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⚡️ add API and Input validation #8

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merged 6 commits into from
Dec 19, 2023
Merged

⚡️ add API and Input validation #8

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d58f1f4
⚡️ add express api server
juanesarango Dec 12, 2023
9286d9d
🔧 add validation with Joi
juanesarango Dec 12, 2023
cb00b15
🔧 validate and better error handling
juanesarango Dec 12, 2023
68ef55a
🔧 add /ipssm endpoint
juanesarango Dec 19, 2023
485ab87
🔧 gitignore serverless artifacts
juanesarango Dec 19, 2023
cb0fd0b
🔧 gitignore serverless artifacts
juanesarango Dec 19, 2023
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -6,4 +6,7 @@ dist

# Data test files
test/data/*-out.*
test.csv
test.csv

# Serverless artifacts
.serverless
14 changes: 6 additions & 8 deletions README.md
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Expand Up @@ -7,9 +7,9 @@

<!-- badges: end -->

# ipssm (js)
# ipssm API and CLI

Javascript/Node Package for the Molecular International Prognostic Scoring System (IPSS-M) for Myelodysplastic Syndromes.
API and CLI of the Molecular International Prognostic Scoring System (IPSS-M) for Myelodysplastic Syndromes.

- For the R package, see [papaemmelab/ipssm](https://github.com/papaemmelab/ipssm).

Expand All @@ -19,11 +19,11 @@ Javascript/Node Package for the Molecular International Prognostic Scoring Syste

- [📖 IPSS-M Publication](#page_with_curl-ipss-m-publication)
- [🚀 Installation instructions](#rocket-installation-instructions)
- [💥 IPSS-M Usage](#boom-ipss-m-usage)
- [💥 IPSS-M Usage](#boom-ipss-m-javascript-usage)
- [🔥 Compute IPSS-M](#fire-compute-ipss-m)
- [⚡️ IPSS-R and IPSS-R (Age adjusted)](#zap-ipss-r-and-ipss-r-age-adjusted)
- [🎯 Annotating batch from CSV/Excel file](#dart-annotating-batch-from-csvexcel-file)
- [🦾 Using the command line interface](#mechanical_arm-using-the-command-line-interface)
- [🦾 Using the command line interface](#mechanical_arm-using-the-command-line-interface-cli)
- [🗒️ Input Variables Definition](#spiral_notepad-input-variables-definition)
- [❓ Question](#question-question)

Expand All @@ -41,7 +41,7 @@ Javascript/Node Package for the Molecular International Prognostic Scoring Syste
npm install ipssm
```

## :boom: IPSS-M Usage
## :boom: IPSS-M Javascript Usage

### :fire: Compute IPSS-M

Expand Down Expand Up @@ -192,7 +192,7 @@ const outputFile = 'IPSSMexample.annotated.xlsx'
await annotateFile(inputFile, outputFile)
```

### :mechanical_arm: Using the command line interface
### :mechanical_arm: Using the command line interface (CLI)

You can use the command line interface to annotate a file with patients, where each row is a patient and each column is a variable.

Expand All @@ -218,8 +218,6 @@ Options:

## :spiral_notepad: Input Variables Definition



| Category | Variable Explanation | Variable | Unit | Possible Value |
|----------------------------|-------------------------------|--------------|------------------------------|-------------------------------------------------------------|
| clinical | Hemoglobin | `HB` | numerical, in g/dL | [`4`-`20`] |
Expand Down
3 changes: 3 additions & 0 deletions deploy.sh
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#!/bin/bash

serverless deploy --aws-profile arangooj-cloud
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