Move content to sysadmin manual

doc/Glossary.md

@@ -135,7 +135,7 @@ A service that controls access between two or more networks.
 
 ## Genie Python
 
-An implementation of the [OpenGenie](http://www.opengenie.org) scripting language in Python, or at least its commands specific to instrument control.  Documentation [here](http://shadow.nd.rl.ac.uk/genie_python/sphinx/genie_python.html).
+An implementation of the [OpenGenie](http://www.opengenie.org) scripting language in Python, or at least its commands specific to instrument control.  Documentation at {external+genie_python:doc}`genie_python`.
 
 ## GIT
 

doc/Overview.md

@@ -29,7 +29,7 @@ overview/Links-and-Resources
 - [General IOC information](IOCs): Everything you could possibly want to know about IOCs in general, creation and conventions
 - [Specific Device IOC](Specific-IOCs): Detailed information about specific IOCs & scientific hardware
 - [Project Tools](Tools): Developer-facing tools which have proven useful for the project
-- [System Administration & Hardware](/Systems): All about the physical & virtual computers on which IBEX runs
+- {external+sysadmin:doc}`System Administration & Hardware <index>`: All about the physical & virtual computers on which IBEX runs
 
 ## Documentation & Processes
 

doc/Providing-Support.md

@@ -173,7 +173,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
 
   1. There are a few things that have services which run, especially the databases, and it is possible after a crash/other restart that these don't start up again, starting task manager as an administrator should allow you to start the service in question
   1. If it is not one of our services (e.g. swipe systems, ERA), we cannot resolve the issue, escalate as appropriate (TODO: Make sure the different escalation methods are documented)
-  1. If the MCR news service isn't working, then so long as there is space, restarting our [webserver](/systems/Webserver) may help.
+  1. If the MCR news service isn't working, then so long as there is space, restarting our {external+sysadmin:doc}`systems/Webserver` may help.
 
 </details>
 

doc/Web.md

@@ -6,10 +6,8 @@
 
 webdashboard/Web-Dashboard
 webdashboard/PVWS
-webdashboard/ISIS-Info-Slack
-webdashboard/MCR-News-in-Teams
 ```
 
 ```{seealso}
-- [WebServer](systems/Webserver) for the physical computer where the [PVWS](webdashboard/PVWS) instance, which the [Web Dashboard](webdashboard/Web-Dashboard) relies on, is hosted.
+- {external+sysadmin:doc}`systems/Webserver` for the physical computer where the [PVWS](webdashboard/PVWS) instance, which the [Web Dashboard](webdashboard/Web-Dashboard) relies on, is hosted.
 ```

doc/client/troubleshooting/PV-Manager-and-Observers-Logging.md

@@ -15,7 +15,7 @@ To help debug the PVObserver and lower levels you can build a version of the GUI
     - org.csstudio.utilities.pvmanager.epics
 1. This will now print out debug statements all containing the text Ticket2162
 1. The logs can be filtered using a python program below (this program is very rough, don't forget to change the date)
-1. This can be combined with Wireshark (see [Network traffic](/tools/Network-traffic)) to analyse traffic if needed
+1. This can be combined with Wireshark to analyse traffic if needed
 
 Example log output from disconnection to reconnection
 

doc/conf.py

@@ -113,4 +113,7 @@
     "ibex_bluesky_core": ("https://isiscomputinggroup.github.io/ibex_bluesky_core/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "secop": ("https://sampleenvironment.github.io/secop-site/", None),
+    # This inventory needs to be periodically updated (manually) if new pages are added or
+    # page layouts changed.
+    "sysadmin": ("https://shadow.nd.rl.ac.uk/ibex_sysadmin_manual/", "sysadmin_manual.inv"),
 }

doc/deployment/Deploy.md

@@ -16,5 +16,4 @@ deploy/Reviewing-Deploy-Tickets
 deploy/Upgrade-ISISICP
 deploy/Upgrade-Java
 deploy/Installing-and-Upgrading-MySQL
-deploy/NPort-install
 ```

doc/deployment/Patch.md

@@ -8,7 +8,3 @@ How to patch or hotfix a new change onto an instrument which already has IBEX.
 
 patch/*
 ```
-
-:::{seealso}
-See also [powershell remoting](/systems/inst_control/PS-Remote) for a script to apply patches to many instruments simultaneously.
-:::

doc/index.md

@@ -35,7 +35,6 @@ Web
 System-components
 IOCs
 Specific-IOCs
-Systems
 ```
 
 ```{toctree}

doc/overview/First-Time-Build.md

@@ -288,4 +288,4 @@ Download and install latest stable version from https://wixtoolset.org/docs/wix3
 ### Add your SSH key to the `keys` repository
 
 Adding an SSH key to the [keys repository](https://github.com/isiscomputinggroup/keys) can be used to give
-passwordless access to instrument machines. Follow the instructions [here](/tools/SSH-keys).
+passwordless access to instrument machines. Follow the instructions {external+sysadmin:doc}`services/SSH-keys`.

doc/overview/Links-and-Resources.md

@@ -29,7 +29,7 @@
 - {external+ibex_user_manual:doc}`IBEX user manual <index>`
 - [IBEX Project Board for Issues](https://github.com/ISISComputingGroup/IBEX/projects/1)
 - [Stream Protocol Page](http://epics.web.psi.ch/software/streamdevice/doc/)
-- [genie_python reference](http://shadow.nd.rl.ac.uk/genie_python/sphinx/genie_python.html)
+- {external+genie_python:doc}`genie_python reference <genie_python>`
 - [nagios](https://varanus.nd.rl.ac.uk/nagios/)
 - [EPICS WIKI](https://wiki-ext.aps.anl.gov/epics/index.php/RRM_3-14)
 - [Current program version, servers and settings](http://beamlog.nd.rl.ac.uk/inst_summary.xml)
@@ -53,7 +53,6 @@ A non-exhaustive collection of troubleshooting pages.
 * [Database](/system_components/mysql/Database-Troubleshooting)
 * [Web Dashboard](#webdashboard_troubleshooting)
 * [genie_python](/scripting/genie_python/genie_python-Troubleshooting)
-* [Computer](/systems/inst_control/Computer-Troubleshooting) (e.g. the NDX)
-* [ICAT and TopCAT](/systems/external/ICAT-Troubleshooting)
+* {external+sysadmin:doc}`index`
 * [Mini-inst](/system_components/startup/Mini-inst-Troubleshooting)
 * [Where are the log files](/iocs/troubleshooting/Log-file-location)

doc/overview/New-Starters.md

@@ -101,7 +101,6 @@ Some pages to read over:
 Pages to skim over. Read in detail only when needed:
 
 - [Settings and Configurations](../system_components/Settings-and-Configurations)
-- [Data Generation and Storage](../systems/inst_control/Data-Generation-and-Storage-on-Instrument-PCs-(NDX's))
 - [Information for User Scientists](https://github.com/ISISComputingGroup/IBEX/wiki)
 
 Every section after this line contains reference information that you do not necessarily have to read before you do your first ticket, but it is where you should take a look when you find out you need to learn new things in order to do your work.

doc/processes/retrospective-notes/Retrospective-Notes-2020.11.11.md

@@ -49,5 +49,5 @@ Yes, this is a good idea. Call the file `Sprintreview_start_<date>`. Add start a
 
 - We are happy that POLREF is now running on IBEX and SURF is planning to use it this cycle.
 - We are making good progress on SANS2D. Different groups coordinating well with each other (us, scientists, network team, ...)
-- We are excited about Windows 10 updates. Build is "mostly" automated, process is now documented [(Link)](/systems/inst_control/mdt/Building-a-windows-10-instrument-machine-from-MDT), everyone should in principle be able to set this up.
+- We are excited about Windows 10 updates. Build is "mostly" automated, process is now documented on SysAdmin manual, everyone should in principle be able to set this up.
 - What to do with trivial support issues? Creating a ticket every time seems like a lot of overhead --> Put them in a teams channel, then record them permanently in a ticket at the end of the sprint. `support-issues` channel has now been created

doc/system_components/journal_viewer/Journal-Viewer-Data.md

@@ -1,7 +1,7 @@
 # Journal Viewer data
 
-The ISISICP writes run summaries to an XML journal file on the instrument, these files are in c:/data but are then copied to the archive and stored under Instrument/logs/journal. 
+The ISISICP writes run summaries to an XML journal file on the instrument, these files are in `c:/data` but are then copied to the archive and stored under `Instrument/logs/journal`. 
 
-The windows archive is smb mounted onto a linux server [(`sparrowhawk.nd.rl.ac.uk`, which we maintain)](/systems/Sparrowhawk) and served to the lab as https://data.isis.rl.ac.uk/journals/ where programs such as Mantid and "standalone journal viewer" can access it. This machine runs on the facilities hyper-v cluster, technology department look after it from a server patching point of view and if there are major operating system issues. Try rebooting the server via the hyper-v console manager, if that doesn't work (e.g. drops into a recovery console talking about disk errors) then contact "Technology IT Support" on outlook. It seems that emails to "Technology IT Support" are only accepted from certain accounts, ISIS experiment controls looking not to be one of them at the moment.
+The windows archive is smb mounted onto a linux server ({external+sysadmin:doc}`systems/linux_support_systems/Sparrowhawk`) and served to the lab as https://data.isis.rl.ac.uk/journals/ where programs such as Mantid and "standalone journal viewer" can access it. This machine runs on the facilities hyper-v cluster, technology department look after it from a server patching point of view and if there are major operating system issues. Try rebooting the server via the hyper-v console manager, if that doesn't work (e.g. drops into a recovery console talking about disk errors) then contact "Technology IT Support" on outlook. It seems that emails to "Technology IT Support" are only accepted from certain accounts, ISIS experiment controls looking not to be one of them at the moment.
 
 Journals can be accessed remotely (outside the lab) by users using https://shadow.nd.rl.ac.uk/journals/. More documentation on this is available at `\\isis\shares\isis_experiment_controls\web_dashboard_history.docx`