Ability to specify external command to generate acquisition uid

[ryansanford]

Included in this PR

• New option uid_ext_command to specify external command to run.
• Single non-deterministic file from acquisition source files will be used in the command.
• Non-zero or empty string returned by command will prevent acquisition from being uploaded.
• Non-zero exit of external command will fail and abort reap attempt

Actions Before Merge

• Create Proof Of Concept
• Decide final implementation details
• Add final implementation details here...
• Abort and fail reap attempt on external command error

[ryansanford]

@gsfr
I don't like the current implementation of assuming source dicoms will be in a folder named the same as the zip, however, it was the quickest path to this POC so I didn't have to worry about state set before the zip is created, and after it's created and we have the metadata object. I feel strongly that this option does belong in the dicom_reaper or lower module, and not orthanc_reaper.

How would you feel about passing a set_acq_uid() function down to dcm.pkg_series that could be used if provided? I'm open to other approaches, as my python-foo is still weak.

[gsfr]

Rebased and added a new commit. This is untested and likely buggy, but I wanted to show it to you, @ryansanford, for feedback on general approach.

Command line looks like this:

--metadata acquisition "Referring Physician" ReferringPhysicianName

[ryansanford]

@gsfr Thanks. I should be able to check this out before I leave.

[ryansanford]

@gsfr pushed change to fix an issue with subprocess call. Feel free to refactor to more elegant approach. I only tested that narrow use case. I'll review with a more critical eye tomorrow.

[gsfr]

Thanks. I'm going to refactor that just a tad. Also note that I have updated the original description of this PR. I don't think that an empty string return value should prevent reaping. Non-zero exit also doesn't currently prevent reaping, but it probably should.

[gsfr]

What is the purpose of the latest commit? Does the previous code not work?

http://stackoverflow.com/q/10563613

[ryansanford]

@gsfr I pushed a change so a single file from the series gets passed, rather than the original filename that's no longer valid after it's renamed.

Behavior with a non-zero return from the external command is an empty metadata value and does not prevent the upload. It would be nice to have a defined return/exception interface on pkg_series() so we can fail the operation with predictable results to any callers.

[gsfr]

My bad on the first point and agreed on the second point. I can take that on once you agree on the general design and have tested the current implementation.

[ryansanford]

Thanks for the python tip @gsfr

I agree with the general design. Cursory testing with static, dicom tag name, and external command is working for me.

👍

[gsfr]

@ryansanford I've added basic error handling. Please give it a whirl. We now error out on non-zero return of external command and proceed zero return, even with an empty string.

--metadata acquisition CustomFieldName @true