Fix masking/reviewfiles endpoint, I broke it earlierIt calls the File.from_raw(), which now expects a path, but
the reviewfiles function had not been updated to return a path.
Make ream reconnect to postgres on dropped connectionPreviously a dropped connection would leave ream stuck (set_file_status
swallowed the error and the next loop iteration would hit the dead
cursor forever). Now we wrap the connection in a Db helper that
reconnects with exponential backoff up to a 5min deadline, then
sys.exit so the supervisor restarts us. set_file_status retries the
insert after reconnect so we don't lose the in-flight file's s...
Pull request #421: Report QUeries for nifti filesMerge in PT/oneposda from niftiReportQueries to master
* commit 'd50799bf46319da4bf382b87e89857f349995200':
Report QUeries for nifti files
Pull request #420: Dciodvfy fixMerge in PT/oneposda from dciodvfy-fix to master
* commit 'b6710b006d99395cc5204a25ff5ec77575487c9c':
Remove fix display with no errors
Update macro to append the fix on to the dciodvfy error
Updated Fix to remove the error text and add IGNORE for blank fixes
Update posda.main.file.insert_file_via_api to be more resilientIt no longer gives up immediately if it cannot insert a file
via the API, instead retrying after an increasing delay, up
to max_attempts (default 5). The delay goes 1s, 2s, 4s, 8s, etc.
Pull request #418: Macro fixMerge in PT/oneposda from macro-fix to master
* commit '4bf85e4ae022977a802f10cf98be6497cbd4e4f3':
Fix line endings
Update dcio macro to insert error into fix column when no fix found
Fix bug in dciodvfy macro
Pull request #416: fix for StructFix assuming CTMerge in PT/oneposda from 311structfix to master
* commit 'bb59ce2bb66649c66d426c5493cb20aeec52ae8c':
fix for StructFix assuming CT
Pull request #415: Add ability to generate initial anon from DEID recipeMerge in PT/oneposda from feature/TADMIN-1623-utilize-the-pydicom-deid-package-to-replace-posda-initial-anonymization-code to master
* commit '2fd12f61d906275c0334e7791742d6f9c377da20':
Add ability to generate initial anon from DEID recipe
Add dicom_edit_compare to API import/file, and improve stabilityThis commit reworks the import/file and import/file_in_place API
endpoints to use a single transaction while writing to the various
tables (file, file_location, etc). This _should_ prevent an issue we
have been seeing where occasionally a file entry will be written but no
file_location entry.
Additionally, this commit adds the query parameters from_file_digest and
subprocess_invocation_id to t...
NewApplyMasks.py: added new IEC output count check, and more loggingSpecifically, it now reports its status better via the Activity Task
Status mechanism.
Update nifti/visualreview to return only unreviewed filesThis is a temp change, it really needs to have a filter option
for status (and maybe other things)
Pull request #413: Dicom patmap improvementsMerge in PT/oneposda from dicom_patmap_improvements to master
* commit 'a50d3dd41ef9291b0181484ed7d6e601c7d9391d':
fixes for null values"
more sql fixes
bugfix3
bugfix2
bugfix
Pull request #412: Path bug dupes repairMerge in PT/oneposda from path_bug_dupes_repair to master
* commit '9c792c67b3f168747a6eec2f1a5c1f8c6d0422b2':
fix to allow removal only run
re-ordered code blocks in commit edits to avoid adding extra copies of files to the new tp
changes to queries using patient mapping to check for active status on select and add upload id on insert
updates for PM pk changes
Quasar Jarosz
Sonya Utecht