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Make a live test OpenREM site available for users to try

Issue #158 resolved
David Platten created an issue

I thought it would be a good idea to have a live test system set up so that potential users can have a proper look at it and a bit of a play. Ideally it would have the plots on too...

Comments (37)

  1. Ed McDonagh

    I'd love that. Couldn't do it on my edshosting servers because I don't have that level of access to install software.

    If you've not ever used Amazon EC2 then they have a free usage tier, which means you can run a tiny Linux instance for a year for free, just paying for any time you upgrade it to a larger spec, which I do on my EC2 server whenever I do anything in it as otherwise it is too slow.

    However, that would only work for 12 months, then I think I pay about $20/month. I used up my free year ages ago.

    Another option if I had fibre at home would be to host it at home on a spare box. But I don't, and probably won't any time soon.

    Do you have any ideas?

  3. Ed McDonagh

    Looks interesting. I've not used a red hat/yum based system for nearly 10 years I think!

    It looks like we can use a custom domain, so demo.openrem.org would be good. I can set the dns accordingly.

  5. Ed McDonagh

    I've been doing some research as and when I can this afternoon. Using OpenShift would mean we wouldn't be able to use Celery/RabbitMQ as far as I can see.

    Now, one might see that as an advantage as it makes it easier in terms of cleaning up the sample data to remove any institutional or staff information.

    But I strongly believe from our experience with using the system that exporting the data in a useful way for detailed analysis is the power of OpenREM, and one of the major things that separates it from the commercial alternatives, at least to non-developer physicists. If you can't demonstrate that element, that would be a shame.

    That's not to say it wouldn't still be useful!

    I'll be driving from Dublin back to London tomorrow, so I won't be able to checkout OpenShift till Friday at the earliest.

  6. David Platten reporter

    OK, I've got it working. See: http://demo-openremdemo.rhcloud.com/openrem/

    I used the instructions here as a basis: http://stackoverflow.com/questions/26871381/deploying-a-local-django-app-using-openshift

    I had to lengthen the name field in the auth_permission table of the database, as mentioned here: https://groups.google.com/forum/#!topic/openrem/TCFFaKHLlPk. I used the psql command in a SSH with the following method: http://sniptools.com/databases/resize-a-column-in-a-postgresql-table-without-changing-data.

    Just need some data to go in it now. @edmcdonagh, do you fancy putting together some CT rsdr files that have dummy hospital names in?

  8. David Platten reporter

    Yes: you can log in with 'demo' as the username and password. I've only given this user viewing rights so that we don't run into problems with the export not working - although I haven't yet tried exporting to see what happens.

  9. Ed McDonagh

    There won't be any errors, it will just redirect to the export page and the export task will never appear.

  10. David Platten reporter

    @edmcdonagh, you should now be able to access the OpenREM demo on OpenShift: I've made you an administrator. You can clone the git repository for the site to your local computer using the details you'll see on the site. Whenever you push any changes from your local copy back to the repository OpenShift rebuilds the live site with your changes immediately.

  11. David Platten reporter

    I've put some anonymised DX data onto the site. the dx.py extractor failed to begin with: I had to change the os.environ['DJANGO_SETTINGS_MODULE'] value from 'openrem.openremproject.settings' to 'openremproject.settings' for it to work. I have since changed this value in the other extractor files for the OpenShift version.

  13. Ed McDonagh

    I think we might be able to do the exports too - we could use the free tier of cloudamqp.com. We can leave that for phase two, but I think we should upload data in the knowledge that it might in future be downloaded...

  14. Ed McDonagh

    I think OpenREM isn't 'installed' as such, rather it is placed(!) on the server. Therefore the scripts won't be installed anywhere that can be executed, hence why you need to use the extractors directly and why the import path failed for the settings file.

  15. David Platten reporter

    It's great to see the demo site with an openrem.org url. Also sounds like it may be good news on the export front.

    I got the scripts working on the server by changing "from openrem.remapp.extractors import dx" to "from remapp.extractors import dx" in the openrem_dx.py file. I don't think it initially worked because the folder structure isn't the same as it is in a proper install.

    You may also notice that there are several "static" folders - they couldn't be found by the OpenShift system when in their usual place, so I put some copies in other places until it worked...

  17. David Platten reporter

    If I'm going to generate fake data, I should probably populate fields like exposure index, patient weight, height etc too, so that it's a complete set.

  18. Ed McDonagh

    If you do, it would have to have some correlation to make sense, particularly when we reintroduce dose/size scatter plots. Mmmm...

  20. David Platten reporter

    I've created some more artificial data and put it in the demo system. There are several variations of chest exposure.

    The patient's age is randomly generated. Their weight is then based on this - lower for the younger patients, and also dropping off for the older patients. The DAP, mAs and REX are also related to the patient weight.

    I have written the patient weight into the appropriate tag in my DICOM files, but it seems that the dx extractor doesn't try and obtain this value at the moment.

  21. David Platten reporter

    Thanks for the reply. I will have another go at OpenShift today. I also agree with what you say about being able to export data. It would be good to have a demo site that could export.

  22. David Platten reporter

    Wow, I sent the above message via e-mail 5 days ago - looks like there has been a problem with outgoing messages!

  23. Ed McDonagh

    I did think 1.45 in the morning was an odd time to be making comments, and that it didn't really make sense as we've rather moved on since!

  24. David Platten reporter

    I have just recreated the database for the demo site: it is now empty. I had put 9000+ radiographic studies in, and it had ground to a halt - issues with OpenShift I think. I will repopulate with 200 examples of a selection of studies tomorrow.

  27. Ed McDonagh

    Can we add a link to openrem.org somewhere at the top or the bottom? Some sort of 'What is OpenREM? Find out more here' type of thing. Just in case someone manages to get to demo.openrem.org without going via the parent site.

  29. David Platten reporter

    There is now a link in the footer before the copyright message, "Find out more about OpenREM at openrem.org."

  31. David Platten reporter

    Done: the demo username and password now appears automatically in the appropriate boxes. It can be over-ridden with different values by the user if needed.

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Type
proposal
Priority
major
Status
resolved
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Milestone
0.5.1
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