diff --git a/docs/404.html b/docs/404.html index 45f9b3aa06..992b87b47a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -23,7 +23,7 @@ - + diff --git a/docs/BreedbaseManual.pdf b/docs/BreedbaseManual.pdf index cbd7281542..f50de500ed 100644 Binary files a/docs/BreedbaseManual.pdf and b/docs/BreedbaseManual.pdf differ diff --git a/docs/BreedbaseManual.tex b/docs/BreedbaseManual.tex index 42e719e501..37a86718c6 100644 --- a/docs/BreedbaseManual.tex +++ b/docs/BreedbaseManual.tex @@ -85,7 +85,7 @@ \title{Breedbase User Manual} \author{Breedbase team} -\date{2025-09-09} +\date{2025-10-23} \begin{document} \maketitle @@ -134,18 +134,18 @@ \subsection{Verifying first that you do not already have an account}\label{verif Before creating an account, please verify first that you don't already have an account. You can use ``Search'' menu to check if you already registered as a user. -In the ``Search'' menu, selecting the ``People'' tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, clicking the ``Login'' button. If you have forgotten your password, you can retrieve it by clicking the ``Forgot your password?'' link on the login page. +In the ``Search'' menu, selecting the ``People'' tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, continue by clicking the ``Login'' button. If you have forgotten your password, you can retrieve it by clicking the ``Forgot your password?'' link on the login page. \hypertarget{creating-a-user-account-1}{% \subsection{Creating a user account}\label{creating-a-user-account-1}} -On the right of the toolbar, clicking on ``Login.'' It will take you to the login page. On the login page, clicking on the link ``sign up for an account.'' It will take you to the page below: +On the right of the toolbar, click on ``Login'', which will take you to the login dialog. On the login dialog, click on the link ``sign up for an account.'' It will take you to the page below: \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image331} \end{center} -Filling in all of the information, then clicking ``Create Account.'' +Filling in all of the information, then click ``Create Account.'' -After you submit the information, an email will be sent to the provided email address. Checking your email and clicking on the link to activate your account. +After you submit the information, an email will be sent to the provided email address. Check your email and click on the link to activate your account. \hypertarget{managing-your-account}{% \section{Managing your Account}\label{managing-your-account}} @@ -153,7 +153,7 @@ \section{Managing your Account}\label{managing-your-account}} \hypertarget{login}{% \subsection{Login}\label{login}} -To login, clicking the ``Login'' link in the toolbar on any page and enter your username and password. +To login, click the ``Login'' link in the toolbar on any page and enter your username and password. If you have forgotten your password, you can retrieve it by clicking the ``Forgot your password?'' link on the login page. @@ -162,13 +162,13 @@ \subsection{Login}\label{login}} \hypertarget{editing-account-settings}{% \subsection{Editing Account Settings}\label{editing-account-settings}} -Account settings can be edited by clicking on the ``my profile'' link displayed as your user name, on the right of the toolbar. You must login, in order to access and change account settings. +Account settings can be edited by clicking on the ``my profile'' link displayed as your user name, on the right of the toolbar. You must be logged in order to access and change account settings. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image261} \end{center} You can add personal information to your account using the ``View or update personal information'' link. -To change your password, username, or your contact email, clicking on ``Update account information'' link. You must provide your old password before you can make any changes. +To change your password, username, or your contact email, click on ``Update account information'' link. You must provide your old password before you can make any changes. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image144} \end{center} @@ -189,7 +189,7 @@ \subsection{Changing Your Account Status: From ``User'' to ``Submitter''}\label{ Post to the forum \end{itemize} -To upgrade your account status to ``submitter,'' contact the database curators using the ``contact'' link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotype data and images. +To upgrade your account status to ``submitter,'' contact the database curators using the ``contact'' link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotypic data and images. \hypertarget{submitting-feedback-on-an-sgn-database}{% \subsection{Submitting Feedback on an SGN Database}\label{submitting-feedback-on-an-sgn-database}} @@ -199,7 +199,7 @@ \subsection{Submitting Feedback on an SGN Database}\label{submitting-feedback-on \hypertarget{menu-layout}{% \section{Menu Layout}\label{menu-layout}} -SGN Database websites have a toolbar on the top of each page with a number of menus for convenient access of major functions. The menus, as pictured below, are ``search,'' ``manage,'' ``analyze,'' and ``maps.'' The toolbar also provides a quick search, a ``log in'' button, and a ``new user'' button. +SGN Database websites have a toolbar on the top of each page with a number of menus for convenient access of major functions. The menus, as pictured below, are ``search,'' ``manage,'' ``analyze,'' and ``maps.'' The toolbar also provides a quick search, a ``log in'' button, and a ``new user'' button. The menus can be customized for each instance, so they may not appear exactly as shown on your instance; for example, most instances do not have a map menu. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image270} \end{center} @@ -298,7 +298,7 @@ \subsubsection*{Analyze}\label{analyze}} \hypertarget{working-with-lists}{% \section{Working with Lists}\label{working-with-lists}} -Lists are collections of identifiers that are stored in the database. Lists can be composed of accessions, plots, traits, locations, and trials. Lists are attached to the individual user's account, and can only be created and seen by the user while logged in. SGN databases make heavy use of lists in a number of tools on the website. For example, trials are created using lists of accessions. +Lists are collections of identifiers that are stored in the database. Lists can be composed of accessions, plots, traits, locations, and trials. A given list can only contain one type of items, for example, all items have to be of type location in a list of locations. Lists are attached to the individual user's account, and can only be created and seen by the user while logged in, however, lists can be made public for all other users to see. SGN databases make heavy use of lists in a number of tools on the website. For example, trials are created using lists of accessions. \hypertarget{creating-lists}{% \subsection{Creating lists}\label{creating-lists}} @@ -309,11 +309,11 @@ \subsection{Creating lists}\label{creating-lists}} \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_start} \end{center} -To create a new list, enter the name of your new list and then clicking on the ``New List'' button. The name of the list can be anything, but should be unique and should be something to help you easily identify. +To create a new list, enter the name of your new list and then click on the ``New List'' button. The name of the list can be anything, but should be unique and should be something to help you easily identify the list. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_new_list} \end{center} -You can find the list that you entered on the ``Your Lists'' page. To add items to your list, click on the ``View'' icon to open ``List Contents'' page. +If the list already exists, it will appear on the ``Your Lists'' dialog. To add items to your list, click on the ``View'' icon to open the ``List Contents'' section. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_view_list} \end{center} @@ -321,7 +321,7 @@ \subsection{Creating lists}\label{creating-lists}} \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_add_items} \end{center} -The page will be updated and will display your items in a table at the bottom of the page. It is possible to sort the list if you need. +The page will be updated and will display your items in a table at the bottom of the dialog It is possible to sort the list if you need. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_added_items} \end{center} @@ -335,12 +335,12 @@ \subsection{Creating lists}\label{creating-lists}} Note that a list cannot contain duplicate elements. If a duplicate item is entered, the list manager will inform the user that the element is already in the list and will not add it again. -Another easy way to create a list is to use \ref{search-wizard}, which can be accessed from the Search menu. +Another easy way to create a list is to use the \ref{search-wizard}, which can be accessed from the Search menu. \hypertarget{viewing-and-editing-lists}{% \subsection{Viewing and editing lists}\label{viewing-and-editing-lists}} -Lists can be viewed and edited using the ``Lists'' link on the toolbar. Clicking on the link will open a window that displays all of your lists, as well as an option to create new lists. +Lists can be viewed and edited using the ``Lists'' link on the toolbar. Clicking on the link will open a dialog that displays all of your lists, as well as an option to create new lists. \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image71} \end{center} diff --git a/docs/basic-website-usage.html b/docs/basic-website-usage.html index da08ab9daf..eeea10acd0 100644 --- a/docs/basic-website-usage.html +++ b/docs/basic-website-usage.html @@ -23,7 +23,7 @@ - + @@ -379,30 +379,30 @@

1.1 Creating a User Account

1.1.1 Verifying first that you do not already have an account

Before creating an account, please verify first that you don’t already have an account. You can use “Search” menu to check if you already registered as a user.

-

In the “Search” menu, selecting the “People” tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, clicking the “Login” button. If you have forgotten your password, you can retrieve it by clicking the “Forgot your password?” link on the login page.

+

In the “Search” menu, selecting the “People” tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, continue by clicking the “Login” button. If you have forgotten your password, you can retrieve it by clicking the “Forgot your password?” link on the login page.

1.1.2 Creating a user account

-

On the right of the toolbar, clicking on “Login.” It will take you to the login page. On the login page, clicking on the link “sign up for an account.” It will take you to the page below:

+

On the right of the toolbar, click on “Login”, which will take you to the login dialog. On the login dialog, click on the link “sign up for an account.” It will take you to the page below:

-

Filling in all of the information, then clicking “Create Account.”

-

After you submit the information, an email will be sent to the provided email address. Checking your email and clicking on the link to activate your account.

+

Filling in all of the information, then click “Create Account.”

+

After you submit the information, an email will be sent to the provided email address. Check your email and click on the link to activate your account.

1.2 Managing your Account

1.2.1 Login

-

To login, clicking the “Login” link in the toolbar on any page and enter your username and password.

+

To login, click the “Login” link in the toolbar on any page and enter your username and password.

If you have forgotten your password, you can retrieve it by clicking the “Forgot your password?” link on the login page.

1.2.2 Editing Account Settings

-

Account settings can be edited by clicking on the “my profile” link displayed as your user name, on the right of the toolbar. You must login, in order to access and change account settings.

+

Account settings can be edited by clicking on the “my profile” link displayed as your user name, on the right of the toolbar. You must be logged in order to access and change account settings.

You can add personal information to your account using the “View or update personal information” link.

-

To change your password, username, or your contact email, clicking on “Update account information” link. You must provide your old password before you can make any changes.

+

To change your password, username, or your contact email, click on “Update account information” link. You must provide your old password before you can make any changes.

@@ -414,7 +414,7 @@

1.2.3 Changing Your Account Statu
  • Post comments on pages
  • Post to the forum
    • -

    To upgrade your account status to “submitter,” contact the database curators using the “contact” link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotype data and images.

    +

    To upgrade your account status to “submitter,” contact the database curators using the “contact” link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotypic data and images.

    1.2.4 Submitting Feedback on an SGN Database

    @@ -423,7 +423,7 @@

    1.2.4 Submitting Feedback on an S