Merge pull request #155 from USEPA/dev

DEV > STG 12/05/2025

Author: bridirks

.github/workflows/security-scan.yml

@@ -18,7 +18,7 @@ jobs:
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          format: openapi
-         target: 'https://api-ccte-stg.epa.gov/docs/exposure.json'
+         target: 'https://ctx-api-stg.ccte.epa.gov/docs/exposure.json'
          cmd_options: '-a'
        env:
          ZAP_AUTH_HEADER_VALUE: "x-api-key=${{ secrets.X_API_KEY }}" 

CONTRIBUTING.md

@@ -1,4 +1,3 @@
-
 Thank you for considering contributing to this project! Contributions are welcome and appreciated. Please follow the guidelines below to ensure a smooth collaboration.
 
 ## How to Contribute
@@ -52,8 +51,6 @@ This project is licensed under the [MIT License](LICENSE.md). By contributing to
 - If you have any questions or need assistance, feel free to reach out to the project maintainers.
 - We appreciate your time and effort in contributing to this project!
 - Happy coding!
-- 
-
 
 
 

README.md

@@ -1,14 +1,22 @@
-# Exposure Microservice (ccte-api-exposure)
+# Computational Toxicology and Exposure (CTX) APIs - CTX Exposure API
 
-## Overview
-The Exposure Microservice is a RESTful API designed to manage and provide Exposure data. It interacts with a PostgreSQL database and offers various endpoints for Exposure-related operations.
+<!-- badges: start -->
+[![Active](http://img.shields.io/badge/Status-Active-green.svg)](https://comptox.epa.gov/ctx-api/exposure/health) 
+<!-- badges: end -->
 
-## Available Data
-Data underlying the Exposure API comes from the Chemicals and Products Database (CPDat) [Learn more: The Chemical and Products Database, a resource for exposure-relevant data on chemicals in consumer products](https://www.nature.com/articles/sdata2018125) and predictions from EPA’s Quantitative Structure Use Relationship (QSUR) models [Learn more: High-throughput screening of chemicals as functional substitutes using structure-based classification models](https://pubs.rsc.org/en/content/articlelanding/2017/gc/c6gc02744j).
+## Welcome to the GitHub repository for the CTX Exposure API
 
-For exposure-related questions, contact the Chemical Exposure Knowledgebase team (chemexpo.support@epa.gov).
+Originating from the US EPA's Center of Computational Toxicology and Exposure (CCTE), the CTX Exposure API is a RESTful API designed to manage and provide Exposure data. It interacts with a PostgreSQL database and offers various endpoints for Exposure-related operations. More information on the CTX API development and utility, as well as guidance on how to technically access and use them, is available here: https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis
 
-## Technologies Used
+- If you would like to report a bug or have other questions related to the CTX APIs, please contact the [CTX API Admins](mailto:[email protected]).
+- If you are interested in contributing, please submit a issue or start a discussion. See [CONTRIBUTING](https://github.com/USEPA/ccte-api-hazard/blob/dev/CONTRIBUTING.md) for more information.
+
+### Available Data
+Data underlying the Exposure API comes from the [Chemicals and Products Database (CPDat)](https://www.nature.com/articles/sdata2018125), the Multimedia Monitoring Database (MMDB)](https://epa.figshare.com/articles/dataset/Multimedia_Monitoring_Database_MMDB_/17065024), [httk](https://github.com/USEPA/CompTox-ExpoCast-httk) simulation data, and predictions from Systematic Empirical Evaluation of Models (SEEM) and [Quantitative Structure Use Relationship (QSUR) models](https://github.com/HumanExposure/qsur).
+
+For exposure-related questions, review the [ChemExpo User guide](https://comptox.epa.gov/chemexpo/static/user_guide/) or contact the [Chemical Exposure Knowledgebase team](mailto:[email protected]).
+
+### Technologies Used
 - **Java**: Programming language used for the development of the application.
 - **Spring Boot**: Framework used to create stand-alone, production-grade Spring-based applications.
 - **Spring Data JPA**: Part of the Spring Data family, used to simplify data access and persistence.
@@ -20,21 +28,21 @@ For exposure-related questions, contact the Chemical Exposure Knowledgebase team
 - **Swagger/OpenAPI**: Used for API documentation and testing.
 - **Testcontainers**: Java library used for integration testing with Docker containers.
 
-## Configuration
+### Configuration
 The application configuration is managed through properties files. The main configuration file is `application.properties`, and environment-specific configurations can be added as needed.
 
-## Build and Deployment
+### Build and Deployment
 The project uses Maven for build and deployment processes. Continuous integration and deployment can be set up using tools like GitHub Actions.
 
-## Getting Started
+### Getting Started
 To build and run the project locally, use the following Maven commands:
 
 ```sh
 mvn clean install
 mvn spring-boot:run
 ```
 
-## Project Structure
+### Project Structure
 ```plaintext
 src/
 ├── main/
@@ -51,7 +59,7 @@ src/
 └── test/
 ```
 
-## Dependencies
+### Dependencies
 - `spring-boot-starter-web`
 - `spring-boot-starter-data-rest`
 - `spring-boot-starter-data-jpa`
@@ -64,11 +72,5 @@ src/
 - `testcontainers`
 - `jackson-datatype-hibernate6`
 
-## Contributing
-Contributions are welcome! Please read the `CONTRIBUTING.md` file for guidelines.
-
-## Contact
-For any inquiries, please contact the project maintainer. **[Rashid, Asif](https://github.com/asif-rashid)** , **[Dirks, Brianna](https://github.com/bridirks)**, **[Feshuk, Madison](https://github.com/madison-feshuk)**
-
 ## Disclaimer
 The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government. 

src/main/java/gov/epa/ccte/api/exposure/config/OpenApiConfig.java

@@ -14,21 +14,21 @@
 @Configuration
 @OpenAPIDefinition(
         info = @Info(
-                title = "Computational Toxicology and Exposure Data APIs - Exposure",
-                description = "The Exposure APIs are part of a set of public computational toxicology and exposure APIs and provide exposure data through a set of API endpoints.",
+                title = "Computational Toxicology and Exposure (CTX) APIs - CTX Exposure API",
+                description = "The CTX Exposure API is part of US EPA's Computational Toxicology and Exposure APIs. The CTX Exposure API provides programmtic access to exposure data through a set of endpoints.",
                 contact = @Contact(
                         name = "",
                         url = "",
                         email = ""),
-                version = "1.0.0"
+                version = "1.1.1"
         ),
         servers = { @Server(url = "${application.api-url}", description = "${application.api-env}")}
 )
 @SecurityScheme(
         type = SecuritySchemeType.APIKEY,
         name = "api_key",
         in = SecuritySchemeIn.HEADER,
-        description = "Each API call should have api_key, Contact author for getting the new api_key. ",
+        description = "Each API request requires an api_key. Contact the CTX API Admin to request an API Key.",
         paramName = "x-api-key"
 )
 public class OpenApiConfig {

src/main/java/gov/epa/ccte/api/exposure/web/rest/CCDApi.java

@@ -28,48 +28,46 @@
  * REST controller for getting available CCD Data Resources.
  */
 @Tag(name = "CCD Data Resource",
-        description = "API endpoints for CompTox Chemicals Dashboard exposure tabs.")
+        description = "Collection of endpoints used to populate CompTox Chemicals Dashboard (CCD) Exposure tabs.")
 @SecurityRequirement(name = "api_key")
 @RequestMapping( value = "exposure/ccd", produces = MediaType.APPLICATION_JSON_VALUE )
 public interface CCDApi {
 
-    @Operation(summary = "Find Chemical Weight Fractions data by dtxsid", description = "return Chemical Weight Fractions data for requested dtxsid")
+    @Operation(summary = "Get Chemical Weight Fractions data by DTXSID", description = "return Chemical Weight Fractions data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDChemicalWeightFractions.class}))),
     })
     @RequestMapping(value = "/chem-weight-fractions/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<CCDChemicalWeightFractions> getChemicalWeightFractionsByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find General Use Keywords data by dtxsid", description = "return General Use Keywords data for requested dtxsid")
+    @Operation(summary = "Get General Use Keywords data by DTXSID", description = "return General Use Keywords data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDGeneralUseKeywords.class}))),
     })
     @RequestMapping(value = "/keywords/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<CCDGeneralUseKeywords> getGeneralUseKeywordsByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find Product Use Category data by dtxsid", description = "return Product Use Category data for requested dtxsid")
+    @Operation(summary = "Get Product Use Category data by DTXSID", description = "return Product Use Category data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDProductUseCategory.class}))),
     })
     @RequestMapping(value = "/puc/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<CCDProductUseCategory> getProductUseCategoryByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find Reported Functional Use data by dtxsid", description = "return Reported Functional Use data for requested dtxsid")
+    @Operation(summary = "Get Reported Functional Use data by DTXSID", description = "return Reported Functional Use data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDReportedFunctionalUse.class}))),
     })
     @RequestMapping(value = "/functional-use/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<CCDReportedFunctionalUse> getReportedFunctionalUseByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find Biomonitoring data by dtxsid with ccd projection", 
-    		   description = "return NHANES Inferences for requested dtxsid" +
-                             "there is an available projection for ccd exposure biomonitoring page:" +
-    				         "ccd-biomonitoring" +
-                             "If no projection is specified, the default CCDBiomonitoring data will be returned")
+    @Operation(summary = "Get Biomonitoring data by DTXSID with CCD projection", 
+    		   description = "return NHANES inferences data for requested DTXSID. There is an available projection aligned with what's available on the CCD Exposure Biomonitoring tab: ccd-biomonitoring. " +
+                             "If no projection is specified, a default CCDBiomonitoring projection will be returned.")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDBiomonitoring.class, CCDBiomonitoringAll.class}))),
@@ -81,7 +79,7 @@ List<?> getBiomonitoringDataByDtxsid(@Parameter(required = true, description = "
             	                                "If omitted, the default CCDBiomonitoring data is returned.")
             	                        @RequestParam(value = "projection", required = false) String projection);
 
-    @Operation(summary = "Find Production Volume data by dtxsid", description = "return Production Volume data for requested dtxsid")
+    @Operation(summary = "Get Production Volume data by DTXSID", description = "return Production Volume data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {CCDProductionVolume.class}))),

src/main/java/gov/epa/ccte/api/exposure/web/rest/DemoExpoPredictionApi.java

@@ -20,12 +20,12 @@
  * REST controller for getting the {@link gov.epa.ccte.api.exposure.domain.DemoExpoPrediction}s.
  */
 @Tag(name = "Demographic Exposure Prediction Resource",
-        description = "API endpoints for demographic prediction in exposure data.")
+        description = "Collection of endpoints with SEEM demographic exposure prediction data. SEEM (Systematic Empirical Evaluation of Models) is a framework developed by the US EPA to predict exposure to chemicals across the general population and demographic subsets of the US.")
 @SecurityRequirement(name = "api_key")
 @RequestMapping( value = "exposure/seem/demographic", produces = MediaType.APPLICATION_JSON_VALUE)
 public interface DemoExpoPredictionApi {
 
-    @Operation(summary = "Find demographic prediction SEEMs data by dtxsid", description = "return demographic prediction SEEMs data for requested dtxsid")
+    @Operation(summary = "Get SEEM Demographic Exposure Prediction data by DTXSID", description = "return SEEM demographic prediction data for requested DTXSID")
     @ApiResponses(value = {
             @ApiResponse(responseCode = "200", description = "OK", content = @Content(mediaType = "application/json",
                     schema = @Schema(oneOf = {DemoExpoPrediction.class}))),
@@ -36,7 +36,7 @@ List<?> getDemoExpoPredictionByDtxsid(@Parameter(required = true, description =
     									@Parameter(description = "Specifies whether to use projection. Optional: ccd-demographic.")
     									@RequestParam(value = "projection", required = false) String projection);
 
-    @Operation(summary = "Find demographic prediction SEEMs data by batch of dtxsids", description = "return demographic prediction SEEMs data for requested dtxsids")
+    @Operation(summary = "Get SEEM Demographic Exposure Prediction data for batch of DTXSIDs", description = "return SEEM demographic prediction data for requested DTXSIDs")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK", content = @Content(mediaType = "application/json",
                     schema = @Schema(oneOf = {DemoExpoPrediction.class}))),

src/main/java/gov/epa/ccte/api/exposure/web/rest/ExposureApi.java

@@ -7,8 +7,8 @@
 /**
  * REST controller for getting the {@link ExposureResource}s.
  */
-@Tag(name = "Exposure Data Resource",
-        description = "API endpoint for checking database connection of exposure application.")
+@Tag(name = "Exposure Data Health Resource",
+        description = "Endpoint for checking health of database connection used by CTX Exposure API")
 public interface ExposureApi {
     @GetMapping("/exposure/health")
     ResponseEntity<?> health();

src/main/java/gov/epa/ccte/api/exposure/web/rest/FunctionalUseApi.java

@@ -22,36 +22,36 @@
  * REST controller for getting the {@link gov.epa.ccte.api.exposure.domain.FunctionalUse}s.
  */
 @Tag(name = "Functional Use Resource",
-        description = "API endpoints for functional use in exposure data.")
+        description = "Collection of endpoints with functional use data. Functional use describes a chemical's role in a product or process, which can help determine exposure pathways used to assess chemical exposure. These curated data are sourced from US EPA's Chemicals and Products Database (CPDat).")
 @SecurityRequirement(name = "api_key")
 @RequestMapping( value = "exposure/functional-use", produces = MediaType.APPLICATION_JSON_VALUE )
 public interface FunctionalUseApi {
 
-    @Operation(summary = "Find functional-use data by dtxsid", description = "return functional-use data for requested dtxsid")
+    @Operation(summary = "Get functional use data by DTXSID", description = "return functional use data for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
             		schema=@Schema(oneOf = {FunctionalUse.class}))),
     })
     @RequestMapping(value = "/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<FunctionalUse> getFunctionalUseByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find functional-use categories", description = "return all functional-use categories")
+    @Operation(summary = "Get functional use categories", description = "return all functional use categories")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK", content = @Content(mediaType = "application/json",
                     schema = @Schema(oneOf = {FunctionalUseCategory.class}))),
     })
     @RequestMapping(value = "/category", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<FunctionalUseCategory> getFunctionalUseCategory();
 
-    @Operation(summary = "Find functional-use probability by dtxsid", description = "return functional-use probability for requested dtxsid")
+    @Operation(summary = "Get functional use probability by DTXSID", description = "return functional use probability for requested DTXSID")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK", content = @Content(mediaType = "application/json",
                     schema = @Schema(oneOf = {QsurDataAll.class}))),
     })
     @RequestMapping(value = "/probability/search/by-dtxsid/{dtxsid}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     List<QsurDataAll> getFunctionalUseProbabilityByDtxsid(@Parameter(required = true, description = "DSSTox Substance Identifier", example = "DTXSID0020232") @PathVariable("dtxsid") String dtxsid);
 
-    @Operation(summary = "Find functional-use data by batch of dtxsids", description = "return functional-use data  for requested dtxsids.")
+    @Operation(summary = "Get functional-use data for a batch of DTXSIDs", description = "return functional-use data for requested DTXSIDs")
     @ApiResponses(value= {
             @ApiResponse(responseCode = "200", description = "OK",  content = @Content( mediaType = "application/json",
                     schema=@Schema(oneOf = {FunctionalUse.class}))),