feat: 15.2.3 bug fix release

CHANGELOG.md

@@ -5,6 +5,13 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v15.2.3 - 2024-11-20
+
+## Bug Fixes:
+
+- Restricted forbidden characters in Guided Mode datasets to avoid JSON save file issues.
+- Moved guidedSaveProgress to trigger after every successful page exit for broader save coverage.
+
 ## v15.2.2 - 2024-10-09
 
 ## Bug Fixes:
@@ -58,7 +65,7 @@
 ## Bug fixes:
 
 - Fixed an issue where the standalone manifest generator fails to generate manifests due to the manifest_files directory not being cleared prior to generation.
 - Fixed an issue where the cod eto fixe the upload failing was reverted prior to release.
 
 ## v15.0.1 - 2024-05-30
 
@@ -106,7 +113,7 @@
 
 ## v13.1.3 - 2024-02-29
 
 ## Feature Addditions:
 
 - Announcements have been redesigned to convey updates and fixes clearly.
 - Added the ability to generate a copy of a dataset's manifest files locally within the organize datasets feature.
@@ -137,7 +144,7 @@
 ## Feature Additions:
 
 - Users can generate datasets on their computer/local device in Guided Mode without having to sign in with a Pennsieve account.
 - Pennsieve API Key names are more unique to resolve myriad of issues that come from having multiple users on one computer and from having one user with acccounts across multiple computers.
 - Switching workspaces resets FFM UI to default state.
 
 ## Bug fixes:
@@ -148,7 +155,7 @@
 
 ## Feature Additions:
 
 - SODA added the ability for users to generate a local copy of their datasets for review to Guided Mode. This should assist users in ensuring their dataset is organized per their criteria before commiting to uploading their dataset to Pennsieve.
 - SODA has been converted to ESM and is using Electron-Vite for bundling.
 
 ## v.12.5.0 - 2023-01-04
@@ -221,7 +228,7 @@
 - Curate and Share button's icon has been updated to be more intuitive. Changing color when it is selected.
 - Return to progress button that appears in the nav bar will correctly update the navigation menu depending where the user navigates.
 - Move item pop up has a max height preventing users from endlessly scrolling to confirm their move.
 - Disseminate calender does not hide anymore when checkbox to awknowledge sharing with the curation team. (Should only be modified by the embargo checkbox)
 - Sweet alert icons for Prepare Metadata -> No 'metadata' file found in root directory will all be the same icon.
 
 ## Removed:
@@ -372,7 +379,7 @@
 - FFM: Imported metadata files not resetting upon changing a dataset has been patched.
 
 - The ability for deleting all files selected has been fixed.
 - Taxonomy endpoint has been patched to look up names and return response corrently.
 
 ## Feature Additions:
 
@@ -456,7 +463,7 @@
 
 ## Bug fixes:
 
 - Manual Windows build creation to fix an issue with the back-end not connectiong on Windows.
 
 ## v.9.4.0 - 2022-11-02
 
@@ -555,10 +562,10 @@
 - Prepare Metadata - Create manifest.xlsx: Automated synchronization between manifest files and their Pennsieve dataset. E.g., if a file is removed from a dataset, the file's corresponding manifest file entry will be removed.
 - Prepare Metadata - Create manifest.xlsx: Empty columns are dropped from manifest files once the user generates their files locally or on Pennsieve.
 - Prepare Metadata - Create manifest.xlsx: Preview manifest files locally before they are uploaded to Pennsieve.
 - Prepare Metadata - Create manifest.xlsx: Generate manfiest files locally in your directory of choice.
 - Guided Mode - added the ability to edit auto-generated manifest files in a spreadsheet like UI.
 - Freeform Mode - Ability to add your dataset to a collection has been added. Intended to better group datasets.
 - Image optimzation for banner images. Image sizes that exceed over 2048 x 2048 will be prompted to scale the image accordingly for upload.
 
 ## Bug fixes:
 

package.json

@@ -1,7 +1,7 @@
 {
   "name": "soda-for-sparc",
   "procductName": "SODA for SPARC",
-  "version": "15.2.2",
+  "version": "15.2.3",
   "description": "Keep Calm and Curate",
   "main": "./out/main/index.js",
   "author": "SODA Team",

src/pyflask/startup/minimumApiVersion.py

@@ -8,7 +8,7 @@ def get_api_version():
     """
 
 
-    return {'version': os.getenv('API_VERSION', "15.2.2")}
+    return {'version': os.getenv('API_VERSION', "15.2.3")}
 
 
 

src/renderer/src/scripts/guided-mode/guided-curate-dataset.js

@@ -1095,11 +1095,15 @@ const savePageChanges = async (pageBeingLeftID) => {
           message: "Please enter a dataset name.",
         });
       }
-      if (check_forbidden_characters_ps(datasetNameInput)) {
+
+      const datasetNameContainsForbiddenCharacters = window.evaluateStringAgainstSdsRequirements(
+        datasetNameInput,
+        "string-contains-forbidden-characters"
+      );
+      if (datasetNameContainsForbiddenCharacters) {
         errorArray.push({
           type: "notyf",
-          message:
-            "A Pennsieve dataset name cannot contain any of the following characters: /:*?'<>.",
+          message: `A Pennsieve dataset name cannot contain any of the following characters: @#$%^&*()+=/\|"'~;:<>{}[]?`,
         });
       }
       if (!datasetSubtitleInput) {
@@ -2101,12 +2105,14 @@ const savePageChanges = async (pageBeingLeftID) => {
       }
     }
 
-    // Save the current version of SODA as the user should be taken back to the first page when the app is updated
-    const currentAppVersion = document.getElementById("version").innerHTML;
-    window.sodaJSONObj["last-version-of-soda-used"] = currentAppVersion;
-
     // Stop any animations that need to be stopped
     startOrStopAnimationsInContainer(pageBeingLeftID, "stop");
+
+    try {
+      await guidedSaveProgress();
+    } catch (error) {
+      log.error(error);
+    }
   } catch (error) {
     guidedSetNavLoadingState(false);
     console.log(error);
@@ -3000,9 +3006,14 @@ const guidedTransitionFromDatasetNameSubtitlePage = () => {
   $("#guided-footer-div").css("display", "flex");
 };
 
-const saveGuidedProgress = async (guidedProgressFileName) => {
+const guidedSaveProgress = async () => {
+  const guidedProgressFileName = window.sodaJSONObj?.["digital-metadata"]?.["name"];
   //return if guidedProgressFileName is not a strnig greater than 0
-  if (typeof guidedProgressFileName !== "string" || guidedProgressFileName.length === 0) {
+  if (
+    !guidedProgressFileName ||
+    typeof guidedProgressFileName !== "string" ||
+    guidedProgressFileName.length === 0
+  ) {
     return;
   }
   //Destination: HOMEDIR/SODA/Guided-Progress
@@ -3026,6 +3037,10 @@ const saveGuidedProgress = async (guidedProgressFileName) => {
   window.sodaJSONObj["subjects-table-data"] = window.subjectsTableData;
   window.sodaJSONObj["samples-table-data"] = window.samplesTableData;
 
+  // Save the current version of SODA as the user should be taken back to the first page when the app is updated
+  const currentAppVersion = document.getElementById("version").innerHTML;
+  window.sodaJSONObj["last-version-of-soda-used"] = currentAppVersion;
+
   window.fs.writeFileSync(guidedFilePath, JSON.stringify(window.sodaJSONObj, null, 2));
 };
 
@@ -3466,7 +3481,7 @@ window.guidedOpenManifestEditSwal = async (highLevelFolderName) => {
       //spreadsheet reply contained results
       await updateManifestJson(highLevelFolderName, result);
       window.electron.ipcRenderer.removeAllListeners("spreadsheet-reply");
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
       renderManifestCards();
     }
   });
@@ -6815,7 +6830,7 @@ window.openPage = async (targetPageID) => {
 
     // Set the last opened page and save it
     window.sodaJSONObj["page-before-exit"] = targetPageID;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
   } catch (error) {
     const eMessage = userErrorMessage(error);
     Swal.fire({
@@ -7537,7 +7552,7 @@ const guidedCheckIfUserNeedsToReconfirmAccountDetails = () => {
   return false;
 };
 
-const guidedGetPageToReturnTo = (sodaJSONObj) => {
+const guidedGetPageToReturnTo = async (sodaJSONObj) => {
   // Set by window.openPage function
   const usersPageBeforeExit = window.sodaJSONObj["page-before-exit"];
 
@@ -7553,7 +7568,11 @@ const guidedGetPageToReturnTo = (sodaJSONObj) => {
   const lastVersionOfSodaUsedOnProgressFile = window.sodaJSONObj["last-version-of-soda-used"];
 
   if (lastVersionOfSodaUsedOnProgressFile != currentSodaVersion) {
-    // If the last time the user worked on the progress file was in a previous version of SODA, then force the user to restart from the first page
+    // If the progress file was last edited in a previous SODA version, reset to the first page
+    await swalShowInfo(
+      "SODA has been updated since you last worked on this dataset.",
+      "You'll be taken to the first page to ensure compatibility with the latest workflow. Your previous work is saved and accessible."
+    );
     return firstPageID;
   }
 
@@ -7876,7 +7895,7 @@ window.guidedResumeProgress = async (datasetNameToResume) => {
     hideSubNavAndShowMainNav(false);
 
     // pageToReturnTo will be set to the page the user will return to
-    const pageToReturnTo = guidedGetPageToReturnTo(window.sodaJSONObj);
+    const pageToReturnTo = await guidedGetPageToReturnTo(window.sodaJSONObj);
 
     await window.openPage(pageToReturnTo);
 
@@ -10546,7 +10565,7 @@ window.openCopySubjectMetadataPopup = async () => {
         window.populateForms(currentSubjectOpenInView, "", "guided");
       }
 
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
     }
   });
 };
@@ -10644,7 +10663,7 @@ window.openCopySampleMetadataPopup = async () => {
       if (currentSampleOpenInView) {
         openModifySampleMetadataPage(currentSampleOpenInView, currentSampleSubjectOpenInView);
       }
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
     }
   });
 };
@@ -12866,7 +12885,7 @@ const renderSubjectsMetadataAsideItems = async () => {
       //check to see if previousSubject is empty
       if (previousSubject) {
         window.addSubject("guided");
-        await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+        await guidedSaveProgress();
       }
 
       window.clearAllSubjectFormFields(window.guidedSubjectsFormDiv);
@@ -12884,7 +12903,7 @@ const renderSubjectsMetadataAsideItems = async () => {
 
       document.getElementById("guided-bootbox-subject-id").value = e.target.innerText;
 
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
     });
   });
 };
@@ -13011,7 +13030,7 @@ const renderSamplesMetadataAsideItems = async () => {
       //check to see if previousSample is empty
       if (previousSample) {
         window.addSample("guided");
-        await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+        await guidedSaveProgress();
       }
 
       //add selected class to clicked element
@@ -13031,7 +13050,7 @@ const renderSamplesMetadataAsideItems = async () => {
         e.target.innerText.split("/")[0]
       );
 
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
     });
   });
 };
@@ -13711,7 +13730,7 @@ const guidedCreateOrRenameDataset = async (bfAccount, datasetName) => {
       // so new metadata can be uploaded to the newly created dataset
       // (This would happen if the user deleted the dataset on Pennsieve)
       window.sodaJSONObj["previously-uploaded-data"] = {};
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
     }
   }
 
@@ -13764,7 +13783,7 @@ const guidedCreateOrRenameDataset = async (bfAccount, datasetName) => {
     //Save the dataset ID generated by pennsieve so the dataset is not re-uploaded when the user
     //resumes progress after failing an upload
     window.sodaJSONObj["digital-metadata"]["pennsieve-dataset-id"] = createdDatasetsID;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     return createdDatasetsID;
   } catch (error) {
@@ -13830,7 +13849,7 @@ const guidedAddDatasetSubtitle = async (bfAccount, datasetName, datasetSubtitle)
     datasetSubtitleUploadText.innerHTML = `Successfully added dataset subtitle: ${datasetSubtitle}`;
     guidedUploadStatusIcon("guided-dataset-subtitle-upload-status", "success");
     window.sodaJSONObj["previously-uploaded-data"]["subtitle"] = datasetSubtitle;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     // Send successful dataset subtitle upload event to Kombucha
     window.electron.ipcRenderer.send(
@@ -13916,7 +13935,7 @@ const guidedAddDatasetDescription = async (
     datasetDescriptionUploadText.innerHTML = `Successfully added dataset description!`;
     guidedUploadStatusIcon("guided-dataset-description-upload-status", "success");
     window.sodaJSONObj["previously-uploaded-data"]["description"] = description;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     // Send successful dataset description upload event to Kombucha
     window.electron.ipcRenderer.send(
@@ -14003,7 +14022,7 @@ const uploadValidBannerImage = async (bfAccount, datasetName, bannerImagePath) =
     datasetBannerImageUploadText.innerHTML = `Successfully added dataset banner image!`;
     guidedUploadStatusIcon("guided-dataset-banner-image-upload-status", "success");
     window.sodaJSONObj["previously-uploaded-data"]["banner-image-path"] = bannerImagePath;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     // Send successful banner image upload event to Kombucha
     window.electron.ipcRenderer.send(
@@ -14096,7 +14115,7 @@ const guidedAddDatasetLicense = async (bfAccount, datasetName, datasetLicense) =
     datasetLicenseUploadText.innerHTML = `Successfully added dataset license: ${datasetLicense}`;
     guidedUploadStatusIcon("guided-dataset-license-upload-status", "success");
     window.sodaJSONObj["previously-uploaded-data"]["license"] = datasetLicense;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     // Send successful license upload event to Kombucha
     window.electron.ipcRenderer.send(
@@ -14169,7 +14188,7 @@ const guidedAddDatasetTags = async (bfAccount, datasetName, tags) => {
     datasetTagsUploadText.innerHTML = `Successfully added dataset tags: ${tags.join(", ")}`;
     guidedUploadStatusIcon("guided-dataset-tags-upload-status", "success");
     window.sodaJSONObj["previously-uploaded-data"]["tags"] = tags;
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
 
     // Send successful tags upload event to Kombucha
     window.electron.ipcRenderer.send(
@@ -15688,7 +15707,7 @@ const guidedUploadDatasetToPennsieve = async () => {
         window.sodaJSONObj["digital-metadata"]["name"];
 
       // Save the window.sodaJSONObj after a successful upload
-      await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+      await guidedSaveProgress();
 
       //Display the click next text
       document.getElementById("guided--verify-files").classList.remove("hidden");
@@ -16493,8 +16512,6 @@ $("#guided-next-button").on("click", async function () {
 
   try {
     await savePageChanges(window.pageBeingLeftID);
-    //Save progress onto local storage with the dataset name as the key
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
 
     //Mark page as completed in JSONObj so we know what pages to load when loading local saves
     //(if it hasn't already been marked complete)
@@ -17087,7 +17104,7 @@ const saveSubPageChanges = async (openSubPageID) => {
         "import";
     }
 
-    await saveGuidedProgress(window.sodaJSONObj["digital-metadata"]["name"]);
+    await guidedSaveProgress();
   } catch (error) {
     guidedSetNavLoadingState(false);
     throw error;

src/renderer/src/scripts/organize-dataset/curate-functions.js

@@ -502,11 +502,8 @@ window.uploadDatasetClickHandler = async (ev) => {
 };
 
 window.handleLocalDatasetImport = async (path) => {
-  console.log("Importing local dataset from path:", path);
   const list = await getFilesAndFolders(path);
-  console.log("List of files and folders:", list);
   const currentFileExplorerPath = window.organizeDSglobalPath.value.trim();
-  console.log("Current file explorer path:", currentFileExplorerPath);
   const builtDatasetStructure = await window.buildDatasetStructureJsonFromImportedData(
     list.folders,
     "dataset_root/", // Use dataset_root as the root folder since we are importing the root in this case

src/renderer/src/scripts/others/renderer.js

@@ -4359,13 +4359,15 @@ const namesOfForbiddenFiles = {
 
 const sparcFolderAndFileRegex = /[\+&\%#]/;
 const identifierConventionsRegex = /^[a-zA-Z0-9-_]+$/;
+const forbiddenCharacters = /[@#$%^&*()+=\/\\|"'~;:<>{}\[\]?]/;
 
 window.evaluateStringAgainstSdsRequirements = (stringToTest, stringCase) => {
   const testCases = {
     "folder-and-file-name-is-valid": !sparcFolderAndFileRegex.test(stringToTest), // returns true if the string is valid
     "file-is-hidden": stringToTest.startsWith("."), // returns true if the string is hidden
     "file-is-in-forbidden-files-list": namesOfForbiddenFiles?.[stringToTest], // returns true if the string is in the forbidden files list
     "string-adheres-to-identifier-conventions": identifierConventionsRegex.test(stringToTest), // returns true if the string adheres to the identifier conventions
+    "string-contains-forbidden-characters": forbiddenCharacters.test(stringToTest), // returns true if the string contains forbidden characters
   };
   return testCases[stringCase];
 };