Create flow diagram of how the system components work together

[David Platten]

I would find it useful to have a diagram that shows how the system components work together. For example:

Populating the database

• Modality sends DICOM objects to OpenREM's store SCP
• The store SCP (Conquest in my case) applies the rules in dicom.ini to each object
• Data from the object is extracted by the appropriate python script or the object is deleted if the extraction rules don't apply
• Calculation of skin dose map occurs if appropriate / possible
• The object is deleted from OpenREM's store

There could be other diagrams for other elements of the system.

Read the docs has Graphviz built-in that can help with this. See http://build-me-the-docs-please.readthedocs.io/en/latest/Using_Sphinx/UsingGraphicsAndDiagramsInSphinx.html

Test doc page to see with in progress: http://docs.openrem.org/en/docsdiagrams/testgraphviz.html

[David Platten]

User guides and examples:

• http://www.graphviz.org/pdf/dotguide.pdf
• http://www.graphviz.org/doc/info/attrs.html
• http://graphs.grevian.org/example
• http://www.tonyballantyne.com/graphs.html
• http://www.linuxdevcenter.com/pub/a/linux/2004/05/06/graphviz_dot.html

[David Platten]

Added a new diagram of the system components. References issue #448

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[David Platten]

Adjusted data extraction diagram to make style match the other one. Also added tooltips. References issue #448

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[David Platten]

Adjusting style of second diagram. References issue #448

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[David Platten]

The tooltips on the second diagram are incorrect - they are duplicates of the tips from the first diagram. It may be that we can only have one diagram per webpage.

See http://docs.openrem.org/en/docsdiagrams/testgraphviz.html

@edmcdonagh, do you have any corrections / omissions / additions to what is there so far?

[David Platten]

There's a list of flowchart shapes here: http://www.conceptdraw.com/How-To-Guide/picture/Designelements-Flowchart.png

I'll adjust the shapes used for each node in the diagrams to better match what is shown in the link above, using the available default shapes (http://www.graphviz.org/doc/info/shapes.html)

[David Platten]

Updating shapes; removing commas. References issue #448

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[David Platten]

Trying to sort out size issue. References issue #448

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[David Platten]

Trying to sort out size issue. References issue #448

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[David Platten]

Trying to sort out size issue. References issue #448

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[David Platten]

Trying to sort out size issue and some shapes. References issue #448

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[David Platten]

Trying to sort out size issue and some shapes. References issue #448

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[David Platten]

Trying to sort out size issue and some shapes. References issue #448

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[David Platten]

Moved Conquest into the server cluster; relabelled the cluster as "Server" to be consistent with other diagram. References issue #448.

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[David Platten]

This site is useful to play with the diagram language: http://www.webgraphviz.com/

[Ed McDonagh]

Is there a system behind the shape choices?

[David Platten]

Yes, I use this site: http://www.conceptdraw.com/How-To-Guide/flowchart-design

Regards,

David

[David Platten]

@edmcdonagh, it would be good to use a proper database symbol for PostgreSQL, but "shape=cylinder" doesn't work on the existing read the docs install. The cylinder shape is now available (http://www.graphviz.org/mantisbt/view.php?id=1867). Is there a way of updating the version of graphviz that read the docs is using so that the cylinder works?

[David Platten]

Combined the two diagrams into one. References issue #448

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[Ed McDonagh]

Seeing if demanding a later version of sphinx will get a later version of graphviz. Refs #448

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[Ed McDonagh]

Didn't work, reverting sphinx version requirement. Even the Sphinx v1.5 docs are produced using Sphinx 1.3.5! Refs #448

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[Ed McDonagh]

No, I don't see a way of doing this @dplatten. Sorry. Maybe a stack-overflow question?

[David Platten]

OK - thanks for checking. I don't think it matters too much for the time being.

[David Platten]

Putting all server nodes in the same cluster to make layout more straightforward for me. References issue #448.

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[Ed McDonagh]

Forgot to reference the issue in the commit: 8d820b4

[Ed McDonagh]

Added alternatives information. Refs #448

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[Ed McDonagh]

Minor mod to wording. Refs #448

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[David Platten]

Updated the layout using two blank nodes and some additional ranking to force a specific horizontal order.

I found the information on forcing a horizontal order here: http://stackoverflow.com/questions/14123259/how-to-enforce-the-left-to-right-node-ordering-in-graphviz-rank-layout

References issue #448.

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[David Platten]

Made nodes a little smaller, and reduced font size. I'm not able to produce a good-looking chart that is much narrower than this at the moment. May re-visit this at the weekend. References issue #448

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[David Platten]

Reverted to larger text size. I'd like to let the user click on the diagram and it open full-size in a new window. References issue #448

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[David Platten]

Updated name of diagram document. Updated link from index. Updated changes files. Fixes issue #448

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[Ed McDonagh]

Refs #448

Adds study time to the CT export module with correct formatting for time and date.

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[Ed McDonagh]

Hi David. Can we modify this to indicate ISIS for Windows and nginx+gunicorn for Linux?

[David Platten]

Updated system diagram in the documents to reflect new recommendations on web servers. Also amended database text. References issue #448, issue #592 and issue #596

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[David Platten]

Amended heading underline. References issue #448

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[David Platten]

@edmcdonagh, would you create a documentation set for the issue448UpdateSystemDiagram branch so that I can check that the changes I've made haven't broken anything?

[Ed McDonagh]

http://docs.openrem.org/en/issue448updatesystemdiagram/

[Ed McDonagh]

Thanks, by the way :)

[David Platten]

Removed link to installing Apache - this is referred to in the web server link anyway. References issue #448, issue #592 and issue #596

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[Ed McDonagh]

Merged in issue448UpdateSystemDiagram (pull request #171)

Issue448UpdateSystemDiagram

Approved-by: Ed McDonagh [e-mail]

Refs #448, #592, #596

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