Knowledge Beacon wrapper for the NDex Bio graph repository
Clone the project:
git clone --recursive https://github.com/NCATS-Tangerine/ndex-beacon.gitThe use of the --recursive flag reflects the use of an embedded ontology submodule. If you get ontology errors at
some future time, you may need to use the git submodule update operation to update this module.
You can run the project directly on your machine or from within a Docker container.
Copy over the server/src/main/resources/{application.properties => application.properties-template file into an application.properties file in the same directory. Configure as needed.
[Optional] For example, reset the port you want to run the beacon on. By default, the port is set to
8076 (localhost:8076). To reset, open server/src/main/resources/application.properties, and change server.port.
Build the project with Gradle (we currently specific a wrapper using Gradle 5.2). From the root folder of the project:
gradle buildIf the build is failing make sure you have pulled all git submodules, you may have missed the --recursive flag when
cloning. If it's still failing check that you're using Gradle version 5.2 or higher, as previous versions may fail.
Once the JAR file has been built you may execute it:
java -jar server/build/libs/ndex-beacon-#.#.#.jar
where #.#.# is the release number of the application (e.g. 1.1.2). (You may also be able to use an astrix as a
wild card, and use the command java -jar server/build/libs/ndex-beacon-*.jar).
You may then view the Swagger UI at http://localhost:8076/beacon/ndex/swagger-ui.html
To run Docker, you'll obviously need to install Docker first in your target Linux operating environment (bare metal server or virtual machine running Linux).
For our installations, we typically use Ubuntu Linux, for which there is an Ubuntu-specific docker installation using the repository. Note that you should have 'curl' installed first before installing Docker:
sudo apt install curl
For other installations, please find instructions specific to your choice of Linux variant, on the Docker site.
In order to ensure that Docker is working correctly, run the following command:
sudo docker run hello-world
This should result in something akin to the following output:
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
ca4f61b1923c: Pull complete
Digest: sha256:be0cd392e45be79ffeffa6b05338b98ebb16c87b255f48e297ec7f98e123905c
Status: Downloaded newer image for hello-world:latest
Hello from Docker!
This message shows that your installation appears to be working correctly.
To generate this message, Docker took the following steps:
1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
(amd64)
3. The Docker daemon created a new container from that image which runs the
executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it
to your terminal.
To try something more ambitious, you can run an Ubuntu container with:
docker run -it ubuntu bash
Share images, automate workflows, and more with a free Docker ID:
https://cloud.docker.com/
For more examples and ideas, visit:
https://docs.docker.com/engine/userguide/
Then with Docker installed, you can build an image from the Dockerfile provided in the main directory of this project.
docker build -t ncats:ndex .Within the Docker container, the Springboot Server is set to run at localhost:8076. You can expose and re-map the
ports when you run a Docker image with the -p flag.
# run it as a daemon...
docker run -d -p 8076:8076 --name ndex ncats:ndexNow open your browser to http://localhost:8076/beacon/ndex/swagger-ui.html to see the application running.
non sequitur: This is not specific to this project, but if your docker build exhibits the following error:
Step 4/6 : RUN apt-get -y update && apt-get -y install default-jre-headless
---> Running in ff3a2bb4b16e
Err:1 http://archive.ubuntu.com/ubuntu bionic InRelease
Temporary failure resolving 'archive.ubuntu.com'
etc., then see the solution here.
This beacon queries for NDEx networks by our search parameters, and then queries those resulting networks again for the desired data. All data that the beacon discovers is cached, and used for the metadata endpoints
The bio.knowledge.server.json package contains the Java implementations of NDEx models. Documentation for the NDEx
data model is here: www.home.ndexbio.org/data-model/
The swagger documentation is here: http://openapi.ndexbio.org/#/
NDEx uses lucene search: https://lucene.apache.org/core/
In NdexClient.java we use a number of endpoints to query nDex:
The BASE URL is http://www.ndexbio.org/v2
NETWORK SEARCH /search/network?start={start}&size={size}
This queries for all networks with the given search term (which is provided in the body of the post request). Among other things, it returns the network ID's for matching networks.
QUERY FOR NODE MATCH /search/network/{networkId}/interconnectquery
We feed a network ID, and it returns all the data (nodes, edges, node attributes, edge attributes, citations, etc.) that match those search terms. Again the search term is given in the body of the post request. This only returns data (nodes, edges, etc.) matches.
QUERY FOR NODE AND EDGES /search/network/{networkId}/query
This functions similarly as interconnectquery, but returns all the data that interconnectquery would plus all nodes and edges and so on that those given nodes are connected to.
NETWORK SUMMARY /network/{networkId}/summary
This endpoint provides a summary of information about the network. We use it to get citation data for the entire network.