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‎.gitignore

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breedpath_sciencedb_bak.tar.bz2
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gitted_sub_projs.tar.bz2

‎Dockerfile.postgres

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FROM postgres:11.1-alpine
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COPY initUserDb.sh /docker-entrypoint-initdb.d/initUserDb.sh
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RUN chmod 755 /docker-entrypoint-initdb.d/initUserDb.sh

‎data_model_definitions/breeding_pool.json

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{
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"model" : "BeedingPool",
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"model" : "BreedingPool",
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"storageType" : "Sql",
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"attributes" : {
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"name" : "String",

‎data_model_definitions/genotype.json

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@@ -1,34 +1,34 @@
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{
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"model" : "Genotype",
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"storageType" : "Sql",
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"attributes" : {
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"name" : "String",
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"description" : "String",
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"model": "Genotype",
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"storageType": "Sql",
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"attributes": {
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"name": "String",
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"description": "String",
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"pedigree_type": "String"
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},
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"associations" : {
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"mother" : {
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"type" : "sql_belongsTo",
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"target" : "Individual",
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"targetKey" : "mother_id",
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"targetStorageType" : "sql",
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"associations": {
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"mother": {
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"type": "sql_belongsTo",
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"target": "Individual",
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"targetKey": "mother_id",
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"targetStorageType": "sql",
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"label": "name",
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"sublabel": "id"
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},
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"father" : {
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"type" : "sql_belongsTo",
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"target" : "Individual",
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"targetKey" : "father_id",
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"targetStorageType" : "sql",
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"father": {
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"type": "sql_belongsTo",
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"target": "Individual",
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"targetKey": "father_id",
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"targetStorageType": "sql",
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"label": "name",
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"sublabel": "id"
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},
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"breeding_pool" : {
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"type" : "sql_belongsTo",
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"target" : "BreedingPool",
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"targetKey" : "breeding_pool_id",
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"targetStorageType" : "sql",
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"breeding_pool": {
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"type": "sql_belongsTo",
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"target": "BreedingPool",
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"targetKey": "breeding_pool_id",
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"targetStorageType": "sql",
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"label": "name",
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"sublabel": "id"
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}

‎data_model_definitions/role.json

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{
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"model" : "Role",
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"storageType" : "SQL",
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"attributes" : {
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"name" : "String",
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"description" : "String"
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},
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"associations" : {
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"users" : {
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"type" : "sql_belongsToMany",
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"target" : "User",
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"targetKey" : "userId",
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"sourceKey" : "roleId",
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"keysIn" : "role_to_user",
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"targetStorageType" : "sql"
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}
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}
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}

‎data_model_definitions/user.json

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{
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"model" : "User",
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"storageType" : "SQL",
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"attributes" : {
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"email" : "String",
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"password" : "String"
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},
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"associations" :{
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"roles" : {
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"type" : "sql_belongsToMany",
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"target" : "Role",
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"targetKey" : "roleId",
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"sourceKey" : "userId",
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"keysIn" : "role_to_user",
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"targetStorageType" : "sql"
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}
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}
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}

‎docker-compose-dev.yml

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version: "3.2"
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services:
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bp_postgres:
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build:
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context: .
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dockerfile: Dockerfile.postgres
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volumes:
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- bp_db_data:/var/lib/postgresql/data
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ports:
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- 5432:5432
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bp_science_db_graphql_server:
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depends_on:
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- bp_postgres
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build:
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context: ./graphql-server
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dockerfile: Dockerfile.graphql_server
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ports:
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- 3000:3000
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environment:
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- PORT=3000
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volumes:
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- ./graphql-server:/usr/src/app
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# Await POSTGRES role and DB creation, migrate schema, then start web
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# server:
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command:
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- ./migrateDbAndStartServer.sh
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bp_science_db_app_server:
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depends_on:
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- bp_postgres
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- bp_science_db_graphql_server
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build:
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context: ./single-page-app
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dockerfile: Dockerfile.app
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ports:
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- 8080:8080
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environment:
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- PORT=8080
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volumes:
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- ./single-page-app:/usr/src/app
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command: npm run dev
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bp_minio:
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image: minio/minio:RELEASE.2019-02-20T22-44-29Z
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volumes:
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- bp_minio_data:/data
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ports:
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- "9000:9000"
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environment:
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MINIO_ACCESS_KEY: minio
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MINIO_SECRET_KEY: minio123
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command: server /data
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volumes:
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bp_db_data:
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bp_minio_data:

‎docker-compose.yml

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version: "3.2"
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services:
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bp_postgres:
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build:
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context: .
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dockerfile: Dockerfile.postgres
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volumes:
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- bp_db_data:/var/lib/postgresql/data
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ports:
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- 5432:5432
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13+
bp_science_db_graphql_server:
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depends_on:
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- bp_postgres
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build:
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context: ./graphql-server
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dockerfile: Dockerfile.graphql_server
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ports:
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- 3000:3000
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environment:
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- PORT=3000
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# Await POSTGRES role and DB creation, migrate schema, then start web
24+
# server:
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command:
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- ./migrateDbAndStartServer.sh
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bp_science_db_app_server:
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depends_on:
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- bp_postgres
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- bp_science_db_graphql_server
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build:
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context: ./single-page-app
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dockerfile: Dockerfile.app
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ports:
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- 8080:8080
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environment:
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- PORT=8080
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command: npm run dev
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bp_minio:
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image: minio/minio:RELEASE.2019-02-20T22-44-29Z
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volumes:
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- bp_minio_data:/data
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ports:
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- "9000:9000"
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environment:
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MINIO_ACCESS_KEY: minio
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MINIO_SECRET_KEY: minio123
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command: server /data
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volumes:
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bp_db_data:
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bp_minio_data:

‎graphql-server/.gitignore

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@@ -12,3 +12,4 @@ models
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models-webservice
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resolvers
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schemas
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test

‎graphql-server/Dockerfile.graphql_server

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FROM node:11.9.0-stretch-slim
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# Create app directory
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WORKDIR /usr/src/app
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# Copy generated code into the skeleton GraphQL-Server
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COPY . .
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# Clone the skeleton project and install dependencies
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RUN apt-get update && apt-get install -y git procps &&\
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chmod u+x ./migrateDbAndStartServer.sh && \
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npm install
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EXPOSE 3000

‎graphql-server/acl_rules.js

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module.exports = {
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aclRules: [{
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roles: 'admin',
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allows: [{
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resources: ['users', 'roles'],
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permissions: '*'
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}]
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},
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{
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roles: 'guest',
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allows: [{
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resources: ['dogs', 'people'],
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permissions: 'read'
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}]
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}]
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roles: 'admin',
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allows: [{
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resources: ['users', 'roles'],
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permissions: '*'
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}]
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},
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{
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roles: 'scientist',
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allows: [{
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resources: ['breeding_pool', 'field_plot', 'genotype',
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'individual', 'marker_data', 'measurement',
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'nuc_acid_library_result', 'sample',
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'sequencing_experiment', 'transcript_count'
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],
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permissions: ['create', 'update', 'delete']
18+
}]
19+
},
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{
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roles: 'guest',
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allows: [{
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resources: ['breeding_pool', 'field_plot', 'genotype',
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'individual', 'marker_data', 'measurement',
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'nuc_acid_library_result', 'sample',
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'sequencing_experiment', 'transcript_count'
27+
],
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permissions: 'read'
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}]
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}
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]
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}

‎graphql-server/config/config.json

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"username": "sciencedb",
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"password": "sciencedb",
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"database": "sciencedb_development",
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"host": "127.0.0.1",
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"host": "bp_postgres",
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"dialect": "postgres",
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"operatorsAliases": false
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},
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"test": {
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"username": "sciencedb",
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"password": "sciencedb",
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"database": "sciencedb_test",
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"host": "postgres",
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"host": "bp_postgres",
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"dialect": "postgres",
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"operatorsAliases": false
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},
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"production": {
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"username": "sciencedb",
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"password": "sciencedb",
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"database": "sciencedb_production",
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"host": "postgres",
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"host": "bp_postgres",
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"dialect": "postgres",
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"operatorsAliases": false
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}

‎graphql-server/config/globals.js

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module.exports = {
2-
LIMIT_RECORDS : process.env.LIMIT_RECORDS || 10000
2+
LIMIT_RECORDS : process.env.LIMIT_RECORDS || 10000,
3+
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MAIL_SERVICE: "gmail",
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MAIL_HOST: "smtp.gmail.com",
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MAIL_ACCOUNT: "[email protected]",
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MAIL_PASSWORD: "SciDbServiceQAZ"
38
}

‎graphql-server/migrateDbAndStartServer.sh

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waited=0
55
until node ./utils/testSequelizeDbServerAvailable.js
66
do
7-
if [ $waited == 240 ]; then
8-
echo -e '\nERROR: Time out reached while waiting for relational database server to be available.\n'
9-
exit 1
10-
fi
11-
sleep 2
12-
waited=$(expr $waited + 2)
7+
if [ $waited == 240 ]; then
8+
echo -e '\nERROR: Time out reached while waiting for relational database server to be available.\n'
9+
exit 1
10+
fi
11+
sleep 2
12+
waited=$(expr $waited + 2)
1313
done
1414

1515
# Run the migrations
1616
if ! ./node_modules/.bin/sequelize db:migrate; then
17-
echo -e '\nERROR: Migrating the relational database(s) caused an error.\n'
18-
exit 1
17+
echo -e '\nERROR: Migrating the relational database(s) caused an error.\n'
18+
exit 1
19+
fi
20+
21+
# Run seeders if needed
22+
if [ -d ./seeders ]; then
23+
if ! ./node_modules/.bin/sequelize db:seed:all; then
24+
echo -e '\nERROR: Seeding the relational database(s) caused an error.\n'
25+
exit 1
26+
fi
1927
fi
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# Start GraphQL-server
22-
npm start
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npm start acl

‎graphql-server/package.json

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"supertest": "^3.1.0",
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"uuidv4": "^2.0.0",
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"xlsx": "^0.12.11",
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"sync-request": "^6.0.0"
38+
"sync-request": "^6.0.0",
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"nodemailer" : "^5.1.1",
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"nodemailer-smtp-transport": "^2.7.4"
3941
},
4042
"devDependencies": {
41-
"mocha": "^5.2.0"
43+
"mocha": "^5.2.0",
44+
"axios": "^0.18.0",
45+
"form-data": "^2.3.2-rc1"
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}
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}

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