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Update docs (#225). #245

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2 changes: 1 addition & 1 deletion docs/app.md
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Expand Up @@ -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 <path to phenopacket file> -f <custom>
-p <path to phenopacket file> -O <path to output directory> -f <custom>
```

The app will append the correct suffix (`.html` or - if the json output option is chosen - `.json`).
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2 changes: 1 addition & 1 deletion docs/json.md
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Expand Up @@ -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.


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21 changes: 10 additions & 11 deletions docs/setup-server.md
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Expand Up @@ -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



Expand Down Expand Up @@ -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
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