Register FIB milling progress#815
Open
tieneupin wants to merge 20 commits into
Open
Conversation
…hat can be run through the 'feedback_callback' function
… database entries
…, and added a new table to record a Murfey-side copy of ISPyB's 'MillingStep' table
…c 'None' for the 'status' field
* GridSquare ID needs to be passed in when creating a new ISPyB record * Need to check if MillingStep update on ISPyB was successful before updating the corresponding Murfey record * Get site number from Pydantic model instead of working it out from first priciples again
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #815 +/- ##
==========================================
+ Coverage 52.39% 52.98% +0.59%
==========================================
Files 97 98 +1
Lines 10461 10684 +223
Branches 1381 1405 +24
==========================================
+ Hits 5481 5661 +180
- Misses 4691 4727 +36
- Partials 289 296 +7 🚀 New features to boost your workflow:
|
tieneupin
force-pushed
the
register-fib-milling-progress
branch
from
f101567 to
b6add3d
Compare
…ead, since the 'MillingStepNameId' requires a DB query
tieneupin
force-pushed
the
register-fib-milling-progress
branch
from
b9ef174 to
acdf448
Compare
tieneupin
force-pushed
the
register-fib-milling-progress
branch
from
acdf448 to
6047bd2
Compare
…o' master dictionary; added test function to check the early exit cases
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Adds new database tables + relationships and workflow functions to support the registration and tracking of the FIB milling process. The AutoTEM metadata read by Murfey will now be registered in ISPyB's new
MillingSteptable, and a local Murfey copy will be created so that Murfey can propagate updates to existing rows.As part of this PR, the ISPyB schema and Python package versions have been bumped to make use of the newly introduced
MillingSteptable.The diff looks huge, but +540 of those lines are due to tests.