fix: Add details about Upload.

docs/FAQs.md

@@ -4,10 +4,10 @@ sidebar_position: 7
 # FAQs
 
 ### How can I submit my data?
-You need to first register to [nmrXiv](https://nmrxiv.org/) with your email id and then submit your data via the automated submission pipeline. Read the [submission guides](http://localhost:3000/docs/category/submission-guides) to get more understanding.
+You need to first register to [nmrXiv](https://nmrxiv.org/) with your email id and then submit your data via the automated submission pipeline. Read the [submission guides](/docs/category/submission-guides) to get more understanding.
 
 ### Do I need to register before submitting the data to nmrXiv?
-Yes, you need to register via your email id or you can also login via Single sign-on with your GitHub or Twitter ID.
+Yes, you need to register via your email id or you can also log in via Single sign-on with your GitHub or Twitter ID.
 
 ### What should be the structure of the folder to be uploaded in nmrXiv?
 
@@ -18,48 +18,48 @@ Yes, you need to register via your email id or you can also login via Single sig
 ### What happens to my data once submitted?
 
 
-### What is public and private project in nmrXiv?
-**Public** projects(including the underline studies and datasets) are visible and accessible to everyone(even to the non-registered user of [nmrXiv](https://nmrxiv.org/)). You can see all the open project [here](https://nmrxiv.org/projects) or can also find it in the Projects tab in the left hand panel of your dashboard.
+### What is a public and private project in nmrXiv?
+**Public** projects(including the underline studies and datasets) are visible and accessible to everyone(even to the non-registered user of [nmrXiv](https://nmrxiv.org/)). You can see all the open projects [here](https://nmrxiv.org/projects) or can also find them in the Projects tab in the left-hand panel of your dashboard.
 
-**Private** projects(including the underline studies and datasets) are only visible and accessible to you or to the members of the team and also to the user with whom you explicitly share the project with.
+**Private** projects(including the underline studies and datasets) are only visible and accessible to you or the members of the team and also to the user with whom you explicitly share the project.
 
 ### What happens when I make my project public?
-If you make your project public you are making it open for access(including the underline studies and datasets) to everyone(even to the non-registered user of [nmrXiv](https://nmrxiv.org/)), but you can define rights by choosing a license for your project. Once your project is made public you cannot edit,delete or change it to private again.
+If you make your project public you are making it open for access(including the underline studies and datasets) to everyone(even to the non-registered user of [nmrXiv](https://nmrxiv.org/)), but you can define rights by choosing a license for your project. Once your project is made public you cannot edit, delete or change it to private again.
 
-### Can I edit my project if once made public?
-You cannot edit the project once it's made public, but you can always create another version of the project and make changes on top it.
+### Can I edit my project once made public?
+You cannot edit the project once it's made public, but you can always create another version of the project and make changes on top of it.
 
-### How can I delete my project,studies or dataset?
+### How can I delete my project, studies or dataset?
 
 
 ### How can I share my project?
-You can share your project with multiple number of users. Not only that you can also choose the type of role you want. Click [here](/docs/submission-guides/sharing) to learn more about sharing.
+You can share your project with multiple users. Not only that you can also choose the type of role you want. Click [here](/docs/submission-guides/sharing) to learn more about sharing.
 
 ### Can I create a team to work on a collaborative project?
-Yes, you can create a [Team](/docs/submission-guides/team) and add as many member as you want. You can also restrict the action of members by assigning different roles. Click [here](/docs/submission-guides/team) to learn more about Team.
+Yes, you can create a [Team](/docs/submission-guides/team) and add as many members as you want. You can also restrict the action of members by assigning different roles. Click [here](/docs/submission-guides/team) to learn more about Team.
 
 
-### What are the different roles I can assign to a member in a team?
+### What are the different roles I can assign to a member of a team?
 Below are the three major roles which you assign to a member. 
-* **Owner** - Can read and/or update including delete the project, study and dataset.
+* **Owner** - Can read and/or update including deleting the project, study and dataset.
 * **Collaborator** -  Can read and/or update project, study and dataset information.
 * **Reviewer** - Can only read project, study and dataset information.
 
 ### How can I delete or edit my account?
-You can edit the basic information in your account by clicking on the `Account` tab from the top right corner drop down in your dashboard. To delete your account please reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/) or write to us at info@nmrxiv.org.
+You can edit the basic information in your account by clicking on the `Account` tab from the top right corner drop-down in your dashboard. To delete your account please reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/) or write to us at info@nmrxiv.org.
 
 ### How can I license my project and how to know which license to choose?
 Licensing your project is important before you make it public. You can choose the license from the license dropdown. Please go through this [discussion](https://github.com/NFDI4Chem/nmrxiv/discussions/123) to learn more about which license to choose.
 
 ### Can I use nmrXiv for my teaching and demo purposes?
-Yes, you can use our [staging site](https://dev.nmrxiv.org) for teaching, demo and also to test most of the features. But please keep it mind this site is just for testing and demonstration purpose only and all your data can be reset anytime.
+Yes, you can use our [staging site](https://dev.nmrxiv.org) for teaching, demoing, and also test most of the features. But please keep in mind this site is just for testing and demonstration purposes only and all your data can be reset anytime.
 To learn more about our environment click [here](docs/developer-guides/deployment/environment).
 
 ### How to report a bug?
 Before reporting a new issue
 * Please read the [documentation](https://docs.nmrxiv.org/) carefully.
-* Search from the existing [issue](https://github.com/NFDI4Chem/nmrxiv/issues) for your bug. [Here](https://docs.github.com/en/issues/tracking-your-work-with-issues/filtering-and-searching-issues-and-pull-requests#searching-for-issues-and-pull-requests) are some tips which can help you to narrow down your search. You can also provide some additional information to any existing issue if it differs. 
+* Search from the existing [issue](https://github.com/NFDI4Chem/nmrxiv/issues) for your bug. [Here](https://docs.github.com/en/issues/tracking-your-work-with-issues/filtering-and-searching-issues-and-pull-requests#searching-for-issues-and-pull-requests) are some tips that can help you to narrow down your search. You can also provide some additional information on any existing issue if it differs. 
 
 #### Reporting a new issue
-Please write to us at info@nmrxiv.org or reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/).
+Please write to us at info@nmrxiv.org or reach out to our [Helpdesk](https://www.nfdi4chem.de/index.php/helpdesk/). We will try to get back to your queries as soon as possible.
 

docs/submission-guides/submission/upload.md

@@ -3,78 +3,40 @@ sidebar_position: 1
 title: Upload
 ---
 
-## Project
+Submitting data to [nmrXiv](https://www.nmrxiv.org) is really simple and just a 3 step process. 
+Before you start submitting data you need to 
+* First register and create an account in [nmrXiv](https://www.nmrxiv.org).
+* Make sure your folder is structured in the format described [here](/docs/submission-guides/submission/folder-structure).
+* Your folder contains files of a supported type.
 
-nmrXiv concept of **Projects** is similar to the concept of the [**Investigation** in **ISA Schema**](https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation) where all the information needed to understand the overall goals and means used in an experiment can be found. Once you have registered your account successfully in nmrXiv, and if you do not want to collaborate with a [Team](https://docs.nmrxiv.org/docs/submission-guides/Teams), the first step, by which you can start, is to create a **Project**.
+Follow the steps below to successfully submit your data.
 
-## Create New Project
-A user can create single or multiple **Projects**, and each **Project** can contain single or multiple [Studies](https://docs.nmrxiv.org/docs/submission-guides/study).
-To create a **Project**, click on the `New Project` button or **Create a new project** tab. 
-![Dashboard](/img/project/dashboard.png) 
+* **Files Upload**
 
-This will pop up a new window where you have to provide the project **Name**, and you can optionally provide a **Description**. The **Description** can be stylized with [Markdown](https://www.markdownguide.org/) in the `Write` view, while the styling effect can be seen in the `Preview` view. You can choose to make your **Project** **Public** or **Private**. If the **Project** is **Private**, then it is accessible (the project only, not the underlying [Studies](https://docs.nmrxiv.org/docs/submission-guides/study)) by you and by the members of the [Team](https://docs.nmrxiv.org/docs/submission-guides/Teams). If it's **Public**, then everyone with the link will be able to access the **Project**.
-Finally you can either `SAVE` your input, or `CANCEL` the process.
-![New Project](/img/project/new-project.png) 
+Click on the `upload` button to open the submission process. Provide basic details about your submission such as project name, description and keywords to categorize your project. Drag and drop your folder and wait for the upload to be completed.
 
-After creating the project, you will be taken back to where it was created (in the dashboard or in a [Team](https://docs.nmrxiv.org/docs/submission-guides/Teams)), where you can see a list of all your available **Projects** sorted from the oldest updated **Project** to the latest updated ones. For each **Project** in the list, you can see its name, privacy, and creation date. On the right side there is an arrow to enter the **Project**
-![Projects List](/img/project/projects-list.png) 
+![File Upload](/img/upload/fileupload.gif)
 
-Here you can see the animated process of creating a **Project**.
-<img src="/img/project/create.gif"/>
+* **Assignement & Meta data**
 
-## View and Update Project Details and Settings
-After creating a **Project**, you can enter that **Project** by clicking the **Project**'s  arrow on the right side of the **Projects** list. This will lead you to a new page where you can find the **Project**'s details, update its settings, and add new [Studies](https://docs.nmrxiv.org/docs/submission-guides/study). 
+In this step you can use [NMRium](https://www.nmrium.org/) to edit your spectra and assign the peaks to the corresponding chemical groups, additionally, you can provide the metadata of the studies and samples. You have a view of all the studies in the project with the datasets they include.
+You can navigate through different datasets(experiments) within the study, visualize and edit the spectrum respectively. Below in the info table you will find all the information extracted by [NMRium](https://www.nmrium.org/) about the NMR experiment.
 
-![Projects Page](/img/project/project-page.png) 
+The `Sample Info` tab shows details including the chemical composition (available molecules and their percentages). In the editor below you can add the structure of your chemical composition or can also import from the SMILES.
 
-### View/Edit Project Details
-By clicking on **View details** on the top left side, a menu opens from the right side containg the same details entered when [creating the **Project**](#create-new-project)   (name, description, privacy) with the possibility to edit them when having the right [role](https://docs.nmrxiv.org/docs/submission-guides/Teams#roles-and-permissions). In addition, you can find a link to the documentation to get more details about sharing **Projects**. [Learn more about sharing](#)
-![Projects Details](/img/project/project-details.png) 
+The `Meta Data` shows an overview of the study's metadata, press on **autogenerate** to auto-generate the description of the study, or can also edit and add manually if needed.
 
-The new addition you can find here is the **Activity** button at the bottom of the menu. By clicking on it, another menu opens from the right side to show a log of all the activites (Changelogs) performed on the project with details on the updater, what was updated, and when. 
-![Projects Activity](/img/project/project-activity.png) 
+![Assignement & Meta data](/img/upload/assignment-metadata.gif)
 
-Here you can see the animated process of view a **Project** details and updating them.
+* **Final step**
 
-<img src="/img/project/update.gif"/>
+After clicking on proceed your data will be now submitted and processed in the background. Give us a few moments for the queue to get processed and you will receive an email once the processing is complete.
+You will be redirected to the final page of the submission workflow where you get the overview summary of the whole project. Here you can edit the existing details and enter other essential information such as defining privacy, choosing release date, and [license](https://github.com/NFDI4Chem/nmrxiv/discussions/123). There is also a quick download link to download your whole project.
+Click on the `Save` button and press `Finish` and you are done!!
 
+![Complete](/img/upload/complete.gif)
 
-### Delete Project (Project Settings)
-To delete your Project, click on the **Project Setting** tab on the right top corner, a new page opens.
-![Delete Project](/img/project/project-delete.png) 
 
-From the new page you can choose to `DELETE PROJECT`. A window pops up to ask you for your password, and to confirm that you really want to delete the project. 
-![Confirm Deletion](/img/project/delete-confirm.png) 
 
 
-:::danger Caution
-Caution: Once your project is deleted, all of its resources and data will be permanently deleted. Before deleting your project, please download any data or information that you wish to retain.
-:::
 
-Here you can see the animated process of deleting a **Project**.
-<img src="/img/project/delete.gif"/>
-
-
-
-
-## Study
-
-nmrXiv concept of **Study** is similar to the concept of the [**Study** in **ISA Schema**](https://isa-specs.readthedocs.io/en/latest/isamodel.html#study) containing information on the subject under study, its characteristics and any treatments applied (The **Subject** in [**ISA**](https://isa-specs.readthedocs.io/en/latest/isamodel.html#) is exclusively a biological object, which we aim at extending in nmrXiv). 
-
-A **Study** contains contextualising information for one or more [Assay](https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay). Metadata about the study design, study factors used, and study protocols are recorded in Study objects, as well as information similarly to the Investigation including title and description of the study, and related people and scholarly publications. For more details, please refer to the [**Study** in **ISA Schema**](https://isa-specs.readthedocs.io/en/latest/isamodel.html#study).
-
-In nmrXiv, **Studies** are contained in [Projects](https://docs.nmrxiv.org/docs/submission-guides/project), where a [Project](https://docs.nmrxiv.org/docs/submission-guides/project) can house one or more **Studies**, and each one of them receives its very own [URL](https://developer.mozilla.org/en-US/docs/Learn/Common_questions/What_is_a_URL). **Studies** can be versioned, command invocations, and metrics.
-
-## Create New Study
-A user can create one or more **Studies**, and each **Study** can contain one or more **Assays**. To create a **Study**, click on the `New Study` button or **Create a new Study** tab. 
-![Projects Page](/img/project/project-page.png) 
-
-This will pop up a new window where you have to provide the study **Name**, and you can optionally provide a **Description**. The **Description** can be stylized with [Markdown](https://www.markdownguide.org/) in the `Write` view, while the styling effect can be seen in the `Preview` view. You can choose to make your **Study** **Public** or **Private**. If the **Study** is **Private**, then it is accessible by you and by the members of the [Team](https://docs.nmrxiv.org/docs/submission-guides/Teams). If it's **Public**, then everyone with the link will be able to access the **Study**.
-Finally you can either `SAVE` your input, or `CANCEL` the process.
-![New Study](/img/study/new-study.png) 
-
-After creating the **Study**, you will be taken back to the [Project](https://docs.nmrxiv.org/docs/submission-guides/project) page, where you can see a list of all your available **Studies** sorted from the oldest updated **Study** to the latest updated ones. For each **Study** in the list, you can see its name, privacy, and creation date. On the right side there is an arrow to enter the **Study**
-![Study List](/img/study/study-list.png) 
-
-Here you can see the animated process of creating a **Study**.
-<img src="/img/study/create.gif"/>