From dea6f590cc46ca1b70ed18a088f32e7cfc4ae8e7 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Fri, 26 Aug 2022 12:08:22 +0900 Subject: [PATCH 1/9] add proxy-api --- .env | 3 + docker-compose.yml | 13 + docker/proxy-api/.node-version | 1 + docker/proxy-api/Dockerfile | 6 + docker/proxy-api/main.js | 64 ++ docker/proxy-api/package-lock.json | 918 +++++++++++++++++++++++++++++ docker/proxy-api/package.json | 19 + 7 files changed, 1024 insertions(+) create mode 100644 .env create mode 100644 docker-compose.yml create mode 100644 docker/proxy-api/.node-version create mode 100644 docker/proxy-api/Dockerfile create mode 100644 docker/proxy-api/main.js create mode 100644 docker/proxy-api/package-lock.json create mode 100644 docker/proxy-api/package.json diff --git a/.env b/.env new file mode 100644 index 0000000..014dfff --- /dev/null +++ b/.env @@ -0,0 +1,3 @@ +ELASTICSEARCH_HOST: "http://es01:9200" +PROXY_API_LOGGER: "on" +PROXY_API_PORT: "4001" diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..b6d8bb0 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,13 @@ +version: '3' +services: + proxy-api: + build: ./docker/proxy-api + ports: + - "4001:4001" + command: npm start + environment: + ELASTICSEARCH_HOST: $ELASTICSEARCH_HOST + LOGGER: $PROXY_API_LOGGER + PORT: $PROXY_API_PORT + depends_on: + - elasticsearch diff --git a/docker/proxy-api/.node-version b/docker/proxy-api/.node-version new file mode 100644 index 0000000..99cdd80 --- /dev/null +++ b/docker/proxy-api/.node-version @@ -0,0 +1 @@ +16.15.0 diff --git a/docker/proxy-api/Dockerfile b/docker/proxy-api/Dockerfile new file mode 100644 index 0000000..d051d85 --- /dev/null +++ b/docker/proxy-api/Dockerfile @@ -0,0 +1,6 @@ +FROM node:16 +WORKDIR /src/proxy-api +COPY . /src/proxy-api +EXPOSE 4001 +RUN npm install +CMD ["bash"] diff --git a/docker/proxy-api/main.js b/docker/proxy-api/main.js new file mode 100644 index 0000000..29278a4 --- /dev/null +++ b/docker/proxy-api/main.js @@ -0,0 +1,64 @@ +import Fastify from 'fastify' +import { Client } from '@elastic/elasticsearch' +import fastifyCors from '@fastify/cors' + +const fastify = Fastify({ + logger: process.env.LOGGER === 'on' ? true : false, +}) + +fastify.register(fastifyCors) + +const client = new Client({ + node: process.env.ELASTICSEARCH_HOST, +}) + +fastify.get('/', async (req) => { + // console.log(req.query) + req.log.info(JSON.stringify(req.query)) + + if (!req.query.q) { + return { hits: [] } + } + + const q = req.query.q.toLowerCase() + + const res = await client.search({ + "size": 1000, + "query": { + "bool": { + "should": [ + { + "wildcard": { + "id": { + "value": `*${q}*` + } + } + }, + { + "wildcard": { + "label": { + "value": `*${q}*` + } + } + }, + ], + "minimum_should_match": 1 + } + } + }) + // console.log(res.hits) + return { + hits: res.hits.hits + } +}) + +const start = async () => { + try { + await fastify.listen(process.env.PORT, '0.0.0.0') + } catch (e) { + fastify.log.error(err) + process.exit(1) + } +} + +start() diff --git a/docker/proxy-api/package-lock.json b/docker/proxy-api/package-lock.json new file mode 100644 index 0000000..6495fca --- /dev/null +++ b/docker/proxy-api/package-lock.json @@ -0,0 +1,918 @@ +{ + "name": "api", + "version": "1.0.0", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "name": "api", + "version": "1.0.0", + "license": "ISC", + "dependencies": { + "@elastic/elasticsearch": "^8.2.0-patch.1", + "@fastify/cors": "^7.0.0", + "fastify": "^3.29.0" + } + }, + "node_modules/@elastic/elasticsearch": { + "version": "8.2.0-patch.1", + "resolved": "https://registry.npmjs.org/@elastic/elasticsearch/-/elasticsearch-8.2.0-patch.1.tgz", + "integrity": "sha512-ROx9WLPoRrJ/NvT3NEz/4ZhzvGRmB1dSvhkNyuQ+LoHSR2kh4CFqFmxoFtJmWN1uqbw8WvQ0AmMCyLbDI04IVA==", + "dependencies": { + "@elastic/transport": "^8.2.0", + "tslib": "^2.4.0" + }, + "engines": { + "node": ">=14" + } + }, + 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diff --git a/docker/proxy-api/package.json b/docker/proxy-api/package.json new file mode 100644 index 0000000..1f9ddf3 --- /dev/null +++ b/docker/proxy-api/package.json @@ -0,0 +1,19 @@ +{ + "name": "api", + "version": "1.0.0", + "description": "", + "main": "index.js", + "scripts": { + "test": "echo \"Error: no test specified\" && exit 1", + "start": "node main.js" + }, + "keywords": [], + "author": "", + "license": "ISC", + "dependencies": { + "@elastic/elasticsearch": "^8.2.0-patch.1", + "@fastify/cors": "^7.0.0", + "fastify": "^3.29.0" + }, + "type": "module" +} From 8ad278bcb791ef04bc46264dce468fc977ba1add Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 29 Sep 2022 23:58:20 +0900 Subject: [PATCH 2/9] add files for es --- .env | 2 + .gitignore | 2 + docker-compose.yml | 12 + docker/elasticsearch/elasticsearch.keystore | Bin 0 -> 199 bytes docker/elasticsearch/elasticsearch.yml | 16 + docker/elasticsearch/entrypoint.sh | 38 + docker/elasticsearch/jvm.options | 82 + docker/elasticsearch/log4j2.properties | 9 + .../templates/bioproject-mapping.json | 2251 +++++++++++++++++ .../templates/biosample-mapping.json | 705 ++++++ .../templates/jga-dac-mapping.json | 249 ++ .../templates/jga-dataset-mapping.json | 360 +++ .../templates/jga-policy-mapping.json | 311 +++ .../templates/jga-study-mapping.json | 419 +++ .../templates/sra-analysis-mapping.json | 865 +++++++ .../templates/sra-experiment-mapping.json | 1059 ++++++++ .../templates/sra-run-mapping.json | 978 +++++++ .../templates/sra-sample-mapping.json | 429 ++++ .../templates/sra-study-mapping.json | 444 ++++ .../templates/sra-submission-mapping.json | 214 ++ 20 files changed, 8445 insertions(+) create mode 100644 .gitignore create mode 100644 docker/elasticsearch/elasticsearch.keystore create mode 100644 docker/elasticsearch/elasticsearch.yml create mode 100755 docker/elasticsearch/entrypoint.sh create mode 100644 docker/elasticsearch/jvm.options create mode 100644 docker/elasticsearch/log4j2.properties create mode 100644 docker/elasticsearch/templates/bioproject-mapping.json create mode 100644 docker/elasticsearch/templates/biosample-mapping.json create mode 100644 docker/elasticsearch/templates/jga-dac-mapping.json create mode 100644 docker/elasticsearch/templates/jga-dataset-mapping.json create mode 100644 docker/elasticsearch/templates/jga-policy-mapping.json create mode 100644 docker/elasticsearch/templates/jga-study-mapping.json create mode 100644 docker/elasticsearch/templates/sra-analysis-mapping.json create mode 100644 docker/elasticsearch/templates/sra-experiment-mapping.json create mode 100644 docker/elasticsearch/templates/sra-run-mapping.json create mode 100644 docker/elasticsearch/templates/sra-sample-mapping.json create mode 100644 docker/elasticsearch/templates/sra-study-mapping.json create mode 100644 docker/elasticsearch/templates/sra-submission-mapping.json diff --git a/.env b/.env index 014dfff..b662537 100644 --- a/.env +++ b/.env @@ -1,3 +1,5 @@ ELASTICSEARCH_HOST: "http://es01:9200" +ELASTICSEARCH_PERSISTENCE_DIR: "./db" +ELASTICSEARCH_LOG_DIR: "./log" PROXY_API_LOGGER: "on" PROXY_API_PORT: "4001" diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e337d9f --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +db +log diff --git a/docker-compose.yml b/docker-compose.yml index b6d8bb0..56a142c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,5 +1,17 @@ version: '3' services: + es01: + image: docker.elastic.co/elasticsearch/elasticsearch:7.15.0 + ports: + - "9200:9200" + - "9300:9300" + volumes: + - ${PWD}/docker/elasticsearch:/usr/share/elasticsearch/config + - ${PWD}/docker/elasticsearch/entrypoint.sh:/usr/local/bin/entrypoint.sh + - ${ELASTICSEARCH_PERSISTENCE_DIR}/elasticsearch:/usr/share/elasticsearch/data + - ${ELASTICSEARCH_LOG_DIR}/elasticsearch:/usr/share/elasticsearch/logs + command: ["bash", "/usr/local/bin/entrypoint.sh"] + proxy-api: build: ./docker/proxy-api ports: diff --git a/docker/elasticsearch/elasticsearch.keystore b/docker/elasticsearch/elasticsearch.keystore new file mode 100644 index 0000000000000000000000000000000000000000..b77bc454e706fb24bbd99889ef355c2e5ce68700 GIT binary patch literal 199 zcmcD&o+B=nnv+;ul9^nbnpl*ap_iRnSzMA|l*+)szyib!lY!Xb#odNUhYj7YRZA(n z+f~0J$;x2m@~E~8&yyxzu)HpPs8# /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/jga_dataset_mapping -d @/usr/share/elasticsearch/config/templates/jga-dataset-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/jga_policy_mapping -d @/usr/share/elasticsearch/config/templates/jga-policy-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/jga_dac_mapping -d @/usr/share/elasticsearch/config/templates/jga-dac-mapping.json > /dev/null 2>&1 + +# BIOPROJECTのマッピング +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/bioproject_mapping -d @/usr/share/elasticsearch/config/templates/bioproject-mapping.json > /dev/null 2>&1 + +# BIOSAMPLEのマッピング +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/biosample_mapping -d @/usr/share/elasticsearch/config/templates/biosample-mapping.json > /dev/null 2>&1 + +# DRAのマッピング +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_submission_mapping -d @/usr/share/elasticsearch/config/templates/sra-submission-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_experiment_mapping -d @/usr/share/elasticsearch/config/templates/sra-experiment-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_analysis_mapping -d @/usr/share/elasticsearch/config/templates/sra-analysis-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_run_mapping -d @/usr/share/elasticsearch/config/templates/sra-run-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_study_mapping -d @/usr/share/elasticsearch/config/templates/sra-study-mapping.json > /dev/null 2>&1 +curl -H "Content-Type:application/json" -XPUT localhost:9200/_index_template/sra_sample_mapping -d @/usr/share/elasticsearch/config/templates/sra-sample-mapping.json > /dev/null 2>&1 + +echo "Finish to input initial data." +tail -f /dev/null diff --git a/docker/elasticsearch/jvm.options b/docker/elasticsearch/jvm.options new file mode 100644 index 0000000..2bb3898 --- /dev/null +++ b/docker/elasticsearch/jvm.options @@ -0,0 +1,82 @@ +################################################################ +## +## JVM configuration +## +################################################################ +## +## WARNING: DO NOT EDIT THIS FILE. If you want to override the +## JVM options in this file, or set any additional options, you +## should create one or more files in the jvm.options.d +## directory containing your adjustments. +## +## See https://www.elastic.co/guide/en/elasticsearch/reference/@project.minor.version@/jvm-options.html +## for more information. +## +################################################################ + + + +################################################################ +## IMPORTANT: JVM heap size +################################################################ +## +## The heap size is automatically configured by Elasticsearch +## based on the available memory in your system and the roles +## each node is configured to fulfill. If specifying heap is +## required, it should be done through a file in jvm.options.d, +## which should be named with .options suffix, and the min and +## max should be set to the same value. For example, to set the +## heap to 4 GB, create a new file in the jvm.options.d +## directory containing these lines: +## +## -Xms4g +## -Xmx4g +## +## See https://www.elastic.co/guide/en/elasticsearch/reference/@project.minor.version@/heap-size.html +## for more information +## +################################################################ + + +################################################################ +## Expert settings +################################################################ +## +## All settings below here are considered expert settings. Do +## not adjust them unless you understand what you are doing. Do +## not edit them in this file; instead, create a new file in the +## jvm.options.d directory containing your adjustments. +## +################################################################ + +## GC configuration +8-13:-XX:+UseConcMarkSweepGC +8-13:-XX:CMSInitiatingOccupancyFraction=75 +8-13:-XX:+UseCMSInitiatingOccupancyOnly + +## G1GC Configuration +# to use G1GC, uncomment the next two lines and update the version on the +# following three lines to your version of the JDK +# 8-13:-XX:-UseConcMarkSweepGC +# 8-13:-XX:-UseCMSInitiatingOccupancyOnly +14-:-XX:+UseG1GC + +## JVM temporary directory +-Djava.io.tmpdir=${ES_TMPDIR} + +## heap dumps + +# generate a heap dump when an allocation from the Java heap fails; heap dumps +# are created in the working directory of the JVM unless an alternative path is +# specified +-XX:+HeapDumpOnOutOfMemoryError + +# specify an alternative path for heap dumps; ensure the directory exists and +# has sufficient space +# @heap.dump.path@ + +# specify an alternative path for JVM fatal error logs +# @error.file@ + +## GC logging +# -Xlog:gc*,gc+age=trace,safepoint:file=@loggc@:utctime,pid,tags:filecount=32,filesize=64m diff --git a/docker/elasticsearch/log4j2.properties b/docker/elasticsearch/log4j2.properties new file mode 100644 index 0000000..46877d0 --- /dev/null +++ b/docker/elasticsearch/log4j2.properties @@ -0,0 +1,9 @@ +status = error + +appender.console.type = Console +appender.console.name = console +appender.console.layout.type = PatternLayout +appender.console.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] %marker%m%n + +rootLogger.level = info +rootLogger.appenderRef.console.ref = console diff --git a/docker/elasticsearch/templates/bioproject-mapping.json b/docker/elasticsearch/templates/bioproject-mapping.json new file mode 100644 index 0000000..9b4b7c0 --- /dev/null +++ b/docker/elasticsearch/templates/bioproject-mapping.json @@ -0,0 +1,2251 @@ +{ + "index_patterns": "bioproject", + "template": { + "settings" : { + "number_of_shards" : "8", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "properties" : { + "properties" : { + "Project" : { + "properties" : { + "Project" : { + "properties" : { + "ProjectDescr" : { + "properties" : { + "Description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "ExternalLink" : { + "properties" : { + "URL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "category" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "dbXREF" : { + "properties" : { + "ID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "db" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Grant" : { + "properties" : { + "Agency" : { + "properties" : { + "abbr" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "GrantId" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Keyword" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "LocusTagPrefix" : { + "properties" : { + "assembly_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "biosample_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "ProjectReleaseDate" : { + "type" : "date" + }, + "Publication" : { + "properties" : { + "DbType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Reference" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "StructuredCitation" : { + "properties" : { + "AuthorSet" : { + "properties" : { + "Author" : { + "properties" : { + "Consortium" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Name" : { + "properties" : { + "First" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Last" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Middle" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Suffix" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + }, + "Journal" : { + "properties" : { + "Issue" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "JournalTitle" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "PagesFrom" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "PagesTo" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Volume" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Year" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "date" : { + "type" : "date" + }, + "id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "status" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "RefSeq" : { + "properties" : { + "AnnotationSource" : { + "properties" : { + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "NomenclatureSource" : { + "properties" : { + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SequenceSource" : { + "properties" : { + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "representation" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Relevance" : { + "properties" : { + "Agricultural" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Environmental" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Evolution" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Industrial" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Medical" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "ModelOrganism" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Other" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "UserTerm" : { + "properties" : { + "category" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "term" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "ProjectID" : { + "properties" : { + "ArchiveID" : { + "properties" : { + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "archive" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "CenterID" : { + "properties" : { + "center" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "LocalID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "submission_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SecondaryArchiveID" : { + "properties" : { + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "archive" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "ProjectType" : { + "properties" : { + "ProjectTypeSubmission" : { + "properties" : { + "IntendedDataTypeSet" : { + "properties" : { + "DataType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Method" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "method_type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Objectives" : { + "properties" : { + "Data" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "data_type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "ProjectDataTypeSet" : { + "properties" : { + "DataType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Target" : { + "properties" : { + "BioSampleSet" : { + "properties" : { + "ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "local_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Organism" : { + "properties" : { + "BiologicalProperties" : { + "properties" : { + "BiologicalSample" : { + "properties" : { + "CultureSample" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TissueSample" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Environment" : { + "properties" : { + "Habitat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OptimumTemperature" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OxygenReq" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Salinity" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TemperatureRange" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Morphology" : { + "properties" : { + "Endospores" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Enveloped" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Gram" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Motility" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Shape" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Phenotype" : { + "properties" : { + "BioticRelationship" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Disease" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TrophicLevel" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Breed" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Cultivar" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "GenomeSize" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "IsolateName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OrganismName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Organization" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "RepliconSet" : { + "properties" : { + "Count" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "repliconType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Ploidy" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Replicon" : { + "properties" : { + "Description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Size" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Type" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isSingle" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "location" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "locationOtherDescr" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "typeOtherDescr" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "order" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Reproduction" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Strain" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Supergroup" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "species" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "taxID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Provider" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "capture" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "material" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "sample_scope" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "ProjectTypeTopAdmin" : { + "properties" : { + "DescriptionSubtypeOther" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Organism" : { + "properties" : { + "BiologicalProperties" : { + "properties" : { + "Environment" : { + "properties" : { + "Habitat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Salinity" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TemperatureRange" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Phenotype" : { + "properties" : { + "Disease" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Breed" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Cultivar" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "GenomeSize" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "IsolateName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OrganismName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Organization" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "RepliconSet" : { + "properties" : { + "Count" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "repliconType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Ploidy" : { + "properties" : { + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Replicon" : { + "properties" : { + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Size" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Type" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isSingle" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "location" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "order" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Reproduction" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Strain" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Supergroup" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "species" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "taxID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "subtype" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "ProjectTypeTopSingleOrganism" : { + "properties" : { + "Organism" : { + "properties" : { + "BiologicalProperties" : { + "properties" : { + "Environment" : { + "properties" : { + "Habitat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OptimumTemperature" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OxygenReq" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Salinity" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TemperatureRange" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Morphology" : { + "properties" : { + "Endospores" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Gram" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Motility" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Shape" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Phenotype" : { + "properties" : { + "BioticRelationship" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Disease" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TrophicLevel" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Cultivar" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "GenomeSize" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "IsolateName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "OrganismName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Organization" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "RepliconSet" : { + "properties" : { + "Count" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "repliconType" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Ploidy" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Replicon" : { + "properties" : { + "Description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Size" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "units" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Type" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "location" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "typeOtherDescr" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "order" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Reproduction" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Strain" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Supergroup" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "species" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "taxID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + } + } + }, + "Submission" : { + "properties" : { + "Description" : { + "properties" : { + "Access" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Hold" : { + "properties" : { + "release_date" : { + "type" : "date" + } + } + }, + "Organization" : { + "properties" : { + "Name" : { + "properties" : { + "abbr" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "org_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "role" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "last_update" : { + "type" : "date" + }, + "submission_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "submitted" : { + "type" : "date" + } + } + } + } + } + } + }, + "sameAs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "status" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "visibility" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } +} diff --git a/docker/elasticsearch/templates/biosample-mapping.json b/docker/elasticsearch/templates/biosample-mapping.json new file mode 100644 index 0000000..8630f65 --- /dev/null +++ b/docker/elasticsearch/templates/biosample-mapping.json @@ -0,0 +1,705 @@ +{ + "index_patterns": "biosample", + "template": { + "settings" : { + "number_of_shards" : "8", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "properties" : { + "properties" : { + "Attributes" : { + "properties" : { + "Attribute" : { + "properties" : { + "attribute_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "display_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "harmonized_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "unit" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Description" : { + "properties" : { + "Comment" : { + "properties" : { + "Paragraph" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Table" : { + "properties" : { + "Body" : { + "properties" : { + "Row" : { + "properties" : { + "Cell" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Caption" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Header" : { + "properties" : { + "Cell" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "class" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "Organism" : { + "properties" : { + "OrganismName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "taxonomy_id" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SampleName" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "Title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "Ids" : { + "properties" : { + "Id" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, 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"jga-dataset", + "template" : { + "settings" : { + "number_of_shards" : "１", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "properties" : { + "properties" : { + "ANALYSIS_REFS" : { + 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"ignore_above" : 256 + } + } + }, + "alias" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "center_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "status" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "visibility" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } +} diff --git a/docker/elasticsearch/templates/jga-policy-mapping.json b/docker/elasticsearch/templates/jga-policy-mapping.json new file mode 100644 index 0000000..6d64686 --- /dev/null +++ b/docker/elasticsearch/templates/jga-policy-mapping.json @@ -0,0 +1,311 @@ +{ + "index_patterns": "jga-policy", + "template" : { + "settings" : { + "number_of_shards" : "１", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + 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: { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SUBMITTER_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "namespace" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "PROCESSING" : { + "properties" : { + "PIPELINE" : { + "properties" : { + "PIPE_SECTION" : { + "properties" : { + "NOTES" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "PREV_STEP_INDEX" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "PROGRAM" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "STEP_INDEX" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "VERSION" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "section_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + }, + "RUN_ATTRIBUTES" : { + "properties" : { + "RUN_ATTRIBUTE" : { + "properties" : { + "TAG" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "UNITS" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "VALUE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "SPOT_DESCRIPTOR" : { + "properties" : { + "SPOT_DECODE_SPEC" : { + "properties" : { + "READ_SPEC" : { + "properties" : { + "BASE_COORD" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "EXPECTED_BASECALL_TABLE" : { + "properties" : { + "BASECALL" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "match_edge" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "max_mismatch" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "min_match" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "read_group_tag" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "base_coord" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "default_length" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "READ_CLASS" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_INDEX" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_LABEL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_TYPE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "RELATIVE_ORDER" : { + "properties" : { + "follows_read_index" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "SPOT_LENGTH" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "TITLE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "alias" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "broker_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "center_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "run_center" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "run_date" : { + "type" : "date" + } + } + }, + "RUN_ATTRIBUTES" : { + "properties" : { + "RUN_ATTRIBUTE" : { + "properties" : { + "TAG" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "VALUE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "SPOT_DESCRIPTOR" : { + "properties" : { + "SPOT_DECODE_SPEC" : { + "properties" : { + "READ_SPEC" : { + "properties" : { + "BASE_COORD" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "EXPECTED_BASECALL_TABLE" : { + "properties" : { + "base_coord" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "default_length" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "READ_CLASS" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_INDEX" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_LABEL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "READ_TYPE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + }, + "TITLE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "alias" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "center_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "run_center" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "run_date" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "status" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "visibility" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } +} diff --git a/docker/elasticsearch/templates/sra-sample-mapping.json b/docker/elasticsearch/templates/sra-sample-mapping.json new file mode 100644 index 0000000..283d0b1 --- /dev/null +++ b/docker/elasticsearch/templates/sra-sample-mapping.json @@ -0,0 +1,429 @@ +{ + "index_patterns": "sra-sample", + "template": { + "settings" : { + "number_of_shards" : "8", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "properties" : { + "properties" : { + "SAMPLE" : { + "properties" : { + "DESCRIPTION" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "IDENTIFIERS" : { + "properties" : { + "EXTERNAL_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "namespace" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "PRIMARY_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "SAMPLE_ATTRIBUTES" : { + "properties" : { + "SAMPLE_ATTRIBUTE" : { + "properties" : { + "TAG" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "UNITS" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "VALUE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "SAMPLE_LINKS" : { + "properties" : { + "SAMPLE_LINK" : { + "properties" : { + "URL_LINK" : { + "properties" : { + "LABEL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "URL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "XREF_LINK" : { + "properties" : { + "DB" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "ID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "LABEL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + }, + "SAMPLE_NAME" : { + "properties" : { + "COMMON_NAME" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "SCIENTIFIC_NAME" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "TAXON_ID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "TITLE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "alias" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "broker_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "center_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "sameAs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } +} diff --git a/docker/elasticsearch/templates/sra-study-mapping.json b/docker/elasticsearch/templates/sra-study-mapping.json new file mode 100644 index 0000000..67b5e35 --- /dev/null +++ b/docker/elasticsearch/templates/sra-study-mapping.json @@ -0,0 +1,444 @@ +{ + "index_patterns": "sra-study", + "template": { + "settings" : { + "number_of_shards" : "8", + "number_of_replicas": "0" + }, + "mappings" : { + "date_detection": false, + "properties" : { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "description" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "distribution" : { + "properties" : { + "contentUrl" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "encodingFormat" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "isPartOf" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "organism" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "properties" : { + "properties" : { + "STUDY" : { + "properties" : { + "DESCRIPTOR" : { + "properties" : { + "CENTER_PROJECT_NAME" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "STUDY_ABSTRACT" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "STUDY_DESCRIPTION" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "STUDY_TITLE" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "STUDY_TYPE" : { + "properties" : { + "existing_study_type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "IDENTIFIERS" : { + "properties" : { + "EXTERNAL_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "label" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "namespace" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "PRIMARY_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SECONDARY_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "SUBMITTER_ID" : { + "properties" : { + "content" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "namespace" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "STUDY_ATTRIBUTES" : { + "properties" : { + "STUDY_ATTRIBUTE" : { + "properties" : { + "TAG" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "VALUE" : { + "type" : "date" + } + } + } + } + }, + "STUDY_LINKS" : { + "properties" : { + "STUDY_LINK" : { + "properties" : { + "URL_LINK" : { + "properties" : { + "LABEL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "URL" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "XREF_LINK" : { + "properties" : { + "DB" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "ID" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + } + } + }, + "accession" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "alias" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "broker_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "center_name" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } + }, + "sameAs" : { + "properties" : { + "identifier" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + }, + "title" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "type" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + }, + "url" : { + "type" : "text", + "fields" : { + "keyword" : { + "type" : "keyword", + "ignore_above" : 256 + } + } + } + } + } + } +} diff --git a/docker/elasticsearch/templates/sra-submission-mapping.json b/docker/elasticsearch/templates/sra-submission-mapping.json new file mode 100644 index 0000000..bec710d --- /dev/null +++ b/docker/elasticsearch/templates/sra-submission-mapping.json @@ -0,0 +1,214 @@ +{ + "index_patterns": "sra-submission", + "template": { + "settings" : { + "number_of_shards" : "8", + "number_of_replicas": "0" + }, + "mappings": { + "date_detection": false, + "properties": { + "dateCreated" : { + "type" : "date" + }, + "dateModified" : { + "type" : "date" + }, + "datePublished" : { + "type" : "date" + }, + "dbXrefs": { + "properties": { + "identifier": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "type": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "url": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + } + } + }, + "distribution": { + "properties": { + "contentUrl": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "encodingFormat": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "type": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + } + } + }, + "identifier": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "isPartOf": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "name": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "organism": { + "properties": { + "identifier": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "name": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + } + } + }, + "properties": { + "properties": { + "SUBMISSION": { + "properties": { + "accession": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "alias": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "broker_name": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "center_name": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "lab_name": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "submission_comment": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + } + } + } + } + }, + "type": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + }, + "url": { + "type": "text", + "fields": { + "keyword": { + "type": "keyword", + "ignore_above": 256 + } + } + } + } + } + } +} From 63ba9e61424d8f0f5ae675c8f6185a08ec35be10 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:13:10 +0900 Subject: [PATCH 3/9] update compose and disable single-node mode --- docker-compose.yml | 28 +++++++++++++++++++++++--- docker/elasticsearch/elasticsearch.yml | 2 +- 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 56a142c..cc048aa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,15 +1,37 @@ version: '3' services: - es01: + elasticsearch01: image: docker.elastic.co/elasticsearch/elasticsearch:7.15.0 ports: - "9200:9200" - "9300:9300" + environment: + node.name: elasticsearch01 + discovery.seed_hosts: elasticsearch02 + cluster.initial_master_nodes: elasticsearch01, elasticsearch02 volumes: - ${PWD}/docker/elasticsearch:/usr/share/elasticsearch/config - ${PWD}/docker/elasticsearch/entrypoint.sh:/usr/local/bin/entrypoint.sh - ${ELASTICSEARCH_PERSISTENCE_DIR}/elasticsearch:/usr/share/elasticsearch/data - - ${ELASTICSEARCH_LOG_DIR}/elasticsearch:/usr/share/elasticsearch/logs + user: ${UID:-1000}:${GID:-0} + command: ["bash", "/usr/local/bin/entrypoint.sh"] + depends_on: + - elasticsearch02 + + elasticsearch02: + image: docker.elastic.co/elasticsearch/elasticsearch:7.15.0 + ports: + - "9201:9200" + - "9301:9300" + environment: + node.name: elasticsearch02 + discovery.seed_hosts: elasticsearch01 + cluster.initial_master_nodes: elasticsearch01, elasticsearch02 + volumes: + - ${PWD}/docker/elasticsearch:/usr/share/elasticsearch/config + - ${PWD}/docker/elasticsearch/entrypoint.sh:/usr/local/bin/entrypoint.sh + - ${ELASTICSEARCH_PERSISTENCE_DIR}/elasticsearch2:/usr/share/elasticsearch/data + user: ${UID:-1000}:${GID:-0} command: ["bash", "/usr/local/bin/entrypoint.sh"] proxy-api: @@ -18,7 +40,7 @@ services: - "4001:4001" command: npm start environment: - ELASTICSEARCH_HOST: $ELASTICSEARCH_HOST + ELASTICSEARCH_HOST: "http://elasticsearch01:9200" LOGGER: $PROXY_API_LOGGER PORT: $PROXY_API_PORT depends_on: diff --git a/docker/elasticsearch/elasticsearch.yml b/docker/elasticsearch/elasticsearch.yml index 6ac8808..5287a92 100644 --- a/docker/elasticsearch/elasticsearch.yml +++ b/docker/elasticsearch/elasticsearch.yml @@ -4,7 +4,7 @@ network.host: 0.0.0.0 # minimum_master_nodes need to be explicitly set when bound on a public IP # set to 1 to allow single node clusters # Details: https://github.com/elastic/elasticsearch/pull/17288 -discovery.type: single-node +#discovery.type: single-node discovery.zen.minimum_master_nodes: 1 From 2ae1a9f5f2c75ae09bbfefa09eacb9bd335c3d14 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:16:27 +0900 Subject: [PATCH 4/9] udpate instruction --- README.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/README.md b/README.md index 106e00c..1b39caf 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,14 @@ # ddbj-ld-proxy Proxy API for DDBJ search ElasticSearch cluster + +## Migration + +``` +$ mkdir db +$ tar xf /path/to/ddbjsearch_elasticsearch.tar --directory ./db +$ ls ./db +elasticsearch +$ mkdir ./db/elasticsearch2 +$ chmod a+w -R ./db +$ docker-compose up +``` \ No newline at end of file From 62ef742ff243c240b5fe3578d8767f9df4ca6985 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:35:19 +0900 Subject: [PATCH 5/9] debug --- .env | 9 ++++----- .gitignore | 2 +- README.md | 9 ++++----- docker-compose.yml | 2 +- 4 files changed, 10 insertions(+), 12 deletions(-) diff --git a/.env b/.env index b662537..83743dd 100644 --- a/.env +++ b/.env @@ -1,5 +1,4 @@ -ELASTICSEARCH_HOST: "http://es01:9200" -ELASTICSEARCH_PERSISTENCE_DIR: "./db" -ELASTICSEARCH_LOG_DIR: "./log" -PROXY_API_LOGGER: "on" -PROXY_API_PORT: "4001" +ELASTICSEARCH_PERSISTENCE_DIR="./data" +ELASTICSEARCH_LOG_DIR="./log" +PROXY_API_LOGGER="on" +PROXY_API_PORT="4001" diff --git a/.gitignore b/.gitignore index e337d9f..328c867 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,2 @@ -db +data log diff --git a/README.md b/README.md index 1b39caf..3a2023e 100644 --- a/README.md +++ b/README.md @@ -4,11 +4,10 @@ Proxy API for DDBJ search ElasticSearch cluster ## Migration ``` -$ mkdir db -$ tar xf /path/to/ddbjsearch_elasticsearch.tar --directory ./db -$ ls ./db +$ tar xf /path/to/ddbjsearch_elasticsearch.tar --directory . +$ ls ./data elasticsearch -$ mkdir ./db/elasticsearch2 -$ chmod a+w -R ./db +$ mkdir ./data/elasticsearch2 +$ chmod a+w -R ./data $ docker-compose up ``` \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index cc048aa..40f6901 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -44,4 +44,4 @@ services: LOGGER: $PROXY_API_LOGGER PORT: $PROXY_API_PORT depends_on: - - elasticsearch + - elasticsearch01 From 8f5a48751fbfe271ec584040173723b838d15f2c Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:40:15 +0900 Subject: [PATCH 6/9] remove quotes --- .env | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.env b/.env index 83743dd..bfa1851 100644 --- a/.env +++ b/.env @@ -1,4 +1,4 @@ -ELASTICSEARCH_PERSISTENCE_DIR="./data" -ELASTICSEARCH_LOG_DIR="./log" -PROXY_API_LOGGER="on" -PROXY_API_PORT="4001" +ELASTICSEARCH_PERSISTENCE_DIR=./data +ELASTICSEARCH_LOG_DIR=./log +PROXY_API_LOGGER=on +PROXY_API_PORT=4001 From 532c5481e8734cc4b8867b02c7705bcbd003393b Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:43:26 +0900 Subject: [PATCH 7/9] max_map_count --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 3a2023e..7bf58fe 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,13 @@ # ddbj-ld-proxy Proxy API for DDBJ search ElasticSearch cluster +## Prerequisites + +``` +# Need root permission +$ sysctl -w vm.max_map_count=262144 +``` + ## Migration ``` From 234c895001287d01689176fee1da1a48b6d27886 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 19:45:47 +0900 Subject: [PATCH 8/9] update --- README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7bf58fe..2739a4e 100644 --- a/README.md +++ b/README.md @@ -3,11 +3,17 @@ Proxy API for DDBJ search ElasticSearch cluster ## Prerequisites +require root permission + ``` -# Need root permission $ sysctl -w vm.max_map_count=262144 ``` +``` +$ cat /etc/sysctl.conf +vm.max_map_count=262144 +``` + ## Migration ``` From fb9d298e256cc62f21e36177b31d1bb4ca692470 Mon Sep 17 00:00:00 2001 From: Tazro Inutano Ohta Date: Thu, 20 Oct 2022 20:06:01 +0900 Subject: [PATCH 9/9] heap 16gb --- docker-compose.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index 40f6901..38790de 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -9,6 +9,7 @@ services: node.name: elasticsearch01 discovery.seed_hosts: elasticsearch02 cluster.initial_master_nodes: elasticsearch01, elasticsearch02 + ES_JAVA_OPTS: "-Xms16g -Xmx16g" volumes: - ${PWD}/docker/elasticsearch:/usr/share/elasticsearch/config - ${PWD}/docker/elasticsearch/entrypoint.sh:/usr/local/bin/entrypoint.sh @@ -27,6 +28,7 @@ services: node.name: elasticsearch02 discovery.seed_hosts: elasticsearch01 cluster.initial_master_nodes: elasticsearch01, elasticsearch02 + ES_JAVA_OPTS: "-Xms16g -Xmx16g" volumes: - ${PWD}/docker/elasticsearch:/usr/share/elasticsearch/config - ${PWD}/docker/elasticsearch/entrypoint.sh:/usr/local/bin/entrypoint.sh