From 097d7f72cc1374ba4e2ff2c0ca5fb38cc4638639 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:56:10 +0200 Subject: [PATCH 1/8] Remove questionnaire feedback settings docs --- .../settings/content/projects.rst | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/docs/applications/data-management-planner/settings/content/projects.rst b/docs/applications/data-management-planner/settings/content/projects.rst index c9eafdb..bd61ee0 100644 --- a/docs/applications/data-management-planner/settings/content/projects.rst +++ b/docs/applications/data-management-planner/settings/content/projects.rst @@ -52,16 +52,6 @@ We can turn **Summary Report** on or off. It is a feature that allows users to g The **Summary Report** shows how many questions are answered and unanswered in each chapter. It can either count all questions in the knowledge model or only the questions required for the project's current phase. Questions from later phases are ignored in the phase-based view. If a parent question is unanswered, its child questions are not counted separately. Chapter results are combined into the total **Summary Report**. -Feedback -======== - -If enabled, users can submit feedback for questions to a configured GitHub repository. The configuration includes the **GitHub Repository Owner**, **GitHub Repository Name**, and **Access Token**. - -.. NOTE:: - - The **Access Token** value is encrypted in the database. - - Project Tagging =============== From a619851046ee902225f5b8c75ec93955130fd888 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:56:41 +0200 Subject: [PATCH 2/8] Document package metadata and selector IDs --- .../data-management-planner/document-templates/list/detail.rst | 2 +- .../data-management-planner/knowledge-models/list/detail.rst | 2 +- .../data-management-planner/projects/list/create.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/applications/data-management-planner/document-templates/list/detail.rst b/docs/applications/data-management-planner/document-templates/list/detail.rst index 856e87d..f2c068a 100644 --- a/docs/applications/data-management-planner/document-templates/list/detail.rst +++ b/docs/applications/data-management-planner/document-templates/list/detail.rst @@ -1,7 +1,7 @@ Document Template Detail ************************ -We can check a document template detail by clicking on a desired template in the :doc:`./index` (or selecting :guilabel:`View detail` from the right dropdown). The detail shows basic information about the template such as its name, ID, version, license, metamodel version, or supported document formats. +We can check a document template detail by clicking on a desired template in the :doc:`./index` (or selecting :guilabel:`View detail` from the right dropdown). The detail shows basic information about the template such as its name, ID, version, license, metamodel version, creation date, or supported document formats. The main part of the detail is the README of the template that should contain basic information and changelog for the template. In the right panel under the basic information, we can navigate to other versions of the document template, navigate to the `FAIR Wizard Registry `__ (if the template is present there), or check compatible knowledge model with the template. diff --git a/docs/applications/data-management-planner/knowledge-models/list/detail.rst b/docs/applications/data-management-planner/knowledge-models/list/detail.rst index cdcd4bc..92c0628 100644 --- a/docs/applications/data-management-planner/knowledge-models/list/detail.rst +++ b/docs/applications/data-management-planner/knowledge-models/list/detail.rst @@ -3,7 +3,7 @@ Knowledge Model Detail ********************** -We can visit a knowledge model detail by clicking on a desired KM in the :doc:`./index` (or selecting :guilabel:`View detail` from the right item menu). The detail shows basic information about the knowledge model such as its name, ID, version, license, metamodel version, or (if applicable) what is the parent knowledge model. +We can visit a knowledge model detail by clicking on a desired KM in the :doc:`./index` (or selecting :guilabel:`View detail` from the right item menu). The detail shows basic information about the knowledge model such as its name, ID, version, license, metamodel version, creation date, or (if applicable) what is the parent knowledge model. The main part of the detail is the README of the KM that should contain basic information and changelog. In the right panel under the basic information, we can navigate to other versions of the KM or navigate to the `FAIR Wizard Registry `__ (if the KM is present there). diff --git a/docs/applications/data-management-planner/projects/list/create.rst b/docs/applications/data-management-planner/projects/list/create.rst index 6597f77..0e46533 100644 --- a/docs/applications/data-management-planner/projects/list/create.rst +++ b/docs/applications/data-management-planner/projects/list/create.rst @@ -34,7 +34,7 @@ So if there are any project templates created in our instance, we can use them t Custom ====== -If there are no project templates available or we don't want to use them, we can choose to create a custom project. We need to give our project a **name** again, but this time we choose a :ref:`knowledge model` from offered options. +If there are no project templates available or we don't want to use them, we can choose to create a custom project. We need to give our project a **name** again, but this time we choose a :ref:`knowledge model` from offered options. The knowledge model selector shows the full knowledge model ID to help distinguish similarly named knowledge models. If the knowledge model has :ref:`question tags`, we can either choose to create questionnaire with all available questions or filter them by the question tags. From abfa1160f31bc3b58dc988df627f56c6d54fda88 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:56:53 +0200 Subject: [PATCH 3/8] Document KM comparison and custom integration replies --- .../data-management-planner/knowledge-models/list/compare.rst | 3 +-- .../projects/list/detail/questionnaire.rst | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/applications/data-management-planner/knowledge-models/list/compare.rst b/docs/applications/data-management-planner/knowledge-models/list/compare.rst index a846ee5..ae3d131 100644 --- a/docs/applications/data-management-planner/knowledge-models/list/compare.rst +++ b/docs/applications/data-management-planner/knowledge-models/list/compare.rst @@ -5,9 +5,8 @@ Knowledge Model Compare We can compare two versions of a knowledge model by clicking :guilabel:`Compare` from the right item menu (three dots) of a specific KM in the :doc:`./index` or from KM :doc:`./detail`. This will open a new page where we can select another KM to compare with. The comparison will show the differences between the two versions, including changes in the name, description, as well as changes in the structure of the KM (e.g. added or removed entities, attributes, etc.). -The comparison can be starter in project migration and in KM list and detail. +The comparison can be started in project migration and in KM list and detail. When we select an item in the comparison, the side panel shows its details, including the UUID. We can use the copy button next to the UUID to copy it. .. TODO:: Add screenshot - diff --git a/docs/applications/data-management-planner/projects/list/detail/questionnaire.rst b/docs/applications/data-management-planner/projects/list/detail/questionnaire.rst index 9472b04..d4c27cd 100644 --- a/docs/applications/data-management-planner/projects/list/detail/questionnaire.rst +++ b/docs/applications/data-management-planner/projects/list/detail/questionnaire.rst @@ -128,7 +128,7 @@ Integration Question Integration question is connected to an external resource where it searches for the answers. The input field works as a search field, so when we start typing something, it will search the external resource and offers us a list of possible answers. -When we pick an answer from the list, we not only have the answer but also **a link to the selected item in the external service**. If the answer we searched for is not there, we can simply keep what we have written in the input field. We just won't have the link with this answer. +When we pick an answer from the list, we not only have the answer but also **a link to the selected item in the external service**. If custom replies are allowed and the answer we searched for is not there, we can simply keep what we have written in the input field. We just won't have the link with this answer. FAIR Wizard marks this as a custom answer, not selected from the integration. .. figure:: questionnaire/integration-question.png @@ -336,4 +336,3 @@ We can click on any of the search results to quickly navigate to that question i :width: 600 Search panel shows all matching questions, answers and other content in real-time. - From e35b54e379c0ee514390452a2b7bf3290560daa1 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:57:07 +0200 Subject: [PATCH 4/8] Update project sharing behavior --- .../data-management-planner/projects/list/detail/sharing.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/applications/data-management-planner/projects/list/detail/sharing.rst b/docs/applications/data-management-planner/projects/list/detail/sharing.rst index 4aa58d4..e54c398 100644 --- a/docs/applications/data-management-planner/projects/list/detail/sharing.rst +++ b/docs/applications/data-management-planner/projects/list/detail/sharing.rst @@ -24,9 +24,9 @@ If we want to only see how sharing is set up or copy the project link, we can us Fast project sharing. -.. NOTE:: +Changes made in the sharing modal are saved after clicking :guilabel:`Save`. We can close the modal without saving by clicking :guilabel:`Cancel`. - When sharing settings are changed, the changes are saved automatically. +When we search for users to add to project sharing, FAIR Wizard also shows user affiliation when it is available. There are different project sharing roles that grant access to different project features: From 76dcd4b501ab4a3eaccc8adef227f137237c8aa0 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:57:20 +0200 Subject: [PATCH 5/8] Update project migration and update indicators --- .../projects/list/detail/settings.rst | 10 ++-- .../projects/list/index.rst | 13 +++-- .../projects/list/migration.rst | 47 ++++--------------- 3 files changed, 21 insertions(+), 49 deletions(-) diff --git a/docs/applications/data-management-planner/projects/list/detail/settings.rst b/docs/applications/data-management-planner/projects/list/detail/settings.rst index ce864b2..bd41531 100644 --- a/docs/applications/data-management-planner/projects/list/detail/settings.rst +++ b/docs/applications/data-management-planner/projects/list/detail/settings.rst @@ -22,7 +22,11 @@ Next, we have **Project Tags**. These can be used for providing some metadata or Default Document Template ========================= -We can set a **default document template** and a **default document format**. These are then used in the :ref:`preview` tab and also pre-selected when creating a :ref:`new document`. +We can set a **default document template** and a **default document format**. These are then used in the :ref:`preview` tab and also pre-selected when creating a :ref:`new document`. The document template selector shows the full document template ID to help distinguish similarly named templates. + +If a newer version of the selected document template is available, FAIR Wizard shows a warning in this section. If the selected template or format is no longer compatible with the project's knowledge model, choose a compatible template and format before saving the settings. + +:guilabel:`Unsupported metamodel` badge can appear when the document template is not compatible with the version of FAIR Wizard. Users should contact the person responsible for document templates or instance administration in this case. Project Template @@ -35,8 +39,6 @@ We can use the project as a :ref:`project template`. If we en Project template options are visible only for users with the :ref:`Manage Project Templates` role permission. -:guilabel:`Unsupported metamodel` badge can appear, when the document template is not compatible with the version of FAIR Wizard. Users should contact the person responsible for document templates or instance administration in this case. - Questionnaire Language ====================== @@ -47,7 +49,7 @@ Changing the questionnaire language changes the knowledge model texts shown in t Knowledge Model =============== -We can see the :ref:`knowledge model` and its tags used for creating the project. If we want to change that, we can simply create a :ref:`project migration`. +We can see the :ref:`knowledge model` and its tags used for creating the project. If a newer version of the knowledge model is available, FAIR Wizard shows a warning in this section. If we want to change the knowledge model, its version, or the selected tags, we can use :ref:`project migration`. Danger Zone diff --git a/docs/applications/data-management-planner/projects/list/index.rst b/docs/applications/data-management-planner/projects/list/index.rst index 9aaaaca..e1e8acd 100644 --- a/docs/applications/data-management-planner/projects/list/index.rst +++ b/docs/applications/data-management-planner/projects/list/index.rst @@ -5,7 +5,10 @@ Project List In the project list, we can see a list of all projects we have access to. Those are the projects where we were assigned to with any role or that are visible by all other logged-in users in the :ref:`project sharing settings`. The projects are filtered to those we are explicitly assigned to by default. -We can see projects name, label :guilabel:`Template` if the project is a template, and icon indicating sharing settings: +We can see project names, label :guilabel:`Template` if the project is a template, update badges, and icons indicating sharing settings: + +- **Outdated KM** - the project uses a knowledge model with a newer version available +- **Outdated DT** - the project uses a document template with a newer version available - **Lock icon** - the project can be only accessed by you - **People icon** - the project is shared with other users, hovering on the icon provides additional information @@ -22,6 +25,7 @@ We can search for specific projects using the search field or filter them using - **Project Tags** - show only the projects that has specific tags assigned - **Knowledge Models** - show only the projects created from a specific knowledge model - **Users** - filter only the projects with specific users assigned to them +- **User Groups** - show only the projects shared with specific user groups, available when Admin Center is enabled .. NOTE:: @@ -35,14 +39,9 @@ By clicking the triple dots on each of the item in the list we can access some a - **Open project** - will simply open the project - **Create project from this template** - will create a new project from the selected project template (this is only available if the project is also a project template) - **Clone** - will create the exact copy of the project -- **Create migration** - will start a :ref:`project migration` +- **Migrate** - will start a :ref:`project migration` - **Delete** - will delete the project (this action cannot be undone) -If there is an ongoing :ref:`project migration`, there are different actions: - -- **Continue migration** - to come back to the ongoing project migration -- **Cancel migration** - to cancel the ongoing project migration - .. raw:: html

Table of Contents

diff --git a/docs/applications/data-management-planner/projects/list/migration.rst b/docs/applications/data-management-planner/projects/list/migration.rst index d4e1aca..6c573eb 100644 --- a/docs/applications/data-management-planner/projects/list/migration.rst +++ b/docs/applications/data-management-planner/projects/list/migration.rst @@ -3,54 +3,25 @@ Project Migration ***************** -Every project is based on a specific :ref:`knowledge model`, its version, and selected tags. Sometimes, we might want to change the knowledge model to a different version (for example, when a new version is released), change the knowledge model (for example, when a new customization is created), or just change the tag selection. Project migration is a process where we can do this. +Every project is based on a specific :ref:`knowledge model`, its version, and selected tags. Sometimes, we might want to change the knowledge model to a different version, change the knowledge model, or just change the tag selection. Project migration is a process where we can do this. -Watch this video to learn more about project migration: +Migrating a Project +=================== -.. youtube:: 536IqCCfLyk - :width: 100% - :align: center - - -Creating a Project Migration -============================ - -We can start a project migration either from the :ref:`project list`, or from the :ref:`project settings`. Sometimes, when there is a newer version of the knowledge model available, we can see a yellow :guilabel:`update available` badge next to the project name. We can click on the badge to start the migration as well. +We can start a project migration either from the :ref:`project list` or from the :ref:`project settings`. When a newer version of the knowledge model is available, we can see an :guilabel:`Outdated KM` badge next to the project name in the project list. .. figure:: migration/create.png - Choosing a new knowledge model for the project when creating a project migration. - - -We can see the **original knowledge model**, its **version**, and selected **question tags** on the left side. On the right side we can choose new values for all of these. After we are satisfied with our selection we can click on :guilabel:`Create` button. - -Note that the original project will remain unchanged until the migration is finished. So we can cancel it anytime before it is finished without affecting the project. - -Project Migration -================= - -The next screen is the project migration itself. We can go through all the changes between the original and the new knowledge model that affects our answers. During this process, we can also add :ref:`todos` if we want to come back to a specific question later, after the migration. - -.. figure:: migration/migration.png - - Reviewing changes during the project migration. + Choosing a new knowledge model for the project. -It is possible that there are no changes to review. This can happen when we don't have all the answers in the questionnaire yet and those we have are not affected by the changes, i.e., all of the questions that we answered are in the original and in the new knowledge model. +We can see the **original knowledge model**, its **version**, and selected **question tags** on the left side. On the right side, we can choose new values for all of these. We can use :guilabel:`Compare` to check the changes between the original and selected knowledge model. -We can leave the migration at any point now and come back to it later. We will see the project twice in the :ref:`project list`, one of them tagged with :guilabel:`migrating` badge. If we open the migrating one (either by clicking the project name or the :guilabel:`migrating` badge), we can come back to the project migration. If we open the other one, we can access the original project, however, only in the read-only mode until the migration is finished or cancelled. +After we are satisfied with our selection, we can click :guilabel:`Migrate`. This updates the project to the selected knowledge model version and tag selection. .. WARNING:: - Named versions are migrated together with the project to new versions of the knowledge model. However it might happen that questions or answers are removed in the new version of the knowledge model. In that case, the named version will not be migrated and will be lost. - - -Cancelling a Project Migration -============================== - -At any point before we finalize the migration, we can decide that we actually don't want to do the migration. We can simply navigate to the :ref:`project list` and choose the :guilabel:`Cancel migration` action on the project tagged with :guilabel:`migrating` badge. This will cancel the migration and the original project will remain unaffected. + Replies associated with questions that are not included in the new project may not be carried over. This can happen when questions or answers were removed in the new knowledge model version or when the selected question tags change which questions are included. -Finishing a Project Migration -============================= -After we resolve all the changes (or if there are no changes to review), we can click on :guilabel:`Finalize migration`. This will complete the project migration applying all the knowledge model changes, and unlocking the project from the read-only mode. \ No newline at end of file +After migrating, the default document template or format may need to be selected again in :ref:`project settings` if the previous selection is no longer compatible with the project's knowledge model. From 1d33b8fe7a28ce19c5481cb8ea857183a3cda937 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 08:57:35 +0200 Subject: [PATCH 6/8] Document MCP role permission and news filtering --- docs/applications/admin-center/settings/system/roles.rst | 3 +++ docs/applications/data-management-planner/profile/news.rst | 3 +-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/applications/admin-center/settings/system/roles.rst b/docs/applications/admin-center/settings/system/roles.rst index 17a55ab..cc00d9c 100644 --- a/docs/applications/admin-center/settings/system/roles.rst +++ b/docs/applications/admin-center/settings/system/roles.rst @@ -77,6 +77,9 @@ The role create/edit form includes these permissions: * - **Use Integration Hub** - Access the Integration Hub and create Value Integrations. - None. + * - **Connect MCP Servers** + - Connect AI assistants using MCP servers to the user's account. + - None. * - **Use Audit Log** - View the Audit Log. - None. diff --git a/docs/applications/data-management-planner/profile/news.rst b/docs/applications/data-management-planner/profile/news.rst index de1e658..026e10d 100644 --- a/docs/applications/data-management-planner/profile/news.rst +++ b/docs/applications/data-management-planner/profile/news.rst @@ -3,10 +3,9 @@ What's New ********** -By selecting the :guilabel:`What's New` option from the :doc:`./index` menu, we can open the News modal. There, we can find information about the most notable updates and changes in FAIR Wizard for each version. +By selecting the :guilabel:`What's New` option from the :doc:`./index` menu, we can open the News modal. There, we can find information about the most notable updates and changes in FAIR Wizard for each version. News can be tailored to role permissions, so users may see entries relevant to features they can access. .. figure:: news/modal.png :width: 500 News modal. - From 13a3ff077c1384ec051203d3fc2bf71652180cf8 Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 09:11:11 +0200 Subject: [PATCH 7/8] Update docs dependencies --- docs/requirements.direct.txt | 1 - docs/requirements.txt | 47 +++++++++--------------------------- 2 files changed, 12 insertions(+), 36 deletions(-) diff --git a/docs/requirements.direct.txt b/docs/requirements.direct.txt index 9124053..5d8ec64 100644 --- a/docs/requirements.direct.txt +++ b/docs/requirements.direct.txt @@ -2,7 +2,6 @@ furo Sphinx sphinx-notfound-page sphinx-prompt -sphinx-toolbox sphinx-reredirects Sphinx-Substitution-Extensions sphinxcontrib-youtube diff --git a/docs/requirements.txt b/docs/requirements.txt index 79d0122..925ddd1 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,57 +1,38 @@ accessible-pygments==0.0.5 alabaster==1.0.0 -anyio==4.9.0 -apeye==1.4.1 -apeye-core==1.1.5 -autodocsumm==0.2.15 +anyio==4.15.0 babel==2.18.0 beartype==0.22.9 beautifulsoup4==4.15.0 -CacheControl==0.14.4 certifi==2026.7.22 -charset-normalizer==3.4.9 -click==8.2.1 +charset-normalizer==3.5.1 +click==8.5.0 colorama==0.4.6 -dict2css==0.6.0 docutils==0.22.4 -domdf_python_tools==3.10.0 -filelock==3.32.2 furo==2025.12.19 h11==0.16.0 -html5lib==1.1 -idna==3.18 -imagesize==2.0.0 +idna==3.19 +imagesize==2.0.1 Jinja2==3.1.6 markdown-it-py==4.2.0 MarkupSafe==3.0.3 mdit-py-plugins==0.6.1 mdurl==0.1.2 -msgpack==1.2.1 myst-parser==5.1.0 -natsort==8.4.0 packaging==26.3 -platformdirs==4.11.0 -Pygments==2.20.0 +Pygments==2.21.0 PyYAML==6.0.3 requests==2.34.2 -roman==5.2 roman-numerals==4.1.0 -ruamel.yaml==0.19.1 -six==1.17.0 -sniffio==1.3.1 snowballstemmer==3.1.1 -soupsieve==2.9.1 +soupsieve==2.9.2 Sphinx==9.1.0 -sphinx-autobuild==2024.10.3 -sphinx-autodoc-typehints==3.5.2 +sphinx-autobuild==2025.8.25 sphinx-basic-ng==1.0.0b2 -sphinx-jinja2-compat==0.4.1 sphinx-notfound-page==1.1.0 sphinx-prompt==1.10.2 sphinx-reredirects==1.1.0 -sphinx-substitution-extensions==2026.8.2 -sphinx-tabs==3.5.0 -sphinx-toolbox==4.3.0 +sphinx-substitution-extensions==2026.8.13.1 sphinxcontrib-applehelp==2.0.0 sphinxcontrib-devhelp==2.0.0 sphinxcontrib-htmlhelp==2.1.0 @@ -59,13 +40,9 @@ sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 sphinxcontrib-youtube==1.5.0 -starlette==0.46.2 -standard-imghdr==3.10.14 -tabulate==0.10.0 -tinycss2==1.5.1 +starlette==1.6.0 typing_extensions==4.16.0 urllib3==2.7.0 -uvicorn==0.34.3 +uvicorn==0.52.4 watchfiles==1.2.0 -webencodings==0.5.1 -websockets==15.0.1 +websockets==17.1 From c9abf264bc2556fd5aafa8310b26b651bd6345df Mon Sep 17 00:00:00 2001 From: krystofkomanec Date: Fri, 4 Sep 2026 09:21:11 +0200 Subject: [PATCH 8/8] 4.34 --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 9855056..6644784 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -22,7 +22,7 @@ author = 'FAIR Wizard Team' # The full version, including alpha/beta/rc tags -version = release = '4.33' +version = release = '4.34' rst_prolog = f"""