JSON API, flask server

.github/workflows/deploy.yml

@@ -0,0 +1,42 @@
+name: Deploy static site to GitHub Pages
+
+on:
+  push:
+    branches:
+      - pyodide # Triggers the workflow on pushes to the pyodide branch
+  workflow_dispatch: # Allows manual triggering from the GitHub UI
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout your repository
+        uses: actions/checkout@v4
+      # Add steps to build your static site (e.g., npm run build)
+      - name: Run deployment script
+        run: |
+          export PYODIDE_VERSION=0.29.3
+          export TARGET_DIR=dist
+          ./deploy_calculator.sh
+      - name: Upload artifact
+        # The contents of the 'build' directory will be uploaded as an artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: 'dist/' # Change this to your build output directory (e.g., public, dist)
+
+  deploy:
+    # Add a dependency to the build job
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write # Grants the GITHUB_TOKEN the necessary permissions to deploy to GitHub Pages
+      id-token: write # Required for OIDC authentication
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4 # This action handles the deployment

.gitignore

@@ -43,3 +43,7 @@ endf/MT.DAT
 endf/PLOT.CHR
 endf/PLOT.SYM
 endf/*.out
+
+# pyodide build cruft
+activation/pyodide
+activation/periodictable_wheel_name.txt

README.md

@@ -13,14 +13,8 @@ available on [github](https://github.com/pkienzle/periodictable).
 Installation
 ============
 
-The activation web frontend is in the activation subdirectory and the cgi
-backend is in cgi-bin. Update the server with something like:
-
-    sudo cp -rp activation/* /var/www/resources/activation
-    sudo cp -p cgi-bin/nact.py /var/www/cgi-bin
-
-The web page uses the date of activate/index.html to show the last
-modification date on the program, so be sure to preserve attributes in copy.
+The activation web frontend is in the activation subdirectory.
+The backend API is in the cgi-bin folder (nact.py)
 
 Be sure the web server is configured to use python 3, with the periodictable
 package updated to the latest version:
@@ -33,15 +27,16 @@ of updates this will also set the last modification date on index.html.
 
 For testing you can run the server from the repository:
 
-    python server.py [host | host:port]
+    pip install flask
+    python flask_server.py [host | host:port]
 
 Additional files:
 
 * endf/* was used to generate the graphs of thermal resonances. It is not
   needed unless you wish to update the graphs, for example, when new versions of
   the endf database are released.
 
-* server.py is used to run a test server for debugging the web application, or
+* flask_server.py is used to run a test server for debugging the web application, or
   showing potential new features to users. See the help inside the file for
   details on running the server.
 
@@ -50,6 +45,19 @@ Additional files:
 
 * cgi-bin/hello.py is a minimal test script for python cgi.
 
+Pyodide implementation
+======================
+You can make a serverless install using pyodide to run the backend API. The `deploy_calculator.sh`
+script will install to `/var/html/resources/activation/index.html`.
+
+To test the pyodide version before deploying, install into a temporary directory:
+```sh
+TARGET_DIR=/tmp/pt bash deploy_calculator.sh
+(cd /tmp/pt && python -m http.server)
+```
+You can then navigate to http://localhost:8000/index.html to view the application.
+
+
 Backend interface
 =================
 
@@ -84,6 +92,25 @@ request = {
 }
 ```
 
+```python
+python_request = {
+    'calculate': "all", # target is "scattering" or "activation" or "all"
+    'sample': 'Co',        # Material
+    'flux': '100000',    # Thermal flux
+    'Cd': '0',           # Cd ratio
+    'fast': '0',         # Thermal/fast ratio
+    'mass': '0',         # Mass
+    'exposure': '1',     # Time on beam
+    'rest': ["0","1","24","360"], # Time off beam
+    'density': '0',      # Density
+    'thickness': '1',    # Thickness
+    'wavelength': '1',   # Source neutrons
+    'xray': 'Cu Ka',     # Source Xrays
+    'decay': '0.001',    # target for "Time to decay below"
+    'abundance': 'IAEA'  # natural abundance tables (IAEA or NIST)
+}
+```
+
 The response is a JSON object with the following fields
 ```javascript
 response = {
@@ -148,119 +175,125 @@ Example
 -------
 
 ```sh
-$ curl -s -d "sample=Co" -X POST https://www.ncnr.nist.gov/cgi-bin/nact.py | python -m json.tool
+$ curl -s -d '{"sample": "Co"}' -H "Content-Type: application/json" -X POST http://localhost:8008/api/calculate | python -m json.tool
 {
-    "sample": {
-        "name": "Co",
-        "density": 8.9,
-        "natural_density": 8.9,
-        "thickness": 1.0,
-        "mass": 1.0,
-        "formula": "Co"
-    },
     "activation": {
-        "flux": 100000.0,
-        "decay_level": 0.001,
-        "total": [
-            0.5088248094656863,
-            0.009706843055148993,
-            1.550197781340068e-05,
-            1.5423998799711213e-05
-        ],
-        "rest": [
-            0,
-            1,
-            24,
-            360
-        ],
+        "Cd": 0.0,
         "activity": [
             {
-                "reaction": "act",
-                "product": "Co-60",
-                "halflife": "5.272 y",
-                "comments": "s for 10m isomer added to ground state",
+                "comments": "",
+                "halflife": "10.5 m",
+                "isotope": "Co-59",
                 "levels": [
-                    1.550756280503848e-05,
-                    1.5507330056885684e-05,
-                    1.5501977813400642e-05,
-                    1.5423998799711213e-05
+                    0.5087467869376632,
+                    0.009690144997026036,
+                    2.6447704770864502e-42,
+                    0.0
                 ],
-                "isotope": "Co-59"
+                "product": "Co-60m+",
+                "reaction": "act"
             },
             {
-                "reaction": "act",
-                "product": "Co-60m+",
-                "halflife": "10.5 m",
-                "comments": "",
+                "comments": "Co-61 prod from Co-60m only",
+                "halflife": "1.65 h",
+                "isotope": "Co-59",
                 "levels": [
-                    0.5088093019028804,
-                    0.009691335725091536,
-                    2.6450954673146495e-42,
-                    0.0
+                    7.305869373119584e-16,
+                    4.799870068457319e-16,
+                    3.0552994658480865e-20,
+                    1.52897407497221e-81
                 ],
-                "isotope": "Co-59"
+                "product": "Co-61",
+                "reaction": "2n"
             },
             {
-                "reaction": "2n",
-                "product": "Co-61",
-                "halflife": "1.65 h",
-                "comments": "Co-61 prod from Co-60m only",
+                "comments": "s for 10m isomer added to ground state",
+                "halflife": "5.272 y",
+                "isotope": "Co-59",
                 "levels": [
-                    7.306767120646388e-16,
-                    4.800459878001244e-16,
-                    3.055674902007567e-20,
-                    1.5291619557875176e-81
+                    1.5505657464889658e-05,
+                    1.5505424745333514e-05,
+                    1.5500073159453058e-05,
+                    1.5422103726672467e-05
                 ],
-                "isotope": "Co-59"
+                "product": "Co-60",
+                "reaction": "act"
             },
             {
-                "reaction": "2n",
-                "product": "Co-61",
-                "halflife": "1.65 h",
                 "comments": "Co-61 prod assuming all Co-60m has decayed to Co-60",
+                "halflife": "1.65 h",
+                "isotope": "Co-59",
                 "levels": [
-                    1.3649499897275873e-16,
-                    8.967560554449202e-17,
-                    5.7081926346341585e-21,
-                    2.8565705754412276e-82
+                    1.3647822848511002e-16,
+                    8.966458753177e-17,
+                    5.707491296308241e-21,
+                    2.8562196022780084e-82
                 ],
-                "isotope": "Co-59"
+                "product": "Co-61",
+                "reaction": "2n"
             }
         ],
+        "decay_level": 0.001,
+        "decay_time": 1.5773360047132599,
         "exposure": 1.0,
-        "decay_time": 1.5773675158317233,
         "fast": 0.0,
-        "Cd": 0.0
+        "flux": 100000.0,
+        "rest": [
+            0,
+            1,
+            24,
+            360
+        ],
+        "total": [
+            0.508762292595129,
+            0.00970565042177194,
+            1.5500073159453095e-05,
+            1.5422103726672467e-05
+        ]
+    },
+    "sample": {
+        "density": 8.9,
+        "formula": "Co",
+        "formula_latex": "Co",
+        "mass": 1.0,
+        "name": "Co",
+        "natural_density": 8.9,
+        "thickness": 1.0
     },
     "scattering": {
-        "sld": {
-            "real": 2.2645416201426363,
-            "imag": 0.009403091502484154,
-            "incoh": 5.632988294016107
+        "contrast_match": {
+            "D2O_fraction": 0.4066002243307043,
+            "sld": 2.2645414633790257
         },
-        "xs": {
-            "coh": 0.07085810248318081,
-            "abs": 1.8806183004968307,
-            "incoh": 0.43843639843243204
-        },
-        "penetration": 0.4184253079898973,
         "neutron": {
-            "wavelength": 1.0,
-            "energy": 81.80420235572412,
-            "velocity": 3956.0339760560055
+            "energy": 81.80421023488275,
+            "velocity": 3956.0340061039888,
+            "wavelength": 1.0
         },
-        "transmission": 9.163767420488476
+        "penetration": 0.4184253369555237,
+        "sld": {
+            "imag": 0.009403090851552168,
+            "incoh": 5.632980055822083,
+            "real": 2.2645414633790257
+        },
+        "transmission": 9.16376893656492,
+        "xs": {
+            "abs": 1.8806181703104334,
+            "coh": 0.07085931929382916,
+            "incoh": 0.4384351463657107
+        }
     },
+    "success": true,
+    "version": "2.0.2",
     "xray_scattering": {
-        "xray": {
-            "wavelength": 1.5418,
-            "energy": 8.041522080237366
-        },
         "sld": {
-            "real": 63.020248367719645,
-            "imag": 9.14097379704212
+            "imag": 9.140742563282087,
+            "real": 63.02025244915057
+        },
+        "xray": {
+            "energy": 8.041522793695698,
+            "wavelength": 1.5418
         }
-    },
-    "success": true
+    }
 }
 ```

activation/api_fetch.js

@@ -0,0 +1,25 @@
+class FetchAPI {
+    response_callback = null;
+    url = null;
+
+    initialize (response_callback, ready_callback=() => {}, url="/api/calculate") {
+        this.response_callback = response_callback;
+        this.url = url;
+        ready_callback();
+    }
+
+    submit(data) {
+        fetch(this.url, {
+            method: "POST",
+            body: JSON.stringify(data),
+            headers: {
+                'Content-Type': 'application/json'
+            }
+        })
+        .then(response => response.json())
+        .then(json => this.response_callback(json))
+        .catch(error => this.response_callback({'success':false,'detail':{'fetch error':error}}));
+    }
+}
+
+const API = new FetchAPI();

activation/api_webworker.js

@@ -0,0 +1,29 @@
+class WebWorkerAPI {
+    response_callback = null;
+    ready_callback = null;
+    url = null;
+    pyodideWorker = null;
+
+    initialize (response_callback, ready_callback=() => {}, url="./webworker.js") {
+        this.response_callback = response_callback;
+        this.ready_callback = ready_callback;
+        this.url = url;
+        this.pyodideWorker = new Worker(this.url, {type: "module"});
+        this.pyodideWorker.onmessage = (event) => {
+            if ('worker_ready' in event.data) {
+                this.ready_callback();
+            }
+            else {
+                this.response_callback(event.data);
+            }
+        }
+    }
+
+    submit(data) {
+        this.pyodideWorker.postMessage({
+            data: data
+        });
+    }
+}
+
+const API = new WebWorkerAPI();