node tool template finished

.github/workflows/docker-image.yml

@@ -0,0 +1,23 @@
+name: Docker Image CI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v2
+    - name: build and push
+      uses: docker/build-push-action@v1
+      with:
+        registry: ghcr.io
+        username: "vforwater"
+        password: ${{ secrets.PAT }}
+        repository: vforwater/tbr_template_node
+        tags: latest,${{ github.ref_name }}

Dockerfile

@@ -1,8 +1,5 @@
 FROM node:18.12.1-buster
 
-# Do anything you need to install tool dependencies here
-RUN echo "Replace this line with a tool"
-
 # create the tool input structure
 RUN mkdir /in
 COPY ./in /in
@@ -11,4 +8,11 @@ RUN mkdir /src
 COPY ./src /src
 
 WORKDIR /src
+
+# install dependencies:  js-yaml and papaparse
+# in node, the dependencies are directly install into /src/
+RUN npm install js-yaml
+RUN npm install papaparse
+
+# run command
 CMD ["node", "run.js"]

in/foo_csv.csv

@@ -0,0 +1,11 @@
+A,B,C,D
+3,14,10,17
+2,0,2,24
+2,17,19,24
+3,13,1,18
+13,13,7,10
+10,7,13,14
+12,12,9,5
+16,24,3,16
+11,3,2,14
+19,4,5,20

in/foo_mat.dat

@@ -0,0 +1,8 @@
+# Created by Octave 6.4.0, Thu Oct 27 08:57:13 2022 UTC <root@b3d554c31921>
+# name: foo_matrix
+# type: matrix
+# rows: 3
+# columns: 2
+ 1 2
+ 3 4
+ 5 6.0999999999999996

in/parameters.json

@@ -1,6 +1,11 @@
 {
     "foobar": {
-        "foo_int": "42",
-        "foo_str": "Foobar"
+        "foo_int": 42,
+        "foo_float": 13.37,
+        "foo_string": "Never eat yellow snow",
+        "foo_enum": "bar",
+        "foo_array": [34, 55, 23, 43, 23],
+        "foo_matrix": "/in/foo_matrix.dat",
+        "foo_csv": "/in/foo_csv.csv"
     }
 }

src/getParameter.js

@@ -1,10 +1,80 @@
-const { PARAM_FILE, CONF_FILE } = process.env;
+const { PARAM_FILE, CONF_FILE, TOOL_RUN } = process.env;
+const fs = require('fs');
+const yaml = require('js-yaml');
+const papa = require('papaparse');
 
 const getParameter = () => {
     // load  parameters file
     const params = require(PARAM_FILE || '/in/parameters.json');
 
-    return params;
+    // if no tool name was passed, return first configured tool
+    const toolName = TOOL_RUN ? TOOL_RUN : Object.keys(params)[0]
+
+    // load the yaml file
+    const config = yaml.load(fs.readFileSync(CONF_FILE || '/src/tool.yml'))
+    const toolConf = config['tools'][toolName]
+
+    // create the kwargs
+    const kwargs = {}
+
+    // foreach param passed
+    Object.entries(params[toolName]).forEach(([key, val]) => {
+        // get the param conf
+        const parConf = toolConf[key]
+
+        // if it is not specified, add anyway
+        if (!parConf) {
+            kwargs[key] = val
+        } else {
+            // parse dates
+            if (['date', 'time', 'datetime'].includes(parConf['type'].toLowerCase())) {
+                kwargs[key] = new Date(val)
+            }
+
+            if (parConf['type'] === 'file') {
+                ext = val.split('.').pop().toLowerCase()
+
+                // switch the file extension
+                // json
+                if (ext === 'json') {
+                    kwargs[key] = require(val)
+                } 
+
+                // dat
+                else if (ext === 'dat') {
+                    raw = fs.readFileSync(val)
+                    const dat = []
+                    raw.split('\n').forEach(line => {
+                        if (!line.startsWith('#')) {
+                            dat.push(line.split(' '))
+                        } 
+                    })
+
+                    // add data
+                    kwargs[key] = dat
+
+                } 
+
+                // read csv data
+                else if (ext === 'csv') {
+                    // 
+                    raw = fs.readFileSync(val).split('\n')
+                    const recs = papa.parse(raw, {header: true})
+
+                    // add 
+                    kwargs[key] = recs
+                }
+
+                // else the tool should handle it
+                else {
+                    // pass the file path anyway, because we don't know this file
+                    kwargs[key] = val
+                }
+            }
+        }
+    })
+
+    return kwargs;
 }
 
 module.exports = getParameter

src/run.js

@@ -9,7 +9,7 @@ params = getParameter();
 // switch the toolName
 if (toolName === 'foobar') {
    console.log('You are running the template directly. Please change the foobar function.')
-   console.log(params[toolName]) 
+   console.log(params) 
 } else {
     console.error(`The toolname ${toolName} is not recognized. Did you forget to implement it?`)
 }

src/tool.yml

@@ -1,10 +1,25 @@
 tools:
   foobar:
-    title: Foobar function
-    description: Dummy default function of a toolbox template
-    version: 1.0
+    title: Foo Bar
+    description: A dummy tool to exemplify the YAML file
+    version: 0.1
     parameters:
-      foo_int:
+      foo_int: 
         type: integer
-      foo_str:
-        type: string
+      foo_float:
+        type: float
+      foo_string:
+        type: string
+      foo_enum:
+        type: enum
+        values:
+          - foo
+          - bar
+          - baz
+      foo_array:
+        type: integer
+        array: true
+      foo_matrix:
+        type: file
+      foo_csv:
+        type: file