feat: codespell: config, workflow + fixing typos #230

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.pdf,*.svg,package-lock.json,*.min.js,*.ipynb,overview-lotties.js
+# ignore-words-list = 

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

CHANGELOG.md

@@ -446,7 +446,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## Bug fixes:
 
 - In organize dataset: When moving files/folders to another location there will be a check if any duplicates are there already.
-- On startup the server will try to connect continuosly. (backOff was replaced)
+- On startup the server will try to connect continuously. (backOff was replaced)
 - Organize dataset: import dataset will correctly check manifest details.
 - Guided Mode: Fixed the automatically generated headers for manifest files
 - Guided Mode: Changed the generated filepath from the filepath on the user's local machine to the path relative to the
@@ -589,7 +589,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Hidden files can now be imported except .DS_Store and Thumbs.db files.
 - The input for renaming or creating a new dataset no longer references undefined function in its HTML.
 - The navigation buttons in each individual Prepare Metadata section have been updated to match the perceived flow from the Prepare Metadata tab.
-- The Add/edit subtitle feature has been updated so that the chracter limit matches the SDS 2.0 specification. This fixes a bug that would cause an error if a user met the character limit enforced by SODA and then tried to add or edit their subtitle.
+- The Add/edit subtitle feature has been updated so that the character limit matches the SDS 2.0 specification. This fixes a bug that would cause an error if a user met the character limit enforced by SODA and then tried to add or edit their subtitle.
 
 ### Known Issues:
 
@@ -842,7 +842,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Fixed an issue where libraries were being loaded out of order leading to errors when opening SODA for the first time.
 - When uploading a dataset, we have now locked the sidebar to prevent accidental clicks that would take you out of the UI.
 - Fixed a bug where loading an award from Airtable would require two attempts.
-- Fixed a bug where macOS version of SODA would run the pre-check message everytime the app lost focus.
+- Fixed a bug where macOS version of SODA would run the pre-check message every time the app lost focus.
 
 ### Known issues:
 
@@ -868,7 +868,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Fixed a bug where manifest file data wasn't being pulled down correctly on Windows.
 - Fixed a bug where .tiff images were not being converted by SODA.
 - Fixed an issue where multiple sample id imports from the primary folder would not work.
-- Fixed a bug where the import primary folder button would dissapear when starting over.
+- Fixed a bug where the import primary folder button would disappear when starting over.
 
 ### Known issues:
 
@@ -912,7 +912,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - Fixed a bug where certain message input boxes would take accidental clicks outside the clickable area and clear the input
 - The dataset_description file will no longer enforce a 5 keyword limit.
-- Fixed a bug where the siebar would open up when exiting a datset curation workflow.
+- Fixed a bug where the siebar would open up when exiting a dataset curation workflow.
 
 ### Known issues:
 

README.md

@@ -86,7 +86,7 @@ SODA is distributed under the MIT License. See [LICENSE](https://github.com/fair
 
 ## Privacy Policy
 
-SODA uses Google Analytics to track user interactions with the application. Tracking is anonymous and no identifying personal information is collected. Tracking is implemented as part of our agreement with the SPARC program to report usage statistics for SODA. Tracking is also used to indentify errors and subsequently improve user experience. To learn more about what is tracked and how we use Google Analytics within SODA, please read our [Privacy Policy](https://github.com/fairdataihub/SODA-for-SPARC/wiki/Privacy-Policy).
+SODA uses Google Analytics to track user interactions with the application. Tracking is anonymous and no identifying personal information is collected. Tracking is implemented as part of our agreement with the SPARC program to report usage statistics for SODA. Tracking is also used to identify errors and subsequently improve user experience. To learn more about what is tracked and how we use Google Analytics within SODA, please read our [Privacy Policy](https://github.com/fairdataihub/SODA-for-SPARC/wiki/Privacy-Policy).
 
 ## Acknowledgements
 

src/pyflask/disseminate/disseminate.py

@@ -23,7 +23,7 @@ def bf_get_doi(selected_bfaccount, selected_bfdataset):
     Function to get current doi for a selected dataset
 
     Args:
-        selected_bfaccount: name of selected Pennsieve acccount (string)
+        selected_bfaccount: name of selected Pennsieve account (string)
         selected_bfdataset: name of selected Pennsieve dataset (string)
     Return:
         Current doi or "None"
@@ -50,7 +50,7 @@ def bf_reserve_doi(selected_bfaccount, selected_bfdataset):
     Function to reserve doi for a selected dataset
 
     Args:
-        selected_bfaccount: name of selected Pennsieve acccount (string)
+        selected_bfaccount: name of selected Pennsieve account (string)
         selected_bfdataset: name of selected Pennsieve dataset (string)
     Return:
         Success or error message

src/pyflask/manageDatasets/manage_datasets.py

@@ -1035,7 +1035,7 @@ def ps_add_permission_team(
     selected_bfaccount, selected_bfdataset, selected_team, selected_role
 ):
     """
-    Function to add/remove permission fo a team to a selected dataset
+    Function to add/remove permission for a team to a selected dataset
 
     Args:
         selected_bfaccount: name of selected Pennsieve account (string)
@@ -1239,7 +1239,7 @@ def bf_get_banner_image(selected_bfaccount, selected_bfdataset):
     Function to get url of current banner image associated with a selected dataset
 
     Args:
-        selected_bfaccount: name of selected Pennsieve acccount (string)
+        selected_bfaccount: name of selected Pennsieve account (string)
         selected_bfdataset: name of selected Pennsieve dataset (string)
     Return:
         url of banner image (string)

src/pyflask/manifest/manifest_writer.py

@@ -481,7 +481,7 @@ def file_manifest_entry(file_key, file, relative_path, dict_folder_manifest):
                 unused_file_name, fileextension = get_name_extension(file_key)
                 # fileextension = name_split[1]
             dict_folder_manifest["file type"].append(fileextension)
-            # addtional metadata
+            # additional metadata
             if "additional-metadata" in file.keys():
                 dict_folder_manifest["Additional Metadata"].append(
                     file["additional-metadata"]
@@ -491,7 +491,7 @@ def file_manifest_entry(file_key, file, relative_path, dict_folder_manifest):
 
             return dict_folder_manifest
 
-        # create local folder to save manifest files temporarly (delete any existing one first)
+        # create local folder to save manifest files temporarily (delete any existing one first)
         if "auto-generated" in soda_json_structure["manifest-files"]:
             if soda_json_structure["manifest-files"]["auto-generated"] == True:
                 manifest_files_structure = (

src/pyflask/namespaces/configureNamespaces.py

@@ -28,7 +28,7 @@ def configure_namespaces():
     Create namespaces for each pysoda file: pysoda ( now manage_datasets), prepare_metadata, etc
     """
 
-    manage_datasets_namespace = Namespace(NamespaceEnum.MANAGE_DATASETS.value, description='Routes for handling manage datsets functionality')
+    manage_datasets_namespace = Namespace(NamespaceEnum.MANAGE_DATASETS.value, description='Routes for handling manage datasets functionality')
     namespaces[NamespaceEnum.MANAGE_DATASETS] = manage_datasets_namespace
 
     curate_datasets_namespace = Namespace(NamespaceEnum.CURATE_DATASETS.value, description='Routes for handling dataset curation')

src/pyflask/prepareMetadata/prepare_metadata.py

@@ -49,11 +49,11 @@
 manifest_folder_path = join(userpath, "SODA", "manifest_files")
 
 ### Sets the TEMPLATE_PATH using SODA-for-SPARC's basepath so that the prepare_metadata section can find
-### the templates stored in file_templates direcotory
+### the templates stored in file_templates directory
 def set_template_path(soda_base_path, soda_resources_path):
     """
     Sets the TEMPLATE_PATH using SODA-for-SPARC's basepath so that the prepare_metadata section can find
-    the templates stored in file_templates direcotory.
+    the templates stored in file_templates directory.
     """
     global TEMPLATE_PATH
 

src/renderer/src/assets/lotties/contact-us-lotties.js

@@ -5,7 +5,7 @@ export const contact_lottie = {
   op: 200,
   w: 1000,
   h: 1000,
-  nm: "Work frome Home Mailing F 2",
+  nm: "Work from Home Mailing F 2",
   ddd: 0,
   assets: [],
   layers: [

src/renderer/src/scripts/metadata-files/readme-changes.js

@@ -42,7 +42,7 @@ window.generateRCFilesHelper = (type) => {
   if (textValue === "") {
     Swal.fire({
       title: "Incomplete information",
-      text: "Plase fill in the textarea.",
+      text: "Please fill in the textarea.",
       heightAuto: false,
       backdrop: "rgba(0,0,0, 0.4)",
       icon: "error",

src/renderer/src/scripts/validator/validator-UI.js

@@ -165,7 +165,7 @@ document.querySelector("#validate-local-dataset-path").addEventListener("click",
     // show confirm button found under the input
     let confirmDatasetBtn = document.querySelector("#validator-confirm-local-dataset-btn");
 
-    // set the field display property to none to remove the field margings
+    // set the field display property to none to remove the field margins
     confirmDatasetBtn.parentElement.style.display = "flex";
   }
 

tools/soda-json-structure/soda-sparc-structure.py

@@ -8,12 +8,12 @@
 dataset-strucuture: contains info about the dataset structure
 
 1. The high-level SPARC folders are included in a "folders" key
-2. Each file/folder info is stored in a key refering to the name of the file/folder (including the extension for files). If user renames the file/folder, this key should change to register that.
+2. Each file/folder info is stored in a key referring to the name of the file/folder (including the extension for files). If user renames the file/folder, this key should change to register that.
 3. The files/folders in each folder are stored in a "files"/"folders" key, respectively.
 4. Each file/folder has a subkey "type" which is a string with value either "virtual" (only for folders, if created in SODA), "local", or "bf"
 5. Each non virtual file/folder has a subkey "path" with is a string with value being the absolute path (for local files) or blackfynn id 
 6. Each non virtual file/folder has a subkey "action" which is an array containing "existing" (if it from an existing local or bf dataset) or "new" (if imported).
-7. If "new", additional "action" could be "renamed". If "existing", addtional "action" could be "renamed", "moved" (if an existing file/folder is moved), and/or "deleted" (if delete is requested in the UI)
+7. If "new", additional "action" could be "renamed". If "existing", additional "action" could be "renamed", "moved" (if an existing file/folder is moved), and/or "deleted" (if delete is requested in the UI)
 8. If provided, a file with have the subkeys "description" and "additional-metadata" each contain a string value to be later included in the manifest files, if requested
 
 """