psdi-data-conversion 0.0.35__py3-none-any.whl → 0.0.37__py3-none-any.whl

psdi_data_conversion/static/javascript/convert_common.js

@@ -3,6 +3,8 @@
   Version 1.0, 17th December 2024
 */
 
+import { disableDirtyForms, enableDirtyForms, initDirtyForms } from "./common.js";
+
 const SECOND = 1000; // Milliseconds
 const CONVERT_TIMEOUT = 60 * SECOND;
 const MEGABYTE = 1024 * 1024;
@@ -31,7 +33,18 @@ var token = "",
 
 export function commonConvertReady(converter) {
     token = sessionStorage.getItem("token");
-    max_file_size = sessionStorage.getItem("max_file_size");
+
+    // Open Babel uniquely has its own maximum file size
+    if (converter == "Open Babel") {
+        max_file_size = sessionStorage.getItem("max_file_size_ob");
+    } else {
+        max_file_size = sessionStorage.getItem("max_file_size");
+    }
+
+    // Set the text for displaying the maximum size
+    if (max_file_size > 0) {
+        $(".max-file-size").text(" (max size " + (max_file_size / MEGABYTE).toFixed(2) + " MB)");
+    }
 
     in_str = sessionStorage.getItem("in_str");
     out_str = sessionStorage.getItem("out_str");
@@ -48,17 +61,25 @@ export function commonConvertReady(converter) {
     $("#heading").html("Convert from \'" + in_ext + "\' (" + in_note + ") to \'" + out_ext + "\' (" + out_note +
         ") using " + converter);
 
+    // Connect the buttons to events
     $("#extCheck").click(setExtCheck);
     $("#requestLog").click(setRequestLog);
+    $("#clearUpload").click(clearUploadedFile);
+
+    // Connect the file upload to event and limit the types it can accept
     $("#fileToUpload").change(checkFile);
+    limitFileType();
+
+    initDirtyForms();
 
-    return [token, max_file_size, in_str, in_ext, out_str, out_ext];
+    return [token, in_str, in_ext, out_str, out_ext];
 }
 
 // Converts user-supplied file to another format and downloads the resulting file
 export function convertFile(form_data, download_fname, fname) {
 
     showSpinner();
+    disableConvertButton();
 
     let convertTimedOut = false;
 
@@ -70,7 +91,12 @@ export function convertFile(form_data, download_fname, fname) {
         contentType: false,
         timeout: CONVERT_TIMEOUT,
         success: async function () {
+
             hideSpinner();
+            enableConvertButton();
+            clearUploadedFile();
+            disableDirtyForms();
+
             if (!convertTimedOut) {
                 await downloadFile(`../downloads/${download_fname}`, download_fname)
 
@@ -109,6 +135,7 @@ export function convertFile(form_data, download_fname, fname) {
         },
         error: function (xmlhttprequest, textstatus, message) {
             hideSpinner();
+            enableConvertButton();
             if (textstatus === "timeout") {
                 convertTimedOut = true;
                 alert("ERROR: Conversion attempt timed out. This may be because the conversion is too complicated, " +
@@ -149,6 +176,13 @@ export function convertFile(form_data, download_fname, fname) {
 
 function setExtCheck(event) {
     extCheck = this.checked;
+
+    // Toggle whether or not the file upload limits uploaded type based on whether or not this box is ticked
+    if (extCheck) {
+        limitFileType();
+    } else {
+        unlimitFileType();
+    }
 }
 
 export function getExtCheck() {
@@ -195,6 +229,9 @@ export function isArchiveExt(ext) {
 // Check that the file meets requirements for upload
 function checkFile(event) {
 
+    // Enable dirty form checking whenever a file is uploaded
+    enableDirtyForms();
+
     let allGood = true;
     let file = this.files[0];
     let message = "";
@@ -226,15 +263,52 @@ function checkFile(event) {
     }
 
     if (allGood) {
-        $("#uploadButton").css({ "background-color": "var(--ifm-color-primary)", "color": "var(--ifm-hero-text-color)" });
-        $("#uploadButton").prop({ disabled: false });
+        enableConvertButton();
     } else {
-        $("#uploadButton").css({ "background-color": "var(--psdi-bg-color-secondary)", "color": "gray" });
-        $("#uploadButton").prop({ disabled: true });
+        disableConvertButton();
         alert(message);
     }
 }
 
+/**
+ * Allow the file upload to only accept the expected type of file
+ */
+function limitFileType() {
+    $("#fileToUpload")[0].accept = "." + in_ext;
+}
+
+/**
+ * Allow the file upload to accept any type of file
+ */
+function unlimitFileType() {
+    $("#fileToUpload")[0].accept = "*";
+}
+
+/**
+ * Clear any uploaded file
+ */
+function clearUploadedFile() {
+    $("#fileToUpload").val('');
+    disableConvertButton();
+}
+
+/**
+ * Enable the "Convert" button
+ */
+function enableConvertButton() {
+    $("#uploadButton").css({ "background-color": "var(--ifm-color-primary)", "color": "var(--ifm-hero-text-color)" });
+    $("#uploadButton").prop({ disabled: false });
+}
+
+
+/**
+ * Disable the "Convert" button
+ */
+function disableConvertButton() {
+    $("#uploadButton").css({ "background-color": "var(--psdi-bg-color-secondary)", "color": "gray" });
+    $("#uploadButton").prop({ disabled: true });
+}
+
 /**
  * Start a download of a file
  * 
@@ -256,7 +330,6 @@ async function downloadFile(path, filename) {
         });
 }
 
-
 /**
  * Show the loading spinner
  */

psdi_data_conversion/static/javascript/convertato.js

@@ -8,14 +8,13 @@
 import { commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt } from "./convert_common.js"
 
 var token = "",
-    max_file_size = 0,
     in_ext = "",
     out_ext = "",
     in_str = "",
     out_str = "";
 
 $(document).ready(function () {
-    [token, max_file_size, in_str, in_ext, out_str, out_ext] = commonConvertReady("Atomsk");
+    [token, in_str, in_ext, out_str, out_ext] = commonConvertReady("Atomsk");
     $("#uploadButton").click(submitFile);
 });
 

psdi_data_conversion/static/javascript/convertc2x.js

@@ -8,14 +8,13 @@
 import { commonConvertReady, convertFile, getExtCheck, splitArchiveExt, isArchiveExt } from "./convert_common.js"
 
 var token = "",
-    max_file_size = 0,
     in_ext = "",
     out_ext = "",
     in_str = "",
     out_str = "";
 
 $(document).ready(function () {
-    [token, max_file_size, in_str, in_ext, out_str, out_ext] = commonConvertReady("c2x");
+    [token, in_str, in_ext, out_str, out_ext] = commonConvertReady("c2x");
     $("#uploadButton").click(submitFile);
 });
 

psdi_data_conversion/static/javascript/format.js

@@ -5,6 +5,7 @@
   This is the JavaScript which makes the Format and Converter Selection gui work.
 */
 
+import { disableDirtyForms, cleanDirtyForms, initDirtyForms, loadServiceMode, loadProductionMode } from "./common.js";
 import {
     getInputFormats, getOutputFormats, getOutputFormatsForInputFormat,
     getInputFormatsForOutputFormat, getConverters, getConverterByName, getLevelChemInfo
@@ -29,12 +30,16 @@ $(document).ready(function () {
 
     sessionStorage.setItem("token", token);
     sessionStorage.setItem("max_file_size", max_file_size);
+    sessionStorage.setItem("max_file_size_ob", max_file_size_ob);
     sessionStorage.setItem("service_mode", service_mode);
     sessionStorage.setItem("production_mode", production_mode);
     sessionStorage.setItem("in_str", "");
     sessionStorage.setItem("out_str", "");
     sessionStorage.setItem("success", "");
 
+    loadServiceMode();
+    loadProductionMode();
+
     $("#fromList").click(populateConversionSuccess);
     $("#toList").click(populateConversionSuccess);
     $("#searchTo").keyup(filterOptions);
@@ -43,6 +48,8 @@ $(document).ready(function () {
     $("#success").click(showConverterDetails);
     $("#resetButton").click(resetAll);
     $("#showButton").click(showQualityDetails);
+
+    initDirtyForms();
 });
 
 /**
@@ -512,6 +519,9 @@ function getFormat(str) {
 
 // Stores chosen formats and switches to the Conversion page
 function goToConversionPage(event) {
+
+    disableDirtyForms();
+
     var path = ``;
 
     if ($("#name").html() == "Open Babel") {
@@ -604,4 +614,6 @@ function resetAll() {
 
     // Populates the "Convert to" selection list
     getOutputFormats().then(formats => populateList(formats, "to"));
+
+    cleanDirtyForms();
 }

psdi_data_conversion/static/javascript/report.js

@@ -5,6 +5,7 @@
   This is the JavaScript which makes the report.htm gui work.
 */
 
+import { disableDirtyForms, initDirtyForms } from "./common.js";
 import { getAllFormats, getConverters } from "./data.js";
 
 var token = "",
@@ -53,6 +54,8 @@ $(document).ready(function () {
     $("#resetButton").click(resetAll);
     $("#resetButton2").click(resetAll);
     $("#reportButton").click(submitUserInput);
+
+    initDirtyForms();
 });
 
 // Included in this file for convenience. When the 'Report' button is clicked, a user's missing conversion report
@@ -131,6 +134,7 @@ function hideConverterDetails() {
 
 // Submits user input
 function submitUserInput() {
+
     const from = $("#searchFrom").val(),
         to = $("#searchTo").val();
 
@@ -205,6 +209,8 @@ function hideOffer() { }
 
 // Submit feedback
 function submitFeedback(data) {
+    disableDirtyForms();
+
     $.post(`/feedback/`, {
         'token': token,
         'data': JSON.stringify(data)

psdi_data_conversion/static/styles/format.css

@@ -146,12 +146,6 @@ select#dark-background option {
   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;

psdi_data_conversion/static/styles/psdi-common.css

@@ -228,7 +228,7 @@ body {
   top       : 0;
   left      : 0;
   background: var(--ifm-background-color);
-  z-index   : 9999;
+  z-index   : 99999;
 }
 
 select,
@@ -412,7 +412,8 @@ h6 {
 }
 
 p {
-  margin: 0 0 1.25rem 0;
+  margin        : 0 0 1.25rem 0;
+  padding-bottom: 0;
 }
 
 .text--center {
@@ -546,9 +547,9 @@ a svg {
 }
 
 .navbar__title h5 {
-  display: unset;
+  display: flex;
   color  : var(--ifm-heading-color);
-  margin : 0 0 0.5rem 0.5rem;
+  margin : 0 0 0.5rem 1.5rem;
 }
 
 .navbar__logo img {
@@ -640,8 +641,11 @@ a svg {
 }
 
 .footer__hline hr {
-  margin: 0.5rem 0;
-  height: 2px;
+  margin             : 0.5rem 0;
+  height             : 2px;
+  border-top-style   : none;
+  border-bottom-style: inset;
+  border-bottom-width: 1px;
 }
 
 .max-width-box .footer__col {

psdi_data_conversion/templates/index.htm

@@ -18,10 +18,13 @@
 
   <script src="https://code.jquery.com/jquery-3.7.1.js" integrity="sha256-eKhayi8LEQwp4NKxN+CfCh+3qOVUtJn3QNZ0TciWLP4="
     crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/jquery.dirtyforms/2.0.0/jquery.dirtyforms.min.js"></script>
+
   {% for item in data %}
   <script>
     const token = "{{item.token}}";
     const max_file_size = "{{item.max_file_size}}";
+    const max_file_size_ob = "{{item.max_file_size_ob}}";
     const service_mode = "{{item.service_mode}}";
     const production_mode = "{{item.production_mode}}";
     document.documentElement.setAttribute("service-mode", service_mode);
@@ -52,8 +55,13 @@
     </div>
   </div>
 
-  <form name="gui">
+  <form name="gui" class="gui">
     <div class="max-width-box">
+      <p>Your one-stop shop for file format conversion, PSDI's Data Conversion Service enables users to seamlessly
+        convert between different file formats and assess the quality of proposed conversions. This is the web version
+        of our service. To find out more about Data Conversion and our other tools, click
+        <a href="https://resources.psdi.ac.uk/resource-themes/7bcc430a-fdc9-413e-bf32-bf163236430b"
+          id="more" target="_blank">here.</a></p>
       <p>Select 'from' and 'to' file formats in the 'Convert from/to' boxes, in either order. Typing where indicated
         filters the options (case insensitive); for example, typing 'can' or 'NON' reduces the number of options to one:
         'can: Canonical SMILES.' If you change your mind about a conversion, it is advisable to click on the 'Reset'
@@ -115,4 +123,4 @@
 
 </body>
 
-</html>
+</html>

psdi_data_conversion/testing/constants.py

@@ -6,7 +6,10 @@ Constants related to unit testing
 
 import os
 
-TEST_DATA_LOC = os.path.abspath("./test_data")
+# Locations relative to the root directory of the project - to ensure the files are found, tests should chdir to this
+# directory before searching for files
 
-INPUT_TEST_DATA_LOC = TEST_DATA_LOC
-OUTPUT_TEST_DATA_LOC = os.path.join(TEST_DATA_LOC, "output")
+TEST_DATA_LOC_IN_PROJECT = "./test_data"
+
+INPUT_TEST_DATA_LOC_IN_PROJECT = TEST_DATA_LOC_IN_PROJECT
+OUTPUT_TEST_DATA_LOC_IN_PROJECT = os.path.join(TEST_DATA_LOC_IN_PROJECT, "output")

psdi_data_conversion/testing/conversion_callbacks.py

@@ -15,8 +15,8 @@ from tempfile import TemporaryDirectory
 from psdi_data_conversion.constants import DATETIME_RE_RAW
 from psdi_data_conversion.file_io import unpack_zip_or_tar
 from psdi_data_conversion.log_utility import string_with_placeholders_matches
-from psdi_data_conversion.testing.constants import OUTPUT_TEST_DATA_LOC
-from psdi_data_conversion.testing.utils import ConversionTestInfo, LibraryConversionTestInfo, check_file_match
+from psdi_data_conversion.testing.constants import OUTPUT_TEST_DATA_LOC_IN_PROJECT
+from psdi_data_conversion.testing.utils import ConversionTestInfo, check_file_match
 
 
 class MultiCallback:
@@ -326,7 +326,7 @@ class CheckException:
     """Callable class which checks an exception raised for its type, status code, and message. Tests will only be
     run on tests with the python library, as that's the only route that provides exceptions."""
 
-    ex_type: type[Exception]
+    ex_type: type[Exception] | None = None
     """The expected type of the raised exception (subclasses of it will also be allowed)"""
 
     ex_message: str | None = None
@@ -339,7 +339,8 @@ class CheckException:
     def __call__(self, test_info: ConversionTestInfo) -> str:
         """Perform the check on the exception"""
 
-        if not isinstance(test_info, LibraryConversionTestInfo):
+        # Skip check on CLA, since this won't catch any exceptions
+        if test_info.run_type == "cla":
             return ""
 
         # Confirm that an exception was indeed raised
@@ -350,7 +351,7 @@ class CheckException:
         l_errors: list[str] = []
 
         # Check the exception type
-        if not issubclass(exc_info.type, self.ex_type):
+        if self.ex_type and not issubclass(exc_info.type, self.ex_type):
             l_errors.append(f"ERROR: Raised exception is of type '{exc_info.type}', but expected '{self.ex_type}'")
 
         exc = exc_info.value
@@ -389,6 +390,6 @@ class MatchOutputFile:
     def __call__(self, test_info: ConversionTestInfo):
         """Run the check comparing the two files"""
 
-        qualified_ex_output_filename = os.path.join(OUTPUT_TEST_DATA_LOC, self.ex_output_filename)
+        qualified_ex_output_filename = os.path.join(OUTPUT_TEST_DATA_LOC_IN_PROJECT, self.ex_output_filename)
 
         return check_file_match(test_info.qualified_out_filename, qualified_ex_output_filename)