README

The Analytical QC application consists of four components:

• Database
• Static content
• Backend
• Frontend

Database

The database contains substance, sample, experiment, and file information along with structured and freeform annotations. It is currently located at ccte-postgres-res.dmap-prod.aws.epa.gov, under database res_gsincl01_qsar and schema sbox_analytical_qc. The DDL file and contents of the database as of 07/02/22 are provided in the db directory of this repository in TSV and SQL format.

Static content (content-server)

Static files are served from a directory by an nginx server, by default on port 82. The directory containing all files is currently located at L:/Lab/NCCT_Richard/Antony Williams/analytical-qc_GFBS_010722/analytical-qc_content-server_static.tar.gz. The contents of this file (~10 GB) should be extracted into the content-server/static directory of this project for deployment.

Backend (server)

A database API served by a Spring Boot web service, by default on port 9091.

Frontend (client)

A frontend interface in Vue.js, running on an nginx server, by default on port 81.

Summary API

Summary API endpoints are provided for substance- and sample-level annotation information (grades at T0 and T4, final stability call, and any text annotation). These are accessible at:

• [backend]/api/substance-annotations/[id|casrn|dtxsid|tox21-id|ncgc-id|bottle-barcode]/[query] (single substance annotation)
• [backend]/api/substance-annotations?pageNo=[no]&pageSize=[size] (all substance annotations, paginated)
• [backend]/api/sample-annotations/[id|tox21-id|ncgc-id|bottle-barcode]/[query] (single sample annotation)
• [backend]/api/sample-annotations?pageNo=[no]&pageSize=[size] (all sample annotations, paginated)

Important

Adding files

The web app interface contains a panel to link files to substances. Files added this way must be manually added to the static content in order to display; otherwise you will see broken links. Files can be added before or after linking in the interface. To add files, copy them into the content-server/static directory of the deployment location, then run docker-compose up -d --build --force-recreate --no-deps content-server to recreate without affecting the server and client services.

scp instructions

Files can be copied onto a remote server using scp (https://linuxize.com/post/how-to-use-scp-command-to-securely-transfer-files/):

1. Open cmd on your local machine.
2. Navigate (cd) to the location of the files to be added.
3. Run scp ./*.pdf [USER]@[HOST]:[DEPLOYMENT_LOCATION]/content-server/static.

Moving the database/redeploying

This application is set up to deploy in Docker using docker-compose. It is now deployed on the v2626umcth819.rtord.epa.gov server. If the database is transferred to a different location or a different user account is used to access it, the app credentials will need to be altered and the services restarted. The current environment variable values are in a .env.local file provided to Tony Williams.

0. Clone this repository into the desired deployment location. 0.5. Extract the static files into the content-server/static directory of this repository.
1. Place the .env.local file in the root directory of this repository.
2. Change the DB_ variables in the .env.local file as needed.
3. Run export $(cat .env.local | xargs) to export the variables in .env.local to your environment.
4. Run docker-compose up --build -d to build and run the services in detached mode.

If the deployment location is not changed, then the services only need to be restarted, not rebuilt, for the changed environment variables to take effect.

Server environment variables

• DB_URL, DB_USER, DB_PASS, DB_SCHEMA: Standard database connection parameters
• DB_DRIVER, DB_DIALECT: Presently for PostgreSQL, made variable to enable compatibility with MySQL systems if needed in the future (MySQL driver included in pom.xml)
• CLIENT_URL: URL of client deployment to enable CORS
• DASHBOARD_API_URL: URL of CCD API to acquire new substance information

Client environment variables

• VUE_APP_SERVER_URL: URL of server deployment
• VUE_APP_CONTENT_SERVER_URL: URL of content-server deployment

Adding new grade/call/structure flag/NMR amenability flag options

New options for grades, calls, structure flags, and NMR amenability flags can be added to the database and will be shown immediately in the interface:

INSERT INTO sbox_analytical_qc.[grades|calls|structure_flags|nmr_amen_flags] (name, description) VALUES ('newname', 'newdescription')

New additions will be automatically colored gray when shown.

Comparing predicted vs. validated LCMS amenability

A side objective of this app was to permit validation of LCMS amenability predictions provided by Charlie Lowe. The interface allows the user to "override" or "validate" the predicted amenability. Amenability predictions (numerical) and user inputs (boolean) are stored in the amenability_predictions table of the database. The following query will retrieve them in summary form:

SELECT s.dtxsid, ap.lcms_amen_neg AS esi_neg_pred, ap.lcms_amen_pos AS esi_pos_pred, ap.lcms_amen_neg_true AS esi_neg_true, ap.lcms_amen_pos_true AS esi_pos_true FROM sbox_analytical_qc.amenability_predictions ap JOIN sbox_analytical_qc.substances s ON s.id = ap.substance_id;