psdi-data-conversion 0.0.32__tar.gz → 0.0.35__tar.gz

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/.github/workflows/ci-cron.yml

@@ -13,7 +13,7 @@ on:
 jobs:
   update-assets:
     name: Update common assets
-    runs-on: ubuntu-latest
+    runs-on: psdi-uk-runners
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/.github/workflows/ci-pr.yml

@@ -13,7 +13,6 @@ on:
       - "Dockerfile"
       - "LICENSE"
       - "**.txt"
-      - "startup.sh"
       - "deploy/**"
       - "scripts/fetch-common-style.*"
       - "scripts/make-index-html.sh"

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/.github/workflows/ci-release.yml

@@ -56,7 +56,7 @@ jobs:
   build:
     needs: [tag]
     name: Build distribution 📦
-    runs-on: ubuntu-latest
+    runs-on: psdi-uk-runners
 
     steps:
       - uses: actions/checkout@v4

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/.github/workflows/job-anchore-scan.yml

@@ -32,7 +32,7 @@ jobs:
       contents: read # for actions/checkout to fetch code
       security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
       actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status
-    runs-on: ubuntu-latest
+    runs-on: psdi-uk-runners
     steps:
     - name: Check out the code
       uses: actions/checkout@v4

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/.github/workflows/job-publish-doc.yml

@@ -26,7 +26,7 @@ jobs:
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
+    runs-on: psdi-uk-runners
     steps:
       - name: Checkout
         uses: actions/checkout@v4

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/CONTRIBUTING.md

@@ -352,17 +352,7 @@ The `ci-release.yml` workflow is planned to publish any new releases to PyPI aft
 
 ## Deployment
 
-The project is currently deployed to two locations: An Azure webserver, which was used in development, and the STFC infrastructure, which will be used in production.
-
-### Azure Deployment
-
-Azure deployment is handled automatically by the `ci-release.yml` workflow, which triggers the `job-deploy-azure.yml` reusable workflow to perform the deployment. This should not need to be edited often.
-
-The Azure host starts the server by running the script `startup.sh`. This script can be edited to set any environmental variables which are set up to control the behaviour of the app.
-
-### STFC Deployment
-
-STFC deployment is handled automatically by the `ci-release.yml` workflow, which triggers the `job-deploy-k8s.yml` reusable workflow to perform the deployment.
+Deployment is handled by the `job-deploy-k8s.yml` reusable workflow, which is triggered from `ci-main.yml` to deploy to dev on each push to `main` and `ci-release.yml` to deploy to staging on each push to `release`. When a push to production is desired, it must be triggered manually by calling the `ci-deploy-production.yml` workflow on the `release` branch (it's set up to fail if run on any other branch).
 
 TODO - Describe details of setup
 

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: psdi_data_conversion
-Version: 0.0.32
+Version: 0.0.35
 Summary: Chemistry file format conversion service, provided by PSDI
-Project-URL: Homepage, https://psdidev2.azurewebsites.net/
+Project-URL: Homepage, https://data-conversion.psdi.ac.uk/
 Project-URL: Documentation, https://psdi-uk.github.io/psdi-data-conversion/
 Project-URL: Repository, https://github.com/PSDI-UK/psdi-data-conversion
 Project-URL: Issues, https://github.com/PSDI-UK/psdi-data-conversion/issues
@@ -249,7 +249,7 @@ Version: Pre-release 2024-02-27
 
 This is the repository for the PSDI PF2 Chemistry File Format Conversion project. The goal of this project is to provide utilities to assist in converting files between the many different file formats used in chemistry, providing information on what converters are available for a given conversion and the expected quality of it, and providing multiple interfaces to perform these conversions. These interfaces are:
 
-- Online web service, available at https://psdidev2.azurewebsites.net
+- Online web service, available at https://data-conversion.psdi.ac.uk/
 - Version of the web app you can download and run locally (e.g. if you need to convert files which exceed the online app's file size limit)
 - Command-line application, to run conversions from a terminal
 - Python library
@@ -319,9 +319,8 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
 - `LICENSE` (Apache Licence version 2.0)
 - `pyproject.toml` (Python project metadata and settings)
 - `README.md` (This file)
-- `requirements.txt` (Requirements for the Azure web app deployment of this project)
+- `requirements.txt` (Requirements for the web app deployment of this project)
 - `run_local.sh` (Helper script to run the web app locally)
-- `startup.sh` (Startup script for the Azure web app)
 
 ## Requirements
 
@@ -567,7 +566,7 @@ The code documentation for the Python library is published online at https://psd
 
 ## Using the Online Conversion Service
 
-Enter https://psdidev2.azurewebsites.net in a browser. Guidance on usage is given on each page of the website.
+Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is given on each page of the website.
 
 ## Running the Python/Flask app locally
 

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/README.md

@@ -4,7 +4,7 @@ Version: Pre-release 2024-02-27
 
 This is the repository for the PSDI PF2 Chemistry File Format Conversion project. The goal of this project is to provide utilities to assist in converting files between the many different file formats used in chemistry, providing information on what converters are available for a given conversion and the expected quality of it, and providing multiple interfaces to perform these conversions. These interfaces are:
 
-- Online web service, available at https://psdidev2.azurewebsites.net
+- Online web service, available at https://data-conversion.psdi.ac.uk/
 - Version of the web app you can download and run locally (e.g. if you need to convert files which exceed the online app's file size limit)
 - Command-line application, to run conversions from a terminal
 - Python library
@@ -74,9 +74,8 @@ This is the repository for the PSDI PF2 Chemistry File Format Conversion project
 - `LICENSE` (Apache Licence version 2.0)
 - `pyproject.toml` (Python project metadata and settings)
 - `README.md` (This file)
-- `requirements.txt` (Requirements for the Azure web app deployment of this project)
+- `requirements.txt` (Requirements for the web app deployment of this project)
 - `run_local.sh` (Helper script to run the web app locally)
-- `startup.sh` (Startup script for the Azure web app)
 
 ## Requirements
 
@@ -322,7 +321,7 @@ The code documentation for the Python library is published online at https://psd
 
 ## Using the Online Conversion Service
 
-Enter https://psdidev2.azurewebsites.net in a browser. Guidance on usage is given on each page of the website.
+Enter https://data-conversion.psdi.ac.uk/ in a browser. Guidance on usage is given on each page of the website.
 
 ## Running the Python/Flask app locally
 

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/content/convert.htm

@@ -10,11 +10,19 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>PSDI Data Conversion Service</title>
   <link rel="icon" type="image/x-icon" href="../img/psdi-icon-dark.svg">
+
   <link href="https://fonts.googleapis.com/css?family=Lato:400" rel="stylesheet" type="text/css">
   <link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:700" rel="stylesheet" type="text/css">
+
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css">
+  <script src="https://cdn.jsdelivr.net/npm/jquery@3.7.1/dist/jquery.slim.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/js/bootstrap.bundle.min.js"></script>
+
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
+
   <link rel="stylesheet" href="../styles/format.css">
   <script src="../javascript/load_accessibility.js"></script>
-  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
   <script src="../javascript/common.js" type="module"></script>
   <script src="../javascript/psdi-common.js" type="module"></script>
 </head>
@@ -99,16 +107,19 @@
       <p id="fileChecking">
       </p>
       <p id="convertFile">
-        <input type="checkbox" checked id="extCheck">Enforce file naming checking to ensure uploaded files (and files
+        <input type="checkbox" checked id="extCheck"> Enforce file naming checking to ensure uploaded files (and files
         contained in archives) all have the correct extension<br>
-        <input type="checkbox" id="requestLog">Also download log file for the conversion<br>
+        <input type="checkbox" id="requestLog"> Also download log file for the conversion<br>
         Select file to convert:
         <br><input type="file" name="fileToUpload" id="fileToUpload"><br>
         If you have sensitive data you might prefer to use
         <a href="download.htm">one of our downloadable tools or Python library</a> rather than uploading your data to
         our service.<br>
-        <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
-          disabled=true>
+        <span class="convert-button-and-spinner">
+          <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
+            disabled=true>
+          <span class="loading-spinner spinner-border"></span>
+        </span>
       </p>
       <div class="medGap"></div>
     </div>

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/content/convertato.htm

@@ -10,11 +10,19 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>PSDI Data Conversion Service</title>
   <link rel="icon" type="image/x-icon" href="../img/psdi-icon-dark.svg">
+
   <link href="https://fonts.googleapis.com/css?family=Lato:400" rel="stylesheet" type="text/css">
   <link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:700" rel="stylesheet" type="text/css">
+
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css">
+  <script src="https://cdn.jsdelivr.net/npm/jquery@3.7.1/dist/jquery.slim.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/js/bootstrap.bundle.min.js"></script>
+
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
+
   <link rel="stylesheet" href="../styles/format.css">
   <script src="../javascript/load_accessibility.js"></script>
-  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
   <script src="../javascript/common.js" type="module"></script>
   <script src="../javascript/psdi-common.js" type="module"></script>
 </head>
@@ -43,16 +51,19 @@
       </p>
       <h6 id="heading"></h6>
       <p id="convertFile">
-        <input type="checkbox" checked id="extCheck">Enforce file naming checking to ensure uploaded files (and files
+        <input type="checkbox" checked id="extCheck"> Enforce file naming checking to ensure uploaded files (and files
         contained in archives) all have the correct extension<br>
-        <input type="checkbox" id="requestLog">Also download log file for the conversion<br>
+        <input type="checkbox" id="requestLog"> Also download log file for the conversion<br>
         Select file to convert:
         <br><input type="file" name="fileToUpload" id="fileToUpload"><br>
         If you have sensitive data you might prefer to use
         <a href="download.htm">one of our downloadable tools or Python library</a> rather than uploading your data to
         our service.<br>
-        <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
-          disabled=true>
+        <span class="convert-button-and-spinner">
+          <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
+            disabled=true>
+          <span class="loading-spinner spinner-border"></span>
+        </span>
       </p>
     </div>
     <div class="largeGap"></div>

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/content/convertc2x.htm

@@ -7,14 +7,23 @@
 <html>
 
 <head>
+
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>PSDI Data Conversion Service</title>
   <link rel="icon" type="image/x-icon" href="../img/psdi-icon-dark.svg">
+
   <link href="https://fonts.googleapis.com/css?family=Lato:400" rel="stylesheet" type="text/css">
   <link href="https://fonts.googleapis.com/css?family=Open+Sans+Condensed:700" rel="stylesheet" type="text/css">
+
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css">
+  <script src="https://cdn.jsdelivr.net/npm/jquery@3.7.1/dist/jquery.slim.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/js/bootstrap.bundle.min.js"></script>
+
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
+
   <link rel="stylesheet" href="../styles/format.css">
   <script src="../javascript/load_accessibility.js"></script>
-  <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
   <script src="../javascript/common.js" type="module"></script>
   <script src="../javascript/psdi-common.js" type="module"></script>
 </head>
@@ -43,16 +52,19 @@
       </p>
       <h6 id="heading"></h6>
       <p id="convertFile">
-        <input type="checkbox" checked id="extCheck">Enforce file naming checking to ensure uploaded files (and files
+        <input type="checkbox" checked id="extCheck"> Enforce file naming checking to ensure uploaded files (and files
         contained in archives) all have the correct extension<br>
-        <input type="checkbox" id="requestLog">Also download log file for the conversion<br>
+        <input type="checkbox" id="requestLog"> Also download log file for the conversion<br>
         Select file to convert:
         <br><input type="file" name="fileToUpload" id="fileToUpload"><br>
         If you have sensitive data you might prefer to use
         <a href="download.htm">one of our downloadable tools or Python library</a> rather than uploading your data to
         our service.<br>
-        <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
-          disabled=true>
+        <span class="convert-button-and-spinner">
+          <input type="button" class="button init-disabled" value=" Convert " name="uploadButton" id="uploadButton"
+            disabled=true>
+          <span class="loading-spinner spinner-border"></span>
+        </span>
       </p>
     </div>
     <div class="largeGap"></div>

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/content/report.htm

@@ -86,7 +86,7 @@
       <div class="smallGap"></div>
       <p>
         To report a missing format or conversion, please use
-        <a href="https://psdidev2.azurewebsites.net/static/content/report.htm?origin=local">the interface on the public
+        <a href="https://data-conversion.psdi.ac.uk/static/content/report.htm?origin=local">the interface on the public
           web app</a>.
       </p>
       <div class="medGap"></div>

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/javascript/convert_common.js

@@ -58,6 +58,8 @@ export function commonConvertReady(converter) {
 // Converts user-supplied file to another format and downloads the resulting file
 export function convertFile(form_data, download_fname, fname) {
 
+    showSpinner();
+
     let convertTimedOut = false;
 
     var jqXHR = $.ajax({
@@ -68,6 +70,7 @@ export function convertFile(form_data, download_fname, fname) {
         contentType: false,
         timeout: CONVERT_TIMEOUT,
         success: async function () {
+            hideSpinner();
             if (!convertTimedOut) {
                 await downloadFile(`../downloads/${download_fname}`, download_fname)
 
@@ -105,6 +108,7 @@ export function convertFile(form_data, download_fname, fname) {
                 })
         },
         error: function (xmlhttprequest, textstatus, message) {
+            hideSpinner();
             if (textstatus === "timeout") {
                 convertTimedOut = true;
                 alert("ERROR: Conversion attempt timed out. This may be because the conversion is too complicated, " +
@@ -216,7 +220,8 @@ function checkFile(event) {
         if (message !== "")
             message += "\n\n";
         message += "The file exceeds the maximum size limit of " + (max_file_size / MEGABYTE).toFixed(2) +
-            " MB; its size is " + (file.size / MEGABYTE).toFixed(2) + " MB.";
+            " MB; its size is " + (file.size / MEGABYTE).toFixed(2) + " MB. Please either log in for an increased " +
+            "file size limit, or see the Downloads page to run the app locally with no limit.";
         allGood = false;
     }
 
@@ -249,4 +254,19 @@ async function downloadFile(path, filename) {
             a.click();
             a.remove();
         });
+}
+
+
+/**
+ * Show the loading spinner
+ */
+function showSpinner() {
+    $(".loading-spinner").css({ display: "inherit" });
+}
+
+/**
+ * Hide the loading spinner
+ */
+function hideSpinner() {
+    $(".loading-spinner").css({ display: "none" });
 }

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/psdi_data_conversion/static/styles/format.css

@@ -144,4 +144,23 @@ select#dark-background option {
 
 [production-mode=False] .dev-only {
   display: none;
+}
+
+.footer__hline hr {
+  border-top-style   : none;
+  border-bottom-style: inset;
+  border-bottom-width: 1px;
+}
+
+/* Convert button and loading spinner */
+.convert-button-and-spinner {
+  display       : flex;
+  flex-direction: row;
+  align-items   : center;
+}
+
+.loading-spinner {
+  display: none;
+  color  : var(--ifm-color-primary);
+  scale  : 75%;
 }

{psdi_data_conversion-0.0.32 → psdi_data_conversion-0.0.35}/pyproject.toml

@@ -48,7 +48,7 @@ doc = ["pdoc3"]
 psdi-data-convert = "psdi_data_conversion.main:main"
 
 [project.urls]
-Homepage = "https://psdidev2.azurewebsites.net/"
+Homepage = "https://data-conversion.psdi.ac.uk/"
 Documentation = "https://psdi-uk.github.io/psdi-data-conversion/"
 Repository = "https://github.com/PSDI-UK/psdi-data-conversion"
 Issues = "https://github.com/PSDI-UK/psdi-data-conversion/issues"
@@ -70,7 +70,6 @@ exclude = [
   "scripts/make-index-html.sh",
   "Dockerfile",
   "requirements.txt",
-  "startup.sh",
 ]
 
 # The following lines run a script which excludes binaries for platforms other than the current from the binary.

psdi_data_conversion-0.0.32/.github/workflows/job-deploy-azure.yml

@@ -1,78 +0,0 @@
-# Reusable workflow intended to be called as a job by other workflows
-
-# Deploys the project to the Azure-hosted web app
-
-# Docs for the Azure Web Apps Deploy action: https://github.com/Azure/webapps-deploy
-# More GitHub Actions for Azure: https://github.com/Azure/actions
-# More info on Python, GitHub Actions, and Azure App Service: https://aka.ms/python-webapps-actions
-
-name: Job - Deploy to Azure
-run-name: Deploy to Azure
-
-on:
-  workflow_call: # allow this workflow to be called from other workflows
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up Python version
-        uses: actions/setup-python@v1
-        with:
-          python-version: "3.12"
-
-      - name: Create and start virtual environment
-        run: |
-          python -m venv venv
-          source venv/bin/activate
-
-      - name: Install dependencies
-        run: pip install -r requirements.txt
-
-      # Optional: Add step to run tests here (PyTest, Django test suites, etc.)
-
-      - name: Zip artifact for deployment
-        run: zip release.zip ./* -r
-
-      - name: Upload artifact for deployment jobs
-        uses: actions/upload-artifact@v4
-        with:
-          name: python-app
-          path: |
-            release.zip
-            !venv/
-
-  deploy:
-    runs-on: ubuntu-latest
-    needs: build
-    environment:
-      name: "production"
-      url: ${{ steps.deploy-to-webapp.outputs.webapp-url }}
-    permissions:
-      id-token: write #This is required for requesting the JWT
-
-    steps:
-      - name: Download artifact from build job
-        uses: actions/download-artifact@v4
-        with:
-          name: python-app
-
-      - name: Unzip artifact for deployment
-        run: unzip release.zip
-
-      - name: Login to Azure
-        uses: azure/login@v2
-        with:
-          client-id: ${{ secrets.AZUREAPPSERVICE_CLIENTID_5D29518D1EE14107A61C0D5316BD180E }}
-          tenant-id: ${{ secrets.AZUREAPPSERVICE_TENANTID_BBA11EDFC02844E1AC766345289C1140 }}
-          subscription-id: ${{ secrets.AZUREAPPSERVICE_SUBSCRIPTIONID_2AA47809BF8D46BD8B6335589DBE4183 }}
-
-      - name: "Deploy to Azure Web App"
-        uses: azure/webapps-deploy@v2
-        id: deploy-to-webapp
-        with:
-          app-name: "PSDIDEV2"
-          slot-name: "production"