diff --git a/.env b/.env index 4d17da5c..db5bef1f 100644 --- a/.env +++ b/.env @@ -1,9 +1,23 @@ DB_NAME=biogenome-db DB_USER=biogenome-user DB_PASS=biogenome-password -DB_HOST=mydatabase + +# declare production db host here +# DB_PROD_HOST= + +# default dev db host +DB_DEV_HOST=mydev-db + DB_PORT=27017 +DB_DUMP=dump_2022-05-18.gz +MONGO_INITDB_ROOT_USERNAME=root +MONGO_INITDB_ROOT_PASSWORD=root +MONGO_INITDB_DATABASE=admin +MONGODB_DATA_DIR=/var/lib/mongodb-data +MONDODB_LOG_DIR=/dev/null + +# change to 'production' or null in prod!! FLASK_ENV=development APP_NAME=RNAmaps API_PORT=80 @@ -14,6 +28,8 @@ THREADS=2 USR=admin JWT_SECRET_KEY=secret_restKey RESTKEY=secretPassword + + PROJECT_ACCESSION=PRJNA533106 PROJECTS=DTOL, VGP EXEC_TIME=600 diff --git a/README.md b/README.md index eb523352..2f7b1ca5 100644 --- a/README.md +++ b/README.md @@ -85,27 +85,31 @@ This project is built with the following stack: ## Getting Started -Before building the application it is necessary to configure the .env file in the project's root directory: -The .env file contains many parts that have to be configured depending on the needs: +By default the portal is configured to retrieve public data under the EBP umbrella (https://www.earthbiogenome.org/) it will load (at building stage) and seed the database with the last dump (/dump-db directory) - The API KEY part: - Configure this part if you want to enter samples locally +If you want to customize the portal follow the steps below: - USER=admin --> Define the user name that will be inserted to access the admin area - JWT_SECRET_KEY=secret_restKey #change this in production!! --> key to encrypt the RESTKEY (below) - RESTKEY=secretPassword #change this in production!! --> password that will be inserted to access the admin area + General configurations: + - Set the ROOT_NODE env variable with the Taxon name you want to use as a root (default: Eukaryota) + + Public data management: + - in the .env file insert the PROJECT_ACCESSION (The INSDC BioProject accession) of the project you want to use as a root: + if the bioproject you want to use as a root is not under the EBP umbrella, you have to comment the volumes of the biogenome_mongo service in the docker-compose-dev file: + - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh + - ./mongo-restore.sh:/docker-entrypoint-initdb.d/mongo-restore.sh + - ./db-dump:/db-dump + - if the same project or sub projects are defined as attributes of the sample metadata (ex: project name: 'YOUR_PROJECT_NAME') submitted in INSDC, set the list of comma separated project names in the PROJECTS env variable (default values: VGP(https://vertebrategenomesproject.org/), DTOL(https://www.darwintreeoflife.org/)) + + -EXEC_TIME: how often, in seconds, the job should be performed it does nothing if PROJECTS OR PROJECT_ACCESSION are empty - The CRONJOB part: - Configure this part if you want to retrieve public data from ENA/BioSamples and/or NCBI (the sample metadata format must be compliant with the ENA checklist). - The cronjob will automatically check for read data in ENA if PROJECTS and/or PROJECT_ACCESSION are present - PROJECTS= --> list of projects (comma separated) wich name figures in the sample metadata submitted to the ENA/BioSamples - PROJECT_ACCESSION --> bioproject accession to retrieve data from NCBI - EXEC_TIME=600 --> how often, in seconds, the job should be performed + NOTE: if you are just interested in local data management remove the default values of PROJECTS and PROJECT_ACCESSION - The DATA PORTAL part: - This part have some default values that can be modified + Local data management: - ROOT_NODE=the INSDC bioproject acccession which will be used as the root project of the application + Configure this part if you want to enter samples locally + USR=admin --> Define the user name that will be inserted to access the admin area + JWT_SECRET_KEY=secret_restKey #change this in production!! --> key to encrypt the RESTKEY (below) + RESTKEY=secretPassword #change this in production!! --> password that will be inserted to access the admin area To add a custom logo and an icon follow this steps: @@ -129,12 +133,14 @@ To get a local copy up and running follow these simple example steps. ### Installation -You need to have docker compose installed (https://docs.docker.com/compose/) +You need to have docker compose installed (https://docs.docker.com/compose/). -1. Configure the .env file as above -2. Run this command in the root directory: - sudo docker-compose -f docker-compose.yml up --build -3. To start creating data go to: /admin from the home page and login +1. Run this command in the root directory: + sudo docker-compose -f docker-compose.dev.yml up --build + + This will load the last generated db dump containing all the public data under the EBP scope (https://www.earthbiogenome.org/) + +2. To start creating data go to: /admin from the home page and login

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@@ -175,11 +181,10 @@ The import function uses the BioSamples API to retrieve samples metadata via the ## Roadmap - [ ] Add Changelog -- [ ] Add JSON schema (OAS docs) -- [X] Add local names management -- [X] Add organism photo management -- [X] Add sample accession import feature -- [ ] Add custom fields management +- [ ] Add API Documentation +- [ ] Add tests (I know..) + + diff --git a/client/src/App.vue b/client/src/App.vue index d24784b1..efb27a30 100644 --- a/client/src/App.vue +++ b/client/src/App.vue @@ -4,6 +4,21 @@ + + +

+ This data portal is an instance of the BioGenome portal software. +

+

+ It tracks the INSDC public data under the Earth BioGenome Project umbrella. +

+
+

+ IMPORTANT: This is NOT the official data portal of the Earth BioGenome Project. + Refer to GoaT to view the Earth BioGenome Project sequencing progress. +

+
+
@@ -25,7 +40,7 @@