Update installation documentation
Yesterday I helped a colleague at another hospital install OpenREM. This flagged a number of issues with the (0.7.4) documentation.
Comments (38)
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reporter -
reporter The list of things to clarify are:
- Erlang is not mentioned in the documentation. You get an error when trying to install RabbitMQ which prompts you to download and install Erlang
- Numpy install could benefit from a reminder to navigate to where you have saved the file prior to the install command
- Under Postgresql setup:
- Setup of a user for the database doesn’t note the privileges the user needs (logging in, creating databases)
- Suggests openremdb as a database name but later uses openrem_db
- Configuring openrem settings the allowed hosts shows an IP address; it could be clearer that it should be the IP address of the OpenREM server itself
- Scheduling celery
- Rewrite as “how to setup” rather than “here’s how it should look when done”
- Suggest the description be put into text to allow copy/paste
- Detail the security options
- No prompts when to install Conquest (or other DICOM software). Likely fits in under Docs »DICOM Store and QR »DICOM Network Configuration
- DICOM store and QR instructions come after the “Now start testing things”
- Instructions for command window querying prompts qrscu.py but should call on openrem_qr.py
- Somewhere along the lines I was missing dicom 0.9.9 and needed to use pip install dicom
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reporter Updated installation documentation based on recent user experience [skip ci]. References issue
#630→ <<cset f8b2c520c6a2>>
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I've changed the view level of the docs associated with this branch to protected - then casual users won't find them. If you know the address (http://docs.openrem.org/en/issue630updateinstalldocs/) you can view them, and if you are logged in to readthedocs they are linked.
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reporter Ok, thanks @edmcdonagh. At which point in the (0.7.4) installation process should the dicom python package be installed? This package wasn't present on the system that I was helping out with yesterday, even though openrem and your pynetdicom package were there.
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Thanks for this @dplatten. This is just the sort of testing we need with the docs!
I think some of the issues may have been dealt with in the current docs maybe? I have certainly tried to reorganise them to make them work better!
In the 0.7.4 docs, pynetdicom was installed as part of the prep. This now happens after OpenREM, partly because it drags in pydicom and gets the latest version. OpenREM is pinned to the <1 pydicom, so if that is installed first pynetdicom is happy with the old version.
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Cross posted. Hopefully my comment will help explain, but I don't understand why it wasn't installed with OpenREM. Or pynetdicom (though the wrong version)
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reporter I've just created a fresh virtualenv on Ubuntu and started to follow the 0.7.4 install prep instructions. I installed numpy, and then tried to install pynetdicom, but was met with an error (see below). I'll test this on Windows too.
(openrem_test) dplatten@newton:~/apps/openrem_test$ pip list Package Version ---------- ------- pip 10.0.1 setuptools 39.1.0 wheel 0.31.1 (openrem_test) dplatten@newton:~/apps/openrem_test$ pip install numpy Collecting numpy Using cached https://files.pythonhosted.org/packages/c0/e7/08f059a00367fd613e4f2875a16c70b6237268a1d6d166c6d36acada8301/numpy-1.14.3-cp27-cp27mu-manylinux1_x86_64.whl Installing collected packages: numpy Successfully installed numpy-1.14.3 (openrem_test) dplatten@newton:~/apps/openrem_test$ pip install https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2 Collecting pynetdicom-0.8.2b2 from https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2 Downloading https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz (47kB) 100% |████████████████████████████████| 51kB 105kB/s Running setup.py (path:/tmp/pip-install-jVEmH8/pynetdicom-0.8.2b2/setup.py) egg_info for package pynetdicom-0.8.2b2 produced metadata for project name pynetdicom. Fix your #egg=pynetdicom-0.8.2b2 fragments. Collecting pydicom>=0.9.7 (from pynetdicom) Downloading https://files.pythonhosted.org/packages/d3/74/f1e9d1b8f86a94a732fed44545e2096580c1719661866bf46df5d0faa3f7/pydicom-1.0.2.tar.gz (6.7MB) 100% |████████████████████████████████| 6.7MB 142kB/s Building wheels for collected packages: pynetdicom, pynetdicom, pydicom Running setup.py bdist_wheel for pynetdicom ... done Stored in directory: /tmp/pip-ephem-wheel-cache-Cc_ope/wheels/25/ce/70/db6c67879ab7e47863c71761cf5708e946ea51936175936263 Running setup.py bdist_wheel for pynetdicom ... error Complete output from command /home/dplatten/apps/openrem_test/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-jVEmH8/pynetdicom/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-2NwnNK --python-tag cp27: Traceback (most recent call last): File "<string>", line 1, in <module> IOError: [Errno 2] No such file or directory: '/tmp/pip-install-jVEmH8/pynetdicom/setup.py' ---------------------------------------- Failed building wheel for pynetdicom Running setup.py clean for pynetdicom Complete output from command /home/dplatten/apps/openrem_test/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-jVEmH8/pynetdicom/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all: Traceback (most recent call last): File "<string>", line 1, in <module> IOError: [Errno 2] No such file or directory: '/tmp/pip-install-jVEmH8/pynetdicom/setup.py' ---------------------------------------- Failed cleaning build dir for pynetdicom Running setup.py bdist_wheel for pydicom ... done Stored in directory: /home/dplatten/.cache/pip/wheels/64/c5/a6/dfde9039d7c59b83cc165848da7580ea68c338da02eee98249 Successfully built pynetdicom pydicom Failed to build pynetdicom Installing collected packages: pydicom, pynetdicom Successfully installed pydicom-1.0.2 pynetdicom-0.8.2b2 (openrem_test) dplatten@newton:~/apps/openrem_test$ pip list Package Version ---------- ------- numpy 1.14.3 pip 10.0.1 pydicom 1.0.2 pynetdicom 0.8.2b2 setuptools 39.1.0 wheel 0.31.1
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I'm wondering if it is an issue with pip 10
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With pip 10.0.1 I had the same messages as you, though it seems they are just noise as the software gets installed just the same.
With pip 9.0.1 I had the following:
root@frp-testpynetdicom1:/home/test# pip -V pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7) root@frp-testpynetdicom1:/home/test# pip install https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2 Collecting pynetdicom-0.8.2b2 from https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz#egg=pynetdicom-0.8.2b2 Cache entry deserialization failed, entry ignored Downloading https://bitbucket.org/edmcdonagh/pynetdicom/get/default.tar.gz (47kB) 100% |################################| 51kB 20kB/s Running setup.py (path:/tmp/pip-build-vKUoRm/pynetdicom-0.8.2b2/setup.py) egg_info for package pynetdicom-0.8.2b2 produced metadata for project name pynetdicom. Fix your #egg=pynetdicom-0.8.2b2 fragments. Collecting pydicom>=0.9.7 (from pynetdicom) Cache entry deserialization failed, entry ignored Installing collected packages: pydicom, pynetdicom Running setup.py install for pynetdicom ... done Successfully installed pydicom-1.0.2 pynetdicom-0.8.2b2
Either way, pydicom 1.0.2 was installed, which is an issue.
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I think the
backupRestorePostgreSQL.rst
could do with aligning with the other db docs, but apart from that I am going to merge in your changes for this beta. -
Adding in note about importance of using our version of pynetdicom, and error messages wth pip10. Refs
#630{skip ci]→ <<cset 28983bf3f1db>>
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Correcting pydicom version number. Refs
#630[skip ci]→ <<cset e39e2d5bc9d5>>
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Tidying up wording for DICOM page. Refs
#630[skip ci] docs only→ <<cset f2dcb70dad8c>>
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Added section to prompt Conquest install in install-prep. Removed link to apache_on_windows that has been deleted. Refs
#630[skip ci] docs only→ <<cset 93245d15d708>>
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@dplatten - I've added http://docs.openrem.org/en/issue630updateinstalldocs/install-prep.html#install-a-dicom-store-service.
I haven't downloaded the current version yet to see what the install instructions are... I've seen on the forum that there is a web based installer for Linux now.
We also need to restructure http://docs.openrem.org/en/issue630updateinstalldocs/netdicom.html as it is a bit of a mess at the moment.
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Note about conquest install, change start using it to refer to import docs. Refs
#630[skip ci] docs only→ <<cset c4f7b9a46367>>
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Moved import-from-file into new doc, intending to put Store and QR sections under import heading... Refs
#630[skip ci] docs only→ <<cset 4c5968ae2f80>>
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Starting to move the conquest and DICOM store docs around. Refs
#630[skip ci] docs only→ <<cset e7cfff46c63b>>
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Forgot the link to the new document. Refs
#630[skip ci] docs only→ <<cset f2c3a67fa539>>
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Linking to the QR docs. Refs
#630[skip ci] docs only→ <<cset f5864a38d4e2>>
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Adding pages for bash/bat file creation for calling scripts from conquest. @dplatten - can you throw some content into conquest-scripts-windows.rst please? Refs
#630[skip ci] docs only→ <<cset 8aab0ed3c20a>>
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Organising the dicom.ini section. Refs
#630[skip ci] docs only→ <<cset b53b189d96a5>>
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Spelling mistake in referencing dicom.ini example doc. Refs
#630. [skip ci] docs only→ <<cset b69d810dbccc>>
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reporter The example Windows dicom.ini file, Lua scripts and batch files assume the user has not used a virtualenv. As they stand, they won't work if the user does use a virtualenv. The Lua scripts will need to be modified to call a batch file that activates the virtualenv and runs the importer; at the moment the importer is run directly within the Lua script. I don't think there's a way of activating a virtualenv from Lua and then running a python command in it. Before I go ahead and update the documentation I will need to check that what I think will work actually does...
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More rearranging of the docs and content. Refs
#630. [skip ci] docs only→ <<cset 111832c96a68>>
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Referenced the remaining existing conquest doc and removed the index reference to netdicom. Refs
#630. [skip ci] docs only→ <<cset 1614269f8458>>
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Thanks for looking into this David. I think the way around that is to specify the python executable - if you do that you don't need to activate the virtualenv. So on linux this command should work:
/home/me/venv/bin/python /home/me/venv/bin/openrem_rdsr.py rdsrfiletoimport.dcm
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I have the import and DICOM docs looking closer to the structure I think I am after now. If you could have a look and comment I'd appreciate it.
http://docs.openrem.org/en/issue630updateinstalldocs/index.html
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@dplatten - I've been trying and failing to install the current version of conquest, which is frustrating! I've been liaising with Marcel via the forum. I will need to demonstrate to myself I can install on linux before I can finalise the docs and release 0.8.
Also, I was thinking that maybe we should drop the recommendation to create the scripts and call them from
dicom.ini
, preferring instead to just recommend a lua script, maybe with a simple version and the some suggestions for your advanced version? -
Minor edit to intro. Refs
#630→ <<cset cfaa3f46d02d>>
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- changed status to resolved
Merged in issue635OrthancExperiment (pull request #198)
Fixes
#630,#635DICOM and Orthanc.Approved-by: David Platten dplatten@gmail.com
→ <<cset 0dcdc304619d>>
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Added refs
#630,#635to changes. Refs#635, [skip ci]→ <<cset e16e571687d9>>
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reporter Revised section on Toshiba CT extractor in the documentation and associated script to more conservative wording and list [skip ci]. References issue
#630→ <<cset 47c174fd9877>>
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reporter Revised section on backing up PostgreSQL before an upgrade following comments from a user [skip ci]. References issue
#630→ <<cset f67ec027743c>>
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Hi @dplatten - do you want to put something in the 0.8.1 release notes about the Toshiba extractor list being more conservative for this release?
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reporter Yep, that would be good. Which file is the release notes?
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I've started a release branch for 0.8.1b1 as I want to get the mammo NHSBSP bug fix out
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Interestingly this Windows-based OpenREM installation is using Celery version 4.1.0, which is working fine.