From be25fdb29ee828ed10f196c44a04dfdb5ad32160 Mon Sep 17 00:00:00 2001 From: mabeckwith Date: Fri, 10 Jul 2026 11:42:56 -0400 Subject: [PATCH] Update docs (#225). --- docs/app.md | 2 +- docs/json.md | 2 +- docs/setup-server.md | 21 ++++++++++----------- 3 files changed, 12 insertions(+), 13 deletions(-) diff --git a/docs/app.md b/docs/app.md index 2175c814..f252d7db 100644 --- a/docs/app.md +++ b/docs/app.md @@ -109,7 +109,7 @@ java -jar maxodiff-cli/target/maxodiff-cli.jar analyze \ If you want to call the output file `custom`, use the `-f` argument ```bash java -jar maxodiff-cli/target/maxodiff-cli.jar analyze \ - -p -f + -p -O -f ``` The app will append the correct suffix (`.html` or - if the json output option is chosen - `.json`). diff --git a/docs/json.md b/docs/json.md index dd619a29..1ffda0dd 100644 --- a/docs/json.md +++ b/docs/json.md @@ -25,7 +25,7 @@ To run the web interface, follow these steps: - Select a phenopacket using the Sample Input box (on the top) - Set the output to **HTML** or **JSON** as desired -- Click the **RUn differential diagnosis calculation** button +- Click the **Run differential diagnosis calculation** button - You should then see a progress bar. diff --git a/docs/setup-server.md b/docs/setup-server.md index 282a7b57..9672f816 100644 --- a/docs/setup-server.md +++ b/docs/setup-server.md @@ -63,7 +63,6 @@ You should now see `maxodiff-html-app` in the list of Containers in the Docker G - The docker process should now be visible at http://localhost:8080/maxodiff. -- To test the single-disease modality tool, use @@ -119,22 +118,22 @@ docker run -it -p 8080:8080 \ ### Testing with Postman -1. maxodiff (standard algorithm) +#### maxodiff (standard algorithm) - To test the container, we can use [postman](https://www.postman.com/). -- Use Postman Desktop app (Note: do not use the Postman Agent app, it is not suited for this) -- Create a new request, set it to POST at http://localhost:8080/api/analyze, -- Set the BODY to JSON and paste the JSON file for a phenopacket -- Click on Send +- Use Postman Desktop app (Note: do not use the Postman Agent app, it is not suited for this). +- Create a new request, set it to POST at http://localhost:8080/api/analyze. +- Set the BODY to JSON and paste the JSON file for a phenopacket. +- Click on Send. - The calculations will take 10 seconds, and then JSON code will be returned. -2. maxodiff single-disease +#### maxodiff single-disease -- enter POST -- use the API http://localhost:8080/api/modality?targetDiseaseId=OMIM:157700. (substitute any OMIM id) -- as body, paste in a complete phenopacket -- click on SEND +- Enter POST. +- Use the API http://localhost:8080/api/modality?targetDiseaseId=OMIM:157700. (substitute any OMIM id). +- As body, paste in a complete phenopacket. +- Click on SEND. - This will return JSON like this: ```json