Update version and changelog

CHANGELOG.md

@@ -6,22 +6,35 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 To see tags and releases, please go to [Tags](https://github.com/AlexJSully/SciGrade/tags) on [GitHub](https://github.com/AlexJSully/SciGrade).
 
+## [1.1.2] - 2024-01-04
+
+Update:
+
+-   Update Sentry version
+-   Update packages
+
+Bug fix:
+
+-   Fixed checking possible correct answers returning null
+-   Fixed issue where if no student information was present, would prevent further use of SciGrade
+-   Fixed issue where service worker would try and register before browser was ready or if the browser did not support service workers
+
 ## [1.1.1] - 2023-08-03
 
 No longer supports Internet Explorer.
 
-**Optimization**:
+Optimization:
 
 -   Added ESLint
 -   Optimized images
 -   Updated web manifest
 
-**Update**:
+Update:
 
 -   Updated OSSAR workflow
 -   Updated packages
 
-**Bug fixes**:
+Bug fixes:
 
 -   Fixed CaptureConsole not found and unable to call CaptureConsole
 -   Fixed TypeError cannot read undefined 0
@@ -30,15 +43,15 @@ No longer supports Internet Explorer.
 
 ## [1.1.0] - 2022-11-03
 
-**A brand new version of the [SciGrade](https://scigrade.com/) has dropped!**
+A brand new version of the [SciGrade](https://scigrade.com/) has dropped!
 
 Version 1.1.0 has now dropped and it includes the ability to do practice genes without an account as well as optimizations and bug fixes.
 
-**Feature**:
+Feature:
 
 -   Can now do practice genes without an account
 
-**Optimization**:
+Optimization:
 
 -   Added Sentry
 -   Added high fetch priority to LCP image
@@ -56,17 +69,17 @@ Version 1.1.0 has now dropped and it includes the ability to do practice genes w
 -   Updated Google Analytics to GA4
 -   Updated robots.txt
 
-**Security**:
+Security:
 
 -   Added Content Security Policy
 -   Added Strict-Transport-Security
 
-**Update**:
+Update:
 
 -   Updated packages
 -   Updated service worker scripts
 
-**Documentation**:
+Documentation:
 
 -   Added CI/CDs and GitHub Actions
 -   Added Quynh (Cathy) Cao's GitHub URL
@@ -76,7 +89,7 @@ Version 1.1.0 has now dropped and it includes the ability to do practice genes w
 -   Updated README
 -   Updated prettier to ignore line endings
 
-**Bug fix**:
+Bug fix:
 
 -   Fixed background size not being read correctly
 -   Fixed being unable to switch login tabs
@@ -91,7 +104,7 @@ Version 1.1.0 has now dropped and it includes the ability to do practice genes w
 
 ## [1.0.7] - 2021-11-22
 
-**A brand new version of the [SciGrade](https://scigrade.com/) has dropped!**
+A brand new version of the [SciGrade](https://scigrade.com/) has dropped!
 
 Version 1.0.7 has now dropped and it includes tons of optimizations and bug fixes
 

CODE_OF_CONDUCT.md

@@ -115,13 +115,13 @@ the community.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
-https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+<https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
 
 Community Impact Guidelines were inspired by [Mozilla's code of conduct
 enforcement ladder](https://github.com/mozilla/diversity).
 
 [homepage]: https://www.contributor-covenant.org
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

EDIT.MD

@@ -1,10 +1,10 @@
-# Welcome to [SciGrade](http://scigrade.com)!
+# Welcome to [SciGrade](http://scigrade.com)
 
 If you opened this document, that means you are most likely interested in how to edit or modify SciGrade. In here, I will go over how you can change, edit and/or modify what makes SciGrade.
 
 I recommend you read our [README](README.md) and [CONTRIBUTING](CONTRIBUTING.md) if you haven't before you start editing SciGrade.
 
-## What’s available with SciGrade and how it works:
+## What’s available with SciGrade and how it works
 
 Everything on SciGrade is generated dynamically on the client side to reduce the number of pages that are needed to be loaded.
 
@@ -34,15 +34,15 @@ There is also a feedback page for practice assignments screen which is displayed
 
 ![feedback example](core/images/EDITmd/004_FeedbackPage.png "Example of the feedback page")
 
-## Example protocol:
+## Example protocol
 
 There is an example protocol for students to follow in the PDF file [LabProtocol](LabProtocol.pdf). It is recommended that you customize it to your teaching class, but the protocol includes all the necessary details for students to follow to understand how to create gRNAs and where they can get the information to input into SciGrade.
 
-## Adding users:
+## Adding users
 
 Only TAs and admins can add new students and only admins can add other admins or TAs. This is done through the account management modal.
 
-### Adding students:
+### Adding students
 
 Multiple students at once can be added through the "Create new class:" card. Within this card, there are three input boxes. A "Choose class" option where you can add to an existing class or create a new class. It is important to note that spaces will be deleted when being added to the MongoDB server once you submit so use capital letters to separate words. To change this, just remove
 
@@ -58,15 +58,15 @@ For student's numbers and emails, there must be an equal amount of each while th
 
 ![adding students](core/images/EDITmd/006_AddStudents.png "Adding students to SciGrade servers")
 
-### Adding a single student:
+### Adding a single student
 
 Adding a single user must be done individually within the "Add single user:" card which can only be accessed by an admin. To change this from being admin only to allowing TAs, within the `openAccountManagement()` in [crispr_script.js](core/scripts/crispr_script.js), change the order of `append_str` or find the `// Admin controls: ` and combine that with the `// TA access to add new students:`.
 
 If you are adding a TA or admin, it recommended you add them to the "AdminTA-List" class. From there, they have to register before you can change the user into a TA or admin from the "Change a user's account type:" card. By default, users are added as students
 
 ![adding students](core/images/EDITmd/007_AddTA.png "Adding a TA to SciGrade servers")
 
-## Marking algorithm:
+## Marking algorithm
 
 SciGrade marks the gRNA strand, PAM sequence, off-target score and the F1 and R1 primers. Using [markAnswers()](core/scripts/crispr_script.js), the student's input into the form on the practice/assignment form will be used to determine the marking.
 
@@ -86,21 +86,21 @@ The following image describes where student's marks come from in the marking alg
 
 ![SciGrade marking algorithm](core/images/EDITmd/005_Algorithm.png "How the SciGrade marking algorithm works")
 
-### Adjusting the marking algorithm:
+### Adjusting the marking algorithm
 
 There are two ways to adjust the marking algorithm
 
 1. Use the "Modify marking controls:" card from the account management modal. Within this modal, you can adjust how the off-target "optimal" value is calculated with two options: "Optimal" and "Custom". Optimal is calculated using the following equation: `Min_optimal = Max_range - (Max_range * 0.2)` where `Max_range` is the highest value of possible feasible off-target scores. While Custom is a custom "optimal" value which can be any number between 0.01 and 100.
    ![modify marking controls](core/images/EDITmd/008_AdjustMarks.png "Example of the account modal modify marking control's card")
 2. Edit the code within [crispr_script.js](core/scripts/crispr_script.js). The following functions are related to marking: `checkAnswers()`, `checkOffTarget(score)`, `checkF1Primers(seq)` and `checkR1Primers(seq)` to determine if answers are correct or not and then `markAnswers()` to assign marks.
 
-### Changing a user's type:
+### Changing a user's type
 
 If you change the MongoDB database, this will not work unless it is structured exactly like ours.
 
 In the "Change a user's account type:" card within the Account module, you can select a user from a class and change this account type from Student or TA or admin (each with their respective properties)
 
-## Downloading marks:
+## Downloading marks
 
 SciGrade has a built-in option to download marks as a CSV (Excel) file. There are two options:
 
@@ -112,7 +112,7 @@ If you wish to change what is visible in the exported CSV file, you can modify i
 1. `generateRestOfIndexTable(whichIndexTable, SimpleComplex)`: Used to generate the template/header for each downloaded CSV mark's file (SimpleComplex is true for marks, false for raw marks)
 2. `generateHiddenStudentDownload(whichClass, whichType)`: Used to fill the template and download the generated CSV mark's file
 
-## Adding new genes:
+## Adding new genes
 
 Currently, there is no interface that allows you to add a new gene from the front-end. Adding a new gene requires access to the MongoDB server and requires the following things:
 
@@ -136,7 +136,7 @@ Add those to the MongoDB server and make sure `loadCRISPRJSON_Files()` within [c
 
 It is important to note that SciGrade's system is meant for human (Homo sapiens) GRCH38 (HG38) gene annotations using the [crispr.mit.edu from Hsu et al., 2013](http://crispr.mit.edu/) algorithm for off-target scoring.
 
-## Connection to MongoDB:
+## Connection to MongoDB
 
 The current version of SciGrade uses MongoDB Atlas as our data hosting service. If you are trying to create your own custom version of SciGrade, I recommend you to create your own MongoDB Atlas cluster ([more information on their website](https://www.mongodb.com/cloud/atlas), including [pricing](https://www.mongodb.com/cloud/atlas/pricing)).
 

LICENSE.md

@@ -75,7 +75,7 @@ modification follow.
 
 ### TERMS AND CONDITIONS
 
-#### 0. Definitions.
+#### 0. Definitions
 
 "This License" refers to version 3 of the GNU General Public License.
 
@@ -115,7 +115,7 @@ work under this License, and how to view a copy of this License. If
 the interface presents a list of user commands or options, such as a
 menu, a prominent item in the list meets this criterion.
 
-#### 1. Source Code.
+#### 1. Source Code
 
 The "source code" for a work means the preferred form of the work for
 making modifications to it. "Object code" means any non-source form of
@@ -156,7 +156,7 @@ regenerate automatically from other parts of the Corresponding Source.
 The Corresponding Source for a work in source code form is that same
 work.
 
-#### 2. Basic Permissions.
+#### 2. Basic Permissions
 
 All rights granted under this License are granted for the term of
 copyright on the Program, and are irrevocable provided the stated
@@ -181,7 +181,7 @@ Conveying under any other circumstances is permitted solely under the
 conditions stated below. Sublicensing is not allowed; section 10 makes
 it unnecessary.
 
-#### 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+#### 3. Protecting Users' Legal Rights From Anti-Circumvention Law
 
 No covered work shall be deemed part of an effective technological
 measure under any applicable law fulfilling obligations under article
@@ -197,7 +197,7 @@ operation or modification of the work as a means of enforcing, against
 the work's users, your or third parties' legal rights to forbid
 circumvention of technological measures.
 
-#### 4. Conveying Verbatim Copies.
+#### 4. Conveying Verbatim Copies
 
 You may convey verbatim copies of the Program's source code as you
 receive it, in any medium, provided that you conspicuously and
@@ -210,7 +210,7 @@ recipients a copy of this License along with the Program.
 You may charge any price or no price for each copy that you convey,
 and you may offer support or warranty protection for a fee.
 
-#### 5. Conveying Modified Source Versions.
+#### 5. Conveying Modified Source Versions
 
 You may convey a work based on the Program, or the modifications to
 produce it from the Program, in the form of source code under the
@@ -245,7 +245,7 @@ beyond what the individual works permit. Inclusion of a covered work
 in an aggregate does not cause this License to apply to the other
 parts of the aggregate.
 
-#### 6. Conveying Non-Source Forms.
+#### 6. Conveying Non-Source Forms
 
 You may convey a covered work in object code form under the terms of
 sections 4 and 5, provided that you also convey the machine-readable
@@ -341,7 +341,7 @@ documented (and with an implementation available to the public in
 source code form), and must require no special password or key for
 unpacking, reading or copying.
 
-#### 7. Additional Terms.
+#### 7. Additional Terms
 
 "Additional permissions" are terms that supplement the terms of this
 License by making exceptions from one or more of its conditions.
@@ -400,7 +400,7 @@ Additional terms, permissive or non-permissive, may be stated in the
 form of a separately written license, or stated as exceptions; the
 above requirements apply either way.
 
-#### 8. Termination.
+#### 8. Termination
 
 You may not propagate or modify a covered work except as expressly
 provided under this License. Any attempt otherwise to propagate or
@@ -428,7 +428,7 @@ this License. If your rights have been terminated and not permanently
 reinstated, you do not qualify to receive new licenses for the same
 material under section 10.
 
-#### 9. Acceptance Not Required for Having Copies.
+#### 9. Acceptance Not Required for Having Copies
 
 You are not required to accept this License in order to receive or run
 a copy of the Program. Ancillary propagation of a covered work
@@ -439,7 +439,7 @@ modify any covered work. These actions infringe copyright if you do
 not accept this License. Therefore, by modifying or propagating a
 covered work, you indicate your acceptance of this License to do so.
 
-#### 10. Automatic Licensing of Downstream Recipients.
+#### 10. Automatic Licensing of Downstream Recipients
 
 Each time you convey a covered work, the recipient automatically
 receives a license from the original licensors, to run, modify and
@@ -464,7 +464,7 @@ rights granted under this License, and you may not initiate litigation
 any patent claim is infringed by making, using, selling, offering for
 sale, or importing the Program or any portion of it.
 
-#### 11. Patents.
+#### 11. Patents
 
 A "contributor" is a copyright holder who authorizes use under this
 License of the Program or a work on which the Program is based. The
@@ -533,7 +533,7 @@ Nothing in this License shall be construed as excluding or limiting
 any implied license or other defenses to infringement that may
 otherwise be available to you under applicable patent law.
 
-#### 12. No Surrender of Others' Freedom.
+#### 12. No Surrender of Others' Freedom
 
 If conditions are imposed on you (whether by court order, agreement or
 otherwise) that contradict the conditions of this License, they do not
@@ -546,7 +546,7 @@ from those to whom you convey the Program, the only way you could
 satisfy both those terms and this License would be to refrain entirely
 from conveying the Program.
 
-#### 13. Use with the GNU Affero General Public License.
+#### 13. Use with the GNU Affero General Public License
 
 Notwithstanding any other provision of this License, you have
 permission to link or combine any covered work with a work licensed
@@ -557,7 +557,7 @@ but the special requirements of the GNU Affero General Public License,
 section 13, concerning interaction through a network will apply to the
 combination as such.
 
-#### 14. Revised Versions of this License.
+#### 14. Revised Versions of this License
 
 The Free Software Foundation may publish revised and/or new versions
 of the GNU General Public License from time to time. Such new versions
@@ -583,7 +583,7 @@ permissions. However, no additional obligations are imposed on any
 author or copyright holder as a result of your choosing to follow a
 later version.
 
-#### 15. Disclaimer of Warranty.
+#### 15. Disclaimer of Warranty
 
 THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
 APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
@@ -595,7 +595,7 @@ PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
 DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
 CORRECTION.
 
-#### 16. Limitation of Liability.
+#### 16. Limitation of Liability
 
 IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
@@ -607,7 +607,7 @@ LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
 TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
 PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
 
-#### 17. Interpretation of Sections 15 and 16.
+#### 17. Interpretation of Sections 15 and 16
 
 If the disclaimer of warranty and limitation of liability provided
 above cannot be given local legal effect according to their terms,

README.md

@@ -12,7 +12,7 @@ SciGrade is an online web-tool that allows students (or any user with access) to
 
 ## Getting Started
 
-It is recommended that you use the web-version available at https://scigrade.com/ but if you want to download and run the SciGrade locally, it is possible though it requires an internet connection to login and accesses the marking form and student information (exclusive for TA's and admins).
+It is recommended that you use the web-version available at <https://scigrade.com/> but if you want to download and run the SciGrade locally, it is possible though it requires an internet connection to login and accesses the marking form and student information (exclusive for TA's and admins).
 
 ## Browser Compatibilities