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3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -12,4 +12,5 @@ beacon/connections/mongo/data/db/*
*.json.gz
adminui/adminclient/migrations/*
adminui/node_modules
*.vcf.bgz
*.vcf.bgz
beacon/conf/conf.py
26 changes: 26 additions & 0 deletions README.md
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Expand Up @@ -6,6 +6,18 @@ Welcome to Beacon v2 Production Implementation (B2PI). This is an application th

Please, go to [B2RI/B2PI docs website](https://b2ri-documentation-demo.ega-archive.org/) to know how to use Beacon v2 Production Implementation.

## New release beacon v2.0-d4012a4 features added

* Models plug in. Beacon PI now accepts different beacon flavours, based on different model specifications. Kicking off with two models: ga4gh beacon v2 default model and EUCAIM.
* Conf now is not affected by further releases. Use your conf and keep it forever.
* Cross queries between collections and non collections now are ready to be performed at full power.
* Schema request now working: feel free to request any schema you'd like for beacon to return.
* Validation on the fly per framework and model(s).
* Configuration of the entities of each entry type now done by .yml files.
* Restart of the app when conf files or generic conf is modified (no need to rebuild).
* Other bug fixes
* Unit tests expanded, with a total of 313 now.

## Main changes from B2RI

* Handlers of the endpoints are classes, not functions
Expand Down Expand Up @@ -86,6 +98,20 @@ And execute the next commands (only the ones you need):
docker exec mongoprod mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /data/caseLevelData.json --collection caseLevelData
```

Alternatively, now also you can have your json gzipped and insert them in a one step injection with the next commands:

```
gunzip --stdout genomicVariations.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection genomicVariations'
gunzip --stdout analyses.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection analyses'
gunzip --stdout biosamples.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection biosamples'
gunzip --stdout datasets.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection datasets'
gunzip --stdout cohorts.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection cohorts'
gunzip --stdout runs.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection runs'
gunzip --stdout individuals.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection individuals'
gunzip --stdout targets.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection targets'
gunzip --stdout caseLevelData.json.gz | docker exec -i mongoprod sh -c 'mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --collection caseLevelData'
```

This loads the JSON files inside of the `data` folder into the MongoDB database container. Each time you import data you will have to create indexes for the queries to run smoothly. Please, check the next point about how to Create the indexes.

#### Create the indexes
Expand Down
2 changes: 1 addition & 1 deletion beacon/conf/api_version.yml
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@@ -1 +1 @@
api_version: v2.0-a7b6f63
api_version: v2.0-548ab64