Merge pull request #84 from mercure-imaging/new-docs

Merge of updated docs
mercure-imaging · Nov 25, 2024 · a192850 · a192850
2 parents 21fd252 + 7ec1065
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diff --git a/docs/conf.py b/docs/conf.py
@@ -9,9 +9,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'mercure'
-copyright = '2019-2023 The "mercure" authors and contributors'
+copyright = '2019-2024 The "mercure" authors and contributors'
 author = ''
-
 def read_version() -> str:
     current_version = "0.0.0"
     version_filepath = os.path.dirname(os.path.realpath(__file__)) + '/../VERSION'
@@ -61,7 +60,7 @@ def read_version() -> str:
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/docs/dashboards.rst b/docs/dashboards.rst
@@ -20,7 +20,7 @@ The health of a mercure server can be monitored using Graphite for data collecti
 
 The diagram shown in the top-left utilizes the data transmitted by the mercure services during each run. If one of the colored blocks disappears for a longer period of time, it indicates that the process might be hanging. Useful are also the other diagrams in the top row, showing pending files and series in the incoming folder as reported by the router module, which can indicate if the server is not able to keep up with the load created by the scanners.
 
-.. image:: dashboards_graphite.png
+.. image:: /images/dashboards/graphite.png
    :width: 550px
    :align: center
    :class: border
@@ -32,7 +32,7 @@ Dispatch Explorer
 
 The Redash dashboard "Dispatch Explorer" allows showing which patient series have been dispatched to a selected target in a selectable time frame. It links to the "Series Events" dashboard that summarizes all information collected for a particular series.
 
-.. image:: dashboards_dispatchexplorer.png
+.. image:: /images/dashboards/dispatchexplorer.png
    :width: 550px
    :align: center
    :class: border
@@ -89,7 +89,7 @@ Last Series Received
 
 The dashboard "Last Series Received" shows the time when the last series from any imaging device has been received. It can be used to detect if there are problems with the DICOM transfer from one of the scanners. The query can be easily modified to provide a trigger for automatic alerts.
 
-.. image:: dashboards_lastseriesreceived.png
+.. image:: /images/dashboards/lastseriesreceived.png
    :width: 550px
    :align: center
    :class: border
@@ -118,7 +118,7 @@ Received Series
 
 The "Received Series" dashboard shows all series that have been received by the router in descending chronological order, with links to the "Series Events" dashboard for details on the series. Using the UI controls on top of the dashboard, series can be searched by patient name, MRN, ACC, and modality.
 
-.. image:: dashboards_receivedseries.png
+.. image:: /images/dashboards/receivedseries.png
    :width: 550px
    :align: center
    :class: border
@@ -176,7 +176,7 @@ Series Events
 
 The "Series Events" dashboard shows all information collected for a particular series, including DICOM tag information on the left side and a journal of how this series has been processed on the right side.
 
-.. image:: dashboards_seriesevents.png
+.. image:: /images/dashboards/seriesevents.png
    :width: 550px
    :align: center
    :class: border
@@ -256,7 +256,7 @@ System Status
 
 The "System Status" dashboard shows all system and webgui events in descending chronological order. Moreover, it shows all error events in the top-right table.
 
-.. image:: dashboards_systemstatus.png
+.. image:: /images/dashboards/systemstatus.png
    :width: 550px
    :align: center
    :class: border

diff --git a/docs/dashboards_dispatchexplorer.png → docs/images/dashboards/dispatchexplorer.png b/docs/dashboards_dispatchexplorer.png → docs/images/dashboards/dispatchexplorer.png
diff --git a/docs/dashboards_graphite.png → docs/images/dashboards/graphite.png b/docs/dashboards_graphite.png → docs/images/dashboards/graphite.png
diff --git a/docs/dashboards_lastseriesreceived.png → .../images/dashboards/lastseriesreceived.png b/docs/dashboards_lastseriesreceived.png → .../images/dashboards/lastseriesreceived.png
diff --git a/docs/dashboards_receivedseries.png → docs/images/dashboards/receivedseries.png b/docs/dashboards_receivedseries.png → docs/images/dashboards/receivedseries.png
diff --git a/docs/dashboards_seriesevents.png → docs/images/dashboards/seriesevents.png b/docs/dashboards_seriesevents.png → docs/images/dashboards/seriesevents.png
diff --git a/docs/dashboards_systemstatus.png → docs/images/dashboards/systemstatus.png b/docs/dashboards_systemstatus.png → docs/images/dashboards/systemstatus.png
diff --git a/docs/header.jpg → docs/images/header.jpg b/docs/header.jpg → docs/images/header.jpg
diff --git a/docs/mercure_logo_w.png → docs/images/mercure_logo_w.png b/docs/mercure_logo_w.png → docs/images/mercure_logo_w.png
diff --git a/docs/scheme.png → docs/images/scheme.png b/docs/scheme.png → docs/images/scheme.png
diff --git a/docs/ui_log.png → docs/images/ui/log.png b/docs/ui_log.png → docs/images/ui/log.png
diff --git a/docs/ui_login.png → docs/images/ui/login.png b/docs/ui_login.png → docs/images/ui/login.png
diff --git a/docs/images/ui/module_add.png b/docs/images/ui/module_add.png
diff --git a/docs/images/ui/module_edit.png b/docs/images/ui/module_edit.png
diff --git a/docs/images/ui/modules.png b/docs/images/ui/modules.png
diff --git a/docs/images/ui/query.png b/docs/images/ui/query.png
diff --git a/docs/ui_queue.png → docs/images/ui/queue.png b/docs/ui_queue.png → docs/images/ui/queue.png
diff --git a/docs/ui_queue_processing.png → docs/images/ui/queue_processing.png b/docs/ui_queue_processing.png → docs/images/ui/queue_processing.png
diff --git a/docs/images/ui/rules/edit.png b/docs/images/ui/rules/edit.png
diff --git a/docs/ui_rules_edit_information.png → docs/images/ui/rules/edit_information.png b/docs/ui_rules_edit_information.png → docs/images/ui/rules/edit_information.png
diff --git a/docs/images/ui/rules/edit_notification.png b/docs/images/ui/rules/edit_notification.png
diff --git a/docs/images/ui/rules/edit_processing.png b/docs/images/ui/rules/edit_processing.png
diff --git a/docs/images/ui/rules/edit_routing.png b/docs/images/ui/rules/edit_routing.png
diff --git a/docs/ui_rules_edit_trigger.png → docs/images/ui/rules/edit_trigger.png b/docs/ui_rules_edit_trigger.png → docs/images/ui/rules/edit_trigger.png
diff --git a/docs/images/ui/rules/rules.png b/docs/images/ui/rules/rules.png
diff --git a/docs/ui_rules_test.png → docs/images/ui/rules/test.png b/docs/ui_rules_test.png → docs/images/ui/rules/test.png
diff --git a/docs/images/ui/status.png b/docs/images/ui/status.png
diff --git a/docs/ui_status_control.png → docs/images/ui/status_control.png b/docs/ui_status_control.png → docs/images/ui/status_control.png
diff --git a/docs/images/ui/target_edit.png b/docs/images/ui/target_edit.png
diff --git a/docs/images/ui/targets.png b/docs/images/ui/targets.png
diff --git a/docs/ui_users.png → docs/images/ui/users.png b/docs/ui_users.png → docs/images/ui/users.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,4 +1,4 @@
-.. image:: header.jpg
+.. image:: /images/header.jpg
    :align: center
    :class: headerimage
 
@@ -7,7 +7,7 @@ mercure DICOM Orchestrator
 
 mercure is a flexible open-source DICOM orchestration platform. It offers an intuitive web-based user interface as well as extensive monitoring options, making it suitable for routine applications that require high availability. It can be used for dispatching DICOM studies to different targets based on easily definable routing rules and for processing DICOM series with custom-developed algorithms, such as inference of AI models for medical imaging. Processing algorithms can either be executed directly on a mercure server (as Docker containers) or can be executed on connected cluster nodes, typically located on premise but possibly also running as cloud instances. Implemented processing modules can be shared via Docker Hub.
 
-.. image:: scheme.png
+.. image:: /images/scheme.png
    :width: 550px
    :align: center
    :class: spacerbottom20
@@ -36,15 +36,16 @@ mercure is a flexible open-source DICOM orchestration platform. It offers an int
 
 .. toctree::
    :caption: User Guide
-   :maxdepth: 2
+   :glob:
 
    intro
    quickstart
    install
-   usage
    advanced
    monitoring
    dashboards
+   new_features
+   usage/index
 
 .. toctree::
    :maxdepth: 1
@@ -76,6 +77,6 @@ mercure is a flexible open-source DICOM orchestration platform. It offers an int
    :maxdepth: 2
 
    environment
-   code
+   source/index
    roadmap
 
diff --git a/docs/intro.rst b/docs/intro.rst
@@ -1,7 +1,7 @@
 What is mercure?
 ================
 
-.. image:: scheme.png
+.. image:: /images/scheme.png
    :width: 550px
    :align: center
 

diff --git a/docs/monitoring.rst b/docs/monitoring.rst
@@ -8,7 +8,7 @@ Log files
 
 All mercure services write detailed logging information into system log files. The most convenient way to review these logs is to use the "Logs" page of the mercure web interface. It shows a separate tab for every mercure service. The log display is updated whenever you switch between tabs or when you click the refresh button on the top-right.
 
-.. image:: ui_log.png
+.. image:: /images/ui/log.png
    :width: 550px
    :align: center
    :class: border

diff --git a/docs/new_features.rst b/docs/new_features.rst
@@ -0,0 +1,31 @@
+New Features
+===============
+
+- Multistep processors
+- Multiple dispatch
+- Rearranged UI
+- Query tool
+- Results files
+- Restart failed dispatch
+- localized timestamps
+- new target types (dicomweb etc)
+- new rule syntax (optional)
+- notifications from results
+- sample dashboards need updating
+- timezone stuff
+- system tag in navbar
+- getdcmtags: additional tags
+- influxdb
+- new receiver algorithm
+- manage.py create users
+- urgent priorities / offpeak
+- notifications templating, emails, PHI
+- json editor
+- "return to sender" target
+- TLS support in receiver
+- logs output in queue page, queue page generally
+
+> Update guide
+
+- update in install.sh to update dependencies, services
+- system status flag for missing services
diff --git a/docs/bookkeeper.rst → docs/source/bookkeeper.rst b/docs/bookkeeper.rst → docs/source/bookkeeper.rst
diff --git a/docs/cleaner.rst → docs/source/cleaner.rst b/docs/cleaner.rst → docs/source/cleaner.rst
diff --git a/docs/common.rst → docs/source/common.rst b/docs/common.rst → docs/source/common.rst
diff --git a/docs/dispatch.rst → docs/source/dispatch.rst b/docs/dispatch.rst → docs/source/dispatch.rst
diff --git a/docs/dispatcher.rst → docs/source/dispatcher.rst b/docs/dispatcher.rst → docs/source/dispatcher.rst
diff --git a/docs/code.rst → docs/source/index.rst b/docs/code.rst → docs/source/index.rst
diff --git a/docs/process.rst → docs/source/process.rst b/docs/process.rst → docs/source/process.rst
diff --git a/docs/processor.rst → docs/source/processor.rst b/docs/processor.rst → docs/source/processor.rst
diff --git a/docs/router.rst → docs/source/router.rst b/docs/router.rst → docs/source/router.rst
diff --git a/docs/routing.rst → docs/source/routing.rst b/docs/routing.rst → docs/source/routing.rst
diff --git a/docs/webgui.rst → docs/source/webgui.rst b/docs/webgui.rst → docs/source/webgui.rst
diff --git a/docs/webinterface.rst → docs/source/webinterface.rst b/docs/webinterface.rst → docs/source/webinterface.rst
diff --git a/docs/support.rst b/docs/support.rst
@@ -11,7 +11,7 @@ We thank `Zulip <https://zulip.com>`_ for sponsoring our project with a free clo
 
 .. container:: bullet
 
-    .. image:: zulip-org-logo.svg
+    .. image:: /images/zulip-org-logo.svg
         :width: 200px
         :align: right
 

diff --git a/docs/ui_modules.png b/docs/ui_modules.png
diff --git a/docs/ui_modules_edit.png b/docs/ui_modules_edit.png
diff --git a/docs/ui_rules.png b/docs/ui_rules.png
diff --git a/docs/ui_rules_edit.png b/docs/ui_rules_edit.png
diff --git a/docs/ui_rules_edit_notification.png b/docs/ui_rules_edit_notification.png
diff --git a/docs/ui_rules_edit_processing.png b/docs/ui_rules_edit_processing.png
diff --git a/docs/ui_rules_edit_routing.png b/docs/ui_rules_edit_routing.png
diff --git a/docs/ui_status.png b/docs/ui_status.png
diff --git a/docs/ui_target_edit.png b/docs/ui_target_edit.png
diff --git a/docs/ui_targets.png b/docs/ui_targets.png