Merge pull request #448 from NUM-Forschungsdatenplattform/develop

Release 1.12.0
NUM-Forschungsdatenplattform · Mar 31, 2023 · a59fb07 · a59fb07
2 parents 9605571 + 495efeb
commit a59fb07
Show file tree

Hide file tree

Showing 159 changed files with 3,013 additions and 1,140 deletions.
diff --git a/docs/01_create_user/01_create_user.md → docs/01_user_account/01_user_account.md b/docs/01_create_user/01_create_user.md → docs/01_user_account/01_user_account.md
@@ -1,4 +1,4 @@
-# Create User
+# User account
 
 Before you can start using CODEX you have to create a new user account for your personal work.
 
@@ -8,7 +8,7 @@ A user account can be created by each indiviual by providing a company or instit
 The domain of your email address (part after the @-symbol) has to be listed in one of the organizations in the portal. If this is not the case, you will receive an according error message upon registration. In such cases, please contact the portal support.
 ```
 
-## Sign up a new user account
+## Create a new user account
 
 To create a new user account navigate to the sign up page which you can find by clicking "SIGN IN"
 at the main naviation. You will be asked to accept storing cookies on your machine. Accept and this
@@ -22,8 +22,10 @@ alt: 'Login page with a red arrow pointing to the registration link'
 Fig 01-01: Position of the register link on Login page
 ```
 
-At the Signup page you will see a form to enter your basic data. All input fields marked with an
-asterisk are required to proceed. 
+At the Signup page you will see a form to enter your basic data. 
+The **project lead** creates new projects, describes them, and manages them through the application process to project completion. He is responsible for defining the cohort and manages the researchers assigned to the project.
+**Researchers** retrieve research data from their assigned projects once the projects are approved and launched. Researchers have no influence on the project description, project application and cohort definition.
+All input fields marked with an asterisk are required to proceed. 
 
 ```{figure} images/sign_up_form_empty.png
 ---
@@ -58,4 +60,21 @@ In the next step click the activation link in the email, that has been sent to y
 
 ```{important}
 After your successful registration you can only see the portals welcome page until your account gets approved. The organization administrator responsible for you is automatically informed via email about your registration. However, the approval is a manual process due to security reasons and therefore can take some time. If you want to see how to approve user accounts go to the section [User management -> Unapproved users](../07_user_management/01_unapproved_users/01_unapproved_users.md)
-```
+```
+
+## Edit your user account
+
+You can always access your user account at the bottom left.
+
+```{figure} images/user_account.png
+---
+alt: 'User account view with details and password change option'
+---
+Fig 01-05: User account view
+```
+
+Within the user account page you can change your First name and your Last name, as well as the passwort by clicking on the "UPDATE PASSWORD" button.
+To save your updated credentials you need to click "SAVE CHANGES".
+
+Within this page you can see (but not change) your E-mail address, organization and current roles.
+
diff --git a/...gin_with_highlighted_register_link.de.png → ...gin_with_highlighted_register_link.de.png b/...gin_with_highlighted_register_link.de.png → ...gin_with_highlighted_register_link.de.png
diff --git a/...gin_with_highlighted_register_link.en.png → ...gin_with_highlighted_register_link.en.png b/...gin_with_highlighted_register_link.en.png → ...gin_with_highlighted_register_link.en.png
diff --git a/..._user/images/sign_up_confirm_email.de.png → ...count/images/sign_up_confirm_email.de.png b/..._user/images/sign_up_confirm_email.de.png → ...count/images/sign_up_confirm_email.de.png
diff --git a/..._user/images/sign_up_confirm_email.en.png → ...count/images/sign_up_confirm_email.en.png b/..._user/images/sign_up_confirm_email.en.png → ...count/images/sign_up_confirm_email.en.png
diff --git a/...ages/sign_up_confirm_email_success.de.png → ...ages/sign_up_confirm_email_success.de.png b/...ages/sign_up_confirm_email_success.de.png → ...ages/sign_up_confirm_email_success.de.png
diff --git a/...ages/sign_up_confirm_email_success.en.png → ...ages/sign_up_confirm_email_success.en.png b/...ages/sign_up_confirm_email_success.en.png → ...ages/sign_up_confirm_email_success.en.png
diff --git a/...ate_user/images/sign_up_email_hint.de.png → ..._account/images/sign_up_email_hint.de.png b/...ate_user/images/sign_up_email_hint.de.png → ..._account/images/sign_up_email_hint.de.png
diff --git a/...ate_user/images/sign_up_email_hint.en.png → ..._account/images/sign_up_email_hint.en.png b/...ate_user/images/sign_up_email_hint.en.png → ..._account/images/sign_up_email_hint.en.png
diff --git a/...ate_user/images/sign_up_form_empty.de.png → ..._account/images/sign_up_form_empty.de.png b/...ate_user/images/sign_up_form_empty.de.png → ..._account/images/sign_up_form_empty.de.png
diff --git a/...ate_user/images/sign_up_form_empty.en.png → ..._account/images/sign_up_form_empty.en.png b/...ate_user/images/sign_up_form_empty.en.png → ..._account/images/sign_up_form_empty.en.png
diff --git a/...ser/images/sign_up_with_open_modal.de.png → ...unt/images/sign_up_with_open_modal.de.png b/...ser/images/sign_up_with_open_modal.de.png → ...unt/images/sign_up_with_open_modal.de.png
diff --git a/...ser/images/sign_up_with_open_modal.en.png → ...unt/images/sign_up_with_open_modal.en.png b/...ser/images/sign_up_with_open_modal.en.png → ...unt/images/sign_up_with_open_modal.en.png
diff --git a/docs/01_user_account/images/user_account.de.png b/docs/01_user_account/images/user_account.de.png
diff --git a/docs/01_user_account/images/user_account.en.png b/docs/01_user_account/images/user_account.en.png
diff --git a/docs/03_search/01_patient_filter/01_patient_filter.md b/docs/03_search/01_patient_filter/01_patient_filter.md
@@ -20,7 +20,7 @@ alt: Screenshot of patient filter
 Fig 03-01-01: Patient filter
 ```
 
-#### 1. Criteria list
+#### 1 - Criteria list
 The various criteria are divided into categories, these can be expanded and collapsed. Detailed information on each individual criterion can be obtained by clicking on the *i* symbol.
 
 To use a criterion and add it to the cohort builder, click it's plus icon. The criterion is then inserted directly into the cohort builder in the active (red bordered) group.
@@ -42,7 +42,7 @@ alt: Screenshot of criteria details dialog
 Fig 03-01-03: Criteria detail view
 ```
 
-#### 2. Cohort builder
+#### 2 - Cohort builder
 
 In the cohort builder, the criteria are inserted in the order you selected/clicked them from the list.
 
@@ -98,7 +98,7 @@ There are also criteria that do not require the entry of parameters, these can b
 ```
 
 
-#### 3. Patients display
+#### 3 - Patients display
 
 This area shows the number of patients in the entire dataset resulting from the configuration of the cohort. To retrieve the patients, you must click the *Retrieve* button. The number of patients is then displayed. Depending on the authorization and if the data is available, the patients are also displayed in a graphical representation.
 

diff --git a/docs/04_projects/02_projects_editor/02_projects_editor.md b/docs/04_projects/02_projects_editor/02_projects_editor.md
@@ -154,8 +154,9 @@ Return parameters are mandatory, in order to save this project you must select a
 
 
 #### Researchers 
-The last section of the project screen is the researchers section, here researchers can be assigned to the project. By clicking the *Add researchers* button.
-
+Select the researchers who are allowed to research on your project by clicking the *Add researchers* button.
+After approval is granted and the project is started, researchers can retrieve data. 
+Even after the project has started, you can still customize the list of authorized researchers.
 
 ```{figure} images/project_researchers.png
 ---

diff --git a/docs/06_criteria/02_criteria_editor/02_criteria_editor.md b/docs/06_criteria/02_criteria_editor/02_criteria_editor.md
@@ -11,7 +11,7 @@ The criteria editor provides functionality to define a criterion, as well as to
 The general information section contains information about the criterion such as:
 
 
-| No  | Field                   | Mandatory |
+| No. | Field                   | Mandatory |
 |-----|-------------------------|-----------|
 | 1   | English title           | Yes       |
 | 2   | English use             | Yes       |

diff --git a/docs/07_user_management/03_available_roles/03_available_roles.md b/docs/07_user_management/03_available_roles/03_available_roles.md
@@ -2,13 +2,13 @@
 
 This section provides an overview of the roles that can be assigned and an indicator, if these are exclusive to the *Super Admin*.
 
-| Role               | Permissions                                   | Super Admin only |
-|--------------------|-----------------------------------------------|------------------|
-| Researcher         | Retrieve data from assigned projects          | No               |
-| Project Lead       | Create, edit and manage projects              | No               |
-| Project Approver   | Approve or deny project applications          | Yes              |
-| Organization Admin | Manage one organization and their users       | No               |
-| Content Editor     | Edit welcome page tiles                       | Yes              |
-| Criteria Editor    | Create and edit criteria                      | Yes              |
-| Manager            | Retrieve data, display exact patient counts   | Yes              |
-| Super Admin        | All permissions, managing all organizations   | Yes              |
+|  Role                |  Permissions                                                                                                                                                                                                                                 |  Super Admin only  |
+|:---------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------|
+|  Researcher          |  Researchers retrieve research data from their assigned projects once the projects are approved and launched. Researchers have no influence on the project description, project application and cohort definition.                           |  No                |
+|  Project Lead        |  The project lead creates new projects, describes them, and manages them through the application process to project completion. He is responsible for defining the cohort and manages the researchers assigned to the project.               |  No                |
+|  Project Approver    | <div>Project approvers have an overview of all projects in their own organization.&nbsp;</div><div>They can accept, revise or reject project proposals.</div>                                                                                |  Yes               |
+|  Organization Admin  | <div>The organization admins can manage their own organization and its users.</div><div>They approve new users, assign roles and can customize the organization's email domain.</div>                                                        |  No                |
+|  Content Editor      |  The content editors can edit the information tiles on the welcome page.                                                                                                                                                                     |  Yes               |
+|  Criteria Editor     |  The criteria editors manage the criteria within the projects that are unlocked for them. You customize criteria categories and create and modify General Specifications and AQL queries using the Criteria Editor.                          |  Yes               |
+|  Manager             |  Managers have access to data and patient search and analysis tools and can determine accurate patient counts.                                                                                                                               |  Yes               |
+|  Super Admin         | <div>The super admins have permissions to manage all users and organizations.</div>                                                                                                                                                          |  Yes               |  
diff --git a/docs/11_support/11_support.md b/docs/11_support/11_support.md
@@ -0,0 +1,4 @@
+# Support
+
+If you need support for using the platform, please contact:
+[email protected]
diff --git a/docs/_gettext/.doctrees/00_glossary/00_glossary.doctree b/docs/_gettext/.doctrees/00_glossary/00_glossary.doctree
diff --git a/docs/_gettext/.doctrees/01_create_user/01_create_user.doctree b/docs/_gettext/.doctrees/01_create_user/01_create_user.doctree
diff --git a/docs/_gettext/.doctrees/01_user_account/01_user_account.doctree b/docs/_gettext/.doctrees/01_user_account/01_user_account.doctree
diff --git a/docs/_gettext/.doctrees/02_welcome/02_welcome.doctree b/docs/_gettext/.doctrees/02_welcome/02_welcome.doctree
diff --git a/docs/_gettext/.doctrees/03_search/01_patient_filter/01_patient_filter.doctree b/docs/_gettext/.doctrees/03_search/01_patient_filter/01_patient_filter.doctree
diff --git a/docs/_gettext/.doctrees/03_search/02_data_filter/02_data_filter.doctree b/docs/_gettext/.doctrees/03_search/02_data_filter/02_data_filter.doctree
diff --git a/docs/_gettext/.doctrees/03_search/03_data_explorer/03_data_explorer.doctree b/docs/_gettext/.doctrees/03_search/03_data_explorer/03_data_explorer.doctree
diff --git a/docs/_gettext/.doctrees/03_search/03_search.doctree b/docs/_gettext/.doctrees/03_search/03_search.doctree
diff --git a/docs/_gettext/.doctrees/04_projects/01_projects_overview/01_projects_overview.doctree b/docs/_gettext/.doctrees/04_projects/01_projects_overview/01_projects_overview.doctree
diff --git a/docs/_gettext/.doctrees/04_projects/02_projects_editor/02_projects_editor.doctree b/docs/_gettext/.doctrees/04_projects/02_projects_editor/02_projects_editor.doctree
diff --git a/docs/_gettext/.doctrees/04_projects/04_projects.doctree b/docs/_gettext/.doctrees/04_projects/04_projects.doctree
diff --git a/...ta_explorer/01_data_explorer_projects_overview/01_data_explorer_projects_overview.doctree b/...ta_explorer/01_data_explorer_projects_overview/01_data_explorer_projects_overview.doctree
diff --git a/.../05_data_explorer/02_data_explorer_data_retrieval/02_data_explorer_data_retrieval.doctree b/.../05_data_explorer/02_data_explorer_data_retrieval/02_data_explorer_data_retrieval.doctree
diff --git a/docs/_gettext/.doctrees/05_data_explorer/05_data_explorer.doctree b/docs/_gettext/.doctrees/05_data_explorer/05_data_explorer.doctree
diff --git a/docs/_gettext/.doctrees/06_criteria/01_criteria_overview/01_criteria_overview.doctree b/docs/_gettext/.doctrees/06_criteria/01_criteria_overview/01_criteria_overview.doctree
diff --git a/docs/_gettext/.doctrees/06_criteria/02_criteria_editor/02_criteria_editor.doctree b/docs/_gettext/.doctrees/06_criteria/02_criteria_editor/02_criteria_editor.doctree
diff --git a/docs/_gettext/.doctrees/06_criteria/03_criteria_categories/03_criteria_categories.doctree b/docs/_gettext/.doctrees/06_criteria/03_criteria_categories/03_criteria_categories.doctree
diff --git a/docs/_gettext/.doctrees/06_criteria/06_criteria.doctree b/docs/_gettext/.doctrees/06_criteria/06_criteria.doctree
diff --git a/docs/_gettext/.doctrees/07_user_management/01_unapproved_users/01_unapproved_users.doctree b/docs/_gettext/.doctrees/07_user_management/01_unapproved_users/01_unapproved_users.doctree
diff --git a/docs/_gettext/.doctrees/07_user_management/02_approved_users/02_approved_users.doctree b/docs/_gettext/.doctrees/07_user_management/02_approved_users/02_approved_users.doctree
diff --git a/docs/_gettext/.doctrees/07_user_management/03_available_roles/03_available_roles.doctree b/docs/_gettext/.doctrees/07_user_management/03_available_roles/03_available_roles.doctree
diff --git a/docs/_gettext/.doctrees/07_user_management/07_user_management.doctree b/docs/_gettext/.doctrees/07_user_management/07_user_management.doctree
diff --git a/...xt/.doctrees/08_organizations/01_organizations_overview/01_organizations_overview.doctree b/...xt/.doctrees/08_organizations/01_organizations_overview/01_organizations_overview.doctree
diff --git a/...ettext/.doctrees/08_organizations/02_organizations_editor/02_organizations_editor.doctree b/...ettext/.doctrees/08_organizations/02_organizations_editor/02_organizations_editor.doctree
diff --git a/docs/_gettext/.doctrees/08_organizations/08_organizations.doctree b/docs/_gettext/.doctrees/08_organizations/08_organizations.doctree
diff --git a/...s/09_content_editor/01_content_editor_welcome_page/01_content_editor_welcome_page.doctree b/...s/09_content_editor/01_content_editor_welcome_page/01_content_editor_welcome_page.doctree
diff --git a/...octrees/09_content_editor/02_content_editor_nav_items/02_content_editor_nav_items.doctree b/...octrees/09_content_editor/02_content_editor_nav_items/02_content_editor_nav_items.doctree
diff --git a/docs/_gettext/.doctrees/09_content_editor/09_content_editor.doctree b/docs/_gettext/.doctrees/09_content_editor/09_content_editor.doctree
diff --git a/docs/_gettext/.doctrees/10_manager_tools/10_manager_tools.doctree b/docs/_gettext/.doctrees/10_manager_tools/10_manager_tools.doctree
diff --git a/docs/_gettext/.doctrees/11_support/11_support.doctree b/docs/_gettext/.doctrees/11_support/11_support.doctree
diff --git a/docs/_gettext/.doctrees/environment.pickle b/docs/_gettext/.doctrees/environment.pickle
diff --git a/docs/_gettext/.doctrees/index.doctree b/docs/_gettext/.doctrees/index.doctree
diff --git a/docs/_gettext/00_glossary/00_glossary.pot b/docs/_gettext/00_glossary/00_glossary.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: NUM CODEX 1.9.0\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2022-11-16 13:15+0100\n"
+"POT-Creation-Date: 2023-02-21 12:47+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <[email protected]>\n"

diff --git a/docs/_gettext/01_create_user/01_create_user.pot b/docs/_gettext/01_create_user/01_create_user.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: NUM CODEX 1.9.0\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2022-11-15 16:01+0100\n"
+"POT-Creation-Date: 2023-03-01 12:25+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <[email protected]>\n"
@@ -57,56 +57,56 @@ msgid "Fig 01-01: Position of the register link on Login page"
 msgstr ""
 
 #: ../01_create_user/01_create_user.md:25
-#: adc62f3862de498f97acf390e956409a
-msgid "At the Signup page you will see a form to enter your basic data. All input fields marked with an asterisk are required to proceed."
+#: 216a952f95b14250b0b6e2d39f0bdfcb
+msgid "At the Signup page you will see a form to enter your basic data.  The **project lead** creates new projects, describes them, and manages them through the application process to project completion. He is responsible for defining the cohort and manages the researchers assigned to the project. **Researchers** retrieve research data from their assigned projects once the projects are approved and launched. Researchers have no influence on the project description, project application and cohort definition. All input fields marked with an asterisk are required to proceed."
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:32
+#: ../01_create_user/01_create_user.md:34
 #: 98557297d6a243e5a8890c405639a80e
 msgid "Sign up page with an empty form for first name, last name, email address, password, password confirm, role, department and additional infos and a checkbox for accepting terms and conditions"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:32
+#: ../01_create_user/01_create_user.md:34
 #: 2033f7dad1db4ac7885008b60e5427ef
 msgid "Fig 01-02: An emtpy Sign up form on initial page visit"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:35
+#: ../01_create_user/01_create_user.md:37
 #: ed4651da5a9b4696b1cc952691610438
 msgid "Additionally you have to aggree with the terms and conditions. If you want to read the terms and conditions you can click the link which opens an overlay with the current version of our terms and conditions that you also can directly accept or decline."
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:43
+#: ../01_create_user/01_create_user.md:45
 #: 20d65b0fd5f247feb8ecd2e66102dacf
 msgid "Sign up page with opened terms and conditions modal with to buttons to accept or decline the terms and conditions at the bottom"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:43
+#: ../01_create_user/01_create_user.md:45
 #: 809afd3156754c7fb3a3628865a2cbc4
 msgid "Fig 01-03: Open Terms and Conditions overlay modal"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:46
+#: ../01_create_user/01_create_user.md:48
 #: d943d3ca7f344b90802907c0fb83f90b
 msgid "Once you have filled out all information about your person and your login information an email will be sent to your provided email address. If the email has been sent to your inbox you will see the following screen:"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:54
+#: ../01_create_user/01_create_user.md:56
 #: 3426ed8120d8474384af4f978d461708
 msgid "After sign up page which informs about a sent email the user should check"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:54
+#: ../01_create_user/01_create_user.md:56
 #: 61d459da9aff41799ad6cd065ce8f4a7
 msgid "Fig 01-04: Hint on sent email to confirm registration"
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:57
+#: ../01_create_user/01_create_user.md:59
 #: f39dca41efb5426ab0c590267a618b0e
 msgid "In the next step click the activation link in the email, that has been sent to you within 5 minutes to activate your account. If you do not get the email or manage to click the link within 5 minutes, you can always resend the email via the page shown above by clicking on the respective link. If you already closed the page, you can log into the portal with the credentials you provided in the registration process (email and password) to see the page again."
 msgstr ""
 
-#: ../01_create_user/01_create_user.md:60
+#: ../01_create_user/01_create_user.md:62
 #: 5765264328054131b17faa8e2ef353aa
 msgid "After your successful registration you can only see the portals welcome page until your account gets approved. The organization administrator responsible for you is automatically informed via email about your registration. However, the approval is a manual process due to security reasons and therefore can take some time. If you want to see how to approve user accounts go to the section [User management -> Unapproved users](../07_user_management/01_unapproved_users/01_unapproved_users.md)"
 msgstr ""