Secret Keyword" @@ -367,6 +408,7 @@ "gen3/bin/kube-setup-dicom.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -375,26 +417,14 @@ "gen3/bin/kube-setup-jenkins.sh": [ { "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_verified": false, - "line_number": 22, - "type": "Secret Keyword" - } - ], - "gen3/bin/kube-setup-jenkins2.sh": [ - { - "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", - "is_verified": false, - "line_number": 18, - "type": "Secret Keyword" - }, - { - "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 22, "type": "Secret Keyword" @@ -403,6 +433,7 @@ "gen3/bin/kube-setup-metadata.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 35, "type": "Secret Keyword" @@ -411,18 +442,21 @@ "gen3/bin/kube-setup-revproxy.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", + "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 55, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 57, "type": "Secret Keyword" @@ -431,18 +465,21 @@ "gen3/bin/kube-setup-secrets.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 79, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 82, "type": "Secret Keyword" }, { "hashed_secret": "6f7531b95bbc99ac25a5cc82edb825f319c5dee8", + "is_secret": false, "is_verified": false, "line_number": 95, "type": "Secret Keyword" @@ -451,12 +488,14 @@ "gen3/bin/kube-setup-sftp.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 36, "type": "Secret Keyword" }, { "hashed_secret": "83d11e3aec005a3b9a2077c6800683e202a95af4", + "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -465,6 +504,7 @@ "gen3/bin/kube-setup-sheepdog.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 33, "type": "Secret Keyword" @@ -473,24 +513,28 @@ "gen3/bin/kube-setup-sower-jobs.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", + "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", + "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 120, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 122, "type": "Secret Keyword" @@ -499,18 +543,21 @@ "gen3/bin/kube-setup-ssjdispatcher.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 117, "type": "Secret Keyword" }, { "hashed_secret": "7992309146efaa8da936e34b0bd33242cd0e9f93", + "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 197, "type": "Secret Keyword" @@ -519,12 +566,14 @@ "gen3/lib/aws.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", + "is_secret": false, "is_verified": false, "line_number": 640, "type": "Secret Keyword" }, { "hashed_secret": "5b4b6c62d3d99d202f095c38c664eded8f640ce8", + "is_secret": false, "is_verified": false, "line_number": 660, "type": "Secret Keyword" @@ -533,12 +582,14 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/apis_configs/fence-config.yaml": [ { "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3", + "is_secret": false, "is_verified": false, "line_number": 33, "type": "Basic Auth Credentials" }, { "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db", + "is_secret": false, "is_verified": false, "line_number": 286, "type": "Secret Keyword" @@ -547,6 +598,7 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/creds.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -555,6 +607,7 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/g3auto/dbfarm/servers.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -563,6 +616,7 @@ "gen3/lib/logs/utils.sh": [ { "hashed_secret": "76143b4ffc8aa2a53f9700ce229f904e69f1e8b5", + "is_secret": false, "is_verified": false, "line_number": 3, "type": "Secret Keyword" @@ -571,6 +625,7 @@ "gen3/lib/manifestDefaults/hatchery/hatchery.json": [ { "hashed_secret": "0da0e0005ca04acb407af2681d0bede6d9406039", + "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -579,12 +634,14 @@ "gen3/lib/onprem.sh": [ { "hashed_secret": "29e52a9bac8f274fa41c51fce9c98eba0dd99cb3", + "is_secret": false, "is_verified": false, "line_number": 68, "type": "Secret Keyword" }, { "hashed_secret": "50f013532a9770a2c2cfdc38b7581dd01df69b70", + "is_secret": false, "is_verified": false, "line_number": 84, "type": "Secret Keyword" @@ -593,12 +650,14 @@ "gen3/lib/secrets/rotate-postgres.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", + "is_secret": false, "is_verified": false, "line_number": 250, "type": "Secret Keyword" @@ -607,42 +666,49 @@ "gen3/lib/testData/etlconvert/expected2.yaml": [ { "hashed_secret": "fe54e5e937d642307ec155b47ac8a214cb40d474", + "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "cea0e701e53c42bede2212b22f58f9ff8324da55", + "is_secret": false, "is_verified": false, "line_number": 13, "type": "Base64 High Entropy String" }, { "hashed_secret": "d98d72830f08c9a8b96ed11d3d96ae9e71b72a26", + "is_secret": false, "is_verified": false, "line_number": 16, "type": "Base64 High Entropy String" }, { "hashed_secret": "667fd45d415f73f4132cf0ed11452beb51117b12", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "c2599d515ba3be74ed58821485ba769fc565e424", + "is_secret": false, "is_verified": false, "line_number": 33, "type": "Base64 High Entropy String" }, { "hashed_secret": "6ec5eb29e2884f0c9731493b38902e37c2d672ba", + "is_secret": false, "is_verified": false, "line_number": 35, "type": "Base64 High Entropy String" }, { "hashed_secret": "99126b74731670a59b663d5320712564ec7b5f22", + "is_secret": false, "is_verified": false, "line_number": 36, "type": "Base64 High Entropy String" @@ -651,6 +717,7 @@ "gen3/test/secretsTest.sh": [ { "hashed_secret": "c2c715092ef59cba22520f109f041efca84b8938", + "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" @@ -659,24 +726,28 @@ "gen3/test/terraformTest.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", + "is_secret": false, "is_verified": false, "line_number": 156, "type": "Secret Keyword" }, { "hashed_secret": "1cc07dccfdf640eb0e403e490a873a5536759009", + "is_secret": false, "is_verified": false, "line_number": 172, "type": "Base64 High Entropy String" }, { "hashed_secret": "185a71a740ef6b9b21c84e6eaa47b89c7de181ef", + "is_secret": false, "is_verified": false, "line_number": 175, "type": "Base64 High Entropy String" }, { "hashed_secret": "329b7cd8191942bedd337107934d365c43a86e6c", + "is_secret": false, "is_verified": false, "line_number": 175, "type": "Secret Keyword" @@ -685,18 +756,21 @@ "kube/services/argocd/values.yaml": [ { "hashed_secret": "27c6929aef41ae2bcadac15ca6abcaff72cda9cd", + "is_secret": false, "is_verified": false, "line_number": 360, "type": "Private Key" }, { "hashed_secret": "edbd5e119f94badb9f99a67ac6ff4c7a5204ad61", + "is_secret": false, "is_verified": false, "line_number": 379, "type": "Secret Keyword" }, { "hashed_secret": "91dfd9ddb4198affc5c194cd8ce6d338fde470e2", + "is_secret": false, "is_verified": false, "line_number": 412, "type": "Secret Keyword" @@ -705,6 +779,7 @@ "kube/services/datadog/values.yaml": [ { "hashed_secret": "4a8ce7ae6a8a7f2624e232b61b18c2ac9789c44b", + "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -713,362 +788,401 @@ "kube/services/fenceshib/fenceshib-configmap.yaml": [ { "hashed_secret": "a985e14b9d6744a2d04f29347693b55c116e478c", + "is_secret": false, "is_verified": false, "line_number": 375, "type": "Base64 High Entropy String" }, { "hashed_secret": "adc747bc5eb82ef4b017f5c3759dcee5aa28c36f", + "is_secret": false, "is_verified": false, "line_number": 376, "type": "Base64 High Entropy String" }, { "hashed_secret": "59b1702ff0eaf92c9271cbd12f587de97df7e13b", + "is_secret": false, "is_verified": false, "line_number": 377, "type": "Base64 High Entropy String" }, { "hashed_secret": "b4a748bbfbbca8925d932a47ab3dcb970d34caf5", + "is_secret": false, "is_verified": false, "line_number": 378, "type": "Base64 High Entropy String" }, { "hashed_secret": "af646701a84f7dd9f0e87753f54def881326e78a", + "is_secret": false, "is_verified": false, "line_number": 379, "type": "Base64 High Entropy String" }, { "hashed_secret": "20c15ad9742124dc06e1612282c49bb443ebcbd9", + "is_secret": false, "is_verified": false, "line_number": 380, "type": "Base64 High Entropy String" }, { "hashed_secret": "9caded71b967a11b7a6cd0f20db91f06f3517d12", + "is_secret": false, "is_verified": false, "line_number": 381, "type": "Base64 High Entropy String" }, { "hashed_secret": "8f19501bc9241b71f7b6db929fb35ab12635dcd7", + "is_secret": false, "is_verified": false, "line_number": 382, "type": "Base64 High Entropy String" }, { "hashed_secret": "d6220f6a55df1ed11c4250f42ab07bb9da20541a", + "is_secret": false, "is_verified": false, "line_number": 383, "type": "Base64 High Entropy String" }, { "hashed_secret": "dadd9b96636f9529f2547d05d754dc310ceba0c3", + "is_secret": false, "is_verified": false, "line_number": 384, "type": "Base64 High Entropy String" }, { "hashed_secret": "3074bc66584550e20c3697a28f67a0762394943c", + "is_secret": false, "is_verified": false, "line_number": 385, "type": "Base64 High Entropy String" }, { "hashed_secret": "823131319b4c4b4688f44d3e832bfa9696f16b52", + "is_secret": false, "is_verified": false, "line_number": 386, "type": "Base64 High Entropy String" }, { "hashed_secret": "015b780cbfb76988caf52de8ac974a6781e53110", + "is_secret": false, "is_verified": false, "line_number": 387, "type": "Base64 High Entropy String" }, { "hashed_secret": "5c8fac33207d74d667680ade09447ea8f43b76d7", + "is_secret": false, "is_verified": false, "line_number": 388, "type": "Base64 High Entropy String" }, { "hashed_secret": "c0c4bb09d8394e8f001e337bd27ccac355433d9e", + "is_secret": false, "is_verified": false, "line_number": 389, "type": "Base64 High Entropy String" }, { "hashed_secret": "f95631bcbbbc56e18487dcb242cfb1b3e74b16a1", + "is_secret": false, "is_verified": false, "line_number": 390, "type": "Base64 High Entropy String" }, { "hashed_secret": "01a692ab6232e0882a313d148981bab58ab98f53", + "is_secret": false, "is_verified": false, "line_number": 391, "type": "Base64 High Entropy String" }, { "hashed_secret": "658060a680d415ce6690ad2c3b622ddb33ddd50a", + "is_secret": false, "is_verified": false, "line_number": 392, "type": "Base64 High Entropy String" }, { "hashed_secret": "80915b0bd9daa5e1f95cad573892980b1b5a2294", + "is_secret": false, "is_verified": false, "line_number": 393, "type": "Base64 High Entropy String" }, { "hashed_secret": "cc55977b293d8cdca8a2c19dfea6874e70057c41", + "is_secret": false, "is_verified": false, "line_number": 394, "type": "Base64 High Entropy String" }, { "hashed_secret": "e400ed02add75dd5f3a8c212857acf12027437d1", + "is_secret": false, "is_verified": false, "line_number": 395, "type": "Base64 High Entropy String" }, { "hashed_secret": "2e819c8baa3b0508a32b77de258655b3f3a6f7cb", + "is_secret": false, "is_verified": false, "line_number": 396, "type": "Base64 High Entropy String" }, { "hashed_secret": "546ed926d58ea5492ab6adb8be94a67aa44ac433", + "is_secret": false, "is_verified": false, "line_number": 397, "type": "Base64 High Entropy String" }, { "hashed_secret": "f056f2deceed268e7af6dbdaf2577079c76e006a", + "is_secret": false, "is_verified": false, "line_number": 398, "type": "Base64 High Entropy String" }, { "hashed_secret": "d75efee28f4798c3a9c6f44b78a8500513ef28b2", + "is_secret": false, "is_verified": false, "line_number": 399, "type": "Base64 High Entropy String" }, { - "hashed_secret": "fbad0bc8f7792b03f89cd3780eb7cf79f284c525", + "hashed_secret": "7803ae08cdc22a5e0b025eff3c9ef0628eedc165", + "is_secret": false, "is_verified": false, "line_number": 419, "type": "Base64 High Entropy String" }, { - "hashed_secret": "3f6480956a775dacb44e2c39aa3d4722a347f7ab", + "hashed_secret": "b8b61e87f5b58b0eeb597b2122ea0cea2ccab3d9", + "is_secret": false, "is_verified": false, "line_number": 420, "type": "Base64 High Entropy String" }, { - "hashed_secret": "17f32ae55b14d708ca121722c2cae37189f19daf", + "hashed_secret": "787745fc904c3bd7eddc3d1aab683a376c13890f", + "is_secret": false, "is_verified": false, "line_number": 423, "type": "Base64 High Entropy String" }, { - "hashed_secret": "08a74689ca077515d406093720a7e5675fb42bb8", + "hashed_secret": "81361d672f238f505a6246ef9b655ee2f48d67e7", + "is_secret": false, "is_verified": false, "line_number": 424, "type": "Base64 High Entropy String" }, { - "hashed_secret": "fa577bb3b2600d2d522dcfea8f1e34896760fcf2", + "hashed_secret": "7c98bff76ac3f273d15ed9bc3dd5294d323ab577", + "is_secret": false, "is_verified": false, "line_number": 425, "type": "Base64 High Entropy String" }, { - "hashed_secret": "37254f15cca211a1bd5f7ceb23de2b3eb8fb33aa", + "hashed_secret": "46038fc88daceed8dd46817ca45c72ae0270fdd4", + "is_secret": false, "is_verified": false, "line_number": 426, "type": "Base64 High Entropy String" }, { - "hashed_secret": "86865593e038509467b91c2d5f36ccc09c3f422b", + "hashed_secret": "acad0c57b4f5cbed1b4863ed06d02784180a9f92", + "is_secret": false, "is_verified": false, "line_number": 427, "type": "Base64 High Entropy String" }, { - "hashed_secret": "a899a8d9e114b2a8e108f90e6a72c056db22489f", + "hashed_secret": "1b57f49a6ee337c16ecd6aabfc0dff3b3821cd09", + "is_secret": false, "is_verified": false, "line_number": 428, "type": "Base64 High Entropy String" }, { - "hashed_secret": "756b4825f886afd83c25563ac9d45f318d695c48", + "hashed_secret": "5b688158be36e8b3f265a462ed599dcf69290084", + "is_secret": false, "is_verified": false, "line_number": 429, "type": "Base64 High Entropy String" }, { - "hashed_secret": "89882eeb0aca97717a7e4afcf4bc08d077813c7f", + "hashed_secret": "965996e12c8b50b3c325d96003e8984a4ece658a", + "is_secret": false, "is_verified": false, "line_number": 430, "type": "Base64 High Entropy String" }, { - "hashed_secret": "347140d7b7ceb4e501c3c9c2ea4f29338e2f145e", + "hashed_secret": "584f0c58e764e948af1a35c9e60447aa0f84c6f5", + "is_secret": false, "is_verified": false, "line_number": 431, "type": "Base64 High Entropy String" }, { - "hashed_secret": "61dbf70eb10d609e60c7b87faf8f755ff48abc46", + "hashed_secret": "bcaf897786d060a675ee9d654a84ae8baf96e9d0", + "is_secret": false, "is_verified": false, "line_number": 432, "type": "Base64 High Entropy String" }, { - "hashed_secret": "24cd54c4b2f58378bba008cb2df68ac663fba7c8", + "hashed_secret": "0c09277fa183e06d32065f9386a3b4190b445df3", + "is_secret": false, "is_verified": false, "line_number": 433, "type": "Base64 High Entropy String" }, { - "hashed_secret": "fa4f9626ae4b98f4b61203c5bafb6f21c9c31e5d", + "hashed_secret": "5a51be06b305d6664e4afd25f21869b0f8b5039b", + "is_secret": false, "is_verified": false, "line_number": 434, "type": "Base64 High Entropy String" }, { - "hashed_secret": "b1370003d9cc1e346c83dba33e0418c7775a0c15", + "hashed_secret": "b38404f8853d734e3d03577b2c1084b4540c8708", + "is_secret": false, "is_verified": false, "line_number": 435, "type": "Base64 High Entropy String" }, { - "hashed_secret": "c66526e195e423a7ba7d68ac661cdcd8600dcd1f", + "hashed_secret": "126ccc602cffcb8292beb57137f7f6719e317b72", + "is_secret": false, "is_verified": false, "line_number": 436, "type": "Base64 High Entropy String" }, { - "hashed_secret": "d29d7044f0944eb30e02cf445f6998e3343dd811", + "hashed_secret": "6681c1d7e1d327642a32cb8864ad51e4b8f981e5", + "is_secret": false, "is_verified": false, "line_number": 437, "type": "Base64 High Entropy String" }, { - "hashed_secret": "80a869460f33722387d8d58e7d9d2e1bbd5d1fe1", - "is_verified": false, - "line_number": 438, - "type": "Base64 High Entropy String" - }, - { - "hashed_secret": "4a06e2a02cbc665adccb4162dc57836895da65b8", + "hashed_secret": "7f7b1f316ece195e5f584fe2faf6f9edc6942c6f", + "is_secret": false, "is_verified": false, "line_number": 439, "type": "Base64 High Entropy String" }, { - "hashed_secret": "ba2549f35835dfa101d3f660f7604dc78e3e226f", + "hashed_secret": "bb908c7bc655057f2edc42815c5dff82e9dea529", + "is_secret": false, "is_verified": false, "line_number": 440, "type": "Base64 High Entropy String" }, { - "hashed_secret": "f354d4ee5fdb94ad29c7b3600264467f45b80eaa", + "hashed_secret": "bc2a0d18e3dd142df7b34e95342d47bf8aadabcb", + "is_secret": false, "is_verified": false, "line_number": 441, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bf17b587868ba7c3db9865b114261b5b8f1df870", + "hashed_secret": "d60f0bcea109bb6edb6e45fd387f5f2c86e49e1a", + "is_secret": false, "is_verified": false, "line_number": 442, "type": "Base64 High Entropy String" }, { - "hashed_secret": "de1fd7a0d32cba528b4d80818c6601f2588d5383", + "hashed_secret": "e549dd40a741557cc1c4e377df0a141354e22688", + "is_secret": false, "is_verified": false, "line_number": 443, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bcad65055f6de654541db2bf27d4e27bd54d94c7", + "hashed_secret": "2dd2486dae84cad50387c20bf687b6fbc6162b58", + "is_secret": false, "is_verified": false, "line_number": 444, "type": "Base64 High Entropy String" }, { - "hashed_secret": "f2e16f2dd532f65f79341342fdf57a093fc408d8", + "hashed_secret": "71622010fc7eb09d9273f59c548bde6a5da5dc0e", + "is_secret": false, "is_verified": false, "line_number": 445, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bb036a679a7d2df9fd2ca57068a446bf7f7dd106", + "hashed_secret": "6f0115cf53bd49ec990c562ac6cbfc452c83cd46", + "is_secret": false, "is_verified": false, "line_number": 446, "type": "Base64 High Entropy String" }, { - "hashed_secret": "5aa6568b1e8185578a6e964f5c322783ad349554", - "is_verified": false, - "line_number": 447, - "type": "Base64 High Entropy String" - }, - { - "hashed_secret": "4d14835ff0b0bf5aad480296cb705c74ac65f413", + "hashed_secret": "70dddd534b2f9bb70871fefe0845b79c3b69363f", + "is_secret": false, "is_verified": false, "line_number": 448, "type": "Base64 High Entropy String" }, { - "hashed_secret": "3f23f77dcf454ad73c4d61c44fd9aa584ef946c1", - "is_verified": false, - "line_number": 451, - "type": "Base64 High Entropy String" - }, - { - "hashed_secret": "1739fe5e5dfcf851b64f8b7b11538f1de29ce0b5", + "hashed_secret": "acf3536b0416aa99608b0be17e87655370ece829", + "is_secret": false, "is_verified": false, - "line_number": 452, + "line_number": 449, "type": "Base64 High Entropy String" }, { - "hashed_secret": "8129db302110714fc735e3494bd82a65690e0963", + "hashed_secret": "1d13ee35c7279c1fae1c6474ed47611994273e41", + "is_secret": false, "is_verified": false, - "line_number": 453, + "line_number": 450, "type": "Base64 High Entropy String" }, { - "hashed_secret": "b48bfc62091164086a703115a0e68bdb09212591", + "hashed_secret": "d38cf89b25bd7378cdb4e00b4b59293001dd500b", + "is_secret": false, "is_verified": false, - "line_number": 454, + "line_number": 451, "type": "Base64 High Entropy String" }, { - "hashed_secret": "a10284feaf27f84081073a3267e3dce24ca7b911", + "hashed_secret": "1648f34ce2f1b563a8ed1c6d5d55b5e76a395903", + "is_secret": false, "is_verified": false, - "line_number": 455, + "line_number": 452, "type": "Base64 High Entropy String" }, { - "hashed_secret": "3fd80f31de4be8dde9d2b421e832c7d4043fd49a", + "hashed_secret": "9bf63f6f49fb01ff80959bc5a60c8688df92cc02", + "is_secret": false, "is_verified": false, - "line_number": 456, + "line_number": 453, "type": "Base64 High Entropy String" } ], "kube/services/jobs/indexd-authz-job.yaml": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", + "is_secret": false, "is_verified": false, "line_number": 87, "type": "Basic Auth Credentials" @@ -1077,12 +1191,14 @@ "kube/services/monitoring/grafana-values.yaml": [ { "hashed_secret": "2ae868079d293e0a185c671c7bcdac51df36e385", + "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "7a64ff8446b06d38dc271019994f13823a2cbcf4", + "is_secret": false, "is_verified": false, "line_number": 166, "type": "Secret Keyword" @@ -1091,6 +1207,7 @@ "kube/services/revproxy/helpers.js": [ { "hashed_secret": "1d278d3c888d1a2fa7eed622bfc02927ce4049af", + "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" @@ -1099,6 +1216,7 @@ "kube/services/revproxy/helpersTest.js": [ { "hashed_secret": "e029d4904cc728879d70030572bf37d4510367cb", + "is_secret": false, "is_verified": false, "line_number": 22, "type": "JSON Web Token" @@ -1107,6 +1225,7 @@ "kube/services/superset/superset-deploy.yaml": [ { "hashed_secret": "96e4aceb7cf284be363aa248a32a7cc89785a9f7", + "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" @@ -1115,12 +1234,14 @@ "kube/services/superset/superset-redis.yaml": [ { "hashed_secret": "4af3596275edcb7cd5cc6c3c38bc10479902a08f", + "is_secret": false, "is_verified": false, "line_number": 165, "type": "Secret Keyword" }, { "hashed_secret": "9fe1c31809da38c55b2b64bfab47b92bc5f6b7b9", + "is_secret": false, "is_verified": false, "line_number": 265, "type": "Secret Keyword" @@ -1129,30 +1250,35 @@ "kube/services/superset/values.yaml": [ { "hashed_secret": "6f803b24314c39062efe38d0c1da8c472f47eab3", + "is_secret": false, "is_verified": false, "line_number": 54, "type": "Secret Keyword" }, { "hashed_secret": "6eae3a5b062c6d0d79f070c26e6d62486b40cb46", + "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" }, { "hashed_secret": "3eb416223e9e69e6bb8ee19793911ad1ad2027d8", + "is_secret": false, "is_verified": false, "line_number": 212, "type": "Secret Keyword" }, { "hashed_secret": "ff55435345834a3fe224936776c2aa15f6ed5358", + "is_secret": false, "is_verified": false, "line_number": 396, "type": "Secret Keyword" }, { "hashed_secret": "98a84a63e5633d17e3b27b69695f87aa7189e9dc", + "is_secret": false, "is_verified": false, "line_number": 503, "type": "Secret Keyword" @@ -1161,240 +1287,280 @@ "package-lock.json": [ { "hashed_secret": "0656ad0df3af4633dc369f13d5e8806973c5fd9d", + "is_secret": false, "is_verified": false, "line_number": 1481, "type": "Base64 High Entropy String" }, { "hashed_secret": "00091d875d922437c5fc9e6067a08e78c2482e87", + "is_secret": false, "is_verified": false, "line_number": 1489, "type": "Base64 High Entropy String" }, { "hashed_secret": "c4e5cc37e115bf7d86e76e3d799705bf691e4d00", + "is_secret": false, "is_verified": false, "line_number": 1521, "type": "Base64 High Entropy String" }, { "hashed_secret": "0512e37fbedf1d16828680a038a241b4780a5c04", + "is_secret": false, "is_verified": false, "line_number": 1547, "type": "Base64 High Entropy String" }, { "hashed_secret": "01868fd50edbfe6eb91e5b01209b543adc6857af", + "is_secret": false, "is_verified": false, "line_number": 1611, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6f48bf1e398deffc7fd31da17c3506b46c97a93", + "is_secret": false, "is_verified": false, "line_number": 1640, "type": "Base64 High Entropy String" }, { "hashed_secret": "85ce358dbdec0996cf3ccd2bf1c6602af68c181e", + "is_secret": false, "is_verified": false, "line_number": 1648, "type": "Base64 High Entropy String" }, { "hashed_secret": "6f9bfb49cb818d2fe07592515e4c3f7a0bbd7e0e", + "is_secret": false, "is_verified": false, "line_number": 1664, "type": "Base64 High Entropy String" }, { "hashed_secret": "7098a3e6d6d2ec0a40f04fe12509c5c6f4c49c0e", + "is_secret": false, "is_verified": false, "line_number": 1683, "type": "Base64 High Entropy String" }, { "hashed_secret": "1664ad175bba1795a7ecad572bae7e0740b94f56", + "is_secret": false, "is_verified": false, "line_number": 1733, "type": "Base64 High Entropy String" }, { "hashed_secret": "1ec4ce2eb945ce2f816dcb6ebdd1e10247f439a3", + "is_secret": false, "is_verified": false, "line_number": 1742, "type": "Base64 High Entropy String" }, { "hashed_secret": "a7af5768a6d936e36f28e1030d7f894d7aaf555e", + "is_secret": false, "is_verified": false, "line_number": 1755, "type": "Base64 High Entropy String" }, { "hashed_secret": "6fbc7dd864586173160874f2a86ca7d2d552cb85", + "is_secret": false, "is_verified": false, "line_number": 1769, "type": "Base64 High Entropy String" }, { "hashed_secret": "81a961f2c89c6209328b74a8768e30fd76c3ac72", + "is_secret": false, "is_verified": false, "line_number": 1855, "type": "Base64 High Entropy String" }, { "hashed_secret": "797d4751c536c421cb82b9f62e0a804af30d78f5", + "is_secret": false, "is_verified": false, "line_number": 1889, "type": "Base64 High Entropy String" }, { "hashed_secret": "0d55babfa89f240142c0adfc7b560500a1d3ae7c", + "is_secret": false, "is_verified": false, "line_number": 1894, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9fdc3025cd10bd8aa4508611e6b7b7a9d650a2c", + "is_secret": false, "is_verified": false, "line_number": 1921, "type": "Base64 High Entropy String" }, { "hashed_secret": "4cf9419259c0ce8eee84b468af3c72db8b001620", + "is_secret": false, "is_verified": false, "line_number": 1950, "type": "Base64 High Entropy String" }, { "hashed_secret": "24816e3eb4308e247bde7c1d09ffb7b79c519b71", + "is_secret": false, "is_verified": false, "line_number": 1983, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9adfe8a333d45f4776fe0eab31608be5d7b6a7d", + "is_secret": false, "is_verified": false, "line_number": 2004, "type": "Base64 High Entropy String" }, { "hashed_secret": "03d6fb388dd1b185129b14221f7127715822ece6", + "is_secret": false, "is_verified": false, "line_number": 2013, "type": "Base64 High Entropy String" }, { "hashed_secret": "ee161bb3f899720f95cee50a5f9ef9c9ed96278b", + "is_secret": false, "is_verified": false, "line_number": 2046, "type": "Base64 High Entropy String" }, { "hashed_secret": "ebeb5b574fa1ed24a40248275e6136759e766466", + "is_secret": false, "is_verified": false, "line_number": 2078, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6a555a428522ccf439fd516ce7c7e269274363f", + "is_secret": false, "is_verified": false, "line_number": 2083, "type": "Base64 High Entropy String" }, { "hashed_secret": "f7f85d9f7c87f1e576dcaf4cf50f35728f9a3265", + "is_secret": false, "is_verified": false, "line_number": 2111, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f1646b60abe74297d2f37a1eee5dc771ad834fc", + "is_secret": false, "is_verified": false, "line_number": 2138, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd933c71e82d5519ae0cb0779b370d02f6935759", + "is_secret": false, "is_verified": false, "line_number": 2143, "type": "Base64 High Entropy String" }, { "hashed_secret": "7090aa59cb52ad1f1810b08c4ac1ddf5c8fce523", + "is_secret": false, "is_verified": false, "line_number": 2150, "type": "Base64 High Entropy String" }, { "hashed_secret": "756444bea4ea3d67844d8ddf58ad32356e9c2430", + "is_secret": false, "is_verified": false, "line_number": 2188, "type": "Base64 High Entropy String" }, { "hashed_secret": "f74135fdd6b8dafdfb01ebbc61c5e5c24ee27cf8", + "is_secret": false, "is_verified": false, "line_number": 2291, "type": "Base64 High Entropy String" }, { "hashed_secret": "56fbae787f4aed7d0632e95840d71bd378d3a36f", + "is_secret": false, "is_verified": false, "line_number": 2303, "type": "Base64 High Entropy String" }, { "hashed_secret": "81cb6be182eb79444202c4563080aee75296a672", + "is_secret": false, "is_verified": false, "line_number": 2308, "type": "Base64 High Entropy String" }, { "hashed_secret": "f0f3f7bce32184893046ac5f8cc80da56c3ca539", + "is_secret": false, "is_verified": false, "line_number": 2317, "type": "Base64 High Entropy String" }, { "hashed_secret": "097893233346336f4003acfb6eb173ee59e648f0", + "is_secret": false, "is_verified": false, "line_number": 2327, "type": "Base64 High Entropy String" }, { "hashed_secret": "bb14c3b4ef4a9f2e86ffdd44b88d9b6729419671", + "is_secret": false, "is_verified": false, "line_number": 2332, "type": "Base64 High Entropy String" }, { "hashed_secret": "71344a35cff67ef081920095d1406601fb5e9b97", + "is_secret": false, "is_verified": false, "line_number": 2340, "type": "Base64 High Entropy String" }, { "hashed_secret": "eb3db6990fd43477a35dfeffc90b3f1ffa83c7bd", + "is_secret": false, "is_verified": false, "line_number": 2349, "type": "Base64 High Entropy String" }, { "hashed_secret": "266288bdc14807b538d1e48a5891e361fa9b4a14", + "is_secret": false, "is_verified": false, "line_number": 2357, "type": "Base64 High Entropy String" }, { "hashed_secret": "800477261175fd21f23e7321923e1fba6ae55471", + "is_secret": false, "is_verified": false, "line_number": 2369, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f0c251b9c2c21454445a98fde6915ceacde2136", + "is_secret": false, "is_verified": false, "line_number": 2387, "type": "Base64 High Entropy String" @@ -1403,6 +1569,7 @@ "tf_files/aws/cognito/README.md": [ { "hashed_secret": "f6920f370a30262b7dd70e97293c73ec89739b70", + "is_secret": false, "is_verified": false, "line_number": 106, "type": "Secret Keyword" @@ -1411,12 +1578,14 @@ "tf_files/aws/commons/README.md": [ { "hashed_secret": "d02e53411e8cb4cd709778f173f7bc9a3455f8ed", + "is_secret": false, "is_verified": false, "line_number": 60, "type": "Secret Keyword" }, { "hashed_secret": "9dc0da3613af850c5a018b0a88a5626fb8888e4e", + "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -1425,6 +1594,7 @@ "tf_files/aws/eks/sample.tfvars": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", + "is_secret": false, "is_verified": false, "line_number": 107, "type": "Hex High Entropy String" @@ -1433,6 +1603,7 @@ "tf_files/aws/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", + "is_secret": false, "is_verified": false, "line_number": 133, "type": "Hex High Entropy String" @@ -1441,12 +1612,14 @@ "tf_files/aws/modules/common-logging/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", + "is_secret": false, "is_verified": false, "line_number": 57, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", + "is_secret": false, "is_verified": false, "line_number": 59, "type": "Hex High Entropy String" @@ -1455,24 +1628,28 @@ "tf_files/aws/modules/common-logging/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", + "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1481,18 +1658,21 @@ "tf_files/aws/modules/common-logging/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" @@ -1501,6 +1681,7 @@ "tf_files/aws/modules/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", + "is_secret": false, "is_verified": false, "line_number": 113, "type": "Hex High Entropy String" @@ -1509,12 +1690,14 @@ "tf_files/aws/modules/management-logs/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", + "is_secret": false, "is_verified": false, "line_number": 54, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", + "is_secret": false, "is_verified": false, "line_number": 56, "type": "Hex High Entropy String" @@ -1523,24 +1706,28 @@ "tf_files/aws/modules/management-logs/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", + "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", + "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1549,36 +1736,42 @@ "tf_files/aws/modules/management-logs/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", + "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "3cf8eb4e9254e1d6cc523da01f8b798b9a83101a", + "is_secret": false, "is_verified": false, "line_number": 6, "type": "Base64 High Entropy String" }, { "hashed_secret": "51118900cd675df1b44f254057398f3e52902a5d", + "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" }, { "hashed_secret": "60a6dfc8d43cd2f5c6292899fc2f94f2d4fc32c4", + "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" @@ -1587,6 +1780,7 @@ "tf_files/aws/slurm/README.md": [ { "hashed_secret": "fd85d792fa56981cf6a8d2a5c0857c74af86e99d", + "is_secret": false, "is_verified": false, "line_number": 83, "type": "Secret Keyword" @@ -1595,6 +1789,7 @@ "tf_files/azure/cloud.tf": [ { "hashed_secret": "7c1a4b52b64e4106041971c345a1f3eab58fb2a4", + "is_secret": false, "is_verified": false, "line_number": 424, "type": "Secret Keyword" @@ -1603,6 +1798,7 @@ "tf_files/gcp-bwg/roots/commons_setup/variables/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", + "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1611,6 +1807,7 @@ "tf_files/gcp-bwg/roots/templates/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", + "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1619,6 +1816,7 @@ "tf_files/gcp-bwg/roots/templates/answerfile-env-tenant.user.tfvars_NO_APP_SETUP": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", + "is_secret": false, "is_verified": false, "line_number": 262, "type": "Secret Keyword" @@ -1627,18 +1825,21 @@ "tf_files/gcp/commons/sample.tfvars": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_secret": false, "is_verified": false, "line_number": 11, "type": "Secret Keyword" }, { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", + "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "253c7b5e7c83a86346fc4501495b130813f08105", + "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" @@ -1647,6 +1848,7 @@ "tf_files/shared/modules/k8s_configs/creds.tpl": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", + "is_secret": false, "is_verified": false, "line_number": 8, "type": "Secret Keyword" diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index 730a3b36e8..71575e3c56 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -1,5 +1,5 @@ import argparse -import copy +import json import sys import requests import pydash @@ -35,16 +35,6 @@ "Buisness Development": "Business Development" } -# repository links -REPOSITORY_STUDY_ID_LINK_TEMPLATE = { - "NIDDK Central": "https://repository.niddk.nih.gov/studies//", - "NIDA Data Share": "https://datashare.nida.nih.gov/study/", - "NICHD DASH": "https://dash.nichd.nih.gov/study/", - "ICPSR": "https://www.icpsr.umich.edu/web/ICPSR/studies/", - "BioSystics-AP": "https://biosystics-ap.com/assays/assaystudy//", -} - - # Defines field that we don't want to include in the filters OMITTED_VALUES_MAPPING = { "study_metadata.human_subject_applicability.gender_applicability": "Not applicable" @@ -124,31 +114,6 @@ def get_client_token(client_id: str, client_secret: str): return token -def get_related_studies(serial_num, hostname): - related_study_result = [] - - if serial_num: - mds = requests.get(f"http://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") - if mds.status_code == 200: - related_study_metadata = mds.json() - - for ( - related_study_metadata_key, - related_study_metadata_value, - ) in related_study_metadata.items(): - title = ( - related_study_metadata_value.get( - "gen3_discovery", {} - ) - .get("study_metadata", {}) - .get("minimal_info", {}) - .get("study_name", "") - ) - link = f"https://{hostname}/portal/discovery/{related_study_metadata_key}/" - related_study_result.append({"title": title, "link": link}) - return related_study_result - - parser = argparse.ArgumentParser() parser.add_argument("--directory", help="CEDAR Directory ID for registering ") @@ -249,67 +214,6 @@ def get_related_studies(serial_num, hostname): mds_res["gen3_discovery"]["study_metadata"].update(cedar_record) mds_res["gen3_discovery"]["study_metadata"]["metadata_location"]["other_study_websites"] = cedar_record_other_study_websites - # setup citations - doi_citation = mds_res["gen3_discovery"]["study_metadata"].get("doi_citation", "") - mds_res["gen3_discovery"]["study_metadata"]["citation"]["heal_platform_citation"] = doi_citation - - - # setup repository_study_link - data_repositories = ( - mds_res.get("study_metadata", {}) - .get("metadata_location", {}) - .get("data_repositories", []) - ) - repository_citation = "Users must also include a citation to the data as specified by the local repository." - repository_citation_additional_text = ' The link to the study page at the local repository can be found in the "Data" tab.' - for repository in data_repositories: - if ( - repository["repository_name"] - and repository["repository_name"] - in REPOSITORY_STUDY_ID_LINK_TEMPLATE - and repository["repository_study_ID"] - ): - repository_study_link = REPOSITORY_STUDY_ID_LINK_TEMPLATE[ - repository["repository_name"] - ].replace("", repository["repository_study_ID"]) - repository.update({"repository_study_link": repository_study_link}) - if repository_citation_additional_text not in repository_citation: - repository_citation += repository_citation_additional_text - if len(data_repositories): - data_repositories[0] = { - **data_repositories[0], - "repository_citation": repository_citation, - } - mds_res["gen3_discovery"]["study_metadata"][ - "metadata_location" - ]["data_repositories"] = data_repositories - - - - # set up related studies - serial_num = None - try: - serial_num = ( - mds_res - .get("nih_reporter", {}) - .get("project_num_split", {}) - .get("serial_num", None) - ) - except Exception: - print(f"Unable to get serial number for study") - - if serial_num == None: - print(f"Unable to get serial number for study") - - related_study_result = get_related_studies(serial_num, hostname) - existing_related_study_result = mds_res.get("related_studies", []) - for related_study in related_study_result: - if related_study not in existing_related_study_result: - existing_related_study_result.append(copy.deepcopy(related_study)) - mds_res["gen3_discovery"][ - "related_studies" - ] = copy.deepcopy(existing_related_study_result) - # merge data from cedar that is not study level metadata into a level higher deleted_keys = [] for key, value in mds_res["gen3_discovery"]["study_metadata"].items(): From 6ee728ad3e375b1a0e521ae256ef13ca29529067 Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Mon, 4 Mar 2024 11:04:31 -0600 Subject: [PATCH 10/21] Automation for Gen3 Discovery AI Service (#2396) * feat(gen3-openai): rough initial testing, no automation for rolling * feat(gen3-discovery-ai): initial deployment * fix(ai): fix setup jq escaping * fix(ai): fix file name * fix(ai): fix deployment configmap * fix(ai): fix configmap * fix(ai): env path * feat(image): use from manifest * chore(ai): better naming * fix(ai): fix mount path for cfg * fix(ai): first attempt to fix issue of needing write volume for chromadb persistance * fix(ai): k8s deploy command * fix(ai): fix duplicate name * chore(ai): don't sent telemetry data * chore(ai): more logging in init * chore(logs): more * fix(ai): mv instead of cp * fix(ai): back to cp, can't mv b/c of readonly * feat(ai): use s3 and service account + role to handle persisted vectorstore data instead of configmap * fix(ai): fix setup * fix(ai): fix setup * fix(ai): fix automation * fix(ai): automation * fix(ai): fix logic for setup * fix(ai): mount storage config and don't use gen3/jq since they're not available * fix(ai): fix wrong path * fix(ai): quotes * fix(ai): quoting * fix(ai): use awshelper for access to aws commands * fix(ai): move files to correct location * fix(ai): only get folder * fix(ai): fix sync * fix(ai): clear folder before syncing * fix(ai): update bucket contents every roll for updates * feat(ai): support TSV loading from manifest config * fix(ai): fix init so aws syncing is done with awshelper image and loading into vectorstore is with service image * fix(ai): fix loading * fix(ai): fix loading * fix(ai): sync all files * feat(ai): add google secret loading and mounting * fix(ai): mount to container, not inits * fix(mount): don't create another dir * fix(mount): don't create another dir * fix(mounts): fix paths * fix(mounts): mount all secrets * fix(secrets): allow .env file to be a secret * fix(secrets): revert failed attempt to support .env * chore(ai): cd to dir with pyproject.toml * chore(ai): try to fix issue with pyproject.toml * fix(ai): actually we need to poetry run * chore(ai): debug lines * chore(ai): debug lines * chore(ai): debug lines * chore(ai): debug lines * chore(ai): debug lines * fix(mount): don't overwrite whole dir * fix(ai): mounts * chore(ai): remove debug lines * fix(ai): remove debug * chore(debug): debug line * chore(debug): remove debug line * feat(ai): add to roll all, fix port in service yaml * fix(ai): fix nginx conf file name * fix(nginx): fix routing for AI service to add trailing slash after "ai" * Update web_whitelist * Update kube-setup-gen3-discovery-ai.sh * Update README.md * Update gen3-discovery-ai-deploy.yaml * Update gen3-discovery-ai-deploy.yaml * Update gen3-discovery-ai-service.yaml * Update kube-setup-gen3-discovery-ai.sh * feat(discovery): update to data load commands and strategy to support markdown --- gen3/bin/kube-roll-all.sh | 6 + gen3/bin/kube-setup-gen3-discovery-ai.sh | 154 +++++++++++++++ kube/services/gen3-discovery-ai/README.md | 42 ++++ .../gen3-discovery-ai-deploy.yaml | 181 ++++++++++++++++++ .../gen3-discovery-ai-service.yaml | 21 ++ .../gen3-discovery-ai-service.conf | 12 ++ 6 files changed, 416 insertions(+) create mode 100644 gen3/bin/kube-setup-gen3-discovery-ai.sh create mode 100644 kube/services/gen3-discovery-ai/README.md create mode 100644 kube/services/gen3-discovery-ai/gen3-discovery-ai-deploy.yaml create mode 100644 kube/services/gen3-discovery-ai/gen3-discovery-ai-service.yaml create mode 100644 kube/services/revproxy/gen3.nginx.conf/gen3-discovery-ai-service.conf diff --git a/gen3/bin/kube-roll-all.sh b/gen3/bin/kube-roll-all.sh index 6a67f2bdd2..1dca87c68c 100644 --- a/gen3/bin/kube-roll-all.sh +++ b/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 diff --git a/gen3/bin/kube-setup-gen3-discovery-ai.sh b/gen3/bin/kube-setup-gen3-discovery-ai.sh new file mode 100644 index 0000000000..44a472a74c --- /dev/null +++ b/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" < "$secretsFolder/base64Authz.txt" + fi + gen3 secrets sync 'setup gen3-discovery-ai-g3auto secrets' +} + +if ! g3k_manifest_lookup '.versions."gen3-discovery-ai"' 2> /dev/null; then + gen3_log_info "kube-setup-gen3-discovery-ai exiting - gen3-discovery-ai service not in manifest" + exit 0 +fi + +# There's no db for this service *yet* +# +# if ! setup_database; then +# gen3_log_err "kube-setup-gen3-discovery-ai bailing out - database failed setup" +# exit 1 +# fi + +setup_storage() { + local saName="gen3-discovery-ai-sa" + g3kubectl create sa "$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" diff --git a/kube/services/gen3-discovery-ai/README.md b/kube/services/gen3-discovery-ai/README.md new file mode 100644 index 0000000000..4c20678e06 --- /dev/null +++ b/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. diff --git a/kube/services/gen3-discovery-ai/gen3-discovery-ai-deploy.yaml b/kube/services/gen3-discovery-ai/gen3-discovery-ai-deploy.yaml new file mode 100644 index 0000000000..dcfe03248a --- /dev/null +++ b/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 diff --git a/kube/services/gen3-discovery-ai/gen3-discovery-ai-service.yaml b/kube/services/gen3-discovery-ai/gen3-discovery-ai-service.yaml new file mode 100644 index 0000000000..b4734c3b8a --- /dev/null +++ b/kube/services/gen3-discovery-ai/gen3-discovery-ai-service.yaml @@ -0,0 +1,21 @@ +kind: Service +apiVersion: v1 +metadata: + name: gen3-discovery-ai-service +spec: + selector: + app: gen3-discovery-ai + release: production + ports: + - protocol: TCP + port: 80 + targetPort: 8089 + name: http + nodePort: null + - protocol: TCP + port: 443 + targetPort: 443 + name: https + nodePort: null + type: ClusterIP + diff --git a/kube/services/revproxy/gen3.nginx.conf/gen3-discovery-ai-service.conf b/kube/services/revproxy/gen3.nginx.conf/gen3-discovery-ai-service.conf new file mode 100644 index 0000000000..42e9a3758b --- /dev/null +++ b/kube/services/revproxy/gen3.nginx.conf/gen3-discovery-ai-service.conf @@ -0,0 +1,12 @@ + location /ai { + if ($csrf_check !~ ^ok-\S.+$) { + return 403 "failed csrf check"; + } + + set $proxy_service "gen3-discovery-ai-service"; + set $upstream http://gen3-discovery-ai-service$des_domain; + rewrite ^/ai/(.*) /$1 break; + proxy_pass $upstream; + proxy_redirect http://$host/ https://$host/ai/; + client_max_body_size 0; + } From 077e475463098416001ebd3ced41ec06d1ee631b Mon Sep 17 00:00:00 2001 From: Aidan Hilt <11202897+AidanHilt@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:21:16 -0500 Subject: [PATCH 11/21] Raising requests for Jenkins pods (#2495) --- .secrets.baseline | 2 +- Jenkinsfile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index b7e06622d6..fbed122fd0 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2024-02-23T20:30:41Z" + "generated_at": "2024-02-23T20:30:41Z", "plugins_used": [ { "name": "AWSKeyDetector" diff --git a/Jenkinsfile b/Jenkinsfile index 4e3470ded6..9c70a2e378 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -99,8 +99,8 @@ spec: resources: requests: cpu: 0.2 - memory: 200Mi - ephemeral-storage: 200Mi + memory: 400Mi + ephemeral-storage: 1Gi env: - name: AWS_DEFAULT_REGION value: us-east-1 From 62894388c1ac907587916462d641788c87226e4a Mon Sep 17 00:00:00 2001 From: Michael Lukowski Date: Thu, 7 Mar 2024 10:42:36 -0600 Subject: [PATCH 12/21] fix cedar ingestion problems (#2494) * fix cedar ingestion problems * add default falue to get statement --------- Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com> --- .secrets.baseline | 360 +++++------------- .../healdata/heal-cedar-data-ingest.py | 101 +++++ 2 files changed, 187 insertions(+), 274 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index fbed122fd0..200b69841f 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,9 +1,9 @@ { "exclude": { - "files": "^.secrets.baseline$", + "files": null, "lines": null }, - "generated_at": "2024-02-23T20:30:41Z", + "generated_at": "2024-03-04T21:42:56Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -61,14 +61,12 @@ "Chef/repo/data_bags/README.md": [ { "hashed_secret": "8a9250639e092d90f164792e35073a9395bff366", - "is_secret": false, "is_verified": false, "line_number": 45, "type": "Secret Keyword" }, { "hashed_secret": "6367c48dd193d56ea7b0baad25b19455e529f5ee", - "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -77,25 +75,22 @@ "Docker/jenkins/Jenkins-CI-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, - "line_number": 121, + "line_number": 124, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins-Worker/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, - "line_number": 143, + "line_number": 139, "type": "Secret Keyword" } ], "Docker/jenkins/Jenkins/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, "line_number": 107, "type": "Secret Keyword" @@ -104,7 +99,6 @@ "Docker/jenkins/Jenkins2/Dockerfile": [ { "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", - "is_secret": false, "is_verified": false, "line_number": 108, "type": "Secret Keyword" @@ -113,7 +107,6 @@ "Docker/sidecar/service.key": [ { "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", - "is_secret": false, "is_verified": false, "line_number": 1, "type": "Private Key" @@ -122,7 +115,6 @@ "Jenkins/Stacks/Jenkins/jenkins.env.sample": [ { "hashed_secret": "eecee33686ac5861c2a7edc8b46bd0e5432bfddd", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -131,7 +123,6 @@ "ansible/roles/awslogs/defaults/main.yaml": [ { "hashed_secret": "9d4e1e23bd5b727046a9e3b4b7db57bd8d6ee684", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Basic Auth Credentials" @@ -140,14 +131,12 @@ "ansible/roles/slurm/README.md": [ { "hashed_secret": "4acfde1ff9c353ba2ef0dbe0df73bda2743cba42", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Base64 High Entropy String" }, { "hashed_secret": "579649582303921502d9e6d3f8755f13fdd2b476", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" @@ -156,7 +145,6 @@ "apis_configs/config_helper.py": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", - "is_secret": false, "is_verified": false, "line_number": 66, "type": "Basic Auth Credentials" @@ -165,7 +153,6 @@ "apis_configs/fence_credentials.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -174,21 +161,18 @@ "apis_configs/fence_settings.py": [ { "hashed_secret": "3ef0fb8a603abdc0b6caac44a23fdc6792f77ddf", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Basic Auth Credentials" }, { "hashed_secret": "b60d121b438a380c343d5ec3c2037564b82ffef3", - "is_secret": false, "is_verified": false, "line_number": 58, "type": "Secret Keyword" }, { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 80, "type": "Basic Auth Credentials" @@ -197,7 +181,6 @@ "apis_configs/indexd_settings.py": [ { "hashed_secret": "0a0d18c85e096611b5685b62bc60ec534d19bacc", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Basic Auth Credentials" @@ -206,7 +189,6 @@ "apis_configs/peregrine_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -215,7 +197,6 @@ "apis_configs/sheepdog_settings.py": [ { "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", - "is_secret": false, "is_verified": false, "line_number": 46, "type": "Basic Auth Credentials" @@ -224,7 +205,6 @@ "doc/Gen3-data-upload.md": [ { "hashed_secret": "b8bd20d4a2701dc3aba0efbbf325f1359392d93e", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -233,7 +213,6 @@ "doc/api.md": [ { "hashed_secret": "625de83a7517422051911680cc803921ff99db90", - "is_secret": false, "is_verified": false, "line_number": 47, "type": "Hex High Entropy String" @@ -242,28 +221,24 @@ "doc/gen3OnK8s.md": [ { "hashed_secret": "2db6d21d365f544f7ca3bcfb443ac96898a7a069", - "is_secret": false, "is_verified": false, "line_number": 113, "type": "Secret Keyword" }, { "hashed_secret": "ff9ee043d85595eb255c05dfe32ece02a53efbb2", - "is_secret": false, "is_verified": false, "line_number": 143, "type": "Secret Keyword" }, { "hashed_secret": "70374248fd7129088fef42b8f568443f6dce3a48", - "is_secret": false, "is_verified": false, "line_number": 170, "type": "Secret Keyword" }, { "hashed_secret": "bcf22dfc6fb76b7366b1f1675baf2332a0e6a7ce", - "is_secret": false, "is_verified": false, "line_number": 189, "type": "Secret Keyword" @@ -272,7 +247,6 @@ "doc/kube-setup-data-ingestion-job.md": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Secret Keyword" @@ -281,7 +255,6 @@ "doc/logs.md": [ { "hashed_secret": "9addbf544119efa4a64223b649750a510f0d463f", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Secret Keyword" @@ -290,7 +263,6 @@ "doc/slurm_cluster.md": [ { "hashed_secret": "2ace62c1befa19e3ea37dd52be9f6d508c5163e6", - "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" @@ -299,14 +271,12 @@ "files/dashboard/usage-reports/package-lock.json": [ { "hashed_secret": "e095101882f706c4de95e0f75c5bcb9666e3f448", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "5422e4f96964d5739998b25ac214520c1b113e5b", - "is_secret": false, "is_verified": false, "line_number": 15, "type": "Base64 High Entropy String" @@ -315,14 +285,12 @@ "gen3/bin/api.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 407, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 477, "type": "Secret Keyword" @@ -331,7 +299,6 @@ "gen3/bin/kube-dev-namespace.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 135, "type": "Secret Keyword" @@ -340,7 +307,6 @@ "gen3/bin/kube-setup-argo.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 206, "type": "Secret Keyword" @@ -349,7 +315,6 @@ "gen3/bin/kube-setup-aurora-monitoring.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Secret Keyword" @@ -358,7 +323,6 @@ "gen3/bin/kube-setup-certs.sh": [ { "hashed_secret": "2e9ee120fd25e31048598693aca91d5473898a99", - "is_secret": false, "is_verified": false, "line_number": 50, "type": "Secret Keyword" @@ -367,14 +331,12 @@ "gen3/bin/kube-setup-dashboard.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 40, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 41, "type": "Secret Keyword" @@ -383,14 +345,12 @@ "gen3/bin/kube-setup-data-ingestion-job.sh": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" }, { "hashed_secret": "8695a632956b1b0ea7b66993dcc98732da39148c", - "is_secret": false, "is_verified": false, "line_number": 102, "type": "Secret Keyword" @@ -399,7 +359,6 @@ "gen3/bin/kube-setup-dicom-server.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 43, "type": "Secret Keyword" @@ -408,23 +367,48 @@ "gen3/bin/kube-setup-dicom.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" } ], + "gen3/bin/kube-setup-gen3-discovery-ai.sh": [ + { + "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", + "is_verified": false, + "line_number": 37, + "type": "Secret Keyword" + }, + { + "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", + "is_verified": false, + "line_number": 71, + "type": "Secret Keyword" + } + ], "gen3/bin/kube-setup-jenkins.sh": [ { "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, + "is_verified": false, + "line_number": 22, + "type": "Secret Keyword" + } + ], + "gen3/bin/kube-setup-jenkins2.sh": [ + { + "hashed_secret": "05ea760643a5c0a9bacb3544dc844ac79938a51f", + "is_verified": false, + "line_number": 18, + "type": "Secret Keyword" + }, + { + "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", "is_verified": false, "line_number": 22, "type": "Secret Keyword" @@ -433,7 +417,6 @@ "gen3/bin/kube-setup-metadata.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 35, "type": "Secret Keyword" @@ -442,21 +425,18 @@ "gen3/bin/kube-setup-revproxy.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 55, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 57, "type": "Secret Keyword" @@ -465,21 +445,18 @@ "gen3/bin/kube-setup-secrets.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 79, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 82, "type": "Secret Keyword" }, { "hashed_secret": "6f7531b95bbc99ac25a5cc82edb825f319c5dee8", - "is_secret": false, "is_verified": false, "line_number": 95, "type": "Secret Keyword" @@ -488,14 +465,12 @@ "gen3/bin/kube-setup-sftp.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 36, "type": "Secret Keyword" }, { "hashed_secret": "83d11e3aec005a3b9a2077c6800683e202a95af4", - "is_secret": false, "is_verified": false, "line_number": 51, "type": "Secret Keyword" @@ -504,7 +479,6 @@ "gen3/bin/kube-setup-sheepdog.sh": [ { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Secret Keyword" @@ -513,28 +487,24 @@ "gen3/bin/kube-setup-sower-jobs.sh": [ { "hashed_secret": "40304f287a52d99fdbe086ad19dbdbf9cc1b3897", - "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" }, { "hashed_secret": "e7064f0b80f61dbc65915311032d27baa569ae2a", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 120, "type": "Secret Keyword" }, { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 122, "type": "Secret Keyword" @@ -543,21 +513,18 @@ "gen3/bin/kube-setup-ssjdispatcher.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 117, "type": "Secret Keyword" }, { "hashed_secret": "7992309146efaa8da936e34b0bd33242cd0e9f93", - "is_secret": false, "is_verified": false, "line_number": 184, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 197, "type": "Secret Keyword" @@ -566,14 +533,12 @@ "gen3/lib/aws.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 640, "type": "Secret Keyword" }, { "hashed_secret": "5b4b6c62d3d99d202f095c38c664eded8f640ce8", - "is_secret": false, "is_verified": false, "line_number": 660, "type": "Secret Keyword" @@ -582,14 +547,12 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/apis_configs/fence-config.yaml": [ { "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Basic Auth Credentials" }, { "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db", - "is_secret": false, "is_verified": false, "line_number": 286, "type": "Secret Keyword" @@ -598,7 +561,6 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/creds.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" @@ -607,7 +569,6 @@ "gen3/lib/bootstrap/templates/Gen3Secrets/g3auto/dbfarm/servers.json": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Secret Keyword" @@ -616,7 +577,6 @@ "gen3/lib/logs/utils.sh": [ { "hashed_secret": "76143b4ffc8aa2a53f9700ce229f904e69f1e8b5", - "is_secret": false, "is_verified": false, "line_number": 3, "type": "Secret Keyword" @@ -625,7 +585,6 @@ "gen3/lib/manifestDefaults/hatchery/hatchery.json": [ { "hashed_secret": "0da0e0005ca04acb407af2681d0bede6d9406039", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -634,14 +593,12 @@ "gen3/lib/onprem.sh": [ { "hashed_secret": "29e52a9bac8f274fa41c51fce9c98eba0dd99cb3", - "is_secret": false, "is_verified": false, "line_number": 68, "type": "Secret Keyword" }, { "hashed_secret": "50f013532a9770a2c2cfdc38b7581dd01df69b70", - "is_secret": false, "is_verified": false, "line_number": 84, "type": "Secret Keyword" @@ -650,14 +607,12 @@ "gen3/lib/secrets/rotate-postgres.sh": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "d3df8a3b08a9de43b73eca1302d50e7a0e5b360f", - "is_secret": false, "is_verified": false, "line_number": 250, "type": "Secret Keyword" @@ -666,49 +621,42 @@ "gen3/lib/testData/etlconvert/expected2.yaml": [ { "hashed_secret": "fe54e5e937d642307ec155b47ac8a214cb40d474", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" }, { "hashed_secret": "cea0e701e53c42bede2212b22f58f9ff8324da55", - "is_secret": false, "is_verified": false, "line_number": 13, "type": "Base64 High Entropy String" }, { "hashed_secret": "d98d72830f08c9a8b96ed11d3d96ae9e71b72a26", - "is_secret": false, "is_verified": false, "line_number": 16, "type": "Base64 High Entropy String" }, { "hashed_secret": "667fd45d415f73f4132cf0ed11452beb51117b12", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "c2599d515ba3be74ed58821485ba769fc565e424", - "is_secret": false, "is_verified": false, "line_number": 33, "type": "Base64 High Entropy String" }, { "hashed_secret": "6ec5eb29e2884f0c9731493b38902e37c2d672ba", - "is_secret": false, "is_verified": false, "line_number": 35, "type": "Base64 High Entropy String" }, { "hashed_secret": "99126b74731670a59b663d5320712564ec7b5f22", - "is_secret": false, "is_verified": false, "line_number": 36, "type": "Base64 High Entropy String" @@ -717,7 +665,6 @@ "gen3/test/secretsTest.sh": [ { "hashed_secret": "c2c715092ef59cba22520f109f041efca84b8938", - "is_secret": false, "is_verified": false, "line_number": 25, "type": "Secret Keyword" @@ -726,28 +673,24 @@ "gen3/test/terraformTest.sh": [ { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 156, "type": "Secret Keyword" }, { "hashed_secret": "1cc07dccfdf640eb0e403e490a873a5536759009", - "is_secret": false, "is_verified": false, "line_number": 172, "type": "Base64 High Entropy String" }, { "hashed_secret": "185a71a740ef6b9b21c84e6eaa47b89c7de181ef", - "is_secret": false, "is_verified": false, "line_number": 175, "type": "Base64 High Entropy String" }, { "hashed_secret": "329b7cd8191942bedd337107934d365c43a86e6c", - "is_secret": false, "is_verified": false, "line_number": 175, "type": "Secret Keyword" @@ -756,21 +699,18 @@ "kube/services/argocd/values.yaml": [ { "hashed_secret": "27c6929aef41ae2bcadac15ca6abcaff72cda9cd", - "is_secret": false, "is_verified": false, "line_number": 360, "type": "Private Key" }, { "hashed_secret": "edbd5e119f94badb9f99a67ac6ff4c7a5204ad61", - "is_secret": false, "is_verified": false, "line_number": 379, "type": "Secret Keyword" }, { "hashed_secret": "91dfd9ddb4198affc5c194cd8ce6d338fde470e2", - "is_secret": false, "is_verified": false, "line_number": 412, "type": "Secret Keyword" @@ -779,7 +719,6 @@ "kube/services/datadog/values.yaml": [ { "hashed_secret": "4a8ce7ae6a8a7f2624e232b61b18c2ac9789c44b", - "is_secret": false, "is_verified": false, "line_number": 23, "type": "Secret Keyword" @@ -788,401 +727,362 @@ "kube/services/fenceshib/fenceshib-configmap.yaml": [ { "hashed_secret": "a985e14b9d6744a2d04f29347693b55c116e478c", - "is_secret": false, "is_verified": false, "line_number": 375, "type": "Base64 High Entropy String" }, { "hashed_secret": "adc747bc5eb82ef4b017f5c3759dcee5aa28c36f", - "is_secret": false, "is_verified": false, "line_number": 376, "type": "Base64 High Entropy String" }, { "hashed_secret": "59b1702ff0eaf92c9271cbd12f587de97df7e13b", - "is_secret": false, "is_verified": false, "line_number": 377, "type": "Base64 High Entropy String" }, { "hashed_secret": "b4a748bbfbbca8925d932a47ab3dcb970d34caf5", - "is_secret": false, "is_verified": false, "line_number": 378, "type": "Base64 High Entropy String" }, { "hashed_secret": "af646701a84f7dd9f0e87753f54def881326e78a", - "is_secret": false, "is_verified": false, "line_number": 379, "type": "Base64 High Entropy String" }, { "hashed_secret": "20c15ad9742124dc06e1612282c49bb443ebcbd9", - "is_secret": false, "is_verified": false, "line_number": 380, "type": "Base64 High Entropy String" }, { "hashed_secret": "9caded71b967a11b7a6cd0f20db91f06f3517d12", - "is_secret": false, "is_verified": false, "line_number": 381, "type": "Base64 High Entropy String" }, { "hashed_secret": "8f19501bc9241b71f7b6db929fb35ab12635dcd7", - "is_secret": false, "is_verified": false, "line_number": 382, "type": "Base64 High Entropy String" }, { "hashed_secret": "d6220f6a55df1ed11c4250f42ab07bb9da20541a", - "is_secret": false, "is_verified": false, "line_number": 383, "type": "Base64 High Entropy String" }, { "hashed_secret": "dadd9b96636f9529f2547d05d754dc310ceba0c3", - "is_secret": false, "is_verified": false, "line_number": 384, "type": "Base64 High Entropy String" }, { "hashed_secret": "3074bc66584550e20c3697a28f67a0762394943c", - "is_secret": false, "is_verified": false, "line_number": 385, "type": "Base64 High Entropy String" }, { "hashed_secret": "823131319b4c4b4688f44d3e832bfa9696f16b52", - "is_secret": false, "is_verified": false, "line_number": 386, "type": "Base64 High Entropy String" }, { "hashed_secret": "015b780cbfb76988caf52de8ac974a6781e53110", - "is_secret": false, "is_verified": false, "line_number": 387, "type": "Base64 High Entropy String" }, { "hashed_secret": "5c8fac33207d74d667680ade09447ea8f43b76d7", - "is_secret": false, "is_verified": false, "line_number": 388, "type": "Base64 High Entropy String" }, { "hashed_secret": "c0c4bb09d8394e8f001e337bd27ccac355433d9e", - "is_secret": false, "is_verified": false, "line_number": 389, "type": "Base64 High Entropy String" }, { "hashed_secret": "f95631bcbbbc56e18487dcb242cfb1b3e74b16a1", - "is_secret": false, "is_verified": false, "line_number": 390, "type": "Base64 High Entropy String" }, { "hashed_secret": "01a692ab6232e0882a313d148981bab58ab98f53", - "is_secret": false, "is_verified": false, "line_number": 391, "type": "Base64 High Entropy String" }, { "hashed_secret": "658060a680d415ce6690ad2c3b622ddb33ddd50a", - "is_secret": false, "is_verified": false, "line_number": 392, "type": "Base64 High Entropy String" }, { "hashed_secret": "80915b0bd9daa5e1f95cad573892980b1b5a2294", - "is_secret": false, "is_verified": false, "line_number": 393, "type": "Base64 High Entropy String" }, { "hashed_secret": "cc55977b293d8cdca8a2c19dfea6874e70057c41", - "is_secret": false, "is_verified": false, "line_number": 394, "type": "Base64 High Entropy String" }, { "hashed_secret": "e400ed02add75dd5f3a8c212857acf12027437d1", - "is_secret": false, "is_verified": false, "line_number": 395, "type": "Base64 High Entropy String" }, { "hashed_secret": "2e819c8baa3b0508a32b77de258655b3f3a6f7cb", - "is_secret": false, "is_verified": false, "line_number": 396, "type": "Base64 High Entropy String" }, { "hashed_secret": "546ed926d58ea5492ab6adb8be94a67aa44ac433", - "is_secret": false, "is_verified": false, "line_number": 397, "type": "Base64 High Entropy String" }, { "hashed_secret": "f056f2deceed268e7af6dbdaf2577079c76e006a", - "is_secret": false, "is_verified": false, "line_number": 398, "type": "Base64 High Entropy String" }, { "hashed_secret": "d75efee28f4798c3a9c6f44b78a8500513ef28b2", - "is_secret": false, "is_verified": false, "line_number": 399, "type": "Base64 High Entropy String" }, { - "hashed_secret": "7803ae08cdc22a5e0b025eff3c9ef0628eedc165", - "is_secret": false, + "hashed_secret": "fbad0bc8f7792b03f89cd3780eb7cf79f284c525", "is_verified": false, "line_number": 419, "type": "Base64 High Entropy String" }, { - "hashed_secret": "b8b61e87f5b58b0eeb597b2122ea0cea2ccab3d9", - "is_secret": false, + "hashed_secret": "3f6480956a775dacb44e2c39aa3d4722a347f7ab", "is_verified": false, "line_number": 420, "type": "Base64 High Entropy String" }, { - "hashed_secret": "787745fc904c3bd7eddc3d1aab683a376c13890f", - "is_secret": false, + "hashed_secret": "17f32ae55b14d708ca121722c2cae37189f19daf", "is_verified": false, "line_number": 423, "type": "Base64 High Entropy String" }, { - "hashed_secret": "81361d672f238f505a6246ef9b655ee2f48d67e7", - "is_secret": false, + "hashed_secret": "08a74689ca077515d406093720a7e5675fb42bb8", "is_verified": false, "line_number": 424, "type": "Base64 High Entropy String" }, { - "hashed_secret": "7c98bff76ac3f273d15ed9bc3dd5294d323ab577", - "is_secret": false, + "hashed_secret": "fa577bb3b2600d2d522dcfea8f1e34896760fcf2", "is_verified": false, "line_number": 425, "type": "Base64 High Entropy String" }, { - "hashed_secret": "46038fc88daceed8dd46817ca45c72ae0270fdd4", - "is_secret": false, + "hashed_secret": "37254f15cca211a1bd5f7ceb23de2b3eb8fb33aa", "is_verified": false, "line_number": 426, "type": "Base64 High Entropy String" }, { - "hashed_secret": "acad0c57b4f5cbed1b4863ed06d02784180a9f92", - "is_secret": false, + "hashed_secret": "86865593e038509467b91c2d5f36ccc09c3f422b", "is_verified": false, "line_number": 427, "type": "Base64 High Entropy String" }, { - "hashed_secret": "1b57f49a6ee337c16ecd6aabfc0dff3b3821cd09", - "is_secret": false, + "hashed_secret": "a899a8d9e114b2a8e108f90e6a72c056db22489f", "is_verified": false, "line_number": 428, "type": "Base64 High Entropy String" }, { - "hashed_secret": "5b688158be36e8b3f265a462ed599dcf69290084", - "is_secret": false, + "hashed_secret": "756b4825f886afd83c25563ac9d45f318d695c48", "is_verified": false, "line_number": 429, "type": "Base64 High Entropy String" }, { - "hashed_secret": "965996e12c8b50b3c325d96003e8984a4ece658a", - "is_secret": false, + "hashed_secret": "89882eeb0aca97717a7e4afcf4bc08d077813c7f", "is_verified": false, "line_number": 430, "type": "Base64 High Entropy String" }, { - "hashed_secret": "584f0c58e764e948af1a35c9e60447aa0f84c6f5", - "is_secret": false, + "hashed_secret": "347140d7b7ceb4e501c3c9c2ea4f29338e2f145e", "is_verified": false, "line_number": 431, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bcaf897786d060a675ee9d654a84ae8baf96e9d0", - "is_secret": false, + "hashed_secret": "61dbf70eb10d609e60c7b87faf8f755ff48abc46", "is_verified": false, "line_number": 432, "type": "Base64 High Entropy String" }, { - "hashed_secret": "0c09277fa183e06d32065f9386a3b4190b445df3", - "is_secret": false, + "hashed_secret": "24cd54c4b2f58378bba008cb2df68ac663fba7c8", "is_verified": false, "line_number": 433, "type": "Base64 High Entropy String" }, { - "hashed_secret": "5a51be06b305d6664e4afd25f21869b0f8b5039b", - "is_secret": false, + "hashed_secret": "fa4f9626ae4b98f4b61203c5bafb6f21c9c31e5d", "is_verified": false, "line_number": 434, "type": "Base64 High Entropy String" }, { - "hashed_secret": "b38404f8853d734e3d03577b2c1084b4540c8708", - "is_secret": false, + "hashed_secret": "b1370003d9cc1e346c83dba33e0418c7775a0c15", "is_verified": false, "line_number": 435, "type": "Base64 High Entropy String" }, { - "hashed_secret": "126ccc602cffcb8292beb57137f7f6719e317b72", - "is_secret": false, + "hashed_secret": "c66526e195e423a7ba7d68ac661cdcd8600dcd1f", "is_verified": false, "line_number": 436, "type": "Base64 High Entropy String" }, { - "hashed_secret": "6681c1d7e1d327642a32cb8864ad51e4b8f981e5", - "is_secret": false, + "hashed_secret": "d29d7044f0944eb30e02cf445f6998e3343dd811", "is_verified": false, "line_number": 437, "type": "Base64 High Entropy String" }, { - "hashed_secret": "7f7b1f316ece195e5f584fe2faf6f9edc6942c6f", - "is_secret": false, + "hashed_secret": "80a869460f33722387d8d58e7d9d2e1bbd5d1fe1", + "is_verified": false, + "line_number": 438, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "4a06e2a02cbc665adccb4162dc57836895da65b8", "is_verified": false, "line_number": 439, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bb908c7bc655057f2edc42815c5dff82e9dea529", - "is_secret": false, + "hashed_secret": "ba2549f35835dfa101d3f660f7604dc78e3e226f", "is_verified": false, "line_number": 440, "type": "Base64 High Entropy String" }, { - "hashed_secret": "bc2a0d18e3dd142df7b34e95342d47bf8aadabcb", - "is_secret": false, + "hashed_secret": "f354d4ee5fdb94ad29c7b3600264467f45b80eaa", "is_verified": false, "line_number": 441, "type": "Base64 High Entropy String" }, { - "hashed_secret": "d60f0bcea109bb6edb6e45fd387f5f2c86e49e1a", - "is_secret": false, + "hashed_secret": "bf17b587868ba7c3db9865b114261b5b8f1df870", "is_verified": false, "line_number": 442, "type": "Base64 High Entropy String" }, { - "hashed_secret": "e549dd40a741557cc1c4e377df0a141354e22688", - "is_secret": false, + "hashed_secret": "de1fd7a0d32cba528b4d80818c6601f2588d5383", "is_verified": false, "line_number": 443, "type": "Base64 High Entropy String" }, { - "hashed_secret": "2dd2486dae84cad50387c20bf687b6fbc6162b58", - "is_secret": false, + "hashed_secret": "bcad65055f6de654541db2bf27d4e27bd54d94c7", "is_verified": false, "line_number": 444, "type": "Base64 High Entropy String" }, { - "hashed_secret": "71622010fc7eb09d9273f59c548bde6a5da5dc0e", - "is_secret": false, + "hashed_secret": "f2e16f2dd532f65f79341342fdf57a093fc408d8", "is_verified": false, "line_number": 445, "type": "Base64 High Entropy String" }, { - "hashed_secret": "6f0115cf53bd49ec990c562ac6cbfc452c83cd46", - "is_secret": false, + "hashed_secret": "bb036a679a7d2df9fd2ca57068a446bf7f7dd106", "is_verified": false, "line_number": 446, "type": "Base64 High Entropy String" }, { - "hashed_secret": "70dddd534b2f9bb70871fefe0845b79c3b69363f", - "is_secret": false, + "hashed_secret": "5aa6568b1e8185578a6e964f5c322783ad349554", + "is_verified": false, + "line_number": 447, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "4d14835ff0b0bf5aad480296cb705c74ac65f413", "is_verified": false, "line_number": 448, "type": "Base64 High Entropy String" }, { - "hashed_secret": "acf3536b0416aa99608b0be17e87655370ece829", - "is_secret": false, + "hashed_secret": "3f23f77dcf454ad73c4d61c44fd9aa584ef946c1", "is_verified": false, - "line_number": 449, + "line_number": 451, "type": "Base64 High Entropy String" }, { - "hashed_secret": "1d13ee35c7279c1fae1c6474ed47611994273e41", - "is_secret": false, + "hashed_secret": "1739fe5e5dfcf851b64f8b7b11538f1de29ce0b5", "is_verified": false, - "line_number": 450, + "line_number": 452, "type": "Base64 High Entropy String" }, { - "hashed_secret": "d38cf89b25bd7378cdb4e00b4b59293001dd500b", - "is_secret": false, + "hashed_secret": "8129db302110714fc735e3494bd82a65690e0963", "is_verified": false, - "line_number": 451, + "line_number": 453, "type": "Base64 High Entropy String" }, { - "hashed_secret": "1648f34ce2f1b563a8ed1c6d5d55b5e76a395903", - "is_secret": false, + "hashed_secret": "b48bfc62091164086a703115a0e68bdb09212591", "is_verified": false, - "line_number": 452, + "line_number": 454, "type": "Base64 High Entropy String" }, { - "hashed_secret": "9bf63f6f49fb01ff80959bc5a60c8688df92cc02", - "is_secret": false, + "hashed_secret": "a10284feaf27f84081073a3267e3dce24ca7b911", "is_verified": false, - "line_number": 453, + "line_number": 455, + "type": "Base64 High Entropy String" + }, + { + "hashed_secret": "3fd80f31de4be8dde9d2b421e832c7d4043fd49a", + "is_verified": false, + "line_number": 456, "type": "Base64 High Entropy String" } ], "kube/services/jobs/indexd-authz-job.yaml": [ { "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", - "is_secret": false, "is_verified": false, "line_number": 87, "type": "Basic Auth Credentials" @@ -1191,14 +1091,12 @@ "kube/services/monitoring/grafana-values.yaml": [ { "hashed_secret": "2ae868079d293e0a185c671c7bcdac51df36e385", - "is_secret": false, "is_verified": false, "line_number": 162, "type": "Secret Keyword" }, { "hashed_secret": "7a64ff8446b06d38dc271019994f13823a2cbcf4", - "is_secret": false, "is_verified": false, "line_number": 166, "type": "Secret Keyword" @@ -1207,7 +1105,6 @@ "kube/services/revproxy/helpers.js": [ { "hashed_secret": "1d278d3c888d1a2fa7eed622bfc02927ce4049af", - "is_secret": false, "is_verified": false, "line_number": 10, "type": "Base64 High Entropy String" @@ -1216,7 +1113,6 @@ "kube/services/revproxy/helpersTest.js": [ { "hashed_secret": "e029d4904cc728879d70030572bf37d4510367cb", - "is_secret": false, "is_verified": false, "line_number": 22, "type": "JSON Web Token" @@ -1225,7 +1121,6 @@ "kube/services/superset/superset-deploy.yaml": [ { "hashed_secret": "96e4aceb7cf284be363aa248a32a7cc89785a9f7", - "is_secret": false, "is_verified": false, "line_number": 38, "type": "Secret Keyword" @@ -1234,14 +1129,12 @@ "kube/services/superset/superset-redis.yaml": [ { "hashed_secret": "4af3596275edcb7cd5cc6c3c38bc10479902a08f", - "is_secret": false, "is_verified": false, "line_number": 165, "type": "Secret Keyword" }, { "hashed_secret": "9fe1c31809da38c55b2b64bfab47b92bc5f6b7b9", - "is_secret": false, "is_verified": false, "line_number": 265, "type": "Secret Keyword" @@ -1250,35 +1143,30 @@ "kube/services/superset/values.yaml": [ { "hashed_secret": "6f803b24314c39062efe38d0c1da8c472f47eab3", - "is_secret": false, "is_verified": false, "line_number": 54, "type": "Secret Keyword" }, { "hashed_secret": "6eae3a5b062c6d0d79f070c26e6d62486b40cb46", - "is_secret": false, "is_verified": false, "line_number": 86, "type": "Secret Keyword" }, { "hashed_secret": "3eb416223e9e69e6bb8ee19793911ad1ad2027d8", - "is_secret": false, "is_verified": false, "line_number": 212, "type": "Secret Keyword" }, { "hashed_secret": "ff55435345834a3fe224936776c2aa15f6ed5358", - "is_secret": false, "is_verified": false, "line_number": 396, "type": "Secret Keyword" }, { "hashed_secret": "98a84a63e5633d17e3b27b69695f87aa7189e9dc", - "is_secret": false, "is_verified": false, "line_number": 503, "type": "Secret Keyword" @@ -1287,280 +1175,240 @@ "package-lock.json": [ { "hashed_secret": "0656ad0df3af4633dc369f13d5e8806973c5fd9d", - "is_secret": false, "is_verified": false, "line_number": 1481, "type": "Base64 High Entropy String" }, { "hashed_secret": "00091d875d922437c5fc9e6067a08e78c2482e87", - "is_secret": false, "is_verified": false, "line_number": 1489, "type": "Base64 High Entropy String" }, { "hashed_secret": "c4e5cc37e115bf7d86e76e3d799705bf691e4d00", - "is_secret": false, "is_verified": false, "line_number": 1521, "type": "Base64 High Entropy String" }, { "hashed_secret": "0512e37fbedf1d16828680a038a241b4780a5c04", - "is_secret": false, "is_verified": false, "line_number": 1547, "type": "Base64 High Entropy String" }, { "hashed_secret": "01868fd50edbfe6eb91e5b01209b543adc6857af", - "is_secret": false, "is_verified": false, "line_number": 1611, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6f48bf1e398deffc7fd31da17c3506b46c97a93", - "is_secret": false, "is_verified": false, "line_number": 1640, "type": "Base64 High Entropy String" }, { "hashed_secret": "85ce358dbdec0996cf3ccd2bf1c6602af68c181e", - "is_secret": false, "is_verified": false, "line_number": 1648, "type": "Base64 High Entropy String" }, { "hashed_secret": "6f9bfb49cb818d2fe07592515e4c3f7a0bbd7e0e", - "is_secret": false, "is_verified": false, "line_number": 1664, "type": "Base64 High Entropy String" }, { "hashed_secret": "7098a3e6d6d2ec0a40f04fe12509c5c6f4c49c0e", - "is_secret": false, "is_verified": false, "line_number": 1683, "type": "Base64 High Entropy String" }, { "hashed_secret": "1664ad175bba1795a7ecad572bae7e0740b94f56", - "is_secret": false, "is_verified": false, "line_number": 1733, "type": "Base64 High Entropy String" }, { "hashed_secret": "1ec4ce2eb945ce2f816dcb6ebdd1e10247f439a3", - "is_secret": false, "is_verified": false, "line_number": 1742, "type": "Base64 High Entropy String" }, { "hashed_secret": "a7af5768a6d936e36f28e1030d7f894d7aaf555e", - "is_secret": false, "is_verified": false, "line_number": 1755, "type": "Base64 High Entropy String" }, { "hashed_secret": "6fbc7dd864586173160874f2a86ca7d2d552cb85", - "is_secret": false, "is_verified": false, "line_number": 1769, "type": "Base64 High Entropy String" }, { "hashed_secret": "81a961f2c89c6209328b74a8768e30fd76c3ac72", - "is_secret": false, "is_verified": false, "line_number": 1855, "type": "Base64 High Entropy String" }, { "hashed_secret": "797d4751c536c421cb82b9f62e0a804af30d78f5", - "is_secret": false, "is_verified": false, "line_number": 1889, "type": "Base64 High Entropy String" }, { "hashed_secret": "0d55babfa89f240142c0adfc7b560500a1d3ae7c", - "is_secret": false, "is_verified": false, "line_number": 1894, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9fdc3025cd10bd8aa4508611e6b7b7a9d650a2c", - "is_secret": false, "is_verified": false, "line_number": 1921, "type": "Base64 High Entropy String" }, { "hashed_secret": "4cf9419259c0ce8eee84b468af3c72db8b001620", - "is_secret": false, "is_verified": false, "line_number": 1950, "type": "Base64 High Entropy String" }, { "hashed_secret": "24816e3eb4308e247bde7c1d09ffb7b79c519b71", - "is_secret": false, "is_verified": false, "line_number": 1983, "type": "Base64 High Entropy String" }, { "hashed_secret": "e9adfe8a333d45f4776fe0eab31608be5d7b6a7d", - "is_secret": false, "is_verified": false, "line_number": 2004, "type": "Base64 High Entropy String" }, { "hashed_secret": "03d6fb388dd1b185129b14221f7127715822ece6", - "is_secret": false, "is_verified": false, "line_number": 2013, "type": "Base64 High Entropy String" }, { "hashed_secret": "ee161bb3f899720f95cee50a5f9ef9c9ed96278b", - "is_secret": false, "is_verified": false, "line_number": 2046, "type": "Base64 High Entropy String" }, { "hashed_secret": "ebeb5b574fa1ed24a40248275e6136759e766466", - "is_secret": false, "is_verified": false, "line_number": 2078, "type": "Base64 High Entropy String" }, { "hashed_secret": "a6a555a428522ccf439fd516ce7c7e269274363f", - "is_secret": false, "is_verified": false, "line_number": 2083, "type": "Base64 High Entropy String" }, { "hashed_secret": "f7f85d9f7c87f1e576dcaf4cf50f35728f9a3265", - "is_secret": false, "is_verified": false, "line_number": 2111, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f1646b60abe74297d2f37a1eee5dc771ad834fc", - "is_secret": false, "is_verified": false, "line_number": 2138, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd933c71e82d5519ae0cb0779b370d02f6935759", - "is_secret": false, "is_verified": false, "line_number": 2143, "type": "Base64 High Entropy String" }, { "hashed_secret": "7090aa59cb52ad1f1810b08c4ac1ddf5c8fce523", - "is_secret": false, "is_verified": false, "line_number": 2150, "type": "Base64 High Entropy String" }, { "hashed_secret": "756444bea4ea3d67844d8ddf58ad32356e9c2430", - "is_secret": false, "is_verified": false, "line_number": 2188, "type": "Base64 High Entropy String" }, { "hashed_secret": "f74135fdd6b8dafdfb01ebbc61c5e5c24ee27cf8", - "is_secret": false, "is_verified": false, "line_number": 2291, "type": "Base64 High Entropy String" }, { "hashed_secret": "56fbae787f4aed7d0632e95840d71bd378d3a36f", - "is_secret": false, "is_verified": false, "line_number": 2303, "type": "Base64 High Entropy String" }, { "hashed_secret": "81cb6be182eb79444202c4563080aee75296a672", - "is_secret": false, "is_verified": false, "line_number": 2308, "type": "Base64 High Entropy String" }, { "hashed_secret": "f0f3f7bce32184893046ac5f8cc80da56c3ca539", - "is_secret": false, "is_verified": false, "line_number": 2317, "type": "Base64 High Entropy String" }, { "hashed_secret": "097893233346336f4003acfb6eb173ee59e648f0", - "is_secret": false, "is_verified": false, "line_number": 2327, "type": "Base64 High Entropy String" }, { "hashed_secret": "bb14c3b4ef4a9f2e86ffdd44b88d9b6729419671", - "is_secret": false, "is_verified": false, "line_number": 2332, "type": "Base64 High Entropy String" }, { "hashed_secret": "71344a35cff67ef081920095d1406601fb5e9b97", - "is_secret": false, "is_verified": false, "line_number": 2340, "type": "Base64 High Entropy String" }, { "hashed_secret": "eb3db6990fd43477a35dfeffc90b3f1ffa83c7bd", - "is_secret": false, "is_verified": false, "line_number": 2349, "type": "Base64 High Entropy String" }, { "hashed_secret": "266288bdc14807b538d1e48a5891e361fa9b4a14", - "is_secret": false, "is_verified": false, "line_number": 2357, "type": "Base64 High Entropy String" }, { "hashed_secret": "800477261175fd21f23e7321923e1fba6ae55471", - "is_secret": false, "is_verified": false, "line_number": 2369, "type": "Base64 High Entropy String" }, { "hashed_secret": "3f0c251b9c2c21454445a98fde6915ceacde2136", - "is_secret": false, "is_verified": false, "line_number": 2387, "type": "Base64 High Entropy String" @@ -1569,7 +1417,6 @@ "tf_files/aws/cognito/README.md": [ { "hashed_secret": "f6920f370a30262b7dd70e97293c73ec89739b70", - "is_secret": false, "is_verified": false, "line_number": 106, "type": "Secret Keyword" @@ -1578,14 +1425,12 @@ "tf_files/aws/commons/README.md": [ { "hashed_secret": "d02e53411e8cb4cd709778f173f7bc9a3455f8ed", - "is_secret": false, "is_verified": false, "line_number": 60, "type": "Secret Keyword" }, { "hashed_secret": "9dc0da3613af850c5a018b0a88a5626fb8888e4e", - "is_secret": false, "is_verified": false, "line_number": 78, "type": "Secret Keyword" @@ -1594,7 +1439,6 @@ "tf_files/aws/eks/sample.tfvars": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 107, "type": "Hex High Entropy String" @@ -1603,7 +1447,6 @@ "tf_files/aws/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 133, "type": "Hex High Entropy String" @@ -1612,14 +1455,12 @@ "tf_files/aws/modules/common-logging/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", - "is_secret": false, "is_verified": false, "line_number": 57, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", - "is_secret": false, "is_verified": false, "line_number": 59, "type": "Hex High Entropy String" @@ -1628,28 +1469,24 @@ "tf_files/aws/modules/common-logging/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1658,21 +1495,18 @@ "tf_files/aws/modules/common-logging/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" @@ -1681,7 +1515,6 @@ "tf_files/aws/modules/eks/variables.tf": [ { "hashed_secret": "83c1003f406f34fba4d6279a948fee3abc802884", - "is_secret": false, "is_verified": false, "line_number": 113, "type": "Hex High Entropy String" @@ -1690,14 +1523,12 @@ "tf_files/aws/modules/management-logs/README.md": [ { "hashed_secret": "83442aa5a16cb1992731c32367ef464564388017", - "is_secret": false, "is_verified": false, "line_number": 54, "type": "Base64 High Entropy String" }, { "hashed_secret": "fd4a4637ac99de2c1d89155d66d1f3de15d231a2", - "is_secret": false, "is_verified": false, "line_number": 56, "type": "Hex High Entropy String" @@ -1706,28 +1537,24 @@ "tf_files/aws/modules/management-logs/lambda_function.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 18, "type": "Hex High Entropy String" }, { "hashed_secret": "4f9fd96d3926f2c53ab0261d33f1d1a85a6a77ff", - "is_secret": false, "is_verified": false, "line_number": 30, "type": "Hex High Entropy String" @@ -1736,42 +1563,36 @@ "tf_files/aws/modules/management-logs/testLambda.py": [ { "hashed_secret": "061765d6854d72f03a6527610d5b6822c9d516de", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "61df81a188bb4dba6ae6128ff7e2c9c6a6f736ef", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Base64 High Entropy String" }, { "hashed_secret": "a4667450661f32f7ad0f06e2f893a8fee9f18e38", - "is_secret": false, "is_verified": false, "line_number": 5, "type": "Hex High Entropy String" }, { "hashed_secret": "3cf8eb4e9254e1d6cc523da01f8b798b9a83101a", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Base64 High Entropy String" }, { "hashed_secret": "51118900cd675df1b44f254057398f3e52902a5d", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" }, { "hashed_secret": "60a6dfc8d43cd2f5c6292899fc2f94f2d4fc32c4", - "is_secret": false, "is_verified": false, "line_number": 6, "type": "Hex High Entropy String" @@ -1780,7 +1601,6 @@ "tf_files/aws/slurm/README.md": [ { "hashed_secret": "fd85d792fa56981cf6a8d2a5c0857c74af86e99d", - "is_secret": false, "is_verified": false, "line_number": 83, "type": "Secret Keyword" @@ -1789,7 +1609,6 @@ "tf_files/azure/cloud.tf": [ { "hashed_secret": "7c1a4b52b64e4106041971c345a1f3eab58fb2a4", - "is_secret": false, "is_verified": false, "line_number": 424, "type": "Secret Keyword" @@ -1798,7 +1617,6 @@ "tf_files/gcp-bwg/roots/commons_setup/variables/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1807,7 +1625,6 @@ "tf_files/gcp-bwg/roots/templates/answerfile-commons_setup-001.template.tfvars": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 231, "type": "Secret Keyword" @@ -1816,7 +1633,6 @@ "tf_files/gcp-bwg/roots/templates/answerfile-env-tenant.user.tfvars_NO_APP_SETUP": [ { "hashed_secret": "f865b53623b121fd34ee5426c792e5c33af8c227", - "is_secret": false, "is_verified": false, "line_number": 262, "type": "Secret Keyword" @@ -1825,21 +1641,18 @@ "tf_files/gcp/commons/sample.tfvars": [ { "hashed_secret": "9f29ed52bc91ba45b309d5234e95edc7ca5286fd", - "is_secret": false, "is_verified": false, "line_number": 11, "type": "Secret Keyword" }, { "hashed_secret": "8db3b325254b6389ca194d829d2fc923dc0a945d", - "is_secret": false, "is_verified": false, "line_number": 26, "type": "Secret Keyword" }, { "hashed_secret": "253c7b5e7c83a86346fc4501495b130813f08105", - "is_secret": false, "is_verified": false, "line_number": 37, "type": "Secret Keyword" @@ -1848,7 +1661,6 @@ "tf_files/shared/modules/k8s_configs/creds.tpl": [ { "hashed_secret": "1f5e25be9b575e9f5d39c82dfd1d9f4d73f1975c", - "is_secret": false, "is_verified": false, "line_number": 8, "type": "Secret Keyword" diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index 71575e3c56..c54f9d5aa0 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -1,4 +1,5 @@ import argparse +import copy import json import sys import requests @@ -40,6 +41,16 @@ "study_metadata.human_subject_applicability.gender_applicability": "Not applicable" } +# repository links +REPOSITORY_STUDY_ID_LINK_TEMPLATE = { + "NIDDK Central": "https://repository.niddk.nih.gov/studies//", + "NIDA Data Share": "https://datashare.nida.nih.gov/study/", + "NICHD DASH": "https://dash.nichd.nih.gov/study/", + "ICPSR": "https://www.icpsr.umich.edu/web/ICPSR/studies/", + "BioSystics-AP": "https://biosystics-ap.com/assays/assaystudy//", +} + + def is_valid_uuid(uuid_to_test, version=4): """ Check if uuid_to_test is a valid UUID. @@ -114,6 +125,31 @@ def get_client_token(client_id: str, client_secret: str): return token +def get_related_studies(serial_num, hostname): + related_study_result = [] + + if serial_num: + mds = requests.get(f"http://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") + if mds.status_code == 200: + related_study_metadata = mds.json() + + for ( + related_study_metadata_key, + related_study_metadata_value, + ) in related_study_metadata.items(): + title = ( + related_study_metadata_value.get( + "gen3_discovery", {} + ) + .get("study_metadata", {}) + .get("minimal_info", {}) + .get("study_name", "") + ) + link = f"https://{hostname}/portal/discovery/{related_study_metadata_key}/" + related_study_result.append({"title": title, "link": link}) + return related_study_result + + parser = argparse.ArgumentParser() parser.add_argument("--directory", help="CEDAR Directory ID for registering ") @@ -214,6 +250,71 @@ def get_client_token(client_id: str, client_secret: str): mds_res["gen3_discovery"]["study_metadata"].update(cedar_record) mds_res["gen3_discovery"]["study_metadata"]["metadata_location"]["other_study_websites"] = cedar_record_other_study_websites + # setup citations + doi_citation = mds_res["gen3_discovery"]["study_metadata"].get("doi_citation", "") + mds_res["gen3_discovery"]["study_metadata"]["citation"]["heal_platform_citation"] = doi_citation + + + # setup repository_study_link + data_repositories = ( + mds_res + .get("gen3_discovery", {}) + .get("study_metadata", {}) + .get("metadata_location", {}) + .get("data_repositories", []) + ) + repository_citation = "Users must also include a citation to the data as specified by the local repository." + repository_citation_additional_text = ' The link to the study page at the local repository can be found in the "Data" tab.' + for repository in data_repositories: + if ( + repository["repository_name"] + and repository["repository_name"] + in REPOSITORY_STUDY_ID_LINK_TEMPLATE + and repository["repository_study_ID"] + ): + repository_study_link = REPOSITORY_STUDY_ID_LINK_TEMPLATE[ + repository["repository_name"] + ].replace("", repository["repository_study_ID"]) + repository.update({"repository_study_link": repository_study_link}) + if repository_citation_additional_text not in repository_citation: + repository_citation += repository_citation_additional_text + if len(data_repositories): + data_repositories[0] = { + **data_repositories[0], + "repository_citation": repository_citation, + } + + mds_res["gen3_discovery"]["study_metadata"][ + "metadata_location" + ]["data_repositories"] = copy.deepcopy(data_repositories) + + + + # set up related studies + serial_num = None + try: + serial_num = ( + mds_res + .get("nih_reporter", {}) + .get("project_num_split", {}) + .get("serial_num", None) + ) + except Exception: + print(f"Unable to get serial number for study") + + if serial_num == None: + print(f"Unable to get serial number for study") + + related_study_result = get_related_studies(serial_num, hostname) + existing_related_study_result = mds_res.get("related_studies", []) + for related_study in related_study_result: + if related_study not in existing_related_study_result: + existing_related_study_result.append(copy.deepcopy(related_study)) + mds_res["gen3_discovery"][ + "related_studies" + ] = copy.deepcopy(existing_related_study_result) + + # merge data from cedar that is not study level metadata into a level higher deleted_keys = [] for key, value in mds_res["gen3_discovery"]["study_metadata"].items(): From 99fc77ac5ee4a36443a9b802d903e6ffaab6f8c7 Mon Sep 17 00:00:00 2001 From: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Date: Thu, 7 Mar 2024 17:32:40 -0600 Subject: [PATCH 13/21] MIDRC-602 Add ecr-access job (#2480) --- .pre-commit-config.yaml | 2 +- .secrets.baseline | 3792 +++++++++++++---- files/scripts/ecr-access-job-requirements.txt | 1 + files/scripts/ecr-access-job.md | 85 + files/scripts/ecr-access-job.py | 177 + gen3/bin/kube-setup-ecr-access-cronjob.sh | 61 + kube/services/jobs/ecr-access-job.yaml | 85 + 7 files changed, 3339 insertions(+), 864 deletions(-) create mode 100644 files/scripts/ecr-access-job-requirements.txt create mode 100644 files/scripts/ecr-access-job.md create mode 100644 files/scripts/ecr-access-job.py create mode 100644 gen3/bin/kube-setup-ecr-access-cronjob.sh create mode 100644 kube/services/jobs/ecr-access-job.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2e3ce795b6..82034495d3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: git@github.com:Yelp/detect-secrets - rev: v0.13.1 + rev: v1.4.0 hooks: - id: detect-secrets args: ['--baseline', '.secrets.baseline'] diff --git a/.secrets.baseline b/.secrets.baseline index 200b69841f..0c4eba0a80 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,19 +1,18 @@ { - "exclude": { - "files": null, - "lines": null - }, - "generated_at": "2024-03-04T21:42:56Z", + "version": "1.4.0", "plugins_used": [ + { + "name": "ArtifactoryDetector" + }, { "name": "AWSKeyDetector" }, { - "name": "ArtifactoryDetector" + "name": "AzureStorageKeyDetector" }, { - "base64_limit": 4.5, - "name": "Base64HighEntropyString" + "name": "Base64HighEntropyString", + "limit": 4.5 }, { "name": "BasicAuthDetector" @@ -22,8 +21,14 @@ "name": "CloudantDetector" }, { - "hex_limit": 3, - "name": "HexHighEntropyString" + "name": "DiscordBotTokenDetector" + }, + { + "name": "GitHubTokenDetector" + }, + { + "name": "HexHighEntropyString", + "limit": 3.0 }, { "name": "IbmCloudIamDetector" @@ -35,21 +40,30 @@ "name": "JwtTokenDetector" }, { - "keyword_exclude": null, - "name": "KeywordDetector" + "name": "KeywordDetector", + "keyword_exclude": "" }, { "name": "MailchimpDetector" }, + { + "name": "NpmDetector" + }, { "name": "PrivateKeyDetector" }, + { + "name": "SendGridDetector" + }, { "name": "SlackDetector" }, { "name": "SoftlayerDetector" }, + { + "name": "SquareOAuthDetector" + }, { "name": "StripeDetector" }, @@ -57,1619 +71,3671 @@ "name": "TwilioKeyDetector" } ], + "filters_used": [ + { + "path": "detect_secrets.filters.allowlist.is_line_allowlisted" + }, + { + "path": "detect_secrets.filters.common.is_baseline_file", + "filename": ".secrets.baseline" + }, + { + "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", + "min_level": 2 + }, + { + "path": "detect_secrets.filters.heuristic.is_indirect_reference" + }, + { + "path": "detect_secrets.filters.heuristic.is_likely_id_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_lock_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_potential_uuid" + }, + { + "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign" + }, + { + "path": "detect_secrets.filters.heuristic.is_sequential_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_swagger_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_templated_secret" + } + ], "results": { "Chef/repo/data_bags/README.md": [ { - "hashed_secret": "8a9250639e092d90f164792e35073a9395bff366", - "is_verified": false, - "line_number": 45, - "type": "Secret Keyword" - }, - { + "type": "Secret Keyword", + "filename": "Chef/repo/data_bags/README.md", "hashed_secret": "6367c48dd193d56ea7b0baad25b19455e529f5ee", "is_verified": false, - "line_number": 51, - "type": "Secret Keyword" + "line_number": 38 } ], - "Docker/jenkins/Jenkins-CI-Worker/Dockerfile": [ + "Docker/sidecar/service.key": [ { - "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "type": "Private Key", + "filename": "Docker/sidecar/service.key", + "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", "is_verified": false, - "line_number": 124, - "type": "Secret Keyword" + "line_number": 1 } ], - "Docker/jenkins/Jenkins-Worker/Dockerfile": [ + "Jenkins/Stacks/Jenkins/jenkins.env.sample": [ { - "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "type": "Secret Keyword", + "filename": "Jenkins/Stacks/Jenkins/jenkins.env.sample", + "hashed_secret": "f41a52528dd2d592d2c05de5f388101c2948aa98", "is_verified": false, - "line_number": 139, - "type": "Secret Keyword" + "line_number": 5 } ], - "Docker/jenkins/Jenkins/Dockerfile": [ + "Jenkinsfile": [ { - "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "type": "Secret Keyword", + "filename": "Jenkinsfile", + "hashed_secret": "c937b6fbb346a51ef679dd02ac5c4863e02bfdbf", "is_verified": false, - "line_number": 107, - "type": "Secret Keyword" - } - ], - "Docker/jenkins/Jenkins2/Dockerfile": [ + "line_number": 144 + }, { - "hashed_secret": "10daf3a26c6a17242a5ab2438a12ebc8276c7603", + "type": "Secret Keyword", + "filename": "Jenkinsfile", + "hashed_secret": "9ce05cf6168d15dfe02aac9ca9e0712c19c9436d", "is_verified": false, - "line_number": 108, - "type": "Secret Keyword" + "line_number": 147 } ], - "Docker/sidecar/service.key": [ + "ansible/roles/slurm/README.md": [ { - "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", + "type": "Base64 High Entropy String", + "filename": "ansible/roles/slurm/README.md", + "hashed_secret": "4acfde1ff9c353ba2ef0dbe0df73bda2743cba42", "is_verified": false, - "line_number": 1, - "type": "Private Key" + "line_number": 86 } ], - "Jenkins/Stacks/Jenkins/jenkins.env.sample": [ + "apis_configs/fence_settings.py": [ { - "hashed_secret": "eecee33686ac5861c2a7edc8b46bd0e5432bfddd", + "type": "Basic Auth Credentials", + "filename": "apis_configs/fence_settings.py", + "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 5, - "type": "Secret Keyword" + "line_number": 80 } ], - "ansible/roles/awslogs/defaults/main.yaml": [ + "apis_configs/peregrine_settings.py": [ { - "hashed_secret": "9d4e1e23bd5b727046a9e3b4b7db57bd8d6ee684", + "type": "Basic Auth Credentials", + "filename": "apis_configs/peregrine_settings.py", + "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 30, - "type": "Basic Auth Credentials" + "line_number": 46 } ], - "ansible/roles/slurm/README.md": [ - { - "hashed_secret": "4acfde1ff9c353ba2ef0dbe0df73bda2743cba42", - "is_verified": false, - "line_number": 86, - "type": "Base64 High Entropy String" - }, + "apis_configs/sheepdog_settings.py": [ { - "hashed_secret": "579649582303921502d9e6d3f8755f13fdd2b476", + "type": "Basic Auth Credentials", + "filename": "apis_configs/sheepdog_settings.py", + "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 86, - "type": "Secret Keyword" + "line_number": 46 } ], - "apis_configs/config_helper.py": [ + "aws-inspec/kubernetes/chef_inspec-cron.yaml": [ { - "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f", + "type": "Secret Keyword", + "filename": "aws-inspec/kubernetes/chef_inspec-cron.yaml", + "hashed_secret": "a3ba27250861948a554629a0e21168821ddfa9f1", "is_verified": false, - "line_number": 66, - "type": "Basic 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kube-setup-ecr-access-cronjob` to set up the ECR access cronjob. + +### What does it do? + +The job runs the `ecr-access-job.py` script. + +This script updates the configuration of ECR repositories so that users can access the repositories that were created for them. + +It queries a DynamoDB table which has the following (simplified) structure: +| user_id | workspace_type | account_id | +| ------------------ | -------------------- | ---------- | +| user1@username.com | Direct Pay | 123456 | +| user2@username.com | Direct Pay | 789012 | +| user1@username.com | Other workspace type | | + +and then allows each AWS account to acccess the appropriate ECR repositories. The users' ECR repositories are based on their username as stored in the table. For example, `user1@username.com`'s ECR repository is assumed to be `nextflow-approved/user1-40username-2ecom`. + +### Access needed + +- "EcrRepoPolicyUpdateRole" role in the account (Acct1) that contains the ECR repositories: + +**Note:** `kube-setup-ecr-access-cronjob.sh` assumes this role already exists. + +Permissions: +``` +{ + "Version": "2012-10-17", + "Statement": [ + { + "Sid": "UpdateEcrRepoPolicy", + "Effect": "Allow", + "Action": "ecr:SetRepositoryPolicy", + "Resource": "arn:aws:ecr:us-east-1::repository/nextflow-approved/*" + } + ] +} +``` + +Trust policy (allows Acct2): +``` +{ + "Version": "2012-10-17", + "Statement": [ + { + "Sid": "AllowAssumingRole", + "Effect": "Allow", + "Principal": { + "AWS": "arn:aws:iam:::root" + }, + "Action": "sts:AssumeRole" + } + ] +} +``` + +- Policy in the account (Acct2) that contains the DynamoDB table (created automatically by `kube-setup-ecr-access-job.sh`): +``` +{ + "Version": "2012-10-17", + "Statement": [ + { + "Sid": "ReadDynamoDB", + "Effect": "Allow", + "Action": [ + "dynamodb:Scan" + ], + "Resource": "arn:aws:dynamodb:::table/" + }, + { + "Sid": "AssumeEcrRole", + "Effect": "Allow", + "Action": [ + "sts:AssumeRole" + ], + "Resource": "arn:aws:iam:::role/" + } + ] +} +``` diff --git a/files/scripts/ecr-access-job.py b/files/scripts/ecr-access-job.py new file mode 100644 index 0000000000..828d94c96b --- /dev/null +++ b/files/scripts/ecr-access-job.py @@ -0,0 +1,177 @@ +""" +See documentation at https://github.com/uc-cdis/cloud-automation/blob/master/files/scripts/ecr-access-job.md +""" + +from decimal import Decimal +import json +import os +from typing import List +import uuid + +import boto3 +from boto3.dynamodb.conditions import Attr + + +REGION = "us-east-1" + +# for local testing. in production, use a service account instead of a key. +MAIN_ACCOUNT_CREDS = {"key_id": os.environ.get("KEY_ID"), "key_secret": os.environ.get("KEY_SECRET")} + + +def escapism(string: str) -> str: + """ + This is a direct translation of Hatchery's `escapism` golang function to python. + We need to escape the username in the same way it's escaped by Hatchery's `escapism` function because + special chars cannot be used in an ECR repo name, and so that the ECR repo generated here matches the + name expected by Hatchery. + """ + safeBytes = "abcdefghijklmnopqrstuvwxyz0123456789" + escaped = "" + for v in string: + if v not in safeBytes: + hexCode = "{0:02x}".format(ord(v)) + escaped += "-" + hexCode + else: + escaped += v + return escaped + + +def get_configs() -> (str, str): + table_name = os.environ.get("PAY_MODELS_DYNAMODB_TABLE") + if not table_name: + raise Exception("Missing 'PAY_MODELS_DYNAMODB_TABLE' environment variable") + + ecr_role_arn = os.environ.get("ECR_ACCESS_JOB_ARN") + if not ecr_role_arn: + raise Exception("Missing 'ECR_ACCESS_JOB_ARN' environment variable") + + return table_name, ecr_role_arn + + +def query_usernames_and_account_ids(table_name: str) -> List[dict]: + """ + Returns: + List[dict]: [ { "user_id": "user1@username.com", "account_id": "123456" } ] + """ + if MAIN_ACCOUNT_CREDS["key_id"]: + session = boto3.Session( + aws_access_key_id=MAIN_ACCOUNT_CREDS["key_id"], + aws_secret_access_key=MAIN_ACCOUNT_CREDS["key_secret"], + ) + else: + session = boto3.Session() + dynamodb = session.resource("dynamodb", region_name=REGION) + table = dynamodb.Table(table_name) + + # get usernames and AWS account IDs from DynamoDB + queried_keys = ["user_id", "account_id"] + filter_expr = Attr("workspace_type").eq("Direct Pay") + proj = ", ".join("#" + key for key in queried_keys) + expr = {"#" + key: key for key in queried_keys} + response = table.scan( + FilterExpression=filter_expr, + ProjectionExpression=proj, + ExpressionAttributeNames=expr, + ) + assert response.get("ResponseMetadata", {}).get("HTTPStatusCode") == 200, response + items = response["Items"] + # if the response is paginated, get the rest of the items + while response["Count"] > 0: + if "LastEvaluatedKey" not in response: + break + response = table.scan( + FilterExpression=filter_expr, + ProjectionExpression=proj, + ExpressionAttributeNames=expr, + ExclusiveStartKey=response["LastEvaluatedKey"], + ) + assert ( + response.get("ResponseMetadata", {}).get("HTTPStatusCode") == 200 + ), response + items.extend(response["Items"]) + + return items + + +def update_access_in_ecr(repo_to_account_ids: List[dict], ecr_role_arn: str) -> None: + # get access to ECR in the account that contains the ECR repos + if MAIN_ACCOUNT_CREDS["key_id"]: + sts = boto3.client( + "sts", + aws_access_key_id=MAIN_ACCOUNT_CREDS["key_id"], + aws_secret_access_key=MAIN_ACCOUNT_CREDS["key_secret"], + ) + else: + sts = boto3.client("sts") + assumed_role = sts.assume_role( + RoleArn=ecr_role_arn, + DurationSeconds=900, # minimum time for aws assume role as per boto docs + RoleSessionName=f"ecr-access-assume-role-{str(uuid.uuid4())[:8]}", + ) + assert "Credentials" in assumed_role, "Unable to assume role" + ecr = boto3.client( + "ecr", + aws_access_key_id=assumed_role["Credentials"]["AccessKeyId"], + aws_secret_access_key=assumed_role["Credentials"]["SecretAccessKey"], + aws_session_token=assumed_role["Credentials"]["SessionToken"], + ) + + # for each ECR repo, whitelist the account IDs so users can access the repo + for repo, account_ids in repo_to_account_ids.items(): + print(f"Allowing AWS accounts {account_ids} to use ECR repository '{repo}'") + policy = { + "Version": "2008-10-17", + "Statement": [ + { + "Sid": "AllowCrossAccountPull", + "Effect": "Allow", + "Principal": { + "AWS": [ + f"arn:aws:iam::{account_id}:root" + for account_id in account_ids + ] + }, + "Action": [ + "ecr:BatchCheckLayerAvailability", + "ecr:BatchGetImage", + "ecr:GetAuthorizationToken", + "ecr:GetDownloadUrlForLayer", + ], + } + ], + } + # Note that this is overwriting the repo policy, not appending to it. This means we can't have 2 dynamodb + # tables pointing at the same set of ECR repos: the repos would only allow the accounts in the table for + # which the script was run most recently. eg QA and Staging can't use the same ECR repos. + # Appending is not possible since this code will eventually rely on Arborist for authorization information + # and we'll need to overwrite in order to remove expired access. + try: + ecr.set_repository_policy( + repositoryName=repo, + policyText=json.dumps(policy), + ) + except Exception as e: + print(f" Unable to update '{repo}'; skipping it: {e}") + + +def main() -> None: + table_name, ecr_role_arn = get_configs() + items = query_usernames_and_account_ids(table_name) + + # construct mapping: { ECR repo url: [ AWS account IDs with access ] } + ecr_repo_prefix = "nextflow-approved" + repo_to_account_ids = { + f"{ecr_repo_prefix}/{escapism(e['user_id'])}": [e["account_id"]] + for e in items + if "account_id" in e + } + print( + "Mapping of ECR repository to allowed AWS accounts:\n", + json.dumps(repo_to_account_ids, indent=2), + ) + + update_access_in_ecr(repo_to_account_ids, ecr_role_arn) + + +if __name__ == "__main__": + main() diff --git a/gen3/bin/kube-setup-ecr-access-cronjob.sh b/gen3/bin/kube-setup-ecr-access-cronjob.sh new file mode 100644 index 0000000000..d23afc862c --- /dev/null +++ b/gen3/bin/kube-setup-ecr-access-cronjob.sh @@ -0,0 +1,61 @@ +#!/bin/bash + +source "${GEN3_HOME}/gen3/lib/utils.sh" +gen3_load "gen3/lib/kube-setup-init" + +setup_ecr_access_job() { + if g3kubectl get configmap manifest-global > /dev/null; then + ecrRoleArn=$(g3kubectl get configmap manifest-global -o jsonpath={.data.ecr-access-job-role-arn}) + fi + if [ -z "$ecrRoleArn" ]; then + gen3_log_err "Missing 'global.ecr-access-job-role-arn' configuration in manifest.json" + return 1 + fi + + local saName="ecr-access-job-sa" + if ! g3kubectl get sa "$saName" > /dev/null 2>&1; then + tempFile="ecr-access-job-policy.json" + cat - > $tempFile < Date: Fri, 8 Mar 2024 16:28:46 -0600 Subject: [PATCH 14/21] Add new middleware url (#2497) * add new middleware url * feat(argo-wrapper): newline --------- Co-authored-by: Andrew Prokhorenkov --- kube/services/argo-wrapper/config.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/kube/services/argo-wrapper/config.ini b/kube/services/argo-wrapper/config.ini index 40ac392fd5..0693ee2e29 100644 --- a/kube/services/argo-wrapper/config.ini +++ b/kube/services/argo-wrapper/config.ini @@ -3,3 +3,4 @@ ARGO_ACCESS_METHOD = access ARGO_HOST = $ARGO_HOST ARGO_NAMESPACE = $ARGO_NAMESPACE COHORT_DEFINITION_BY_SOURCE_AND_TEAM_PROJECT_URL = http://cohort-middleware-service/cohortdefinition-stats/by-source-id/{}/by-team-project?team-project={} +COHORT_MIDDLEWARE_URL = http://cohort-middleware-service From f84581c1fd8899d7cbb09d48464bb6a9a6ceaa47 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Mon, 11 Mar 2024 09:35:52 -0600 Subject: [PATCH 15/21] Update gen3-helpers to fix failing tests (#2443) * updating the awsrole script to better handle variables and flag * adding "migrate to vpc cni" script to cloud-auto * removing script- wrong branch * updating kube-setup-argo script for IRSA * changing the script to get the 3 private ip to account for fargate instances and fix the "ec2 test filter" test * changing -S to -e to verify if docker is the container runtime due to the way that Jenkins pods are setup * testing mount change * testing another mount change * reverting change * mounting containerd instead * modifying jenkins shell commands * reverting ecr change * reverting jenkisfile change and then changing permissions on containerd.sock instead of docker.sock * adding more jobs to the "excludeJob" list * commenting out jupyter metric test as we currently don't use prometheus in most environments * commented out the wrong line in the wrong script * removing terraform test as we are now using Atlantis and Terragrunt to manage our infastructure and will no longer use the "workon" command * fixing snapshot script to grab init containers and all the main containers seperately * updating to use "pip3" instead of /usr/bin/pip3" * changing the evicted pod cleanup to produce no output so the healthcheck will pass in Jenkins. also, adding in the proper path for pip in the pytest stage of the pipeline * trying another method to get rid of the json error when running the gen3 healthcheck test * Update healthcheck.sh moving clear_evicted_pods function call to run inside the healthcheck function --- Jenkinsfile | 12 +- gen3/bin/awsrole.sh | 48 ++-- gen3/bin/healthcheck.sh | 6 +- gen3/bin/kube-setup-argo.sh | 2 +- gen3/lib/logs/snapshot.sh | 2 +- gen3/test/ec2Test.sh | 2 +- gen3/test/ecrTest.sh | 4 +- gen3/test/jobTest.sh | 2 +- gen3/test/jupyterTest.sh | 2 +- gen3/test/terraformTest.sh | 461 ------------------------------------ 10 files changed, 39 insertions(+), 502 deletions(-) delete mode 100644 gen3/test/terraformTest.sh diff --git a/Jenkinsfile b/Jenkinsfile index 9c70a2e378..908c2d01a5 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -134,8 +134,8 @@ spec: readOnly: true mountPath: "/usr/local/share/ca-certificates/cdis/cdis-ca.crt" subPath: "ca.pem" - - name: dockersock - mountPath: "/var/run/docker.sock" + - name: containerdsock + mountPath: "/var/run/containerd/containerd.sock" serviceAccount: jenkins-service serviceAccountName: jenkins-service volumes: @@ -145,9 +145,9 @@ spec: - name: ca-volume secret: secretName: "service-ca" - - name: dockersock + - name: containerdsock hostPath: - path: /var/run/docker.sock + path: /var/run/containerd/containerd.sock ''' defaultContainer 'shell' } @@ -293,8 +293,8 @@ spec: script { try { if(!skipUnitTests) { - sh '/usr/bin/pip3 install boto3 --upgrade --user' - sh '/usr/bin/pip3 install kubernetes --upgrade --user' + sh '/usr/local/bin/pip3 install boto3 --upgrade --user' + sh '/usr/local/bin/pip3 install kubernetes --upgrade --user' sh 'python3 -m pytest cloud-automation/apis_configs/' sh 'python3 -m pytest cloud-automation/gen3/lib/dcf/' sh 'cd cloud-automation/tf_files/aws/modules/common-logging && python3 -m pytest testLambda.py' diff --git a/gen3/bin/awsrole.sh b/gen3/bin/awsrole.sh index 144b7a4fea..dd19ea7a48 100644 --- a/gen3/bin/awsrole.sh +++ b/gen3/bin/awsrole.sh @@ -25,16 +25,16 @@ gen3_awsrole_help() { function gen3_awsrole_ar_policy() { local serviceAccount="$1" shift || return 1 - if [[ ! -z $1 ]]; then - local namespace=$1 + if [[ -z $1 ]] || [[ $1 == -* ]]; then + namespace=$(gen3 db namespace) else - local namespace=$(gen3 db namespace) + namespace=$1 + shift fi local issuer_url local account_id local vpc_name - shift || return 1 - local flag=$1 + local flag=$flag vpc_name="$(gen3 api environment)" || return 1 issuer_url="$(aws eks describe-cluster \ @@ -46,7 +46,7 @@ function gen3_awsrole_ar_policy() { local provider_arn="arn:aws:iam::${account_id}:oidc-provider/${issuer_url}" - if [[ "$flag" == "all_namespaces" ]]; then + if [[ "$flag" == "-all_namespaces" ]]; then # Use a trust policy that allows role to be used by multiple namespaces. cat - < config.tfvars @@ -230,10 +226,14 @@ gen3_awsrole_create() { gen3_log_err "use: gen3 awsrole create roleName saName" return 1 fi - if [[ ! -z $1 ]]; then - local namespace=$1 + if [[ -z $1 ]] || [[ $1 == -* ]]; then + namespace=$(gen3 db namespace) else - local namespace=$(gen3 db namespace) + namespace=$1 + shift + fi + if [[ ! -z $1 ]]; then + flag=$1 fi # do simple validation of name local regexp="^[a-z][a-z0-9\-]*$" @@ -247,13 +247,7 @@ EOF gen3_log_err $errMsg return 1 fi - shift || return 1 - local flag="" - # Check if the "all_namespaces" flag is provided - if [[ "$1" == "-f" || "$1" == "--flag" ]]; then - flag="$2" - shift 2 - fi + # check if the name is already used by another entity local entity_type @@ -271,9 +265,11 @@ EOF fi TF_IN_AUTOMATION="true" - if ! _tfplan_role $rolename $saName $namespace -f $flag; then + + if ! _tfplan_role $rolename $saName $namespace $flag; then return 1 fi + if ! _tfapply_role $rolename; then return 1 fi @@ -422,4 +418,4 @@ gen3_awsrole() { # Let testsuite source file if [[ -z "$GEN3_SOURCE_ONLY" ]]; then gen3_awsrole "$@" -fi +fi \ No newline at end of file diff --git a/gen3/bin/healthcheck.sh b/gen3/bin/healthcheck.sh index 149cb1aaa9..b658ff033b 100644 --- a/gen3/bin/healthcheck.sh +++ b/gen3/bin/healthcheck.sh @@ -137,6 +137,10 @@ gen3_healthcheck() { internetAccessExplicitProxy=false fi + gen3_log_info "Clearing Evicted pods" + sleep 5 + clear_evicted_pods + local healthJson=$(cat - < ". g3kubectl get pods -o json | \ - jq -r '.items | map(select(.status.phase != "Pending" and .status.phase != "Unknown")) | map( {pod: .metadata.name, containers: [(.spec.containers | select(.!=null) | map(.name)), (.spec.initContainers | select(.!=null) | map(.name)) | add ] } ) | map( .pod as $pod | .containers | map( { pod: $pod, cont: .})[]) | map(select(.cont != "pause" and .cont != "jupyterhub"))[] | .pod + " " + .cont' | \ + jq -r '.items | map(select(.status.phase != "Pending" and .status.phase != "Unknown")) | .[] | .metadata.name as $pod | (.spec.containers + .spec.initContainers) | map(select(.name != "pause" and .name != "jupyterhub")) | .[] | {pod: $pod, cont: .name} | "\(.pod) \(.cont)"' | \ while read -r line; do gen3_logs_snapshot_container $line done diff --git a/gen3/test/ec2Test.sh b/gen3/test/ec2Test.sh index 21310a24ca..4981c925cf 100644 --- a/gen3/test/ec2Test.sh +++ b/gen3/test/ec2Test.sh @@ -1,6 +1,6 @@ -if ! EC2_TEST_IP="$(g3kubectl get nodes -o json | jq -r -e '.items[0].status.addresses[] | select(.type == "InternalIP") | .address')" || [[ -z "$EC2_TEST_IP" ]]; then +if ! EC2_TEST_IP="$(g3kubectl get nodes -o json | jq -r -e '.items[3].status.addresses[] | select(.type == "InternalIP") | .address')" || [[ -z "$EC2_TEST_IP" ]]; then gen3_log_err "ec2Test failed to acquire IP address of a k8s node to test against" fi diff --git a/gen3/test/ecrTest.sh b/gen3/test/ecrTest.sh index 91edf798ba..57847abe5e 100644 --- a/gen3/test/ecrTest.sh +++ b/gen3/test/ecrTest.sh @@ -10,8 +10,8 @@ test_ecr_login() { test_ecr_setup() { if [[ -n "$JENKINS_HOME" ]]; then - # give ourselves read/write permissions on /var/run/docker.sock - sudo chmod a+rw /var/run/docker.sock; because $? "ecr_setup modified docker.sock" + # give ourselves permissions on /run/containerd/containerd.sock + sudo chown root:sudo /run/containerd/containerd.sock; because $? "ecr_setup modified containerd.sock" fi } diff --git a/gen3/test/jobTest.sh b/gen3/test/jobTest.sh index 84a4d046b6..bb37b4f723 100644 --- a/gen3/test/jobTest.sh +++ b/gen3/test/jobTest.sh @@ -6,7 +6,7 @@ excludeJob() { local jobKey="$1" local excludeList=( - /aws-bucket- /bucket- /covid19- /data-ingestion- /google- /nb-etl- /remove-objects-from- /replicate- /s3sync- /fence-cleanup + /aws-bucket- /bucket- /covid19- /data-ingestion- /google- /nb-etl- /remove-objects-from- /replicate- /s3sync- /fence-cleanup /etl- /indexd- /metadata- ) for exclude in "${excludeList[@]}"; do if [[ "$it" =~ $exclude ]]; then return 0; fi diff --git a/gen3/test/jupyterTest.sh b/gen3/test/jupyterTest.sh index f0e327d717..db6a626188 100644 --- a/gen3/test/jupyterTest.sh +++ b/gen3/test/jupyterTest.sh @@ -30,7 +30,7 @@ test_jupyter_metrics() { } shunit_runtest "test_jupyter_idle" "jupyter" -shunit_runtest "test_jupyter_metrics" "jupyter" +# shunit_runtest "test_jupyter_metrics" "jupyter" shunit_runtest "test_jupyter_prepuller" "local,jupyter" shunit_runtest "test_jupyter_namespace" "local,jupyter" shunit_runtest "test_jupyter_setup" "jupyter" diff --git a/gen3/test/terraformTest.sh b/gen3/test/terraformTest.sh deleted file mode 100644 index 17bcc03c2b..0000000000 --- a/gen3/test/terraformTest.sh +++ /dev/null @@ -1,461 +0,0 @@ -GEN3_TEST_PROFILE="${GEN3_TEST_PROFILE:-cdistest}" -GEN3_TEST_WORKSPACE="gen3test" -GEN3_TEST_ACCOUNT=707767160287 - -# -# TODO - generalize these tests to setup their own test VPC, -# rather than relying on qaplanetv1 or devplanetv1 being there -# - -# -# Little macos/linux stat wrapper -# -file_mode() { - if [[ $(uname -s) == 'Linux' ]]; then - stat -c %a "$1" - else - stat -f %p "$1" - fi -} - -test_workspace() { - gen3 workon $GEN3_TEST_PROFILE $GEN3_TEST_WORKSPACE; because $? "Calling gen3 workon multiple times should be harmless" - [[ $GEN3_PROFILE = $GEN3_TEST_PROFILE ]]; because $? "gen3 workon sets the GEN3_PROFILE env variable: $GEN3_PROFILE" - [[ $GEN3_WORKSPACE = $GEN3_TEST_WORKSPACE ]]; because $? "gen3 workon sets the GEN3_WORKSPACE env variable: $GEN3_WORKSPACE" - [[ $GEN3_FLAVOR = "AWS" || \ - ($GEN3_FLAVOR == "GCP" && $GEN3_PROFILE =~ ^gcp-) || \ - ($GEN3_FLAVOR == "ONPREM" && $GEN3_PROFILE =~ ^onprem-) ]]; because $? "GEN3_FLAVOR is gcp for gcp-* profiles, else AWS" - [[ $GEN3_FLAVOR != "AWS" || $GEN3_S3_BUCKET = "cdis-state-ac${GEN3_TEST_ACCOUNT}-gen3" || $GEN3_S3_BUCKET = "cdis-terraform-state.account-${GEN3_TEST_ACCOUNT}.gen3" ]]; because $? "gen3 workon sets the GEN3_S3_BUCKET env variable: $GEN3_S3_BUCKET" - [[ (! -z $GEN3_WORKDIR) && -d $GEN3_WORKDIR ]]; because $? "gen3 workon sets the GEN3_WORKDIR env variable, and initializes the folder: $GEN3_WORKDIR" - [[ $(file_mode $GEN3_WORKDIR) =~ 700$ ]]; because $? "gen3 workon sets the GEN3_WORKDIR to mode 0700, because secrets are in there" - gen3 cd && [[ $(pwd) = "$GEN3_WORKDIR" ]]; because $? "gen3 cd should take us to the workspace by default: $(pwd) =? $GEN3_WORKDIR" - for fileName in README.md config.tfvars backend.tfvars; do - [[ -f $fileName ]]; because $? "gen3 workon ensures we have a $fileName - local copy || s3 copy || generated from template" - done - [[ ! -z "$MD5" ]]; because $? "commons.sh sets MD5 to $MD5" - - if [[ $GEN3_TEST_WORKSPACE =~ __custom$ ]]; then - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_WORKDIR" ]]; because $? "a __custom workspace loads from the workspace folder" - elif [[ "$GEN3_TEST_PROFILE" =~ ^gcp- ]]; then - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_HOME/tf_files/gcp/commons" ]]; because $? "a gcp- profile currently only support a commons workspace" - elif [[ "$GEN3_TEST_PROFILE" =~ ^onprem- ]]; then - for fileName in README.md creds.json 00configmap.yaml kube-setup.sh; do - filePath="onprem_scripts/$fileName" - [[ -f $filePath ]]; because $? "gen3 workon ensures we have a $filePath generated from template" - done - else # aws profile - [[ "$GEN3_TFSCRIPT_FOLDER" =~ ^"$GEN3_HOME/tf_files/aws/" ]]; because $? "an aws workspace references the aws/ folder: $GEN3_TFSCRIPT_FOLDER" - fi -} - -workspace_cleanup() { - # try to avoid accidentally erasing the user's data ... - cd /tmp && [[ -n "$GEN3_WORKDIR" && "$GEN3_WORKDIR" =~ /gen3/ && -f "$GEN3_WORKDIR/config.tfvars" ]] && /bin/rm -rf "$GEN3_WORKDIR"; - because $? "was able to cleanup $GEN3_WORKDIR" -} - -test_uservpc_workspace() { - GEN3_TEST_WORKSPACE="${GEN3_TEST_WORKSPACE}_user" - test_workspace - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_HOME/tf_files/aws/user_vpc" ]]; because $? "a _user workspace should use the ./aws/user_vpc resources: $GEN3_TFSCRIPT_FOLDER" - workspace_cleanup -} - -test_usergeneric_workspace() { - GEN3_TEST_WORKSPACE="${GEN3_TEST_WORKSPACE}_usergeneric" - test_workspace - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_HOME/tf_files/aws/user_generic" ]]; because $? "a _usergeneric workspace should use the ./aws/user_generic resources: $GEN3_TFSCRIPT_FOLDER" - cat << EOF > config.tfvars -username="frickjack" -EOF - gen3 tfplan; because $? "_usergeneric tfplan should work"; - workspace_cleanup -} - -test_snapshot_workspace() { - GEN3_TEST_WORKSPACE="${GEN3_TEST_WORKSPACE}_snapshot" - test_workspace - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_HOME/tf_files/aws/rds_snapshot" ]]; because $? "a _snapshot workspace should use the ./aws/rds_snapshot resources: $GEN3_TFSCRIPT_FOLDER" - workspace_cleanup -} - -test_databucket_workspace() { - GEN3_TEST_WORKSPACE="${GEN3_TEST_WORKSPACE}_databucket" - test_workspace - [[ "$GEN3_TFSCRIPT_FOLDER" == "$GEN3_HOME/tf_files/aws/data_bucket" ]]; because $? "a _databucket workspace should use the ./aws/data_bucket resources: $GEN3_TFSCRIPT_FOLDER" - cat - > config.tfvars < config.tfvars < config.tfvars < @ in password -db_password_fence="whatever" - -db_password_gdcapi="whatever" -db_password_sheepdog="whatever" -db_password_peregrine="whatever" - -db_password_indexd="g6pmYkcoR7qECjGoErzVb5gkX3kum0yo" - -# password for write access to indexd -gdcapi_indexd_password="oYva39mIPV5uXskv7jWnKuVZBUFBQcxd" - -fence_snapshot="" -gdcapi_snapshot="" -indexd_snapshot="" -# mailgun for sending alert e-mails -mailgun_api_key="" -mailgun_api_url="" -mailgun_smtp_host="" - -kube_ssh_key="" -EOM - [[ "$(pwd)" =~ "/$GEN3_WORKSPACE"$ ]]; because $? "commons workspace should have base $GEN3_WORKSPACE - $(pwd)" - gen3 tfplan; because $? "tfplan should run even with some invalid config variables" - [[ -f "$GEN3_WORKDIR/plan.terraform" ]]; because $? "'gen3 tfplan' generates a plan.terraform file used by 'gen3 tfapply'" - workspace_cleanup -} - -test_custom_workspace() { - GEN3_TEST_WORKSPACE="${GEN3_TEST_WORKSPACE}__custom" - test_workspace - - local sourceFolder="../../../../../cloud-automation/tf_files/aws/modules/s3-bucket" - if [[ ! -d "$sourceFolder" ]]; then - # Jenkins has a different relative path setup - sourceFolder="../../../../cloud-automation/tf_files/aws/modules/s3-bucket" - fi - cat - > bucket.tf < config.tfvars < config.tfvars < config.tfvars < config.tfvars < config.tfvars < config.tfvars < config.tfvars < config.tfvars < Date: Tue, 12 Mar 2024 10:05:49 -0500 Subject: [PATCH 16/21] Split build-push workflows (#2499) --- .github/workflows/build_awshelper.yaml | 21 +++++++++++++ .github/workflows/build_python3.10.yaml | 23 ++++++++++++++ .github/workflows/build_python3.9.yaml | 23 ++++++++++++++ .github/workflows/image_build_push.yaml | 42 ------------------------- 4 files changed, 67 insertions(+), 42 deletions(-) create mode 100644 .github/workflows/build_awshelper.yaml create mode 100644 .github/workflows/build_python3.10.yaml create mode 100644 .github/workflows/build_python3.9.yaml delete mode 100644 .github/workflows/image_build_push.yaml diff --git a/.github/workflows/build_awshelper.yaml b/.github/workflows/build_awshelper.yaml new file mode 100644 index 0000000000..f42a136109 --- /dev/null +++ b/.github/workflows/build_awshelper.yaml @@ -0,0 +1,21 @@ +name: Build awshelper image + +on: + push: + paths: + - .github/workflows/build_awshelper.yaml + - Docker/awshelper/** + +jobs: + awshelper: + name: Build and push + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + DOCKERFILE_LOCATION: "./Docker/awshelper/Dockerfile" + OVERRIDE_REPO_NAME: "awshelper" + secrets: + ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} + ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} + QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} + QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} + diff --git a/.github/workflows/build_python3.10.yaml b/.github/workflows/build_python3.10.yaml new file mode 100644 index 0000000000..993da14680 --- /dev/null +++ b/.github/workflows/build_python3.10.yaml @@ -0,0 +1,23 @@ +name: Build Python 3.10 image + +on: + push: + paths: + - .github/workflows/build_python3.10.yaml + - Docker/python-nginx/python3.10-buster/** + +jobs: + python_3-10: + name: Build and push + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.10-buster/Dockerfile" + DOCKERFILE_BUILD_CONTEXT: "./Docker/python-nginx/python3.10-buster" + OVERRIDE_REPO_NAME: "python" + OVERRIDE_TAG_NAME: "python3.10-buster-$(echo ${GITHUB_REF#refs/*/} | tr / _)" + secrets: + ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} + ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} + QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} + QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} + diff --git a/.github/workflows/build_python3.9.yaml b/.github/workflows/build_python3.9.yaml new file mode 100644 index 0000000000..5bc8bc4629 --- /dev/null +++ b/.github/workflows/build_python3.9.yaml @@ -0,0 +1,23 @@ +name: Build Python 3.9 image + +on: + push: + paths: + - .github/workflows/build_python3.9.yaml + - Docker/python-nginx/python3.9-buster/** + +jobs: + python_3-9: + name: Build and push + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.9-buster/Dockerfile" + DOCKERFILE_BUILD_CONTEXT: "./Docker/python-nginx/python3.9-buster" + OVERRIDE_REPO_NAME: "python" + OVERRIDE_TAG_NAME: "python3.9-buster-$(echo ${GITHUB_REF#refs/*/} | tr / _)" + secrets: + ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} + ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} + QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} + QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} + diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml deleted file mode 100644 index d5bfea351d..0000000000 --- a/.github/workflows/image_build_push.yaml +++ /dev/null @@ -1,42 +0,0 @@ -name: Build Python Base Images - -on: push - -jobs: - python_3-9: - name: Python 3.9 - uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master - with: - DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.9-buster/Dockerfile" - DOCKERFILE_BUILD_CONTEXT: "./Docker/python-nginx/python3.9-buster" - OVERRIDE_REPO_NAME: "python" - OVERRIDE_TAG_NAME: "python3.9-buster-$(echo ${GITHUB_REF#refs/*/} | tr / _)" - secrets: - ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} - ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} - QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} - QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} - python_3-10: - name: Python 3.10 - uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master - with: - DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.10-buster/Dockerfile" - DOCKERFILE_BUILD_CONTEXT: "./Docker/python-nginx/python3.10-buster" - OVERRIDE_REPO_NAME: "python" - OVERRIDE_TAG_NAME: "python3.10-buster-$(echo ${GITHUB_REF#refs/*/} | tr / _)" - secrets: - ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} - ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} - QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} - QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} - awshelper: - name: AwsHelper - uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master - with: - DOCKERFILE_LOCATION: "./Docker/awshelper/Dockerfile" - OVERRIDE_REPO_NAME: "awshelper" - secrets: - ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} - ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} - QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} - QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} From b2195b1ae6f9d802d346629d126e9d3ba408eccd Mon Sep 17 00:00:00 2001 From: Pauline <4224001+paulineribeyre@users.noreply.github.com> Date: Tue, 12 Mar 2024 10:07:34 -0500 Subject: [PATCH 17/21] fix wf naming --- .github/workflows/build_awshelper.yaml | 2 +- .github/workflows/build_python3.10.yaml | 2 +- .github/workflows/build_python3.9.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_awshelper.yaml b/.github/workflows/build_awshelper.yaml index f42a136109..3d2da5393e 100644 --- a/.github/workflows/build_awshelper.yaml +++ b/.github/workflows/build_awshelper.yaml @@ -8,7 +8,7 @@ on: jobs: awshelper: - name: Build and push + name: awshelper uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/awshelper/Dockerfile" diff --git a/.github/workflows/build_python3.10.yaml b/.github/workflows/build_python3.10.yaml index 993da14680..80d2d76232 100644 --- a/.github/workflows/build_python3.10.yaml +++ b/.github/workflows/build_python3.10.yaml @@ -8,7 +8,7 @@ on: jobs: python_3-10: - name: Build and push + name: Python 3.10 uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.10-buster/Dockerfile" diff --git a/.github/workflows/build_python3.9.yaml b/.github/workflows/build_python3.9.yaml index 5bc8bc4629..540e0d4eca 100644 --- a/.github/workflows/build_python3.9.yaml +++ b/.github/workflows/build_python3.9.yaml @@ -8,7 +8,7 @@ on: jobs: python_3-9: - name: Build and push + name: Python 3.9 uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./Docker/python-nginx/python3.9-buster/Dockerfile" From b6031e029db84ab0190d2a263c16b418b113482d Mon Sep 17 00:00:00 2001 From: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Date: Tue, 12 Mar 2024 12:03:41 -0500 Subject: [PATCH 18/21] Build awshelper workflow: always build (#2501) --- .github/workflows/build_awshelper.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build_awshelper.yaml b/.github/workflows/build_awshelper.yaml index 3d2da5393e..36b5745dbd 100644 --- a/.github/workflows/build_awshelper.yaml +++ b/.github/workflows/build_awshelper.yaml @@ -1,10 +1,8 @@ name: Build awshelper image -on: - push: - paths: - - .github/workflows/build_awshelper.yaml - - Docker/awshelper/** +# Always build this image because it contains all the cloud-automation files. +# Some jobs depend on arbitrary files and we need to test them with updated awshelper images. +on: push jobs: awshelper: From 24492c2d6868ce49a474617544b575a38697d0af Mon Sep 17 00:00:00 2001 From: Aidan Hilt <11202897+AidanHilt@users.noreply.github.com> Date: Tue, 12 Mar 2024 16:23:59 -0400 Subject: [PATCH 19/21] Adding a gen3 db namespace to the temp files so they don't overlap (#2502) --- gen3/bin/kube-setup-revproxy.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gen3/bin/kube-setup-revproxy.sh b/gen3/bin/kube-setup-revproxy.sh index 5db9850a18..fd30b478b3 100644 --- a/gen3/bin/kube-setup-revproxy.sh +++ b/gen3/bin/kube-setup-revproxy.sh @@ -114,8 +114,8 @@ done if g3k_manifest_lookup .argo.argo_server_service_url 2> /dev/null; then argo_server_service_url=$(g3k_manifest_lookup .argo.argo_server_service_url) - g3k_kv_filter "${scriptDir}/gen3.nginx.conf/argo-server.conf" SERVICE_URL "${argo_server_service_url}" > /tmp/argo-server-with-url.conf - filePath="/tmp/argo-server-with-url.conf" + g3k_kv_filter "${scriptDir}/gen3.nginx.conf/argo-server.conf" SERVICE_URL "${argo_server_service_url}" > /tmp/argo-server-with-url$(gen3 db namespace).conf + filePath="/tmp/argo-server-with-url$(gen3 db namespace).conf" if [[ -f "$filePath" ]]; then confFileList+=("--from-file" "$filePath") fi From e979669cd92cf1ecad69f2bc2837a8fed35e2926 Mon Sep 17 00:00:00 2001 From: Mingfei Shao <2475897+mfshao@users.noreply.github.com> Date: Wed, 13 Mar 2024 12:08:30 -0500 Subject: [PATCH 20/21] HP-1310 feat: updated related studies logic (#2498) * feat: updated related studies logic * update --- .../healdata/heal-cedar-data-ingest.py | 174 +++++++++++------- 1 file changed, 107 insertions(+), 67 deletions(-) diff --git a/files/scripts/healdata/heal-cedar-data-ingest.py b/files/scripts/healdata/heal-cedar-data-ingest.py index c54f9d5aa0..e0c4b3c463 100644 --- a/files/scripts/healdata/heal-cedar-data-ingest.py +++ b/files/scripts/healdata/heal-cedar-data-ingest.py @@ -13,7 +13,7 @@ "study_metadata.study_type.study_subject_type": "Subject Type", "study_metadata.human_subject_applicability.gender_applicability": "Gender", "study_metadata.human_subject_applicability.age_applicability": "Age", - "research_program": "Research Program" + "research_program": "Research Program", } # Defines how to handle special cases for values in filters @@ -33,7 +33,7 @@ "Gender Queer": "Genderqueer/gender nonconforming/neither exclusively male nor female", "Intersex": "Genderqueer/gender nonconforming/neither exclusively male nor female", "Intersexed": "Genderqueer/gender nonconforming/neither exclusively male nor female", - "Buisness Development": "Business Development" + "Buisness Development": "Business Development", } # Defines field that we don't want to include in the filters @@ -54,24 +54,25 @@ def is_valid_uuid(uuid_to_test, version=4): """ Check if uuid_to_test is a valid UUID. - + Parameters ---------- uuid_to_test : str version : {1, 2, 3, 4} - + Returns ------- `True` if uuid_to_test is a valid UUID, otherwise `False`. - + """ - + try: uuid_obj = UUID(uuid_to_test, version=version) except ValueError: return False return str(uuid_obj) == uuid_to_test + def update_filter_metadata(metadata_to_update): filter_metadata = [] for metadata_field_key, filter_field_key in FILTER_FIELD_MAPPINGS.items(): @@ -83,20 +84,21 @@ def update_filter_metadata(metadata_to_update): print(filter_field_values) raise TypeError("Neither a string nor a list") for filter_field_value in filter_field_values: - if (metadata_field_key, filter_field_value) in OMITTED_VALUES_MAPPING.items(): + if ( + metadata_field_key, + filter_field_value, + ) in OMITTED_VALUES_MAPPING.items(): continue if filter_field_value in SPECIAL_VALUE_MAPPINGS: filter_field_value = SPECIAL_VALUE_MAPPINGS[filter_field_value] - filter_metadata.append({"key": filter_field_key, "value": filter_field_value}) + filter_metadata.append( + {"key": filter_field_key, "value": filter_field_value} + ) filter_metadata = pydash.uniq(filter_metadata) metadata_to_update["advSearchFilters"] = filter_metadata # Retain these from existing tags save_tags = ["Data Repository"] - tags = [ - tag - for tag in metadata_to_update["tags"] - if tag["category"] in save_tags - ] + tags = [tag for tag in metadata_to_update["tags"] if tag["category"] in save_tags] # Add any new tags from advSearchFilters for f in metadata_to_update["advSearchFilters"]: if f["key"] == "Gender": @@ -111,25 +113,30 @@ def update_filter_metadata(metadata_to_update): def get_client_token(client_id: str, client_secret: str): try: token_url = f"http://revproxy-service/user/oauth2/token" - headers = {'Content-Type': 'application/x-www-form-urlencoded'} - params = {'grant_type': 'client_credentials'} - data = 'scope=openid user data' + headers = {"Content-Type": "application/x-www-form-urlencoded"} + params = {"grant_type": "client_credentials"} + data = "scope=openid user data" token_result = requests.post( - token_url, params=params, headers=headers, data=data, + token_url, + params=params, + headers=headers, + data=data, auth=(client_id, client_secret), ) - token = token_result.json()["access_token"] + token = token_result.json()["access_token"] except: raise Exception("Could not get token") return token -def get_related_studies(serial_num, hostname): +def get_related_studies(serial_num, guid, hostname): related_study_result = [] if serial_num: - mds = requests.get(f"http://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000") + mds = requests.get( + f"http://revproxy-service/mds/metadata?nih_reporter.project_num_split.serial_num={serial_num}&data=true&limit=2000" + ) if mds.status_code == 200: related_study_metadata = mds.json() @@ -137,15 +144,22 @@ def get_related_studies(serial_num, hostname): related_study_metadata_key, related_study_metadata_value, ) in related_study_metadata.items(): + if related_study_metadata_key == guid or ( + related_study_metadata_value["_guid_type"] != "discovery_metadata" + and related_study_metadata_value["_guid_type"] + != "unregistered_discovery_metadata" + ): + # do nothing for self, or for archived studies + continue title = ( - related_study_metadata_value.get( - "gen3_discovery", {} - ) + related_study_metadata_value.get("gen3_discovery", {}) .get("study_metadata", {}) .get("minimal_info", {}) .get("study_name", "") ) - link = f"https://{hostname}/portal/discovery/{related_study_metadata_key}/" + link = ( + f"https://{hostname}/portal/discovery/{related_study_metadata_key}/" + ) related_study_result.append({"title": title, "link": link}) return related_study_result @@ -180,7 +194,7 @@ def get_related_studies(serial_num, hostname): print("Getting CEDAR client access token") access_token = get_client_token(client_id, client_secret) -token_header = {"Authorization": 'bearer ' + access_token} +token_header = {"Authorization": "bearer " + access_token} limit = 10 offset = 0 @@ -192,16 +206,21 @@ def get_related_studies(serial_num, hostname): print("Directory ID is not in UUID format!") sys.exit(1) -while((limit + offset <= total)): +while limit + offset <= total: # Get the metadata from cedar to register print("Querying CEDAR...") - cedar = requests.get(f"http://revproxy-service/cedar/get-instance-by-directory/{dir_id}?limit={limit}&offset={offset}", headers=token_header) + cedar = requests.get( + f"http://revproxy-service/cedar/get-instance-by-directory/{dir_id}?limit={limit}&offset={offset}", + headers=token_header, + ) # If we get metadata back now register with MDS if cedar.status_code == 200: metadata_return = cedar.json() if "metadata" not in metadata_return: - print("Got 200 from CEDAR wrapper but no metadata in body, something is not right!") + print( + "Got 200 from CEDAR wrapper but no metadata in body, something is not right!" + ) sys.exit(1) total = metadata_return["metadata"]["totalCount"] @@ -209,13 +228,17 @@ def get_related_studies(serial_num, hostname): print(f"Successfully got {returned_records} record(s) from CEDAR directory") for cedar_record in metadata_return["metadata"]["records"]: # get the appl id from cedar for querying in our MDS - cedar_appl_id = pydash.get(cedar_record, "metadata_location.nih_application_id") + cedar_appl_id = pydash.get( + cedar_record, "metadata_location.nih_application_id" + ) if cedar_appl_id is None: print("This record doesn't have appl_id, skipping...") continue # Get the metadata record for the nih_application_id - mds = requests.get(f"http://revproxy-service/mds/metadata?gen3_discovery.study_metadata.metadata_location.nih_application_id={cedar_appl_id}&data=true") + mds = requests.get( + f"http://revproxy-service/mds/metadata?gen3_discovery.study_metadata.metadata_location.nih_application_id={cedar_appl_id}&data=true" + ) if mds.status_code == 200: mds_res = mds.json() @@ -234,9 +257,13 @@ def get_related_studies(serial_num, hostname): if mds_res["_guid_type"] == "discovery_metadata": print("Metadata is already registered. Updating MDS record") elif mds_res["_guid_type"] == "unregistered_discovery_metadata": - print("Metadata has not been registered. Registering it in MDS record") + print( + "Metadata has not been registered. Registering it in MDS record" + ) else: - print(f"This metadata data record has a special GUID type \"{mds_res['_guid_type']}\" and will be skipped") + print( + f"This metadata data record has a special GUID type \"{mds_res['_guid_type']}\" and will be skipped" + ) continue if "clinicaltrials_gov" in cedar_record: @@ -244,21 +271,27 @@ def get_related_studies(serial_num, hostname): del cedar_record["clinicaltrials_gov"] # some special handing for this field, because its parent will be deleted before we merging the CEDAR and MDS SLMD to avoid duplicated values - cedar_record_other_study_websites = cedar_record.get("metadata_location", {}).get("other_study_websites", []) + cedar_record_other_study_websites = cedar_record.get( + "metadata_location", {} + ).get("other_study_websites", []) del cedar_record["metadata_location"] mds_res["gen3_discovery"]["study_metadata"].update(cedar_record) - mds_res["gen3_discovery"]["study_metadata"]["metadata_location"]["other_study_websites"] = cedar_record_other_study_websites + mds_res["gen3_discovery"]["study_metadata"]["metadata_location"][ + "other_study_websites" + ] = cedar_record_other_study_websites # setup citations - doi_citation = mds_res["gen3_discovery"]["study_metadata"].get("doi_citation", "") - mds_res["gen3_discovery"]["study_metadata"]["citation"]["heal_platform_citation"] = doi_citation - + doi_citation = mds_res["gen3_discovery"]["study_metadata"].get( + "doi_citation", "" + ) + mds_res["gen3_discovery"]["study_metadata"]["citation"][ + "heal_platform_citation" + ] = doi_citation # setup repository_study_link data_repositories = ( - mds_res - .get("gen3_discovery", {}) + mds_res.get("gen3_discovery", {}) .get("study_metadata", {}) .get("metadata_location", {}) .get("data_repositories", []) @@ -275,8 +308,13 @@ def get_related_studies(serial_num, hostname): repository_study_link = REPOSITORY_STUDY_ID_LINK_TEMPLATE[ repository["repository_name"] ].replace("", repository["repository_study_ID"]) - repository.update({"repository_study_link": repository_study_link}) - if repository_citation_additional_text not in repository_citation: + repository.update( + {"repository_study_link": repository_study_link} + ) + if ( + repository_citation_additional_text + not in repository_citation + ): repository_citation += repository_citation_additional_text if len(data_repositories): data_repositories[0] = { @@ -284,36 +322,28 @@ def get_related_studies(serial_num, hostname): "repository_citation": repository_citation, } - mds_res["gen3_discovery"]["study_metadata"][ - "metadata_location" - ]["data_repositories"] = copy.deepcopy(data_repositories) - - + mds_res["gen3_discovery"]["study_metadata"]["metadata_location"][ + "data_repositories" + ] = copy.deepcopy(data_repositories) # set up related studies serial_num = None try: serial_num = ( - mds_res - .get("nih_reporter", {}) + mds_res.get("nih_reporter", {}) .get("project_num_split", {}) .get("serial_num", None) ) except Exception: - print(f"Unable to get serial number for study") - - if serial_num == None: - print(f"Unable to get serial number for study") + print("Unable to get serial number for study") - related_study_result = get_related_studies(serial_num, hostname) - existing_related_study_result = mds_res.get("related_studies", []) - for related_study in related_study_result: - if related_study not in existing_related_study_result: - existing_related_study_result.append(copy.deepcopy(related_study)) - mds_res["gen3_discovery"][ - "related_studies" - ] = copy.deepcopy(existing_related_study_result) + if serial_num is None: + print("Unable to get serial number for study") + related_study_result = get_related_studies( + serial_num, mds_record_guid, hostname + ) + mds_res["gen3_discovery"]["related_studies"] = copy.deepcopy(related_study_result) # merge data from cedar that is not study level metadata into a level higher deleted_keys = [] @@ -324,29 +354,39 @@ def get_related_studies(serial_num, hostname): for key in deleted_keys: del mds_res["gen3_discovery"]["study_metadata"][key] - mds_discovery_data_body = update_filter_metadata(mds_res["gen3_discovery"]) + mds_discovery_data_body = update_filter_metadata( + mds_res["gen3_discovery"] + ) mds_cedar_register_data_body["gen3_discovery"] = mds_discovery_data_body if mds_clinical_trials: - mds_cedar_register_data_body["clinicaltrials_gov"] = {**mds_cedar_register_data_body.get("clinicaltrials_gov", {}), **mds_clinical_trials} + mds_cedar_register_data_body["clinicaltrials_gov"] = { + **mds_cedar_register_data_body.get("clinicaltrials_gov", {}), + **mds_clinical_trials, + } mds_cedar_register_data_body["_guid_type"] = "discovery_metadata" print(f"Metadata {mds_record_guid} is now being registered.") - mds_put = requests.put(f"http://revproxy-service/mds/metadata/{mds_record_guid}", + mds_put = requests.put( + f"http://revproxy-service/mds/metadata/{mds_record_guid}", headers=token_header, - json = mds_cedar_register_data_body + json=mds_cedar_register_data_body, ) if mds_put.status_code == 200: print(f"Successfully registered: {mds_record_guid}") else: - print(f"Failed to register: {mds_record_guid}. Might not be MDS admin") + print( + f"Failed to register: {mds_record_guid}. Might not be MDS admin" + ) print(f"Status from MDS: {mds_put.status_code}") else: print(f"Failed to get information from MDS: {mds.status_code}") - + else: - print(f"Failed to get information from CEDAR wrapper service: {cedar.status_code}") + print( + f"Failed to get information from CEDAR wrapper service: {cedar.status_code}" + ) if offset + limit == total: break From ec6510ff37b03662497ac5e651b36d70f4101e68 Mon Sep 17 00:00:00 2001 From: Jian <52763034+tianj7@users.noreply.github.com> Date: Wed, 13 Mar 2024 16:30:06 -0500 Subject: [PATCH 21/21] add alt text to maintenance page images (#2500) --- files/dashboard/maintenance-page/index.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/files/dashboard/maintenance-page/index.html b/files/dashboard/maintenance-page/index.html index a3e34479b7..fac49e64e1 100644 --- a/files/dashboard/maintenance-page/index.html +++ b/files/dashboard/maintenance-page/index.html @@ -16,7 +16,7 @@
@@ -27,12 +27,12 @@

This site is under maintenance...

Please check back later.

- + A shiba dog looking into the distance
- - + Gen3 Data Commons + Center for Translational Data Science at the University of Chicago