Speedrichr

This is the API backend for Enrichr. It supports faster in memory data structures to take the load of the database instance.

This file should be extracted into the /src/main/webapp/WEB-INF/data/ folder.

Building a new image and updating gene list files

The data used by Speedrichr are stored directly in the docker image. You can download the gmt files from an S3 bucket s3://maayanlab-public/enrichr (ask Daniel for access) To update or add a new GMT file the following steps have to be taken:

1. Update the file: /src/main/webapp/WEB-INF/data/datasetStatistics.json

Add information about the new file in the format of:

{
    "geneCoverage": number of genes,
    "genesPerTerm": average  number of genes,
    "libraryName": name of gene set (same as GMT file name without file ending),
    "link": url of resource,
    "numTerms": number of gene lists,
    "categoryId": category from "categories" at the end of the file
}

Example:

{
    "geneCoverage": 17464,
    "genesPerTerm": 63,
    "libraryName": "DisGeNET",
    "link": "https://www.disgenet.org",
    "numTerms": 9828,
    "categoryId": 7
}

2. Add GMT file to folder: /src/main/webapp/WEB-INF/data/genelibs

3. Build new docker image and push to docker hub. Go to /docker folder and execute ./buildContainer.sh This will also launch a local version of Speedrichr at port 8666 and can be tested at localhost.

   Example: http://localhost:8666/speedrichr/api/datasetStatistics