Merge pull request #370 from fairdataihub/staging

feat: 15.2.3 bug fix release

Author: aaronm-2112

CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to SODA will be documented in this file.
 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:

package-lock.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",

package.json

@@ -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/pyflask/startup/minimumApiVersion.py

@@ -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/guided-mode/guided-curate-dataset.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/organize-dataset/curate-functions.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];
 };