From 7e1f17482ef39c8e22ea8590e3d4f76e7655429a Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 13:40:21 -0400 Subject: [PATCH 01/34] initial commit --- .../deployments/overtureQuickstart.sh | 52 ++++++++ .../serviceScripts/arrangerSetup.sh | 8 ++ .../serviceScripts/elasticsearchSetup.sh | 45 +++++++ .../serviceScripts/keycloakDbSetup.sh | 18 +++ .../serviceScripts/maestroSetup.sh | 9 ++ .../serviceScripts/songDbSetup.sh | 13 ++ conductorScripts/serviceScripts/songSetup.sh | 9 ++ conductorScripts/serviceScripts/stageSetup.sh | 9 ++ .../02732061-9daf-5a64-99f5-c550320c7916.json | 1 + .../190e1812-563f-5158-9b35-0925edea4a1d.json | 1 + .../22a0f109-77ac-5c09-b3e4-26a783e898c1.json | 1 + .../2c7b355a-c47b-5cd6-8268-f3ace739eef6.json | 1 + .../38a0187c-203a-5669-83b8-d074e7362783.json | 1 + .../41bde62d-e63e-5b4a-a8ea-58aa63b1e6e9.json | 1 + .../44a53c0b-4622-5602-a958-338891712724.json | 1 + .../4ec2c13a-e03d-516c-b393-ece343963eb9.json | 1 + .../4fd0be6f-ce25-521a-9a54-1dbc2318ce05.json | 1 + .../59291c9f-0b02-575a-85b7-501e54951e63.json | 1 + .../5b431188-0ba3-53a2-88db-5b5a710d4a74.json | 1 + .../603d285a-9070-51da-bb9d-d32b3429c9db.json | 1 + .../726a01c6-a491-5213-9b4a-22a8d431337a.json | 1 + .../79f178e4-c033-59c5-82df-c460ec7b19d6.json | 1 + .../998f068b-0856-539e-86c3-a392e4ea171d.json | 1 + .../9ec6bdd4-1265-5e98-ae1d-57f76abeb483.json | 1 + .../a9e44028-6858-5e85-96eb-c57873da6658.json | 1 + .../ae23ca2d-d8f8-5e05-bdac-c9e0ec1bd275.json | 1 + .../b08d8ad0-1dfc-5559-9233-b78091fff52f.json | 1 + .../b2dec936-af54-5b2c-9ab9-7502b94191d0.json | 1 + .../b4b672be-f917-504b-b4e3-c4d6d580af06.json | 1 + .../b8cdb477-995e-55cc-88ce-3e1f9b0de1d9.json | 1 + .../bba25936-6d51-5b24-be2c-6af6d462c434.json | 1 + .../bf14635d-e43e-5dfd-b977-f2735e98f7e3.json | 1 + .../c0ecacdb-92c1-5e37-b949-24e9acfb50e2.json | 1 + .../e3ef7c5a-244e-5323-acd0-94d66c2f0125.json | 1 + .../e45bed7a-552d-5076-9507-405c51b2f196.json | 1 + .../e9e7922a-a102-5381-be8f-b020e6045877.json | 1 + .../fa6ed231-77fe-5b2b-8df4-f32f8d526208.json | 1 + .../ff7b8ca2-2b43-5503-b407-35dc8b0591b0.json | 1 + docker-compose.yml | 112 +----------------- .../data-keycloak-db/base/16384/16385 | Bin 8192 -> 8192 bytes .../base/16384/pg_internal.init | Bin 155936 -> 155936 bytes .../data-keycloak-db/global/pg_control | Bin 8192 -> 8192 bytes .../data-keycloak-db/global/pg_internal.init | Bin 23840 -> 23840 bytes .../pg_logical/replorigin_checkpoint | Bin 0 -> 8 bytes .../data-keycloak-db/pg_stat/db_0.stat | Bin 0 -> 1670 bytes .../data-keycloak-db/pg_stat/db_16384.stat | Bin 0 -> 30715 bytes .../data-keycloak-db/pg_stat/global.stat | Bin 0 -> 1335 bytes .../data-keycloak-db/pg_stat_tmp/db_0.stat | Bin 1670 -> 0 bytes .../pg_stat_tmp/db_13780.stat | Bin 5185 -> 0 bytes .../pg_stat_tmp/db_16384.stat | Bin 32195 -> 0 bytes .../data-keycloak-db/pg_stat_tmp/global.stat | Bin 1335 -> 0 bytes .../pg_wal/000000010000000000000001 | Bin 16777216 -> 16777216 bytes .../data-keycloak-db/pg_xact/0000 | Bin 8192 -> 8192 bytes .../data-keycloak-db/postmaster.pid | 8 -- .../data-song-db/base/16384/1255 | Bin 630784 -> 630784 bytes .../data-song-db/base/16384/16588 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16601 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16614 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16765 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16947 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16949 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16954 | Bin 16384 -> 16384 bytes .../data-song-db/base/16384/16961 | Bin 16384 -> 16384 bytes .../data-song-db/base/16384/2606 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/2619 | Bin 172032 -> 172032 bytes .../data-song-db/base/16384/pg_internal.init | Bin 141820 -> 141820 bytes .../data-song-db/global/pg_control | Bin 8192 -> 8192 bytes .../data-song-db/pg_stat/db_0.stat | Bin 0 -> 1526 bytes .../data-song-db/pg_stat/db_16384.stat | Bin 0 -> 18595 bytes .../data-song-db/pg_stat/global.stat | Bin 0 -> 607 bytes .../data-song-db/pg_stat_tmp/db_0.stat | Bin 2033 -> 0 bytes .../data-song-db/pg_stat_tmp/db_16384.stat | Bin 26200 -> 0 bytes .../data-song-db/pg_stat_tmp/global.stat | Bin 607 -> 0 bytes .../pg_wal/000000010000000000000001 | Bin 16777216 -> 16777216 bytes persistentStorage/data-song-db/pg_xact/0000 | Bin 8192 -> 8192 bytes persistentStorage/data-song-db/postmaster.pid | 8 -- 76 files changed, 198 insertions(+), 123 deletions(-) create mode 100755 conductorScripts/deployments/overtureQuickstart.sh create mode 100755 conductorScripts/serviceScripts/arrangerSetup.sh create mode 100755 conductorScripts/serviceScripts/elasticsearchSetup.sh create mode 100755 conductorScripts/serviceScripts/keycloakDbSetup.sh create mode 100755 conductorScripts/serviceScripts/maestroSetup.sh create mode 100755 conductorScripts/serviceScripts/songDbSetup.sh create mode 100755 conductorScripts/serviceScripts/songSetup.sh create mode 100755 conductorScripts/serviceScripts/stageSetup.sh create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/190e1812-563f-5158-9b35-0925edea4a1d.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/22a0f109-77ac-5c09-b3e4-26a783e898c1.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/2c7b355a-c47b-5cd6-8268-f3ace739eef6.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/38a0187c-203a-5669-83b8-d074e7362783.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/41bde62d-e63e-5b4a-a8ea-58aa63b1e6e9.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/44a53c0b-4622-5602-a958-338891712724.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/4ec2c13a-e03d-516c-b393-ece343963eb9.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/4fd0be6f-ce25-521a-9a54-1dbc2318ce05.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/59291c9f-0b02-575a-85b7-501e54951e63.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/5b431188-0ba3-53a2-88db-5b5a710d4a74.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/603d285a-9070-51da-bb9d-d32b3429c9db.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/726a01c6-a491-5213-9b4a-22a8d431337a.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/79f178e4-c033-59c5-82df-c460ec7b19d6.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/998f068b-0856-539e-86c3-a392e4ea171d.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/9ec6bdd4-1265-5e98-ae1d-57f76abeb483.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/a9e44028-6858-5e85-96eb-c57873da6658.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/ae23ca2d-d8f8-5e05-bdac-c9e0ec1bd275.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/b08d8ad0-1dfc-5559-9233-b78091fff52f.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/b2dec936-af54-5b2c-9ab9-7502b94191d0.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/b4b672be-f917-504b-b4e3-c4d6d580af06.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/b8cdb477-995e-55cc-88ce-3e1f9b0de1d9.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/bba25936-6d51-5b24-be2c-6af6d462c434.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/bf14635d-e43e-5dfd-b977-f2735e98f7e3.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/c0ecacdb-92c1-5e37-b949-24e9acfb50e2.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/e3ef7c5a-244e-5323-acd0-94d66c2f0125.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/e45bed7a-552d-5076-9507-405c51b2f196.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/e9e7922a-a102-5381-be8f-b020e6045877.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/fa6ed231-77fe-5b2b-8df4-f32f8d526208.json create mode 100644 configurationFiles/elasticsearchConfigs/es-docs/ff7b8ca2-2b43-5503-b407-35dc8b0591b0.json create mode 100644 persistentStorage/data-keycloak-db/pg_logical/replorigin_checkpoint create mode 100644 persistentStorage/data-keycloak-db/pg_stat/db_0.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat/db_16384.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat/global.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_0.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_13780.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_16384.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/global.stat delete mode 100644 persistentStorage/data-keycloak-db/postmaster.pid create mode 100644 persistentStorage/data-song-db/pg_stat/db_0.stat create mode 100644 persistentStorage/data-song-db/pg_stat/db_16384.stat create mode 100644 persistentStorage/data-song-db/pg_stat/global.stat delete mode 100644 persistentStorage/data-song-db/pg_stat_tmp/db_0.stat delete mode 100644 persistentStorage/data-song-db/pg_stat_tmp/db_16384.stat delete mode 100644 persistentStorage/data-song-db/pg_stat_tmp/global.stat delete mode 100644 persistentStorage/data-song-db/postmaster.pid diff --git a/conductorScripts/deployments/overtureQuickstart.sh b/conductorScripts/deployments/overtureQuickstart.sh new file mode 100755 index 00000000..3939397d --- /dev/null +++ b/conductorScripts/deployments/overtureQuickstart.sh @@ -0,0 +1,52 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the Overture QuickStart ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Database Setups +rs /scripts/serviceScripts/songDbSetup.sh +rs /scripts/serviceScripts/keycloakDbSetup.sh + +# Elasticsearch Setup +rs /scripts/serviceScripts/elasticSearchSetup.sh + +# Song Setup +rs /scripts/serviceScripts/songSetup.sh + +# Update Conductor to Healthy Status +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Maestro +rs /scripts/serviceScripts/maestroSetup.sh + +# Check Arranger +rs /scripts/serviceScripts/arrangerSetup.sh + +# Check Stage +rs /scripts/serviceScripts/stageSetup.sh + +# Success & Next Steps +rs /scripts/serviceScripts/successQuickStart.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Overture QuickStart Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" +echo -e "\033[1m🌐 Front-end Portal:\033[0m" +echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" +echo -e "\033[1m📚 Overture Platform Guides:\033[0m" +echo -e " \033[1;32mhttps://www.overture.bio/documentation/guides/\033[0m\n" +echo -e "\033[1m🛠️ QuickStart Information:\033[0m" +echo -e " Check the \033[1;33mdocker-compose.yml\033[0m file for details on this QuickStart," +echo -e " including links to relevant sections of our deployment guide.\n" \ No newline at end of file diff --git a/conductorScripts/serviceScripts/arrangerSetup.sh b/conductorScripts/serviceScripts/arrangerSetup.sh new file mode 100755 index 00000000..a2f2ecb6 --- /dev/null +++ b/conductorScripts/serviceScripts/arrangerSetup.sh @@ -0,0 +1,8 @@ +#!/bin/sh + + echo -e "\033[1;35m[9/10]\033[0m Checking if Arranger is reachable" + until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do + echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 + done + echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" diff --git a/conductorScripts/serviceScripts/elasticsearchSetup.sh b/conductorScripts/serviceScripts/elasticsearchSetup.sh new file mode 100755 index 00000000..e0f3b741 --- /dev/null +++ b/conductorScripts/serviceScripts/elasticsearchSetup.sh @@ -0,0 +1,45 @@ +#!/bin/sh + +# Wait for Elasticsearch +echo -e "\033[1;35m[3/10]\033[0m Waiting for Elasticsearch (this may take a few minutes)" +sleep 20 +until curl -s -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/_cluster/health" > /dev/null; do + echo -e "\033[1;36mElasticsearch:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Elasticsearch is reachable" + +# Set up Elasticsearch index template +echo -e "\033[1;35m[4/10]\033[0m Setting up Elasticsearch index template" +if ! curl -s -u elastic:myelasticpassword "http://elasticsearch:9200/_template/index_template" | grep -q "\"index_patterns\""; then + curl -s -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/_template/index_template" \ + -H "Content-Type: application/json" -d @/usr/share/elasticsearch/config/quickstart_index_template.json > /dev/null && + echo -e "\033[1;32mSuccess:\033[0m Elasticsearch index template created successfully" +else + echo -e "\033[1;36mElasticsearch:\033[0m Index template already exists, skipping creation" +fi + +# Set up Elasticsearch index and alias (needs failure check) +echo -e "\033[1;35m[5/10]\033[0m Setting up Elasticsearch index and alias" +echo -e "\033[1;36mElasticsearch:\033[0m Checking if Elasticsearch index exists" +if ! curl -s -f -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/overture-quickstart-index" > /dev/null 2>&1; then + echo -e "\033[1;32mElasticsearch:\033[0m Creating Elasticsearch index and alias" + response=$(curl -s -w "\n%{http_code}" -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/overture-quickstart-index" \ + -H "Content-Type: application/json" -d "{\"aliases\": {\"file_centric\": {\"is_write_index\": true}}}") + http_code=$(echo "$response" | tail -n1) + body=$(echo "$response" | sed '$d') + echo -e "\033[1;32mSuccess:\033[0m Index and alias created successfully, Elasticsearch setup complete" +else + echo -e "\033[1;36mElasticsearch:\033[0m Index already exists, skipping creation" +fi + +# Importing Elasticsearch Documents +echo -e "\033[1;35m[6/10]\033[0m Importing Elasticsearch Documents" +for f in ./es-docs/*.json; do + object_id=$(basename "$f" .json) + curl --user elastic:myelasticpassword -sL -X POST \ + -H "Content-Type: application/json" \ + "http://elasticsearch:9200/overture-quickstart-index/_doc/$object_id" \ + -d "@$f" > /dev/null +done +echo -e "\033[1;32mSuccess:\033[0m Document import complete" diff --git a/conductorScripts/serviceScripts/keycloakDbSetup.sh b/conductorScripts/serviceScripts/keycloakDbSetup.sh new file mode 100755 index 00000000..94929d3d --- /dev/null +++ b/conductorScripts/serviceScripts/keycloakDbSetup.sh @@ -0,0 +1,18 @@ +#!/bin/sh + +# Create missing empty directories not tracked by git and needed by postgres +echo -e "\033[1;35m[2/10]\033[0m Setting up empty directories for Keycloaks postgres database" +mkdir -p keycloak/db-folder-init/pg_tblspc +mkdir -p keycloak/db-folder-init/pg_stat +mkdir -p keycloak/db-folder-init/pg_replslot +mkdir -p keycloak/db-folder-init/pg_dynshmem +mkdir -p keycloak/db-folder-init/pg_twophase +mkdir -p keycloak/db-folder-init/pg_notify +mkdir -p keycloak/db-folder-init/pg_serial +mkdir -p keycloak/db-folder-init/pg_snapshots +mkdir -p keycloak/db-folder-init/pg_commit_ts +mkdir -p keycloak/db-folder-init/pg_wal/archive_status +mkdir -p keycloak/db-folder-init/pg_logical/snapshots +mkdir -p keycloak/db-folder-init/pg_logical/mappings +echo -e "\033[1;32mSuccess:\033[0m Keycloak Databases ready" + diff --git a/conductorScripts/serviceScripts/maestroSetup.sh b/conductorScripts/serviceScripts/maestroSetup.sh new file mode 100755 index 00000000..dfb72438 --- /dev/null +++ b/conductorScripts/serviceScripts/maestroSetup.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +# Check Maestro +echo -e "\033[1;35m[8/10]\033[0m Checking if Maestro is reachable (this may take a few minutes)" +until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study/demo" -H "accept: */*" -d "{}" | grep -q "true"; do + echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" \ No newline at end of file diff --git a/conductorScripts/serviceScripts/songDbSetup.sh b/conductorScripts/serviceScripts/songDbSetup.sh new file mode 100755 index 00000000..a95e6a50 --- /dev/null +++ b/conductorScripts/serviceScripts/songDbSetup.sh @@ -0,0 +1,13 @@ +#!/bin/sh + +# Create missing empty directories not tracked by git and needed by postgres +echo -e "\033[1;35m[1/10]\033[0m Setting up empty directories for Songs postgres database" +mkdir -p song/db-folder-init/pg_tblspc +mkdir -p song/db-folder-init/pg_stat +mkdir -p song/db-folder-init/pg_replslot +mkdir -p song/db-folder-init/pg_twophase +mkdir -p song/db-folder-init/pg_snapshots +mkdir -p song/db-folder-init/pg_commit_ts +mkdir -p song/db-folder-init/pg_logical/snapshots +mkdir -p song/db-folder-init/pg_logical/mappings +echo -e "\033[1;32mSuccess:\033[0m Song Databases ready" diff --git a/conductorScripts/serviceScripts/songSetup.sh b/conductorScripts/serviceScripts/songSetup.sh new file mode 100755 index 00000000..8a2772f9 --- /dev/null +++ b/conductorScripts/serviceScripts/songSetup.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +# Check for Song +echo -e "\033[1;35m[7/10]\033[0m Checking if Song is ready" +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do + echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 2 seconds" + sleep 20 +done +echo -e "\033[1;32mSuccess:\033[0m Song is now reachable" diff --git a/conductorScripts/serviceScripts/stageSetup.sh b/conductorScripts/serviceScripts/stageSetup.sh new file mode 100755 index 00000000..89ba4467 --- /dev/null +++ b/conductorScripts/serviceScripts/stageSetup.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +# Check Stage +echo -e "\033[1;35m[10/10]\033[0m Checking if Stage is reachable" + until curl -s -o /dev/null -w "%{http_code}" "http://stage:3000" | grep -q "200"; do + echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" + sleep 10 + done +echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" \ No newline at end of file diff --git a/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json b/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json new file mode 100644 index 00000000..56c836ba --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json @@ -0,0 +1 @@ +{"object_id": "02732061-9daf-5a64-99f5-c550320c7916", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "CRAM", "file_access": "controlled", "analysis": {"analysis_id": "4ab918ab-a6e9-4cc8-b918-aba6e98cc8b1", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110840020, "first_published_at": 1720110840007, 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"00000000-0000-0000-0000-0000000009198"}], "sessionId": "SI9198", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "Mutect2 Variant Calling", "workflowVersion": "0.1.1.1", "workflowShortName": "Mutect2Variant"}}, "file": {"name": "SP919811.indel.vcf.gz", "md5sum": "b32991cae3845c0b38ff42dc6179a5c1", "size": 17405, "data_type": "Raw InDel Calls", "index_file": {"object_id": "05dc857c-1a01-5a47-9bbb-ceddad8da90a", "name": "SP919811.indel.vcf.gz.tbi", "file_type": "TBI", "md5sum": "c0e92c3059a3dd763c72a1e633c08b4a", "data_type": "Raw InDel Calls", "size": 159, "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "4d1c2bd5-79cd-5448-bbb2-ada6ad4a5cb4", "submitter_donor_id": "DO9198", "gender": "Male", "specimens": [{"specimen_id": "f4e34423-3588-52b0-9c3d-6ba37b5302ce", "specimen_type": "Metastatic tumour - additional metastatic", "submitter_specimen_id": "SP919811", "samples": [{"sample_id": "f4e34423-3588-52b0-9c3d-6ba37b5302ce", "submitter_sample_id": "SP919811", "sample_type": "Amplified DNA", "matched_normal_submitter_sample_id": "SP919801"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Blood derived"}]}], "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/configurationFiles/elasticsearchConfigs/es-docs/fa6ed231-77fe-5b2b-8df4-f32f8d526208.json b/configurationFiles/elasticsearchConfigs/es-docs/fa6ed231-77fe-5b2b-8df4-f32f8d526208.json new file mode 100644 index 00000000..0277cd7b --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/fa6ed231-77fe-5b2b-8df4-f32f8d526208.json @@ -0,0 +1 @@ +{"object_id": "fa6ed231-77fe-5b2b-8df4-f32f8d526208", "study_id": "demo", "data_type": "Raw InDel Calls", "file_type": "VCF", "file_access": "controlled", "analysis": {"analysis_id": "b110074f-4337-41b3-9007-4f433761b39f", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110406367, "first_published_at": 1720110406356, "published_at": 1720110406356, "experiment": {"model": "SEQUEL IIe", "platform": "PacBio", "sequencingDate": "2021-03-08T19:00:00.000Z", "sequencingCenter": "CGTA", "experimentalStrategy": "WXS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:26:46.356908"}], "collaborator": [{"name": "MICR", "contactEmail": "susannorton@micr.ca"}], "createdAt": "2024-07-04T16:19:32.104094", "donor": {"primarySite": "Hematopoietic and reticuloendothelial systems", "vitalStatus": "Alive", "causeOfDeath": null, "survivalTime": null, "primaryDiagnosis": [{"followUp": [{"relapseType": null, "intervalOfFollowUp": 67, "submitterFollowUpId": "FO744301", "submitterTreatmentId": "TR744301", "diseaseStatusAtFollowUp": "Complete remission"}], "treatment": [{"chemotherapy": [{"drugName": "Azacitidine "}], "treatmentType": ["Chemotherapy"], "treatmentDuration": 70, "responseToTreatment": "Disease progression", "submitterTreatmentId": "TR744301", "treatmentStartInterval": 21}], "ageAtDiagnosis": 57, "cancerTypeCode": "C88.3", "clinicalStageGroup": "Stage IIC", "clinicalTumourStagingSystem": "AJCC 7th edition", "submitterPrimaryDiagnosisId": "PD744301"}], "submitterDonorId": "DO7443"}, "publication": {"doi": "10.1093/nar/gkae188", "publication": "NAR"}, "specimen": {"tumourGrade": "G1", "submitterSpecimenId": "SP744302", "tumourGradingSystem": "ISUP grading system", "specimenAnatomicLocation": "C47", "submitterPrimaryDiagnosisId": "PD744301"}, "workflow": {"runId": "RI7443", "inputs": [{"analysisType": "sequencing_alignment", "normalAnalysisId": "00000000-0000-0000-0000-0000000007443", "tumourAnalysisId": "00000000-0000-0000-0000-0000000007443"}], "sessionId": "SI7443", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "Mutect2 Variant Calling", "workflowVersion": "0.1.1.1", "workflowShortName": "Mutect2Variant"}}, "file": {"name": "SP744312.indel.vcf.gz", "md5sum": "d713f83a36ff6d95a49268905b8a0206", "size": 17380, "data_type": "Raw InDel Calls", "index_file": {"object_id": "11fe277d-454b-51be-a6c8-9a890e2e332c", "name": "SP744312.indel.vcf.gz.tbi", "file_type": "TBI", "md5sum": "0fffe3a8969892bebfb92554748d1d60", "data_type": "Raw InDel Calls", "size": 151, "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "6ac5fc9e-88db-5837-9e57-3f048980ce90", "submitter_donor_id": "DO7443", "gender": "Male", "specimens": [{"specimen_id": "cf6006da-3fde-5945-afc4-635924a26800", "specimen_type": "Metastatic tumour - additional metastatic", "submitter_specimen_id": "SP744312", "samples": [{"sample_id": "cf6006da-3fde-5945-afc4-635924a26800", "submitter_sample_id": "SP744312", "sample_type": "ctDNA", "matched_normal_submitter_sample_id": "SP744302"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Blood derived"}]}], "dataCategory": "Simple Nucelotide Variation", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/configurationFiles/elasticsearchConfigs/es-docs/ff7b8ca2-2b43-5503-b407-35dc8b0591b0.json b/configurationFiles/elasticsearchConfigs/es-docs/ff7b8ca2-2b43-5503-b407-35dc8b0591b0.json new file mode 100644 index 00000000..86e30a23 --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/ff7b8ca2-2b43-5503-b407-35dc8b0591b0.json @@ -0,0 +1 @@ +{"object_id": "ff7b8ca2-2b43-5503-b407-35dc8b0591b0", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "BAM", "file_access": "controlled", "analysis": {"analysis_id": "d7fe62b5-3bab-47b0-be62-b53bab77b0e7", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110461116, "first_published_at": 1720110461106, "published_at": 1720110461106, "experiment": {"model": "SEQUEL IIe", "platform": "PacBio", "sequencingDate": "2021-03-08T19:00:00.000Z", "sequencingCenter": "CGTA", "experimentalStrategy": "WGS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:27:41.106551"}], "collaborator": [{"name": "MICR", "contactEmail": "susannorton@micr.ca"}], "createdAt": "2024-07-04T16:19:40.628302", "donor": {"primarySite": "Bronchus and lung", "vitalStatus": "Alive", "causeOfDeath": null, "survivalTime": null, "primaryDiagnosis": [{"followUp": [{"relapseType": null, "intervalOfFollowUp": 74, "submitterFollowUpId": "FO745301", "submitterTreatmentId": "TR745301", "diseaseStatusAtFollowUp": "Relapse or recurrence"}], "treatment": [{"treatmentType": ["Hormonal therapy"], "hormoneTherapy": [{"drugName": "Letrozole "}], "treatmentDuration": 32, "responseToTreatment": "Partial response", "submitterTreatmentId": "TR745301", "treatmentStartInterval": 38}], "ageAtDiagnosis": 30, "cancerTypeCode": "C34.3", "clinicalStageGroup": "Stage IB1", "clinicalTumourStagingSystem": "FIGO staging system", "submitterPrimaryDiagnosisId": "PD745301"}, {"followUp": [{"relapseType": null, "intervalOfFollowUp": 46, "submitterFollowUpId": "FO745302", "submitterTreatmentId": "TR745302", "diseaseStatusAtFollowUp": "Relapse or recurrence"}], "treatment": [{"chemotherapy": [{"drugName": "Tamoxifen "}], "treatmentType": ["Chemotherapy"], "treatmentDuration": 44, "responseToTreatment": "Disease progression", "submitterTreatmentId": "TR745302", "treatmentStartInterval": 82}], "ageAtDiagnosis": 20, "cancerTypeCode": "C34.8", "clinicalStageGroup": "Stage III", "clinicalTumourStagingSystem": "Ann Arbor staging system", "submitterPrimaryDiagnosisId": "PD745302"}], "submitterDonorId": "DO7453"}, "publication": {"doi": "10.1093/nar/gkae188", "publication": "NAR"}, "specimen": {"tumourGrade": "G3", "submitterSpecimenId": "SP745301", "tumourGradingSystem": "Four-tier grading system", "specimenAnatomicLocation": "C11", "submitterPrimaryDiagnosisId": "PD745301"}, "workflow": {"runId": "RI7453", "inputs": [{"analysisId": "00000000-0000-0000-0000-0000000007453", "analysisType": "sequencing_experiment"}], "sessionId": "SI7453", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "BWA mem2 Alignment", "workflowVersion": "0.8", "workflowShortName": "BWAmem2Aln"}}, "file": {"name": "SP745311.bam", "md5sum": "7df44e073f73923d05893764889039d2", "size": 125255, "data_type": "Aligned Reads", "index_file": {"object_id": "a36547ca-da4a-5591-a0fc-4e11e03a829c", "name": "SP745311.bam.bai", "file_type": "BAI", "md5sum": "dd2b54ec315db4ef29ffeec3777fc8a0", "data_type": "Aligned Reads", "size": 27160, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "663b8536-90a9-51d3-abda-695771e751d0", "submitter_donor_id": "DO7453", "gender": "Male", "specimens": [{"specimen_id": "6473c26f-b273-5172-9bb0-7e95ea9f5020", "specimen_type": "Metastatic tumour", "submitter_specimen_id": "SP745311", "samples": [{"sample_id": "6473c26f-b273-5172-9bb0-7e95ea9f5020", "submitter_sample_id": "SP745311", "sample_type": "Total DNA", "matched_normal_submitter_sample_id": "SP745301"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Blood derived - peripheral blood"}]}], "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 5134f693..bc406fd6 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -13,116 +13,13 @@ services: - ./persistentStorage/data-keycloak-db:/keycloak/db-folder-init - ./persistentStorage/data-song-db:/song/db-folder-init - ./configurationFiles/elasticsearchConfigs/quickstart_index_template.json:/usr/share/elasticsearch/config/quickstart_index_template.json + - ./configurationFiles/elasticsearchConfigs/es-docs:/es-docs + - ./conductorScripts/:/scripts - ./health:/health command: > sh -c ' set -e - - echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" - echo -e "\033[1;36m║ Welcome to the Overture QuickStart ║\033[0m" - echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" - # Create missing empty directories not tracked by git and needed by postgres - echo -e "\033[1;35m[1/7]\033[0m Setting up empty directories for postgres" - mkdir -p keycloak/db-folder-init/pg_tblspc - mkdir -p keycloak/db-folder-init/pg_stat - mkdir -p keycloak/db-folder-init/pg_replslot - mkdir -p keycloak/db-folder-init/pg_dynshmem - mkdir -p keycloak/db-folder-init/pg_twophase - mkdir -p keycloak/db-folder-init/pg_notify - mkdir -p keycloak/db-folder-init/pg_serial - mkdir -p keycloak/db-folder-init/pg_snapshots - mkdir -p keycloak/db-folder-init/pg_commit_ts - mkdir -p keycloak/db-folder-init/pg_wal/archive_status - mkdir -p keycloak/db-folder-init/pg_logical/snapshots - mkdir -p keycloak/db-folder-init/pg_logical/mappings - mkdir -p song/db-folder-init/pg_tblspc - mkdir -p song/db-folder-init/pg_stat - mkdir -p song/db-folder-init/pg_replslot - mkdir -p song/db-folder-init/pg_twophase - mkdir -p song/db-folder-init/pg_snapshots - mkdir -p song/db-folder-init/pg_commit_ts - mkdir -p song/db-folder-init/pg_logical/snapshots - mkdir -p song/db-folder-init/pg_logical/mappings - echo -e "\033[1;32mSuccess:\033[0m Databases ready" - - # Wait for Elasticsearch - echo -e "\033[1;35m[2/7]\033[0m Waiting for Elasticsearch (this may take a few minutes)" - sleep 20 - until curl -s -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/_cluster/health" > /dev/null; do - echo -e "\033[1;36mElasticsearch:\033[0m Not yet reachable, checking again in 30 seconds" - sleep 30 - done - echo -e "\033[1;32mSuccess:\033[0m Elasticsearch is reachable" - - # Set up Elasticsearch index template - echo -e "\033[1;35m[3/7]\033[0m Setting up Elasticsearch index template" - if ! curl -s -u elastic:myelasticpassword "http://elasticsearch:9200/_template/index_template" | grep -q "\"index_patterns\"" > /dev/null; then - curl -s -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/_template/index_template" -H "Content-Type: application/json" -d @/usr/share/elasticsearch/config/quickstart_index_template.json > /dev/null && - echo -e "\033[1;32mSuccess:\033[0m Elasticsearch index template created successfully" - else - echo -e "\033[1;36mElasticsearch:\033[0m Index template already exists, skipping creation" - fi - - # Set up Elasticsearch index and alias (needs failure check) - echo -e "\033[1;35m[4/7]\033[0m Setting up Elasticsearch index and alias" - echo -e "\033[1;36mElasticsearch:\033[0m Checking if Elasticsearch index exists" - if ! curl -s -f -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/overture-quickstart-index" > /dev/null 2>&1; then - echo -e "\033[1;32mElasticsearch:\033[0m Creating Elasticsearch index and alias" - response=$$(curl -s -w "\n%{http_code}" -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/overture-quickstart-index" -H "Content-Type: application/json" -d "{\"aliases\": {\"file_centric\": {\"is_write_index\": true}}}") - http_code=$$(echo "$$response" | tail -n1) - body=$$(echo "$$response" | sed "$$d") - echo -e "\033[1;32mSuccess:\033[0m Index and alias created successfully, Elasticsearch setup complete" - else - echo -e "\033[1;36mElasticsearch:\033[0m Index already exists, skipping creation" - fi - - # Check for Song - echo -e "\033[1;35m[5/7]\033[0m Checking if Song is ready" - until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do - echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 2 seconds" - sleep 20 - done - echo -e "\033[1;32mSuccess:\033[0m Song is now reachable" - - # Updating health status of the conductor image - # This health file signals container readiness, fulfilling dependencies for search & discovery components, Maestro, Arranger & Stage - echo "healthy" > /health/conductor_health - echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" - - # Check Maestro - echo -e "\033[1;35m[6/8]\033[0m Checking if Maestro is reachable (this may take a few minutes)" - until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study/demo" -H "accept: */*" -d "{}" | grep -q "true"; do - echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" - sleep 30 - done - echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" - - # Check Arranger - echo -e "\033[1;35m[7/8]\033[0m Checking if Arranger is reachable" - until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do - echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 10 seconds" - sleep 10 - done - echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" - - # Check Stage - echo -e "\033[1;35m[8/8]\033[0m Checking if Stage is reachable" - until curl -s -o /dev/null -w "%{http_code}" "http://stage:3000" | grep -q "200"; do - echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" - sleep 10 - done - echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" - echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" - echo -e "\033[1;36m║ Overture QuickStart Setup Complete ║\033[0m" - echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" - echo -e "\033[1m🌐 Front-end Portal:\033[0m" - echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" - echo -e "\033[1m📚 Overture Platform Guides:\033[0m" - echo -e " \033[1;32mhttps://www.overture.bio/documentation/guides/\033[0m\n" - echo -e "\033[1m🛠️ QuickStart Information:\033[0m" - echo -e " Check the \033[1;33mdocker-compose.yml\033[0m file for details on this QuickStart," - echo -e " including links to relevant sections of our deployment guide.\n" - rm /health/conductor_health + chmod +x scripts/deployments/overtureQuickstart.sh && scripts/deployments/overtureQuickstart.sh exit 0 ' healthcheck: @@ -548,4 +445,5 @@ services: NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE: file NEXT_PUBLIC_ARRANGER_INDEX: file_centric NEXT_PUBLIC_ARRANGER_API_URL: http://arranger-server:5050 - NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS: repositories.code, analysis.analysis_id, object_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id \ No newline at end of file + NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS: repositories.code, analysis.analysis_id, object_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id + \ No newline at end of file diff --git a/persistentStorage/data-keycloak-db/base/16384/16385 b/persistentStorage/data-keycloak-db/base/16384/16385 index 47276c98cf4cf8d8e749475c49242e16df5143ae..0c5613ef4a4a41427571dd90806c5e39464cbd5c 100644 GIT binary patch delta 22 ccmZp0XmDU-0D>D=HnQ!LXHsODd`#X707>Nrpa1{> delta 22 ccmZp0XmDU-0D^|%jcohmnSL`*J|=Gk07du)zyJUM 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Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 15:33:41 -0400 Subject: [PATCH 02/34] updated with docker profiles + profile specific automation --- Makefile | 8 ++++ .../{overtureQuickstart.sh => platform.sh} | 3 -- conductorScripts/deployments/stageDev.sh | 37 ++++++++++++++++++ docker-compose.yml | 38 +++++++++++++++---- 4 files changed, 76 insertions(+), 10 deletions(-) create mode 100644 Makefile rename conductorScripts/deployments/{overtureQuickstart.sh => platform.sh} (96%) create mode 100755 conductorScripts/deployments/stageDev.sh diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..3526ca4d --- /dev/null +++ b/Makefile @@ -0,0 +1,8 @@ +platform: + PROFILE=platform docker compose --profile platform up --attach conductor + +stageDev: + PROFILE=stageDev docker compose --profile stageDev up --attach conductor + +down: + docker compose down diff --git a/conductorScripts/deployments/overtureQuickstart.sh b/conductorScripts/deployments/platform.sh similarity index 96% rename from conductorScripts/deployments/overtureQuickstart.sh rename to conductorScripts/deployments/platform.sh index 3939397d..75036b02 100755 --- a/conductorScripts/deployments/overtureQuickstart.sh +++ b/conductorScripts/deployments/platform.sh @@ -33,9 +33,6 @@ rs /scripts/serviceScripts/arrangerSetup.sh # Check Stage rs /scripts/serviceScripts/stageSetup.sh -# Success & Next Steps -rs /scripts/serviceScripts/successQuickStart.sh - # Remove Health Check File rm /health/conductor_health diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deployments/stageDev.sh new file mode 100755 index 00000000..76908877 --- /dev/null +++ b/conductorScripts/deployments/stageDev.sh @@ -0,0 +1,37 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the StageDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Elasticsearch Setup +rs /scripts/serviceScripts/elasticSearchSetup.sh + +# Update Conductor to Healthy Status +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Arranger +rs /scripts/serviceScripts/arrangerSetup.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Stage Dev Dependency Setup Complete ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run stage locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/stage.git\033[0m\n" +echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m3️⃣ Rename \033[1;32m.env.stageDev\033[0m to \033[1;32m.env:\033[0m\n" +echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index bc406fd6..bb3fd3eb 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,10 +1,6 @@ services: - # ====================================== - # Conductor - # -------------------------------------- - # Orchestrates setup with health checks, data population and logging - # -------------------------------------- conductor: + profiles: ["platform", "stageDev"] image: alpine/curl:8.8.0 container_name: conductor ports: @@ -16,10 +12,28 @@ services: - ./configurationFiles/elasticsearchConfigs/es-docs:/es-docs - ./conductorScripts/:/scripts - ./health:/health + environment: + - PROFILE=${PROFILE:-platform} command: > sh -c ' set -e - chmod +x scripts/deployments/overtureQuickstart.sh && scripts/deployments/overtureQuickstart.sh + echo "Profile is set to: $PROFILE" + case "$PROFILE" in + platform) + echo "Running platform deployment..." + chmod +x scripts/deployments/platform.sh + scripts/deployments/platform.sh + ;; + stageDev) + echo "Running stage development environment..." + scripts/deployments/stageDev.sh + ;; + *) + echo "Invalid profile: $PROFILE. Available options are 'platform' or 'stageDev'." + exit 1 + ;; + esac + exit 0 ' healthcheck: @@ -40,6 +54,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: + profiles: ["platform"] depends_on: - conductor image: postgres:14 @@ -65,6 +80,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: + profiles: ["platform"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 @@ -104,6 +120,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-kafka # -------------------------------------- kafka: + profiles: ["platform"] image: confluentinc/cp-kafka:7.6.1 container_name: kafka platform: linux/amd64 @@ -137,6 +154,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song-db: + profiles: ["platform"] image: postgres:11.1 container_name: song-db platform: linux/amd64 @@ -162,6 +180,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song: + profiles: ["platform"] image: ghcr.io/overture-stack/song-server:5.2.0 container_name: song platform: linux/amd64 @@ -216,6 +235,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#setting-up-object-storage # -------------------------------------- minio: + profiles: ["platform"] image: minio/minio:RELEASE.2018-05-11T00-29-24Z container_name: minio platform: linux/amd64 @@ -240,6 +260,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-score # -------------------------------------- score: + profiles: ["platform"] image: ghcr.io/overture-stack/score-server:5.11.0 container_name: score platform: linux/amd64 @@ -296,6 +317,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-elasticsearch # -------------------------------------- elasticsearch: + profiles: ["platform", "stageDev"] image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1 container_name: elasticsearch platform: linux/amd64 @@ -328,6 +350,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-maestro # -------------------------------------- maestro: + profiles: ["platform"] image: ghcr.io/overture-stack/maestro:4.3.0 container_name: maestro platform: linux/amd64 @@ -377,6 +400,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-arranger # -------------------------------------- arranger-server: + profiles: ["platform", stageDev] image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.33 container_name: arranger-server platform: linux/amd64 @@ -413,6 +437,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-stage # -------------------------------------- stage: + profiles: ["platform"] image: ghcr.io/overture-stack/stage:a211593 container_name: stage platform: linux/amd64 @@ -446,4 +471,3 @@ services: NEXT_PUBLIC_ARRANGER_INDEX: file_centric NEXT_PUBLIC_ARRANGER_API_URL: http://arranger-server:5050 NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS: repositories.code, analysis.analysis_id, object_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id - \ No newline at end of file From dec119b125c967efdce534133e04d25db4a8c9f9 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 15:46:29 -0400 Subject: [PATCH 03/34] renamed deployment directory to deploymentScripts --- .../{deployments => deploymentScripts}/platform.sh | 0 .../{deployments => deploymentScripts}/stageDev.sh | 0 docker-compose.yml | 7 ++++--- 3 files changed, 4 insertions(+), 3 deletions(-) rename conductorScripts/{deployments => deploymentScripts}/platform.sh (100%) rename conductorScripts/{deployments => deploymentScripts}/stageDev.sh (100%) diff --git a/conductorScripts/deployments/platform.sh b/conductorScripts/deploymentScripts/platform.sh similarity index 100% rename from conductorScripts/deployments/platform.sh rename to conductorScripts/deploymentScripts/platform.sh diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deploymentScripts/stageDev.sh similarity index 100% rename from conductorScripts/deployments/stageDev.sh rename to conductorScripts/deploymentScripts/stageDev.sh diff --git a/docker-compose.yml b/docker-compose.yml index bb3fd3eb..bb7ab0c8 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,12 +21,13 @@ services: case "$PROFILE" in platform) echo "Running platform deployment..." - chmod +x scripts/deployments/platform.sh - scripts/deployments/platform.sh + chmod +x scripts/deploymentScripts/platform.sh + scripts/deploymentScripts/platform.sh ;; stageDev) echo "Running stage development environment..." - scripts/deployments/stageDev.sh + chmod +x scripts/deploymentScripts/stageDev.sh + scripts/deploymentScripts/stageDev.sh ;; *) echo "Invalid profile: $PROFILE. Available options are 'platform' or 'stageDev'." From d385df289530618ce16bce58f129ad77799db118 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 16:45:23 -0400 Subject: [PATCH 04/34] added arrangerDev profile --- Makefile | 3 ++ .../deploymentScripts/arrangerDev.sh | 37 +++++++++++++++++++ .../deploymentScripts/stageDev.sh | 8 ++-- docker-compose.yml | 17 +++++---- 4 files changed, 54 insertions(+), 11 deletions(-) create mode 100755 conductorScripts/deploymentScripts/arrangerDev.sh diff --git a/Makefile b/Makefile index 3526ca4d..4775039d 100644 --- a/Makefile +++ b/Makefile @@ -4,5 +4,8 @@ platform: stageDev: PROFILE=stageDev docker compose --profile stageDev up --attach conductor +arrangerDev: + PROFILE=arrangerDev docker compose --profile arrangerDev up --attach conductor + down: docker compose down diff --git a/conductorScripts/deploymentScripts/arrangerDev.sh b/conductorScripts/deploymentScripts/arrangerDev.sh new file mode 100755 index 00000000..1745f183 --- /dev/null +++ b/conductorScripts/deploymentScripts/arrangerDev.sh @@ -0,0 +1,37 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔═════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the ArrangerDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚═════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Elasticsearch Setup +rs /scripts/serviceScripts/elasticSearchSetup.sh + +# Update Conductor to Healthy Status +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Stack +rs /scripts/serviceScripts/stageSetup.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Arranger Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run Arranger locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/arranger.git\033[0m\n" +echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m3️⃣ Rename \033[1;32m.env.arrangerDev\033[0m to \033[1;32m.env:\033[0m\n" +echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deploymentScripts/stageDev.sh b/conductorScripts/deploymentScripts/stageDev.sh index 76908877..90de0a3a 100755 --- a/conductorScripts/deploymentScripts/stageDev.sh +++ b/conductorScripts/deploymentScripts/stageDev.sh @@ -25,10 +25,10 @@ rm /health/conductor_health # Success and Next Steps echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" -echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Stage Dev Dependency Setup Complete ║\033[0m" -echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" -echo -e "\033[1m1️⃣ To run stage locally, start by cloning the repo:\033[0m\n" +echo -e "\033[1;36m╔═══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Stage Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run Stage locally, start by cloning the repo:\033[0m\n" echo -e " \033[1;32mgit clone https://github.com/overture-stack/stage.git\033[0m\n" echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" echo -e " \033[1;32mnpm ci\033[0m\n" diff --git a/docker-compose.yml b/docker-compose.yml index bb7ab0c8..33172a4d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,6 +1,6 @@ services: conductor: - profiles: ["platform", "stageDev"] + profiles: ["platform", "songDev", "scoreDev", "maestroDev", "arrangerDev", "stageDev"] image: alpine/curl:8.8.0 container_name: conductor ports: @@ -25,12 +25,17 @@ services: scripts/deploymentScripts/platform.sh ;; stageDev) - echo "Running stage development environment..." + echo "Running Stage development environment..." chmod +x scripts/deploymentScripts/stageDev.sh scripts/deploymentScripts/stageDev.sh ;; + arrangerDev) + echo "Running Arranger development environment..." + chmod +x scripts/deploymentScripts/arrangerDev.sh + scripts/deploymentScripts/arrangerDev.sh + ;; *) - echo "Invalid profile: $PROFILE. Available options are 'platform' or 'stageDev'." + echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." exit 1 ;; esac @@ -318,7 +323,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-elasticsearch # -------------------------------------- elasticsearch: - profiles: ["platform", "stageDev"] + profiles: ["platform", "stageDev", "arrangerDev"] image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1 container_name: elasticsearch platform: linux/amd64 @@ -438,15 +443,13 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-stage # -------------------------------------- stage: - profiles: ["platform"] + profiles: ["platform", "arrangerDev"] image: ghcr.io/overture-stack/stage:a211593 container_name: stage platform: linux/amd64 depends_on: conductor: condition: service_healthy - arranger-server: - condition: service_started ports: - "3000:3000" environment: From e16d1975234c90f907fdd4e799d10f649297bea0 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 17:30:21 -0400 Subject: [PATCH 05/34] added maestroDev profile --- Makefile | 3 ++ .../deploymentScripts/arrangerDev.sh | 2 +- .../deploymentScripts/maestroDev.sh | 36 +++++++++++++++++++ .../serviceScripts/keycloakDbSetup.sh | 1 - conductorScripts/serviceScripts/songSetup.sh | 4 +-- docker-compose.yml | 19 ++++++---- 6 files changed, 54 insertions(+), 11 deletions(-) create mode 100755 conductorScripts/deploymentScripts/maestroDev.sh diff --git a/Makefile b/Makefile index 4775039d..508f0402 100644 --- a/Makefile +++ b/Makefile @@ -7,5 +7,8 @@ stageDev: arrangerDev: PROFILE=arrangerDev docker compose --profile arrangerDev up --attach conductor +maestroDev: + PROFILE=maestroDev docker compose --profile maestroDev up --attach conductor + down: docker compose down diff --git a/conductorScripts/deploymentScripts/arrangerDev.sh b/conductorScripts/deploymentScripts/arrangerDev.sh index 1745f183..c77b89ed 100755 --- a/conductorScripts/deploymentScripts/arrangerDev.sh +++ b/conductorScripts/deploymentScripts/arrangerDev.sh @@ -17,7 +17,7 @@ rs /scripts/serviceScripts/elasticSearchSetup.sh echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" -# Check Stack +# Check Stage rs /scripts/serviceScripts/stageSetup.sh # Remove Health Check File diff --git a/conductorScripts/deploymentScripts/maestroDev.sh b/conductorScripts/deploymentScripts/maestroDev.sh new file mode 100755 index 00000000..803ff5da --- /dev/null +++ b/conductorScripts/deploymentScripts/maestroDev.sh @@ -0,0 +1,36 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the MaestroDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# KeycloakDb Setup +rs /scripts/serviceScripts/keycloakDbSetup.sh + +# SongDb Setup +rs /scripts/serviceScripts/songDbSetup.sh + +# Song Setup +rs /scripts/serviceScripts/songSetup.sh + +# Elasticsearch Setup +rs /scripts/serviceScripts/elasticSearchSetup.sh + +# Success and Next Steps +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Maestro Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run Maestro locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/maestro.git\033[0m\n" +echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m3️⃣ Rename \033[1;32m.env.maestroDev\033[0m to \033[1;32m.env:\033[0m\n" +echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/serviceScripts/keycloakDbSetup.sh b/conductorScripts/serviceScripts/keycloakDbSetup.sh index 94929d3d..35e8efdd 100755 --- a/conductorScripts/serviceScripts/keycloakDbSetup.sh +++ b/conductorScripts/serviceScripts/keycloakDbSetup.sh @@ -15,4 +15,3 @@ mkdir -p keycloak/db-folder-init/pg_wal/archive_status mkdir -p keycloak/db-folder-init/pg_logical/snapshots mkdir -p keycloak/db-folder-init/pg_logical/mappings echo -e "\033[1;32mSuccess:\033[0m Keycloak Databases ready" - diff --git a/conductorScripts/serviceScripts/songSetup.sh b/conductorScripts/serviceScripts/songSetup.sh index 8a2772f9..5ec68974 100755 --- a/conductorScripts/serviceScripts/songSetup.sh +++ b/conductorScripts/serviceScripts/songSetup.sh @@ -1,9 +1,9 @@ #!/bin/sh - + # Check for Song echo -e "\033[1;35m[7/10]\033[0m Checking if Song is ready" until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do - echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 2 seconds" + echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 20 seconds" sleep 20 done echo -e "\033[1;32mSuccess:\033[0m Song is now reachable" diff --git a/docker-compose.yml b/docker-compose.yml index 33172a4d..296898b9 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -34,6 +34,11 @@ services: chmod +x scripts/deploymentScripts/arrangerDev.sh scripts/deploymentScripts/arrangerDev.sh ;; + maestroDev) + echo "Running Maestro development environment..." + chmod +x scripts/deploymentScripts/maestroDev.sh + scripts/deploymentScripts/maestroDev.sh + ;; *) echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." exit 1 @@ -60,7 +65,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: - profiles: ["platform"] + profiles: ["platform", "maestroDev"] depends_on: - conductor image: postgres:14 @@ -86,7 +91,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: - profiles: ["platform"] + profiles: ["platform", "maestroDev"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 @@ -126,7 +131,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-kafka # -------------------------------------- kafka: - profiles: ["platform"] + profiles: ["platform", maestroDev] image: confluentinc/cp-kafka:7.6.1 container_name: kafka platform: linux/amd64 @@ -160,7 +165,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song-db: - profiles: ["platform"] + profiles: ["platform", "maestroDev"] image: postgres:11.1 container_name: song-db platform: linux/amd64 @@ -186,7 +191,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song: - profiles: ["platform"] + profiles: ["platform", "maestroDev"] image: ghcr.io/overture-stack/song-server:5.2.0 container_name: song platform: linux/amd64 @@ -323,7 +328,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-elasticsearch # -------------------------------------- elasticsearch: - profiles: ["platform", "stageDev", "arrangerDev"] + profiles: ["platform", "stageDev", "arrangerDev", "maestroDev"] image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1 container_name: elasticsearch platform: linux/amd64 @@ -406,7 +411,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-arranger # -------------------------------------- arranger-server: - profiles: ["platform", stageDev] + profiles: ["platform", "stageDev"] image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.33 container_name: arranger-server platform: linux/amd64 From 0c18601974a28b211078919653b4ce42a3adcd89 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 17:40:03 -0400 Subject: [PATCH 06/34] re-renamed scripts folders, updated scripts accordingly --- .../arrangerDev.sh | 4 ++-- .../maestroDev.sh | 8 ++++---- .../platform.sh | 14 +++++++------- .../stageDev.sh | 4 ++-- .../arrangerSetup.sh | 0 .../elasticsearchSetup.sh | 0 .../keycloakDbSetup.sh | 0 .../{serviceScripts => services}/maestroSetup.sh | 0 .../{serviceScripts => services}/songDbSetup.sh | 0 .../{serviceScripts => services}/songSetup.sh | 0 .../{serviceScripts => services}/stageSetup.sh | 0 docker-compose.yml | 16 ++++++++-------- 12 files changed, 23 insertions(+), 23 deletions(-) rename conductorScripts/{deploymentScripts => deployments}/arrangerDev.sh (95%) rename conductorScripts/{deploymentScripts => deployments}/maestroDev.sh (89%) rename conductorScripts/{deploymentScripts => deployments}/platform.sh (85%) rename conductorScripts/{deploymentScripts => deployments}/stageDev.sh (94%) rename conductorScripts/{serviceScripts => services}/arrangerSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/elasticsearchSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/keycloakDbSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/maestroSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/songDbSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/songSetup.sh (100%) rename conductorScripts/{serviceScripts => services}/stageSetup.sh (100%) diff --git a/conductorScripts/deploymentScripts/arrangerDev.sh b/conductorScripts/deployments/arrangerDev.sh similarity index 95% rename from conductorScripts/deploymentScripts/arrangerDev.sh rename to conductorScripts/deployments/arrangerDev.sh index c77b89ed..876485f0 100755 --- a/conductorScripts/deploymentScripts/arrangerDev.sh +++ b/conductorScripts/deployments/arrangerDev.sh @@ -11,14 +11,14 @@ rs() { } # Elasticsearch Setup -rs /scripts/serviceScripts/elasticSearchSetup.sh +rs /scripts/services/elasticSearchSetup.sh # Update Conductor to Healthy Status echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Stage -rs /scripts/serviceScripts/stageSetup.sh +rs /scripts/services/stageSetup.sh # Remove Health Check File rm /health/conductor_health diff --git a/conductorScripts/deploymentScripts/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh similarity index 89% rename from conductorScripts/deploymentScripts/maestroDev.sh rename to conductorScripts/deployments/maestroDev.sh index 803ff5da..c34bffb5 100755 --- a/conductorScripts/deploymentScripts/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -11,16 +11,16 @@ rs() { } # KeycloakDb Setup -rs /scripts/serviceScripts/keycloakDbSetup.sh +rs /scripts/services/keycloakDbSetup.sh # SongDb Setup -rs /scripts/serviceScripts/songDbSetup.sh +rs /scripts/services/songDbSetup.sh # Song Setup -rs /scripts/serviceScripts/songSetup.sh +rs /scripts/services/songSetup.sh # Elasticsearch Setup -rs /scripts/serviceScripts/elasticSearchSetup.sh +rs /scripts/services/elasticSearchSetup.sh # Success and Next Steps echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" diff --git a/conductorScripts/deploymentScripts/platform.sh b/conductorScripts/deployments/platform.sh similarity index 85% rename from conductorScripts/deploymentScripts/platform.sh rename to conductorScripts/deployments/platform.sh index 75036b02..186f3cc8 100755 --- a/conductorScripts/deploymentScripts/platform.sh +++ b/conductorScripts/deployments/platform.sh @@ -11,27 +11,27 @@ rs() { } # Database Setups -rs /scripts/serviceScripts/songDbSetup.sh -rs /scripts/serviceScripts/keycloakDbSetup.sh +rs /scripts/services/songDbSetup.sh +rs /scripts/services/keycloakDbSetup.sh # Elasticsearch Setup -rs /scripts/serviceScripts/elasticSearchSetup.sh +rs /scripts/services/elasticSearchSetup.sh # Song Setup -rs /scripts/serviceScripts/songSetup.sh +rs /scripts/services/songSetup.sh # Update Conductor to Healthy Status echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Maestro -rs /scripts/serviceScripts/maestroSetup.sh +rs /scripts/services/maestroSetup.sh # Check Arranger -rs /scripts/serviceScripts/arrangerSetup.sh +rs /scripts/services/arrangerSetup.sh # Check Stage -rs /scripts/serviceScripts/stageSetup.sh +rs /scripts/services/stageSetup.sh # Remove Health Check File rm /health/conductor_health diff --git a/conductorScripts/deploymentScripts/stageDev.sh b/conductorScripts/deployments/stageDev.sh similarity index 94% rename from conductorScripts/deploymentScripts/stageDev.sh rename to conductorScripts/deployments/stageDev.sh index 90de0a3a..cb8df4e0 100755 --- a/conductorScripts/deploymentScripts/stageDev.sh +++ b/conductorScripts/deployments/stageDev.sh @@ -11,14 +11,14 @@ rs() { } # Elasticsearch Setup -rs /scripts/serviceScripts/elasticSearchSetup.sh +rs /scripts/services/elasticSearchSetup.sh # Update Conductor to Healthy Status echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Arranger -rs /scripts/serviceScripts/arrangerSetup.sh +rs /scripts/services/arrangerSetup.sh # Remove Health Check File rm /health/conductor_health diff --git a/conductorScripts/serviceScripts/arrangerSetup.sh b/conductorScripts/services/arrangerSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/arrangerSetup.sh rename to conductorScripts/services/arrangerSetup.sh diff --git a/conductorScripts/serviceScripts/elasticsearchSetup.sh b/conductorScripts/services/elasticsearchSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/elasticsearchSetup.sh rename to conductorScripts/services/elasticsearchSetup.sh diff --git a/conductorScripts/serviceScripts/keycloakDbSetup.sh b/conductorScripts/services/keycloakDbSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/keycloakDbSetup.sh rename to conductorScripts/services/keycloakDbSetup.sh diff --git a/conductorScripts/serviceScripts/maestroSetup.sh b/conductorScripts/services/maestroSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/maestroSetup.sh rename to conductorScripts/services/maestroSetup.sh diff --git a/conductorScripts/serviceScripts/songDbSetup.sh b/conductorScripts/services/songDbSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/songDbSetup.sh rename to conductorScripts/services/songDbSetup.sh diff --git a/conductorScripts/serviceScripts/songSetup.sh b/conductorScripts/services/songSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/songSetup.sh rename to conductorScripts/services/songSetup.sh diff --git a/conductorScripts/serviceScripts/stageSetup.sh b/conductorScripts/services/stageSetup.sh similarity index 100% rename from conductorScripts/serviceScripts/stageSetup.sh rename to conductorScripts/services/stageSetup.sh diff --git a/docker-compose.yml b/docker-compose.yml index 296898b9..cf5afb45 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,23 +21,23 @@ services: case "$PROFILE" in platform) echo "Running platform deployment..." - chmod +x scripts/deploymentScripts/platform.sh - scripts/deploymentScripts/platform.sh + chmod +x scripts/deployments/platform.sh + scripts/deployments/platform.sh ;; stageDev) echo "Running Stage development environment..." - chmod +x scripts/deploymentScripts/stageDev.sh - scripts/deploymentScripts/stageDev.sh + chmod +x scripts/deployments/stageDev.sh + scripts/deployments/stageDev.sh ;; arrangerDev) echo "Running Arranger development environment..." - chmod +x scripts/deploymentScripts/arrangerDev.sh - scripts/deploymentScripts/arrangerDev.sh + chmod +x scripts/deployments/arrangerDev.sh + scripts/deployments/arrangerDev.sh ;; maestroDev) echo "Running Maestro development environment..." - chmod +x scripts/deploymentScripts/maestroDev.sh - scripts/deploymentScripts/maestroDev.sh + chmod +x scripts/deployments/maestroDev.sh + scripts/deployments/maestroDev.sh ;; *) echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." From b2b72abe6d2721f91890d7eacf315e09b960e3f4 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 17:59:36 -0400 Subject: [PATCH 07/34] added songDev profile --- Makefile | 3 +++ conductorScripts/deployments/songDev.sh | 30 +++++++++++++++++++++++++ docker-compose.yml | 20 +++++++++-------- 3 files changed, 44 insertions(+), 9 deletions(-) create mode 100755 conductorScripts/deployments/songDev.sh diff --git a/Makefile b/Makefile index 508f0402..7a594f00 100644 --- a/Makefile +++ b/Makefile @@ -10,5 +10,8 @@ arrangerDev: maestroDev: PROFILE=maestroDev docker compose --profile maestroDev up --attach conductor +songDev: + PROFILE=songDev docker compose --profile songDev up --attach conductor + down: docker compose down diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh new file mode 100755 index 00000000..e8dde021 --- /dev/null +++ b/conductorScripts/deployments/songDev.sh @@ -0,0 +1,30 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔═════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the SongDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚═════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# KeycloakDb Setup +rs /scripts/services/keycloakDbSetup.sh + +# SongDb Setup +rs /scripts/services/songDbSetup.sh + +# Success and Next Steps +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;36m╔═══════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Song Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run Song locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0m\n" +echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m3️⃣ Rename \033[1;32m.env.songDev\033[0m to \033[1;32m.env:\033[0m\n" +echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index cf5afb45..737ba3ad 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -39,12 +39,16 @@ services: chmod +x scripts/deployments/maestroDev.sh scripts/deployments/maestroDev.sh ;; + songDev) + echo "Running Maestro development environment..." + chmod +x scripts/deployments/songDev.sh + scripts/deployments/songDev.sh + ;; *) echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." exit 1 ;; esac - exit 0 ' healthcheck: @@ -65,7 +69,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: - profiles: ["platform", "maestroDev"] + profiles: ["platform", "songDev" ,"maestroDev"] depends_on: - conductor image: postgres:14 @@ -91,7 +95,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: - profiles: ["platform", "maestroDev"] + profiles: ["platform", "songDev" ,"maestroDev"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 @@ -131,7 +135,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-kafka # -------------------------------------- kafka: - profiles: ["platform", maestroDev] + profiles: ["platform", "maestroDev"] image: confluentinc/cp-kafka:7.6.1 container_name: kafka platform: linux/amd64 @@ -165,7 +169,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song-db: - profiles: ["platform", "maestroDev"] + profiles: ["platform", "maestroDev", "songDev"] image: postgres:11.1 container_name: song-db platform: linux/amd64 @@ -246,7 +250,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#setting-up-object-storage # -------------------------------------- minio: - profiles: ["platform"] + profiles: ["platform", "songDev"] image: minio/minio:RELEASE.2018-05-11T00-29-24Z container_name: minio platform: linux/amd64 @@ -271,15 +275,13 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-score # -------------------------------------- score: - profiles: ["platform"] + profiles: ["platform", "songDev"] image: ghcr.io/overture-stack/score-server:5.11.0 container_name: score platform: linux/amd64 depends_on: keycloak: condition: service_started - song: - condition: service_started ports: - "8087:8087" environment: From 252f34e6c0010414fe317e48f752f09389c42df9 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 18:17:34 -0400 Subject: [PATCH 08/34] added scoreDev profile --- conductorScripts/deployments/scoreDev.sh | 33 ++++++++++++++++++++++++ docker-compose.yml | 19 ++++++++------ 2 files changed, 44 insertions(+), 8 deletions(-) create mode 100755 conductorScripts/deployments/scoreDev.sh diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh new file mode 100755 index 00000000..79699ead --- /dev/null +++ b/conductorScripts/deployments/scoreDev.sh @@ -0,0 +1,33 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the scoreDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# KeycloakDb Setup +rs /scripts/services/keycloakDbSetup.sh + +# SongDb Setup +rs /scripts/services/songDbSetup.sh + +# Song Setup +rs /scripts/services/songSetup.sh + +# Success and Next Steps +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;36m╔══════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Score Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════╝\033[0m" +echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/score.git\033[0m\n" +echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m3️⃣ Rename \033[1;32m.env.scoreDev\033[0m to \033[1;32m.env:\033[0m\n" +echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 737ba3ad..3a93e8e0 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -40,10 +40,15 @@ services: scripts/deployments/maestroDev.sh ;; songDev) - echo "Running Maestro development environment..." + echo "Running Song development environment..." chmod +x scripts/deployments/songDev.sh scripts/deployments/songDev.sh ;; + scoreDev) + echo "Running Score development environment..." + chmod +x scripts/deployments/scoreDev.sh + scripts/deployments/scoreDev.sh + ;; *) echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." exit 1 @@ -69,7 +74,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: - profiles: ["platform", "songDev" ,"maestroDev"] + profiles: ["platform", "songDev" , "scoreDev" ,"maestroDev"] depends_on: - conductor image: postgres:14 @@ -95,7 +100,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: - profiles: ["platform", "songDev" ,"maestroDev"] + profiles: ["platform", "songDev", "scoreDev", "maestroDev"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 @@ -169,7 +174,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song-db: - profiles: ["platform", "maestroDev", "songDev"] + profiles: ["platform", "songDev", "scoreDev", "maestroDev"] image: postgres:11.1 container_name: song-db platform: linux/amd64 @@ -195,15 +200,13 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song: - profiles: ["platform", "maestroDev"] + profiles: ["platform", "scoreDev", "maestroDev"] image: ghcr.io/overture-stack/song-server:5.2.0 container_name: song platform: linux/amd64 depends_on: keycloak: condition: service_started - kafka: - condition: service_started song-db: condition: service_healthy ports: @@ -250,7 +253,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#setting-up-object-storage # -------------------------------------- minio: - profiles: ["platform", "songDev"] + profiles: ["platform", "scoreDev", "songDev"] image: minio/minio:RELEASE.2018-05-11T00-29-24Z container_name: minio platform: linux/amd64 From edab084efc564f9b61c06586762011506b68a2eb Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 20 Sep 2024 18:20:16 -0400 Subject: [PATCH 09/34] updated make file and added a .bat file for windows users --- Makefile | 5 ++++- make.bat | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+), 1 deletion(-) create mode 100644 make.bat diff --git a/Makefile b/Makefile index 7a594f00..71c8bd46 100644 --- a/Makefile +++ b/Makefile @@ -13,5 +13,8 @@ maestroDev: songDev: PROFILE=songDev docker compose --profile songDev up --attach conductor +scoreDev: + PROFILE=scoreDev docker compose --profile scoreDev up --attach conductor + down: - docker compose down + PROFILE=platform docker compose --profile platform down diff --git a/make.bat b/make.bat new file mode 100644 index 00000000..1fd591ce --- /dev/null +++ b/make.bat @@ -0,0 +1,51 @@ +@echo off +setlocal enabledelayedexpansion + +if "%1"=="" goto help + +if "%1"=="platform" ( + set PROFILE=platform + goto run +) +if "%1"=="stageDev" ( + set PROFILE=stageDev + goto run +) +if "%1"=="arrangerDev" ( + set PROFILE=arrangerDev + goto run +) +if "%1"=="maestroDev" ( + set PROFILE=maestroDev + goto run +) +if "%1"=="songDev" ( + set PROFILE=songDev + goto run +) +if "%1"=="scoreDev" ( + set PROFILE=scoreDev + goto run +) +if "%1"=="down" ( + set PROFILE=platfrom + docker compose down + goto :eof +) + +goto help + +:run +docker compose --profile %PROFILE% up --attach conductor +goto :eof + +:help +echo Usage: build.bat [target] +echo Available targets: +echo platform +echo stageDev +echo arrangerDev +echo maestroDev +echo songDev +echo scoreDev +echo down \ No newline at end of file From ad42f4c44939534a458006b474cf03f2ba7552bc Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 23 Sep 2024 11:36:40 -0400 Subject: [PATCH 10/34] update to readme --- README.md | 74 +++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 55 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index b35e004c..2156ebdc 100644 --- a/README.md +++ b/README.md @@ -1,33 +1,69 @@ -# Overture QuickStart +# Conductor -The Overture QuickStart provides those interested in gaining hands-on experience using an Overture platform a fast and frictionless local installation. +Conductor is a flexible Docker Compose setup that simplifies the process of spinning up Overture development and deployment configurations using Docker profiles and extensible scripting events. -## Getting Started +## Key Features -**1. Download and configure Docker Desktop** +- **Profile-based Deployments**: Uses Docker profiles to manage different environment setups. +- **Conductor-driven Execution**: The Conductor service executes ordered scripts based on the `PROFILE` environment variable. -In Docker Desktop click the cog icon , then resources. We recommend at minimum setting your CPU limit to 8, memory to 8GB, swap to 2GB, with64GB of virtual disk space available. If you have Docker already installed ensure it is up to date. +## Getting Started -**2. Clone the QuickStart Repository** +**1. Clone the repo branch** -```bash -git clone https://github.com/overture-stack/composer.git && cd composer ``` +git clone -b concerto https://github.com/overture-stack/composer.git && cd composer +``` + +**2. Run one of the following commands to spin up different environments:** + +| Environment | Unix/macOS | Windows | +|-------------|------------|---------| +| Overture Platform | `make platform` | `make.bat platform` | +| Stage Dev | `make stageDev` | `make.bat stageDev` | +| Arranger Dev | `make arrangerDev` | `make.bat arrangerDev` | +| Maestro Dev | `make maestroDev` | `make.bat maestroDev` | +| Song Dev | `make songDev` | `make.bat songDev` | +| Score Dev | `make scoreDev` | `make.bat scoreDev` | -**3. Run the Docker Compose with attach mode enabled** +Each command spins up complementary services for the specified development environment. -```bash -docker compose up --attach conductor +## Repository Structure + +``` +. +├── conductorScripts/ +│ ├── deployments +│ └── services +├── configurationFiles/ +│ ├── arrangerConfigs +│ ├── elasticsearchConfigs +│ └── keycloakConfigs +├── guideMaterials +├── persistentStorage/ +│ ├── data-keycloak-db +│ ├── data-minio +│ └── data-song-db +├── Makefile +└── make.bat ``` -Your portal will be accessible from your `localhost:3000` +- **`conductorScripts/`** Contains scripts for orchestrating the deployment process. + - `deployments/`: Scripts that execute service scripts sequentially based on the deployment configuration. These also include custom post-deployment logs with essential next steps for the deployment scenario. + - `services/`: Modular scripts for individual service setup tasks. Each file is named according to its purpose, with inline comments documenting the code. + +- **`configurationFiles/`** Stores all required configuration files, including: + - `arrangerConfigs/`: Configuration files specific to Arranger. + - `elasticsearchConfigs/`: Configuration files for Elasticsearch, encompassing indexing mappings and documents for seeding data. + - `keycloakConfigs/`: Configuration files for Keycloak, including preconfigured realm files and Overture API key provider details. + +- **`guideMaterials/`** Supplementary folders and files for use with the [Overture guides](https://www.overture.bio/documentation/guides/). -## Rational +- **`persistentStorage/`** Directory for storing persistent data during container startups and restarts. These folders come pre-loaded with mock data. + - `data-keycloak-db/`: Persistent local storage for the Keycloak database. + - `data-minio/`: Persistent local storage for MinIO object storage. + - `data-song-db/`: Persistent local storage for the Song database. -With Overture we want to provide new users the following: +- **`Makefile`** Contains make commands for Unix-based systems (macOS, Linux) to streamline Docker operations. -|Purpose|Solution| -|---|---| -| **A way to look at it**|[Overture Demo Portal](https://demo.overture.bio/)| -| **A way to try it**| Overture QuickStart | -| **A way to own it**| [Product Documentation](https://www.overture.bio/documentation/) *and* [Platform Guides](https://github.com/overture-stack/website/pull/385)| +- **`make.bat`** Windows equivalent of the Makefile, featuring batch commands tailored for Windows systems. From afc2219458c36bc2f4437a112e91c368330875b0 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Thu, 26 Sep 2024 21:01:07 -0400 Subject: [PATCH 11/34] partial update to scripts removed unnecessary env variables --- conductorScripts/deployments/arrangerDev.sh | 17 +++++++++++------ conductorScripts/deployments/platform.sh | 8 +++++++- conductorScripts/deployments/stageDev.sh | 5 +++-- conductorScripts/services/arrangerSetup.sh | 2 +- conductorScripts/services/elasticsearchSetup.sh | 10 +++++----- conductorScripts/services/keycloakDbSetup.sh | 4 ++-- conductorScripts/services/maestroSetup.sh | 2 +- conductorScripts/services/songDbSetup.sh | 4 ++-- conductorScripts/services/songSetup.sh | 2 +- conductorScripts/services/stageSetup.sh | 2 +- docker-compose.yml | 5 ----- 11 files changed, 34 insertions(+), 27 deletions(-) diff --git a/conductorScripts/deployments/arrangerDev.sh b/conductorScripts/deployments/arrangerDev.sh index 876485f0..ba602be1 100755 --- a/conductorScripts/deployments/arrangerDev.sh +++ b/conductorScripts/deployments/arrangerDev.sh @@ -24,14 +24,19 @@ rs /scripts/services/stageSetup.sh rm /health/conductor_health # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable\n" echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" echo -e "\033[1;36m║ Arranger Dev Service Setup Complete ║\033[0m" -echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m\n" echo -e "\033[1m1️⃣ To run Arranger locally, start by cloning the repo:\033[0m\n" echo -e " \033[1;32mgit clone https://github.com/overture-stack/arranger.git\033[0m\n" -echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd arranger\033[0m\n" +echo -e "\033[1m3️⃣ Copy the example environment file:\033[0m\n" +echo -e " \033[1;32mcp .env.arrangerDev .env\033[0m\n" +echo -e "\033[1m4️⃣ Install the dependencies:\033[0m\n" echo -e " \033[1;32mnpm ci\033[0m\n" -echo -e "\033[1m3️⃣ Rename \033[1;32m.env.arrangerDev\033[0m to \033[1;32m.env:\033[0m\n" -echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file +echo -e "\033[1m5️⃣ Bootstrap the project:\033[0m\n" +echo -e " \033[1;32mnpm run bootstrap\033[0m\n" +echo -e "\033[1m6️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run server\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/platform.sh b/conductorScripts/deployments/platform.sh index 186f3cc8..18f4e866 100755 --- a/conductorScripts/deployments/platform.sh +++ b/conductorScripts/deployments/platform.sh @@ -11,13 +11,16 @@ rs() { } # Database Setups +echo -e "\033[1;35m[1/6]\033[0m Starting up postgres databases" rs /scripts/services/songDbSetup.sh rs /scripts/services/keycloakDbSetup.sh # Elasticsearch Setup +echo -e "\033[1;35m[2/6]\033[0m Setting up Elasticsearch" rs /scripts/services/elasticSearchSetup.sh # Song Setup +echo -e "\033[1;35m[3/6]\033[0m Starting up Song" rs /scripts/services/songSetup.sh # Update Conductor to Healthy Status @@ -25,12 +28,15 @@ echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Maestro +echo -e "\033[1;35m[4/6]\033[0m Starting up Maestro (this may take a few minutes)" rs /scripts/services/maestroSetup.sh # Check Arranger +echo -e "\033[1;35m[5/6]\033[0m Setting up Arranger" rs /scripts/services/arrangerSetup.sh # Check Stage +echo -e "\033[1;35m[6/6]\033[0m Checking on Stage" rs /scripts/services/stageSetup.sh # Remove Health Check File @@ -46,4 +52,4 @@ echo -e "\033[1m📚 Overture Platform Guides:\033[0m" echo -e " \033[1;32mhttps://www.overture.bio/documentation/guides/\033[0m\n" echo -e "\033[1m🛠️ QuickStart Information:\033[0m" echo -e " Check the \033[1;33mdocker-compose.yml\033[0m file for details on this QuickStart," -echo -e " including links to relevant sections of our deployment guide.\n" \ No newline at end of file +echo -e " including links to relevant sections of our deployment guide.\n" diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deployments/stageDev.sh index cb8df4e0..2863c989 100755 --- a/conductorScripts/deployments/stageDev.sh +++ b/conductorScripts/deployments/stageDev.sh @@ -11,6 +11,7 @@ rs() { } # Elasticsearch Setup +echo -e "\033[1;35m[1/2]\033[0m Setting up Elasticsearch" rs /scripts/services/elasticSearchSetup.sh # Update Conductor to Healthy Status @@ -18,16 +19,16 @@ echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Arranger +echo -e "\033[1;35m[2/2]\033[0m Setting up Arranger" rs /scripts/services/arrangerSetup.sh # Remove Health Check File rm /health/conductor_health # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" echo -e "\033[1;36m╔═══════════════════════════════════════╗\033[0m" echo -e "\033[1;36m║ Stage Dev Service Setup Complete ║\033[0m" -echo -e "\033[1;36m╚═══════════════════════════════════════╝\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════════╝\033[0m\n" echo -e "\033[1m1️⃣ To run Stage locally, start by cloning the repo:\033[0m\n" echo -e " \033[1;32mgit clone https://github.com/overture-stack/stage.git\033[0m\n" echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" diff --git a/conductorScripts/services/arrangerSetup.sh b/conductorScripts/services/arrangerSetup.sh index a2f2ecb6..93be94f0 100755 --- a/conductorScripts/services/arrangerSetup.sh +++ b/conductorScripts/services/arrangerSetup.sh @@ -1,6 +1,6 @@ #!/bin/sh - echo -e "\033[1;35m[9/10]\033[0m Checking if Arranger is reachable" + echo -e "Checking if Arranger is reachable" until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 20 seconds" sleep 20 diff --git a/conductorScripts/services/elasticsearchSetup.sh b/conductorScripts/services/elasticsearchSetup.sh index e0f3b741..6587a161 100755 --- a/conductorScripts/services/elasticsearchSetup.sh +++ b/conductorScripts/services/elasticsearchSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Wait for Elasticsearch -echo -e "\033[1;35m[3/10]\033[0m Waiting for Elasticsearch (this may take a few minutes)" +echo -e "\033[1;36mElasticsearch:\033[0m Starting up (this may take a few minutes)" sleep 20 until curl -s -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/_cluster/health" > /dev/null; do echo -e "\033[1;36mElasticsearch:\033[0m Not yet reachable, checking again in 30 seconds" @@ -10,7 +10,7 @@ done echo -e "\033[1;32mSuccess:\033[0m Elasticsearch is reachable" # Set up Elasticsearch index template -echo -e "\033[1;35m[4/10]\033[0m Setting up Elasticsearch index template" +echo -e "Setting up the Elasticsearch index template" if ! curl -s -u elastic:myelasticpassword "http://elasticsearch:9200/_template/index_template" | grep -q "\"index_patterns\""; then curl -s -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/_template/index_template" \ -H "Content-Type: application/json" -d @/usr/share/elasticsearch/config/quickstart_index_template.json > /dev/null && @@ -20,10 +20,10 @@ else fi # Set up Elasticsearch index and alias (needs failure check) -echo -e "\033[1;35m[5/10]\033[0m Setting up Elasticsearch index and alias" +echo -e "Setting up the Elasticsearch index and alias" echo -e "\033[1;36mElasticsearch:\033[0m Checking if Elasticsearch index exists" if ! curl -s -f -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/overture-quickstart-index" > /dev/null 2>&1; then - echo -e "\033[1;32mElasticsearch:\033[0m Creating Elasticsearch index and alias" + echo -e "\033[1;36mElasticsearch:\033[0m Creating Elasticsearch index and alias" response=$(curl -s -w "\n%{http_code}" -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/overture-quickstart-index" \ -H "Content-Type: application/json" -d "{\"aliases\": {\"file_centric\": {\"is_write_index\": true}}}") http_code=$(echo "$response" | tail -n1) @@ -34,7 +34,7 @@ else fi # Importing Elasticsearch Documents -echo -e "\033[1;35m[6/10]\033[0m Importing Elasticsearch Documents" +echo -e "Importing Elasticsearch Documents" for f in ./es-docs/*.json; do object_id=$(basename "$f" .json) curl --user elastic:myelasticpassword -sL -X POST \ diff --git a/conductorScripts/services/keycloakDbSetup.sh b/conductorScripts/services/keycloakDbSetup.sh index 35e8efdd..f4fdfb00 100755 --- a/conductorScripts/services/keycloakDbSetup.sh +++ b/conductorScripts/services/keycloakDbSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Create missing empty directories not tracked by git and needed by postgres -echo -e "\033[1;35m[2/10]\033[0m Setting up empty directories for Keycloaks postgres database" +echo -e "Setting up empty directories for Keycloaks postgres database" mkdir -p keycloak/db-folder-init/pg_tblspc mkdir -p keycloak/db-folder-init/pg_stat mkdir -p keycloak/db-folder-init/pg_replslot @@ -14,4 +14,4 @@ mkdir -p keycloak/db-folder-init/pg_commit_ts mkdir -p keycloak/db-folder-init/pg_wal/archive_status mkdir -p keycloak/db-folder-init/pg_logical/snapshots mkdir -p keycloak/db-folder-init/pg_logical/mappings -echo -e "\033[1;32mSuccess:\033[0m Keycloak Databases ready" +echo -e "\033[1;32mSuccess:\033[0m Keycloak Database ready" diff --git a/conductorScripts/services/maestroSetup.sh b/conductorScripts/services/maestroSetup.sh index dfb72438..5eaff6d2 100755 --- a/conductorScripts/services/maestroSetup.sh +++ b/conductorScripts/services/maestroSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Check Maestro -echo -e "\033[1;35m[8/10]\033[0m Checking if Maestro is reachable (this may take a few minutes)" +echo -e "Checking if Maestro is reachable (this may take a few minutes)" until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study/demo" -H "accept: */*" -d "{}" | grep -q "true"; do echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" sleep 30 diff --git a/conductorScripts/services/songDbSetup.sh b/conductorScripts/services/songDbSetup.sh index a95e6a50..9f6cb51d 100755 --- a/conductorScripts/services/songDbSetup.sh +++ b/conductorScripts/services/songDbSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Create missing empty directories not tracked by git and needed by postgres -echo -e "\033[1;35m[1/10]\033[0m Setting up empty directories for Songs postgres database" +echo -e "Setting up empty directories for Songs postgres database" mkdir -p song/db-folder-init/pg_tblspc mkdir -p song/db-folder-init/pg_stat mkdir -p song/db-folder-init/pg_replslot @@ -10,4 +10,4 @@ mkdir -p song/db-folder-init/pg_snapshots mkdir -p song/db-folder-init/pg_commit_ts mkdir -p song/db-folder-init/pg_logical/snapshots mkdir -p song/db-folder-init/pg_logical/mappings -echo -e "\033[1;32mSuccess:\033[0m Song Databases ready" +echo -e "\033[1;32mSuccess:\033[0m Song Database ready" diff --git a/conductorScripts/services/songSetup.sh b/conductorScripts/services/songSetup.sh index 5ec68974..42105c5e 100755 --- a/conductorScripts/services/songSetup.sh +++ b/conductorScripts/services/songSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Check for Song -echo -e "\033[1;35m[7/10]\033[0m Checking if Song is ready" +echo -e "Checking if Song is ready" until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 20 seconds" sleep 20 diff --git a/conductorScripts/services/stageSetup.sh b/conductorScripts/services/stageSetup.sh index 89ba4467..1e44f7fd 100755 --- a/conductorScripts/services/stageSetup.sh +++ b/conductorScripts/services/stageSetup.sh @@ -1,7 +1,7 @@ #!/bin/sh # Check Stage -echo -e "\033[1;35m[10/10]\033[0m Checking if Stage is reachable" +echo -e "Checking if Stage is reachable" until curl -s -o /dev/null -w "%{http_code}" "http://stage:3000" | grep -q "200"; do echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" sleep 10 diff --git a/docker-compose.yml b/docker-compose.yml index 3a93e8e0..44c91b91 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -438,9 +438,6 @@ services: ES_HOST: http://elasticsearch:9200 ES_USER: elastic ES_PASS: myelasticpassword - # Stage Variables - REACT_APP_BASE_URL: http://stage:3000 - REACT_APP_ARRANGER_ADMIN_ROOT: http://arranger-server:5050/graphql # ================================================================================== # F. Discovery (Stage) @@ -478,8 +475,6 @@ services: NEXT_PUBLIC_KEYCLOAK_CLIENT_ID: webclient KEYCLOAK_CLIENT_SECRET: ikksyrYaKX07acf4hpGrpKWcUGaFkEdM NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE: dms - # Score Variables - NEXT_PUBLIC_SCORE_API_URL: http://score:8087 # Arranger Variables NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE: file NEXT_PUBLIC_ARRANGER_INDEX: file_centric From 45d48bb538d5e3eda8fa00540b2c3dd4dda6bad5 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 30 Sep 2024 21:53:52 -0400 Subject: [PATCH 12/34] updated scripts and improved logging --- conductorScripts/deployments/arrangerDev.sh | 5 +- conductorScripts/deployments/maestroDev.sh | 28 +++++------ conductorScripts/deployments/platform.sh | 49 ++++++++++++------- conductorScripts/deployments/scoreDev.sh | 27 +++++----- conductorScripts/deployments/songDev.sh | 28 +++++------ conductorScripts/deployments/stageDev.sh | 37 +++++++++++--- .../{arrangerSetup.sh => arrangerCheck.sh} | 0 conductorScripts/services/keycloakCheck.sh | 8 +++ conductorScripts/services/keycloakDbSetup.sh | 4 +- .../{maestroSetup.sh => maestroCheck.sh} | 0 conductorScripts/services/minioCheck.sh | 7 +++ conductorScripts/services/scoreCheck.sh | 8 +++ .../services/{songSetup.sh => songCheck.sh} | 1 - conductorScripts/services/songDbSetup.sh | 5 +- .../services/{stageSetup.sh => stageCheck.sh} | 0 docker-compose.yml | 12 ++--- 16 files changed, 134 insertions(+), 85 deletions(-) rename conductorScripts/services/{arrangerSetup.sh => arrangerCheck.sh} (100%) create mode 100755 conductorScripts/services/keycloakCheck.sh rename conductorScripts/services/{maestroSetup.sh => maestroCheck.sh} (100%) create mode 100755 conductorScripts/services/minioCheck.sh create mode 100755 conductorScripts/services/scoreCheck.sh rename conductorScripts/services/{songSetup.sh => songCheck.sh} (88%) rename conductorScripts/services/{stageSetup.sh => stageCheck.sh} (100%) diff --git a/conductorScripts/deployments/arrangerDev.sh b/conductorScripts/deployments/arrangerDev.sh index ba602be1..4e1b720a 100755 --- a/conductorScripts/deployments/arrangerDev.sh +++ b/conductorScripts/deployments/arrangerDev.sh @@ -11,6 +11,7 @@ rs() { } # Elasticsearch Setup +echo -e "\033[1;35m[1/2]\033[0m Setting up Elasticsearch" rs /scripts/services/elasticSearchSetup.sh # Update Conductor to Healthy Status @@ -18,13 +19,13 @@ echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Stage -rs /scripts/services/stageSetup.sh +echo -e "\033[1;35m[2/2]\033[0m Checking Stage" +rs /scripts/services/stageCheck.sh # Remove Health Check File rm /health/conductor_health # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable\n" echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" echo -e "\033[1;36m║ Arranger Dev Service Setup Complete ║\033[0m" echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m\n" diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh index c34bffb5..9be67b89 100755 --- a/conductorScripts/deployments/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -10,27 +10,21 @@ rs() { chmod +x "$1" && "$1" } -# KeycloakDb Setup +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Song & Keycloak databases" rs /scripts/services/keycloakDbSetup.sh - -# SongDb Setup rs /scripts/services/songDbSetup.sh -# Song Setup -rs /scripts/services/songSetup.sh +# Song Check +echo -e "\033[1;35m[2/4]\033[0m Checking Song" +rs /scripts/services/songCheck.sh # Elasticsearch Setup -rs /scripts/services/elasticSearchSetup.sh +echo -e "\033[1;35m[3/4]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticsearchSetup.sh + +# Check Keycloak +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" -echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Maestro Dev Service Setup Complete ║\033[0m" -echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m" -echo -e "\033[1m1️⃣ To run Maestro locally, start by cloning the repo:\033[0m\n" -echo -e " \033[1;32mgit clone https://github.com/overture-stack/maestro.git\033[0m\n" -echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" -echo -e " \033[1;32mnpm ci\033[0m\n" -echo -e "\033[1m3️⃣ Rename \033[1;32m.env.maestroDev\033[0m to \033[1;32m.env:\033[0m\n" -echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/platform.sh b/conductorScripts/deployments/platform.sh index 18f4e866..401d0f3d 100755 --- a/conductorScripts/deployments/platform.sh +++ b/conductorScripts/deployments/platform.sh @@ -1,9 +1,9 @@ #!/bin/sh # Welcome -echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Welcome to the Overture QuickStart ║\033[0m" -echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" +echo -e "\033[1;36m╔═══════════════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the Overture Platform QuickStart ║\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════════════════════╝\033[0m" # rs = "Run Script" a simple function to apply permissions and run scripts rs() { @@ -11,33 +11,45 @@ rs() { } # Database Setups -echo -e "\033[1;35m[1/6]\033[0m Starting up postgres databases" +echo -e "\033[1;35m[1/9]\033[0m Setting up Song & Keycloak databases" rs /scripts/services/songDbSetup.sh rs /scripts/services/keycloakDbSetup.sh -# Elasticsearch Setup -echo -e "\033[1;35m[2/6]\033[0m Setting up Elasticsearch" -rs /scripts/services/elasticSearchSetup.sh +# Minio Check +echo -e "\033[1;35m[2/9]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/9]\033[0m Checking on Score" +rs /scripts/services/scoreCheck.sh # Song Setup -echo -e "\033[1;35m[3/6]\033[0m Starting up Song" -rs /scripts/services/songSetup.sh +echo -e "\033[1;35m[4/9]\033[0m Checking on Song" +rs /scripts/services/songCheck.sh -# Update Conductor to Healthy Status +# Elasticsearch Setup +echo -e "\033[1;35m[5/9]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticSearchSetup.sh + +# Update Conductor to Healthy Status, this signals search and exploration services (maestro, arranger, stage) to startup echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" -# Check Maestro -echo -e "\033[1;35m[4/6]\033[0m Starting up Maestro (this may take a few minutes)" -rs /scripts/services/maestroSetup.sh +# Check Stage +echo -e "\033[1;35m[7/9]\033[0m Checking Stage" +rs /scripts/services/stageCheck.sh # Check Arranger -echo -e "\033[1;35m[5/6]\033[0m Setting up Arranger" -rs /scripts/services/arrangerSetup.sh +echo -e "\033[1;35m[6/9]\033[0m Checking Arranger" +rs /scripts/services/arrangerCheck.sh -# Check Stage -echo -e "\033[1;35m[6/6]\033[0m Checking on Stage" -rs /scripts/services/stageSetup.sh +# Check Maestro +echo -e "\033[1;35m[8/9]\033[0m Checking Maestro" +rs /scripts/services/maestroCheck.sh + +# Check Keycloak +echo -e "\033[1;35m[9/9]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh # Remove Health Check File rm /health/conductor_health @@ -46,6 +58,7 @@ rm /health/conductor_health echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" echo -e "\033[1;36m║ Overture QuickStart Setup Complete ║\033[0m" echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" +echo -e "\n" echo -e "\033[1m🌐 Front-end Portal:\033[0m" echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" echo -e "\033[1m📚 Overture Platform Guides:\033[0m" diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh index 79699ead..439d0244 100755 --- a/conductorScripts/deployments/scoreDev.sh +++ b/conductorScripts/deployments/scoreDev.sh @@ -10,24 +10,21 @@ rs() { chmod +x "$1" && "$1" } -# KeycloakDb Setup +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Song & Keycloak databases" rs /scripts/services/keycloakDbSetup.sh - -# SongDb Setup rs /scripts/services/songDbSetup.sh +# Minio Check +echo -e "\033[1;35m[2/4]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + # Song Setup -rs /scripts/services/songSetup.sh +echo -e "\033[1;35m[3/6]\033[0m Checking Song" +rs /scripts/services/songCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" -echo -e "\033[1;36m╔══════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Score Dev Service Setup Complete ║\033[0m" -echo -e "\033[1;36m╚══════════════════════════════════╝\033[0m" -echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" -echo -e " \033[1;32mgit clone https://github.com/overture-stack/score.git\033[0m\n" -echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" -echo -e " \033[1;32mnpm ci\033[0m\n" -echo -e "\033[1m3️⃣ Rename \033[1;32m.env.scoreDev\033[0m to \033[1;32m.env:\033[0m\n" -echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh index e8dde021..b581f053 100755 --- a/conductorScripts/deployments/songDev.sh +++ b/conductorScripts/deployments/songDev.sh @@ -10,21 +10,21 @@ rs() { chmod +x "$1" && "$1" } -# KeycloakDb Setup +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Song and Keycloak databases" rs /scripts/services/keycloakDbSetup.sh - -# SongDb Setup rs /scripts/services/songDbSetup.sh +# Minio Check +echo -e "\033[1;35m[2/4]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/4]\033[0m Checking Score" +rs /scripts/services/scoreCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + # Success and Next Steps -echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" -echo -e "\033[1;36m╔═══════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Song Dev Service Setup Complete ║\033[0m" -echo -e "\033[1;36m╚═══════════════════════════════════╝\033[0m" -echo -e "\033[1m1️⃣ To run Song locally, start by cloning the repo:\033[0m\n" -echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0m\n" -echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" -echo -e " \033[1;32mnpm ci\033[0m\n" -echo -e "\033[1m3️⃣ Rename \033[1;32m.env.songDev\033[0m to \033[1;32m.env:\033[0m\n" -echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deployments/stageDev.sh index 2863c989..98440a05 100755 --- a/conductorScripts/deployments/stageDev.sh +++ b/conductorScripts/deployments/stageDev.sh @@ -10,8 +10,12 @@ rs() { chmod +x "$1" && "$1" } +# Keycloak Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Keycloak database" +rs /scripts/services/keycloakDbSetup.sh + # Elasticsearch Setup -echo -e "\033[1;35m[1/2]\033[0m Setting up Elasticsearch" +echo -e "\033[1;35m[2/4]\033[0m Setting up Elasticsearch" rs /scripts/services/elasticSearchSetup.sh # Update Conductor to Healthy Status @@ -19,8 +23,12 @@ echo "healthy" > /health/conductor_health echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" # Check Arranger -echo -e "\033[1;35m[2/2]\033[0m Setting up Arranger" -rs /scripts/services/arrangerSetup.sh +echo -e "\033[1;35m[3/4]\033[0m Checking Arranger" +rs /scripts/services/arrangerCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh # Remove Health Check File rm /health/conductor_health @@ -29,10 +37,25 @@ rm /health/conductor_health echo -e "\033[1;36m╔═══════════════════════════════════════╗\033[0m" echo -e "\033[1;36m║ Stage Dev Service Setup Complete ║\033[0m" echo -e "\033[1;36m╚═══════════════════════════════════════╝\033[0m\n" + echo -e "\033[1m1️⃣ To run Stage locally, start by cloning the repo:\033[0m\n" echo -e " \033[1;32mgit clone https://github.com/overture-stack/stage.git\033[0m\n" -echo -e "\033[1m2️⃣ Then install the dependencies by running:\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd stage\033[0m\n" + +echo -e "\033[1m3️⃣ Copy the example environment file:\033[0m\n" +echo -e " \033[1;32mcp .env.arrangerDev .env\033[0m\n" + +echo -e "\033[1m4️⃣ Install the dependencies:\033[0m\n" echo -e " \033[1;32mnpm ci\033[0m\n" -echo -e "\033[1m3️⃣ Rename \033[1;32m.env.stageDev\033[0m to \033[1;32m.env:\033[0m\n" -echo -e "\033[1m4️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run dev\033[0m\n" \ No newline at end of file + +echo -e "\033[1m This will require:\033[0m" +echo -e "\033[1;34m - Node v16 or higher\033[0m" +echo -e "\033[1;34m - npm v8.3.0 or higher\033[0m\n" + +echo -e "\033[1m5️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" + +echo -e "\033[1mYour development server will be accessible at:\n" +echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" diff --git a/conductorScripts/services/arrangerSetup.sh b/conductorScripts/services/arrangerCheck.sh similarity index 100% rename from conductorScripts/services/arrangerSetup.sh rename to conductorScripts/services/arrangerCheck.sh diff --git a/conductorScripts/services/keycloakCheck.sh b/conductorScripts/services/keycloakCheck.sh new file mode 100755 index 00000000..4cf752d1 --- /dev/null +++ b/conductorScripts/services/keycloakCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +# Check for Keycloak +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://keycloak:8080/health/live")" = "200" ]; do + echo -e "\033[1;36mKeycloak:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Keycloak is reachable" diff --git a/conductorScripts/services/keycloakDbSetup.sh b/conductorScripts/services/keycloakDbSetup.sh index f4fdfb00..2b901f14 100755 --- a/conductorScripts/services/keycloakDbSetup.sh +++ b/conductorScripts/services/keycloakDbSetup.sh @@ -4,6 +4,7 @@ echo -e "Setting up empty directories for Keycloaks postgres database" mkdir -p keycloak/db-folder-init/pg_tblspc mkdir -p keycloak/db-folder-init/pg_stat +mkdir -p keycloak/db-folder-init/pg_stat_tmp mkdir -p keycloak/db-folder-init/pg_replslot mkdir -p keycloak/db-folder-init/pg_dynshmem mkdir -p keycloak/db-folder-init/pg_twophase @@ -13,5 +14,4 @@ mkdir -p keycloak/db-folder-init/pg_snapshots mkdir -p keycloak/db-folder-init/pg_commit_ts mkdir -p keycloak/db-folder-init/pg_wal/archive_status mkdir -p keycloak/db-folder-init/pg_logical/snapshots -mkdir -p keycloak/db-folder-init/pg_logical/mappings -echo -e "\033[1;32mSuccess:\033[0m Keycloak Database ready" +mkdir -p keycloak/db-folder-init/pg_logical/mappings \ No newline at end of file diff --git a/conductorScripts/services/maestroSetup.sh b/conductorScripts/services/maestroCheck.sh similarity index 100% rename from conductorScripts/services/maestroSetup.sh rename to conductorScripts/services/maestroCheck.sh diff --git a/conductorScripts/services/minioCheck.sh b/conductorScripts/services/minioCheck.sh new file mode 100755 index 00000000..8af12e6d --- /dev/null +++ b/conductorScripts/services/minioCheck.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://minio:9000/minio/health/live")" = "200" ]; do + echo -e "\033[1;36mMinio:\033[0m Not yet reachable, checking again in 15 seconds" + sleep 15 +done +echo -e "\033[1;32mSuccess:\033[0m Minio is reachable" diff --git a/conductorScripts/services/scoreCheck.sh b/conductorScripts/services/scoreCheck.sh new file mode 100755 index 00000000..cba7bcec --- /dev/null +++ b/conductorScripts/services/scoreCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +# Check for Score +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://score:8087/download/ping" -H "accept: */*" -H "Authorization: 68fb42b4-f1ed-4e8c-beab-3724b99fe528" -H "User-Agent: unknown")" = "200" ]; do + echo -e "\033[1;36mScore:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 +done +echo -e "\033[1;32mSuccess:\033[0m Score is now reachable" diff --git a/conductorScripts/services/songSetup.sh b/conductorScripts/services/songCheck.sh similarity index 88% rename from conductorScripts/services/songSetup.sh rename to conductorScripts/services/songCheck.sh index 42105c5e..fd515161 100755 --- a/conductorScripts/services/songSetup.sh +++ b/conductorScripts/services/songCheck.sh @@ -1,7 +1,6 @@ #!/bin/sh # Check for Song -echo -e "Checking if Song is ready" until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 20 seconds" sleep 20 diff --git a/conductorScripts/services/songDbSetup.sh b/conductorScripts/services/songDbSetup.sh index 9f6cb51d..c79148df 100755 --- a/conductorScripts/services/songDbSetup.sh +++ b/conductorScripts/services/songDbSetup.sh @@ -4,10 +4,9 @@ echo -e "Setting up empty directories for Songs postgres database" mkdir -p song/db-folder-init/pg_tblspc mkdir -p song/db-folder-init/pg_stat -mkdir -p song/db-folder-init/pg_replslot +mkdir -p song/db-folder-init/pg_stat_tmp mkdir -p song/db-folder-init/pg_twophase mkdir -p song/db-folder-init/pg_snapshots mkdir -p song/db-folder-init/pg_commit_ts -mkdir -p song/db-folder-init/pg_logical/snapshots +mkdir -p song/db-folder-init/pg_logical/snapshotss mkdir -p song/db-folder-init/pg_logical/mappings -echo -e "\033[1;32mSuccess:\033[0m Song Database ready" diff --git a/conductorScripts/services/stageSetup.sh b/conductorScripts/services/stageCheck.sh similarity index 100% rename from conductorScripts/services/stageSetup.sh rename to conductorScripts/services/stageCheck.sh diff --git a/docker-compose.yml b/docker-compose.yml index 44c91b91..e846a54b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -10,7 +10,7 @@ services: - ./persistentStorage/data-song-db:/song/db-folder-init - ./configurationFiles/elasticsearchConfigs/quickstart_index_template.json:/usr/share/elasticsearch/config/quickstart_index_template.json - ./configurationFiles/elasticsearchConfigs/es-docs:/es-docs - - ./conductorScripts/:/scripts + - ./conductorScripts:/scripts - ./health:/health environment: - PROFILE=${PROFILE:-platform} @@ -58,10 +58,10 @@ services: ' healthcheck: test: ["CMD", "test", "-f", "/health/conductor_health"] - interval: 30s - timeout: 10s + interval: 5s + timeout: 40s retries: 100 - start_period: 45s + start_period: 30s # ================================================================================== # OAuth (KeyCloak) @@ -74,7 +74,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: - profiles: ["platform", "songDev" , "scoreDev" ,"maestroDev"] + profiles: ["platform", "songDev" , "scoreDev" ,"maestroDev", "stageDev"] depends_on: - conductor image: postgres:14 @@ -100,7 +100,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: - profiles: ["platform", "songDev", "scoreDev", "maestroDev"] + profiles: ["platform", "songDev", "scoreDev", "maestroDev", "stageDev"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 From d005302671bab3d84f1463b3153706c52e38a570 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 30 Sep 2024 22:08:04 -0400 Subject: [PATCH 13/34] spacing --- conductorScripts/deployments/arrangerDev.sh | 2 +- conductorScripts/services/stageCheck.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conductorScripts/deployments/arrangerDev.sh b/conductorScripts/deployments/arrangerDev.sh index 4e1b720a..80f4eafe 100755 --- a/conductorScripts/deployments/arrangerDev.sh +++ b/conductorScripts/deployments/arrangerDev.sh @@ -40,4 +40,4 @@ echo -e " \033[1;32mnpm ci\033[0m\n" echo -e "\033[1m5️⃣ Bootstrap the project:\033[0m\n" echo -e " \033[1;32mnpm run bootstrap\033[0m\n" echo -e "\033[1m6️⃣ Run the development server:\033[0m\n" -echo -e " \033[1;32mnpm run server\033[0m\n" \ No newline at end of file +echo -e " \033[1;32mnpm run server\033[0m\n" diff --git a/conductorScripts/services/stageCheck.sh b/conductorScripts/services/stageCheck.sh index 1e44f7fd..f07d08b9 100755 --- a/conductorScripts/services/stageCheck.sh +++ b/conductorScripts/services/stageCheck.sh @@ -6,4 +6,4 @@ echo -e "Checking if Stage is reachable" echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" sleep 10 done -echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" \ No newline at end of file +echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" From 342bf65a31d65958dc69e60cbdcbaf8111f5ceb3 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Tue, 1 Oct 2024 11:26:21 -0400 Subject: [PATCH 14/34] minor updates --- conductorScripts/deployments/songDev.sh | 26 ++++++++++++++++++++ conductorScripts/deployments/stageDev.sh | 2 +- conductorScripts/services/keycloakDbSetup.sh | 2 +- conductorScripts/services/maestroCheck.sh | 2 +- 4 files changed, 29 insertions(+), 3 deletions(-) diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh index b581f053..aec047b0 100755 --- a/conductorScripts/deployments/songDev.sh +++ b/conductorScripts/deployments/songDev.sh @@ -28,3 +28,29 @@ echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" rs /scripts/services/keycloakCheck.sh # Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ SongDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Song locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd song\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1mThis will require:\033[0m" +echo -e "\033[1;34m - JDK11\033[0m" +echo -e "\033[1;34m - Maven3\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32mcd song-server/\033[0m\n" +echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=noSecurityDev,default,score-client-cred\033[0m\n" + +echo -e "\033[1mYour development server will be accessible at:\n" +echo -e " \033[1;32mhttp://localhost:8080\033[0m\n" + +echo -e "\033[1mSongs Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:8080/swagger-ui.html\033[0m\n" diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deployments/stageDev.sh index 98440a05..d36544fc 100755 --- a/conductorScripts/deployments/stageDev.sh +++ b/conductorScripts/deployments/stageDev.sh @@ -45,7 +45,7 @@ echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" echo -e " \033[1;32mcd stage\033[0m\n" echo -e "\033[1m3️⃣ Copy the example environment file:\033[0m\n" -echo -e " \033[1;32mcp .env.arrangerDev .env\033[0m\n" +echo -e " \033[1;32mcp .env.stageDev .env\033[0m\n" echo -e "\033[1m4️⃣ Install the dependencies:\033[0m\n" echo -e " \033[1;32mnpm ci\033[0m\n" diff --git a/conductorScripts/services/keycloakDbSetup.sh b/conductorScripts/services/keycloakDbSetup.sh index 2b901f14..3af80fa0 100755 --- a/conductorScripts/services/keycloakDbSetup.sh +++ b/conductorScripts/services/keycloakDbSetup.sh @@ -14,4 +14,4 @@ mkdir -p keycloak/db-folder-init/pg_snapshots mkdir -p keycloak/db-folder-init/pg_commit_ts mkdir -p keycloak/db-folder-init/pg_wal/archive_status mkdir -p keycloak/db-folder-init/pg_logical/snapshots -mkdir -p keycloak/db-folder-init/pg_logical/mappings \ No newline at end of file +mkdir -p keycloak/db-folder-init/pg_logical/mappings diff --git a/conductorScripts/services/maestroCheck.sh b/conductorScripts/services/maestroCheck.sh index 5eaff6d2..7a60c551 100755 --- a/conductorScripts/services/maestroCheck.sh +++ b/conductorScripts/services/maestroCheck.sh @@ -6,4 +6,4 @@ until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" sleep 30 done -echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" \ No newline at end of file +echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" From dd0973375399b2c1fef47bdc3aea6728c188137e Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 7 Oct 2024 13:01:27 -0400 Subject: [PATCH 15/34] updated updated host port on songDb --- conductorScripts/deployments/scoreDev.sh | 21 ++++++++++++++++++++- conductorScripts/deployments/songDev.sh | 11 ++--------- docker-compose.yml | 8 +++++--- 3 files changed, 27 insertions(+), 13 deletions(-) diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh index 439d0244..fb9b589b 100755 --- a/conductorScripts/deployments/scoreDev.sh +++ b/conductorScripts/deployments/scoreDev.sh @@ -2,7 +2,7 @@ # Welcome echo -e "\033[1;36m╔════════════════════════════════════╗\033[0m" -echo -e "\033[1;36m║ Welcome to the scoreDev QuickStart ║\033[0m" +echo -e "\033[1;36m║ Welcome to the ScoreDev QuickStart ║\033[0m" echo -e "\033[1;36m╚════════════════════════════════════╝\033[0m" # rs = "Run Script" a simple function to apply permissions and run scripts @@ -28,3 +28,22 @@ echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" rs /scripts/services/keycloakCheck.sh # Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ ScoreDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/score.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd score\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32mcd score-server/\033[0m\n" +echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev\033[0m\n" + +echo -e "\033[1mScores Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:8087/swagger-ui.html\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh index aec047b0..912ddf19 100755 --- a/conductorScripts/deployments/songDev.sh +++ b/conductorScripts/deployments/songDev.sh @@ -38,19 +38,12 @@ echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0 echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" echo -e " \033[1;32mcd song\033[0m\n" -echo -e "\033[1m3️⃣ Build the application:\033[0m\n" +echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" -echo -e "\033[1mThis will require:\033[0m" -echo -e "\033[1;34m - JDK11\033[0m" -echo -e "\033[1;34m - Maven3\033[0m\n" - echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" echo -e " \033[1;32mcd song-server/\033[0m\n" -echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=noSecurityDev,default,score-client-cred\033[0m\n" - -echo -e "\033[1mYour development server will be accessible at:\n" -echo -e " \033[1;32mhttp://localhost:8080\033[0m\n" +echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=default,dev,secure\033[0m\n" echo -e "\033[1mSongs Swagger UI can be accessed from:\n" echo -e " \033[1;32mhttp://localhost:8080/swagger-ui.html\033[0m\n" diff --git a/docker-compose.yml b/docker-compose.yml index e846a54b..c9288234 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -78,8 +78,8 @@ services: depends_on: - conductor image: postgres:14 - container_name: keycloak-db platform: linux/amd64 + container_name: keycloak-db environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 @@ -175,11 +175,13 @@ services: # -------------------------------------- song-db: profiles: ["platform", "songDev", "scoreDev", "maestroDev"] + depends_on: + - conductor image: postgres:11.1 container_name: song-db platform: linux/amd64 - depends_on: - - conductor + ports: + - "5434" environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 From 5987124716fa253370c92e3ba5c7f50bba60c394 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 7 Oct 2024 13:22:05 -0400 Subject: [PATCH 16/34] updated updated host port on songDb --- docker-compose.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index c9288234..f248441c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -180,8 +180,6 @@ services: image: postgres:11.1 container_name: song-db platform: linux/amd64 - ports: - - "5434" environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 From 886630e621757558e9d1387e476b92e363478fee Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 7 Oct 2024 13:48:22 -0400 Subject: [PATCH 17/34] updated script for generating empty postgres directories --- conductorScripts/services/songDbSetup.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conductorScripts/services/songDbSetup.sh b/conductorScripts/services/songDbSetup.sh index c79148df..8d1b1950 100755 --- a/conductorScripts/services/songDbSetup.sh +++ b/conductorScripts/services/songDbSetup.sh @@ -10,3 +10,5 @@ mkdir -p song/db-folder-init/pg_snapshots mkdir -p song/db-folder-init/pg_commit_ts mkdir -p song/db-folder-init/pg_logical/snapshotss mkdir -p song/db-folder-init/pg_logical/mappings +mkdir -p song/db-folder-init/pg_replslot +mkdir -p song/db-folder-init/pg_logical/snapshots From 8667609024f308798fd3536f0133a046dba2fed4 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 7 Oct 2024 14:14:08 -0400 Subject: [PATCH 18/34] fixed port and songDev script --- conductorScripts/deployments/songDev.sh | 5 ++--- docker-compose.yml | 2 ++ 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh index 912ddf19..879ca012 100755 --- a/conductorScripts/deployments/songDev.sh +++ b/conductorScripts/deployments/songDev.sh @@ -38,12 +38,11 @@ echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0 echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" echo -e " \033[1;32mcd song\033[0m\n" -echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" +echo -e "\033[1m3️⃣ Build the application \033[1;34m(Requires JDK11)\033[0m:\033[0m\n" echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" -echo -e " \033[1;32mcd song-server/\033[0m\n" -echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=default,dev,secure\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -Dspring-boot.run.profiles=default,dev,secure -pl song-server\033[0m\n" echo -e "\033[1mSongs Swagger UI can be accessed from:\n" echo -e " \033[1;32mhttp://localhost:8080/swagger-ui.html\033[0m\n" diff --git a/docker-compose.yml b/docker-compose.yml index f248441c..93638a26 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -180,6 +180,8 @@ services: image: postgres:11.1 container_name: song-db platform: linux/amd64 + ports: + - "5433:5432" environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 From a8f19a2a5577a44a9e97e6274fc8cbf1567ce64e Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 7 Oct 2024 16:29:26 -0400 Subject: [PATCH 19/34] added healthcheck file removal at startup --- conductorScripts/deployments/platform.sh | 3 +++ conductorScripts/services/healthcheckCleanup.sh | 4 ++++ 2 files changed, 7 insertions(+) create mode 100755 conductorScripts/services/healthcheckCleanup.sh diff --git a/conductorScripts/deployments/platform.sh b/conductorScripts/deployments/platform.sh index 401d0f3d..ded7c1c7 100755 --- a/conductorScripts/deployments/platform.sh +++ b/conductorScripts/deployments/platform.sh @@ -10,6 +10,9 @@ rs() { chmod +x "$1" && "$1" } +# Cleanup any existing healthcheck file +rs scripts/services/healthcheckCleanup.sh + # Database Setups echo -e "\033[1;35m[1/9]\033[0m Setting up Song & Keycloak databases" rs /scripts/services/songDbSetup.sh diff --git a/conductorScripts/services/healthcheckCleanup.sh b/conductorScripts/services/healthcheckCleanup.sh new file mode 100755 index 00000000..b3e30c8f --- /dev/null +++ b/conductorScripts/services/healthcheckCleanup.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +# If the health check file exists on startup it needs to be removed +rm /health/conductor_health 2>/dev/null \ No newline at end of file From d7c0dd830eb126a6f2979b514c972c93952563c8 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Tue, 8 Oct 2024 11:37:30 -0400 Subject: [PATCH 20/34] minor fix to deployment scripts and compose comment --- conductorScripts/deployments/maestroDev.sh | 18 ++++++++++++++++++ conductorScripts/deployments/scoreDev.sh | 3 +-- docker-compose.yml | 6 +++--- 3 files changed, 22 insertions(+), 5 deletions(-) diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh index 9be67b89..d5b508e9 100755 --- a/conductorScripts/deployments/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -28,3 +28,21 @@ echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" rs /scripts/services/keycloakCheck.sh # Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ MaestroDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/maestro.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd score\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -pl maestro-app\033[0m\n" + +echo -e "\033[1mMaestro's Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:11235/api-docsl\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh index fb9b589b..147c6ff6 100755 --- a/conductorScripts/deployments/scoreDev.sh +++ b/conductorScripts/deployments/scoreDev.sh @@ -42,8 +42,7 @@ echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" -echo -e " \033[1;32mcd score-server/\033[0m\n" -echo -e " \033[1;32mmvn spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev -pl score-server\033[0m\n" echo -e "\033[1mScores Swagger UI can be accessed from:\n" echo -e " \033[1;32mhttp://localhost:8087/swagger-ui.html\033[0m\n" \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 93638a26..78c5aabc 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -70,7 +70,7 @@ services: # ====================================== # Keycloak Database # -------------------------------------- - # Pre-populated with a system side API key: 68fb42b4-f1ed-4e8c-beab-3724b99fe528, required for Songs SCORE_ACCESSTOKEN env variable + # Pre-populated with a system wide API key: 68fb42b4-f1ed-4e8c-beab-3724b99fe528, required for Songs SCORE_ACCESSTOKEN env variable # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: @@ -391,7 +391,7 @@ services: MAESTRO_REPOSITORIES_0_CODE: song.overture MAESTRO_REPOSITORIES_0_URL: http://song:8080 MAESTRO_REPOSITORIES_0_NAME: Overture - MAESTRO_REPOSITORIES_0_ORGANIZATION: Overture + MAESTRO_REPOSITORIES_0_ORGANIZATION: OICR MAESTRO_REPOSITORIES_0_COUNTRY: CA # Elasticsearch Variables MAESTRO_ELASTICSEARCH_CLUSTER_NODES: http://elasticsearch:9200 @@ -403,7 +403,7 @@ services: MAESTRO_ELASTICSEARCH_INDEXES_FILECENTRIC_NAME: overture-quickstart-index MAESTRO_ELASTICSEARCH_INDEXES_FILECENTRIC_ALIAS: file_centric MAESTRO_ELASTICSEARCH_CLIENT_BASICAUTH_ENABLED: true - MANAGEMENT_HEALTH_ELASTICSEARCH_ENABLED: "false" + MANAGEMENT_HEALTH_ELASTICSEARCH_ENABLED: false # Spring Variables SPRING_MVC_ASYNC_REQUESTTIMEOUT: -1 SPRINGDOC_SWAGGERUI_PATH: /swagger-api From bac5ef8ed4b500d6d0a854991786147ae7d8e3c5 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Thu, 10 Oct 2024 09:15:42 -0400 Subject: [PATCH 21/34] minor fix to maestro log --- conductorScripts/deployments/maestroDev.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh index d5b508e9..749f2d24 100755 --- a/conductorScripts/deployments/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -36,7 +36,7 @@ echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m echo -e " \033[1;32mgit clone https://github.com/overture-stack/maestro.git\033[0m\n" echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" -echo -e " \033[1;32mcd score\033[0m\n" +echo -e " \033[1;32mcd maestro\033[0m\n" echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" From 2ea8ab1f3294ae02558ba46e4d96434af23de98b Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Tue, 29 Oct 2024 12:46:56 -0400 Subject: [PATCH 22/34] update & tested maestroDev & platform kafka configuration --- conductorScripts/deployments/maestroDev.sh | 18 +++-- conductorScripts/services/kafkaSetup.sh | 21 ++++++ docker-compose.yml | 88 +++++++++++++++------- 3 files changed, 93 insertions(+), 34 deletions(-) create mode 100755 conductorScripts/services/kafkaSetup.sh diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh index 749f2d24..2db11759 100755 --- a/conductorScripts/deployments/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -11,20 +11,28 @@ rs() { } # Keycloak and Song Db Setup -echo -e "\033[1;35m[1/4]\033[0m Setting up Song & Keycloak databases" +echo -e "\033[1;35m[1/6]\033[0m Setting up Song & Keycloak databases" rs /scripts/services/keycloakDbSetup.sh rs /scripts/services/songDbSetup.sh +# Minio Check +echo -e "\033[1;35m[2/6]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/6]\033[0m Checking on Score" +rs /scripts/services/scoreCheck.sh + # Song Check -echo -e "\033[1;35m[2/4]\033[0m Checking Song" +echo -e "\033[1;35m[4/6]\033[0m Checking Song" rs /scripts/services/songCheck.sh # Elasticsearch Setup -echo -e "\033[1;35m[3/4]\033[0m Setting up Elasticsearch" +echo -e "\033[1;35m[5/6]\033[0m Setting up Elasticsearch" rs /scripts/services/elasticsearchSetup.sh # Check Keycloak -echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +echo -e "\033[1;35m[6/6]\033[0m Checking Keycloak" rs /scripts/services/keycloakCheck.sh # Success and Next Steps @@ -45,4 +53,4 @@ echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" echo -e " \033[1;32m./mvnw spring-boot:run -pl maestro-app\033[0m\n" echo -e "\033[1mMaestro's Swagger UI can be accessed from:\n" -echo -e " \033[1;32mhttp://localhost:11235/api-docsl\033[0m\n" \ No newline at end of file +echo -e " \033[1;32mhttp://localhost:11235/api-docs\033[0m\n" \ No newline at end of file diff --git a/conductorScripts/services/kafkaSetup.sh b/conductorScripts/services/kafkaSetup.sh new file mode 100755 index 00000000..2aea3c3c --- /dev/null +++ b/conductorScripts/services/kafkaSetup.sh @@ -0,0 +1,21 @@ +#!/bin/sh + +# Quick check if Kafka is ready +until /bin/kafka-topics --bootstrap-server kafka:9092 --list > /dev/null 2>&1; do + echo -e "\033[1;33mWaiting:\033[0m Kafka not ready yet..." + sleep 5 +done + +# Create topic if it doesn't exist +echo -e "\033[1;36mSetting up Kafka:\033[0m Creating Kafka topic for Song" +/bin/kafka-topics --bootstrap-server kafka:9092 --create --if-not-exists \ + --topic song-analysis \ + --partitions 1 \ + --replication-factor 1 \ + --config cleanup.policy=delete \ + --config retention.ms=604800000 + +# Update healthcheck to just verify +echo "Verifying Kafka topic creation" +/bin/kafka-topics --bootstrap-server kafka:9092 --describe --topic song-analysis +echo -e "\033[1;32mSuccess:\033[0m Kafka Overture Setup Script Complete" \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 78c5aabc..3c405f50 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -140,32 +140,60 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-kafka # -------------------------------------- kafka: - profiles: ["platform", "maestroDev"] - image: confluentinc/cp-kafka:7.6.1 - container_name: kafka - platform: linux/amd64 - ports: - - "9092:9092" - - "29092:29092" - environment: - KAFKA_PROCESS_ROLES: broker,controller - KAFKA_NODE_ID: 1 - KAFKA_LISTENERS: PLAINTEXT://kafka:9092,CONTROLLER://kafka:9093 - KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092 - KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: PLAINTEXT:PLAINTEXT,CONTROLLER:PLAINTEXT - KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT - KAFKA_CONTROLLER_QUORUM_VOTERS: 1@kafka:9093 - KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER - KAFKA_LOG_DIRS: /var/lib/kafka/data - KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1 - KAFKA_AUTO_CREATE_TOPICS_ENABLE: false - KAFKA_NUM_PARTITIONS: 1 - CLUSTER_ID: "q1Sh-9_ISia_zwGINzRvyQ" - healthcheck: - test: ["CMD", "sh", "-c", "echo stats | nc localhost 9092"] - interval: 30s - timeout: 10s - retries: 5 + profiles: ["platform", "maestroDev"] + image: confluentinc/cp-kafka:7.6.1 + container_name: kafka + platform: linux/amd64 + ports: + - "9092:9092" + - "29092:29092" + volumes: + - ./conductorScripts/services/kafkaSetup.sh:/scripts/kafkaSetup.sh + environment: + # Core Kafka Configuration + KAFKA_PROCESS_ROLES: broker,controller + KAFKA_NODE_ID: 1 + KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:29092 + KAFKA_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://0.0.0.0:29092,CONTROLLER://kafka:9093 + KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: PLAINTEXT:PLAINTEXT,EXTERNAL:PLAINTEXT,CONTROLLER:PLAINTEXT + KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT + KAFKA_CONTROLLER_QUORUM_VOTERS: 1@kafka:9093 + KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER + # Storage Configuration + KAFKA_LOG_DIRS: /var/lib/kafka/data + KAFKA_LOG_RETENTION_HOURS: 168 # 7 days + KAFKA_LOG_RETENTION_BYTES: -1 # Unlimited size + # Topic Configuration + KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1 + KAFKA_AUTO_CREATE_TOPICS_ENABLE: false + KAFKA_NUM_PARTITIONS: 1 + KAFKA_DEFAULT_REPLICATION_FACTOR: 1 + KAFKA_MIN_INSYNC_REPLICAS: 1 + # Performance Tuning + KAFKA_MESSAGE_MAX_BYTES: 5242880 # 5MB max message size + KAFKA_REPLICA_FETCH_MAX_BYTES: 5242880 + # Logging Configuration + KAFKA_LOG4J_LOGGERS: "kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO" + KAFKA_LOG4J_ROOT_LOGLEVEL: INFO + # Cluster Configuration + CLUSTER_ID: "q1Sh-9_ISia_zwGINzRvyQ" + command: > + sh -c ' + echo "Setting up Kafka..." + chmod +x /scripts/kafkaSetup.sh + /scripts/kafkaSetup.sh & + + # Start Kafka broker + /etc/confluent/docker/run + ' + healthcheck: + test: + - "CMD-SHELL" + - > + /bin/kafka-topics --bootstrap-server kafka:9092 --list + interval: 10s + timeout: 5s + retries: 10 # ====================================== # Song Database @@ -209,6 +237,8 @@ services: depends_on: keycloak: condition: service_started + kafka: + condition: service_healthy song-db: condition: service_healthy ports: @@ -241,7 +271,7 @@ services: SPRING_DATASOURCE_USERNAME: admin SPRING_DATASOURCE_PASSWORD: admin123 # Kafka Variables - SPRING_KAFKA_BOOTSTRAPSERVERS: http://kafka:9092 + SPRING_KAFKA_BOOTSTRAPSERVERS: kafka:9092 SPRING_KAFKA_TEMPLATE_DEFAULTTOPIC: song-analysis # Swagger Variable SWAGGER_ALTERNATEURL: /swagger-api @@ -255,7 +285,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#setting-up-object-storage # -------------------------------------- minio: - profiles: ["platform", "scoreDev", "songDev"] + profiles: ["platform", "scoreDev", "songDev", "maestroDev"] image: minio/minio:RELEASE.2018-05-11T00-29-24Z container_name: minio platform: linux/amd64 @@ -280,7 +310,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-score # -------------------------------------- score: - profiles: ["platform", "songDev"] + profiles: ["platform", "songDev", "maestroDev"] image: ghcr.io/overture-stack/score-server:5.11.0 container_name: score platform: linux/amd64 From c08a60d28271223fd4da1d49c69e8d172a0fb043 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 11:41:19 -0500 Subject: [PATCH 23/34] updated persistent storage inline with main branch --- .gitignore | 3 ++- .../data-keycloak-db/base/16384/16385 | Bin 8192 -> 8192 bytes .../base/16384/pg_internal.init | Bin 155936 -> 155936 bytes .../data-keycloak-db/global/pg_control | Bin 8192 -> 8192 bytes .../data-keycloak-db/global/pg_internal.init | Bin 23840 -> 23840 bytes .../pg_logical/replorigin_checkpoint | Bin 8 -> 0 bytes .../data-keycloak-db/pg_stat/db_0.stat | Bin 1670 -> 0 bytes .../data-keycloak-db/pg_stat/db_16384.stat | Bin 30715 -> 0 bytes .../data-keycloak-db/pg_stat/global.stat | Bin 1335 -> 0 bytes .../data-keycloak-db/pg_stat_tmp/db_0.stat | Bin 0 -> 1670 bytes .../pg_stat_tmp/db_13780.stat | Bin 0 -> 5185 bytes .../pg_stat_tmp/db_16384.stat | Bin 0 -> 32195 bytes .../data-keycloak-db/pg_stat_tmp/global.stat | Bin 0 -> 1335 bytes .../pg_wal/000000010000000000000001 | Bin 16777216 -> 16777216 bytes .../data-keycloak-db/pg_xact/0000 | Bin 8192 -> 8192 bytes .../data-keycloak-db/postmaster.pid | 8 ++++++++ .../data-song-db/base/16384/1255 | Bin 630784 -> 630784 bytes .../data-song-db/base/16384/16588 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16601 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16614 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16765 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16947 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16949 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/16954 | Bin 16384 -> 16384 bytes .../data-song-db/base/16384/16961 | Bin 16384 -> 16384 bytes .../data-song-db/base/16384/2606 | Bin 8192 -> 8192 bytes .../data-song-db/base/16384/2619 | Bin 172032 -> 172032 bytes .../data-song-db/base/16384/pg_internal.init | Bin 141820 -> 141820 bytes .../data-song-db/global/pg_control | Bin 8192 -> 8192 bytes .../data-song-db/pg_stat/db_0.stat | Bin 1526 -> 0 bytes .../data-song-db/pg_stat/db_16384.stat | Bin 18595 -> 0 bytes .../data-song-db/pg_stat/global.stat | Bin 607 -> 0 bytes .../data-song-db/pg_stat_tmp/db_0.stat | Bin 0 -> 2033 bytes .../data-song-db/pg_stat_tmp/db_16384.stat | Bin 0 -> 26200 bytes .../data-song-db/pg_stat_tmp/global.stat | Bin 0 -> 607 bytes .../pg_wal/000000010000000000000001 | Bin 16777216 -> 16777216 bytes persistentStorage/data-song-db/pg_xact/0000 | Bin 8192 -> 8192 bytes persistentStorage/data-song-db/postmaster.pid | 8 ++++++++ 38 files changed, 18 insertions(+), 1 deletion(-) delete mode 100644 persistentStorage/data-keycloak-db/pg_logical/replorigin_checkpoint delete mode 100644 persistentStorage/data-keycloak-db/pg_stat/db_0.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat/db_16384.stat delete mode 100644 persistentStorage/data-keycloak-db/pg_stat/global.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_0.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_13780.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/db_16384.stat create mode 100644 persistentStorage/data-keycloak-db/pg_stat_tmp/global.stat create mode 100644 persistentStorage/data-keycloak-db/postmaster.pid delete mode 100644 persistentStorage/data-song-db/pg_stat/db_0.stat delete mode 100644 persistentStorage/data-song-db/pg_stat/db_16384.stat delete mode 100644 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z<372`1aIMXUYOuSnuvX6BArqY4XG^}7WKv0a1x{(6-y6P(>?^Ir9< z6*jA9cGxvbU-g(?BTXY#jM(-4@h1w~DHEKXu%_jYO5b&|<(qVoAn{zoZ~J5^x$Abm zeArd)Dvf@($R8qzKC!AutB$|T#@62ow*Sd!p^LU@SoZTZYeS$8#Kw(F=Y_yJTof_=EIil~HuNOstqbp9HZ{`gxpTD@9;yGfu zj9dSms^r)e&v#pv%(0~!KdEJM7~6Bjkc}_rZ@D_pU#Xm&71eI+;SAlP2K?Jv!+V48 z1+fp&Vnozb_w$#qS-pW|gqwVKOttnRRw(dIS^1aQmyEZ(KLdk5Q`s`X+5VH?o2N8x z`|M{55`S=p1urw$my8 Date: Mon, 4 Nov 2024 11:42:33 -0500 Subject: [PATCH 24/34] one less file --- .gitignore | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index a7dfb30e..496ee2ca 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1 @@ -.DS_Store -.env \ No newline at end of file +.DS_Store \ No newline at end of file From c33e93807f0b33b226af935d140755012307768b Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:15:38 -0500 Subject: [PATCH 25/34] Update make.bat Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- make.bat | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/make.bat b/make.bat index 1fd591ce..9e86a98a 100644 --- a/make.bat +++ b/make.bat @@ -48,4 +48,4 @@ echo arrangerDev echo maestroDev echo songDev echo scoreDev -echo down \ No newline at end of file +echo down From 83c9b460b6a3961f217a9255e477a953e2a323aa Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:19:18 -0500 Subject: [PATCH 26/34] Update conductorScripts/services/kafkaSetup.sh Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- conductorScripts/services/kafkaSetup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conductorScripts/services/kafkaSetup.sh b/conductorScripts/services/kafkaSetup.sh index 2aea3c3c..6589fc96 100755 --- a/conductorScripts/services/kafkaSetup.sh +++ b/conductorScripts/services/kafkaSetup.sh @@ -18,4 +18,4 @@ echo -e "\033[1;36mSetting up Kafka:\033[0m Creating Kafka topic for Song" # Update healthcheck to just verify echo "Verifying Kafka topic creation" /bin/kafka-topics --bootstrap-server kafka:9092 --describe --topic song-analysis -echo -e "\033[1;32mSuccess:\033[0m Kafka Overture Setup Script Complete" \ No newline at end of file +echo -e "\033[1;32mSuccess:\033[0m Kafka Overture Setup Script Complete" From 33678092bd17f04526615f6d57477eede0c1b161 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:19:24 -0500 Subject: [PATCH 27/34] Update conductorScripts/services/healthcheckCleanup.sh Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- conductorScripts/services/healthcheckCleanup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conductorScripts/services/healthcheckCleanup.sh b/conductorScripts/services/healthcheckCleanup.sh index b3e30c8f..8cb3521c 100755 --- a/conductorScripts/services/healthcheckCleanup.sh +++ b/conductorScripts/services/healthcheckCleanup.sh @@ -1,4 +1,4 @@ #!/bin/sh # If the health check file exists on startup it needs to be removed -rm /health/conductor_health 2>/dev/null \ No newline at end of file +rm /health/conductor_health 2>/dev/null From 6abb1fd625b78317de97c90a3b46b84e4ac9d8af Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:20:23 -0500 Subject: [PATCH 28/34] Update conductorScripts/deployments/scoreDev.sh Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- conductorScripts/deployments/scoreDev.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh index 147c6ff6..57a045e2 100755 --- a/conductorScripts/deployments/scoreDev.sh +++ b/conductorScripts/deployments/scoreDev.sh @@ -45,4 +45,4 @@ echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" echo -e " \033[1;32m./mvnw spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev -pl score-server\033[0m\n" echo -e "\033[1mScores Swagger UI can be accessed from:\n" -echo -e " \033[1;32mhttp://localhost:8087/swagger-ui.html\033[0m\n" \ No newline at end of file +echo -e " \033[1;32mhttp://localhost:8087/swagger-ui.html\033[0m\n" From 5176039fa308790a773ff64a61e604e0559b6955 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:21:26 -0500 Subject: [PATCH 29/34] Update conductorScripts/deployments/maestroDev.sh Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- conductorScripts/deployments/maestroDev.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh index 2db11759..899a9302 100755 --- a/conductorScripts/deployments/maestroDev.sh +++ b/conductorScripts/deployments/maestroDev.sh @@ -53,4 +53,4 @@ echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" echo -e " \033[1;32m./mvnw spring-boot:run -pl maestro-app\033[0m\n" echo -e "\033[1mMaestro's Swagger UI can be accessed from:\n" -echo -e " \033[1;32mhttp://localhost:11235/api-docs\033[0m\n" \ No newline at end of file +echo -e " \033[1;32mhttp://localhost:11235/api-docs\033[0m\n" From 59a380ba97ecab81bec542664196858308a03e29 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:21:41 -0500 Subject: [PATCH 30/34] Update README.md Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2156ebdc..4da8939d 100644 --- a/README.md +++ b/README.md @@ -64,6 +64,6 @@ Each command spins up complementary services for the specified development envir - `data-minio/`: Persistent local storage for MinIO object storage. - `data-song-db/`: Persistent local storage for the Song database. -- **`Makefile`** Contains make commands for Unix-based systems (macOS, Linux) to streamline Docker operations. +- **`Makefile`** Contains [`make` commands](https://www.gnu.org/software/make/manual/make.html#Overview-of-make) for Unix-based systems (macOS, Linux) to streamline Docker operations. - **`make.bat`** Windows equivalent of the Makefile, featuring batch commands tailored for Windows systems. From 92aec4d72e2e12f0e9d677c852f95ad4e7585bba Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:21:52 -0500 Subject: [PATCH 31/34] Update README.md Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4da8939d..8d828dc8 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Conductor is a flexible Docker Compose setup that simplifies the process of spin ## Getting Started -**1. Clone the repo branch** +**1. Clone the repo's `main` branch** ``` git clone -b concerto https://github.com/overture-stack/composer.git && cd composer From fe7c544d5633b6474b88d5d1475731e9e74c9aca Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 14:25:03 -0500 Subject: [PATCH 32/34] minor indentation fix --- conductorScripts/services/arrangerCheck.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conductorScripts/services/arrangerCheck.sh b/conductorScripts/services/arrangerCheck.sh index 93be94f0..5a9a5709 100755 --- a/conductorScripts/services/arrangerCheck.sh +++ b/conductorScripts/services/arrangerCheck.sh @@ -1,8 +1,8 @@ #!/bin/sh - echo -e "Checking if Arranger is reachable" - until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do - echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 20 seconds" - sleep 20 - done - echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" +echo -e "Checking if Arranger is reachable" + until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do + echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 + done +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" From 1aa9a695f76c0421bb0170cabff2ad0dcb3d781e Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Nov 2024 17:30:34 -0500 Subject: [PATCH 33/34] added gitattributes for CRLF to LF conversion on windows --- .gitattributes | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..fd23a936 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +conductorscripts/**/*.sh text eol=lf \ No newline at end of file From 7830070f9b8239171a6087b947d914c3ca90cdaa Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Tue, 5 Nov 2024 10:00:28 -0500 Subject: [PATCH 34/34] Update .gitattributes Co-authored-by: Anders Richardsson <2107110+justincorrigible@users.noreply.github.com> --- .gitattributes | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitattributes b/.gitattributes index fd23a936..21742c08 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -conductorscripts/**/*.sh text eol=lf \ No newline at end of file +conductorscripts/**/*.sh text eol=lf