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Gpl 714 partial destinations #201

Merged
merged 85 commits into from
Dec 3, 2020
Merged

Gpl 714 partial destinations #201

merged 85 commits into from
Dec 3, 2020

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Chris-Friend
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Changes proposed in this pull request:

  • Add a new cherrypicked-plates/fail endpoint to pull together all data needed for a destination plate failure message. Create this message and send via RabbitMQ
  • Lots of refactoring: pulling out repeated code into shared modules, simplification of implementations, and removing redundant code

Christopher Friend added 30 commits November 26, 2020 15:43
Add and test new beckman/robots API endpoint
6b456a5
Add failure types config option
5f76d48
Add and test new beckman/failure-types API endpoint
3db4db8
Begin implementing the cherrypicked-plates/fail endpoint
e3569ba
Merge branch 'GPL711-update-cp-plate-create-for-events' into GPL-714-…
8fa4e0a 
…partial-destinations
Get samples from DART for failed plate. Test response if this fails
12390da
Merge branch 'GPL711-update-cp-plate-create-for-events' into GPL-714-…
6e4f486 
…partial-destinations

# Conflicts:
#	lighthouse/blueprints/cherrypicked_plates.py
Update error message
76a1d86
Merge branch 'GPL711-update-cp-plate-create-for-events' into GPL-714-…
278bfe8 
…partial-destinations
Test that errors getting DART samples are caught and handled
48315cc
Implement and test getting matching samples from Mongo
d4a66c9
Simplify checking matching sample numbers
c2f92bc
Use helper methods to return different error responses
1dbf9f8
Add checking sample numbers are correct
dc5b2d1
Merge branch 'GPL711-update-cp-plate-create-for-events' into GPL-714-…
0001738 
…partial-destinations
Re-structure code for simplification
007a08d
Merge branch 'GPL711-update-cp-plate-create-for-events' into GPL-714-…
6cb8bab 
…partial-destinations
Begin (re-)adding tests for constructing the message
797efbd
Rename mongo_db get_samples method
4d6ac79
Remove unused method
55552a4
Use for-loop generate function where appropriate
f4516ee
When comparing DART rows and samples, ensure we look for a sample wit…
12c649b 
…h a Positive result
Further code simplification
7cd57a3
Construct sample subjects ready to send in event message
29faf68
Don't map source plates to a local instance for the sake of mapping: …
71c5b5b 
…use the mongo format source plate throughout
Construct source plate message subjects
ac0ecb5
Use serial number for robot subject friendly name. Use plate_event he…
4a086df 
…lper methods for constructing the robot subject
Add new event type constant
7044d2e
Expose and rename method to get message timestamp
80d8cfc
Finish constructing event message
c704486
@harrietc52 harrietc52 linked an issue Dec 2, 2020 that may be closed by this pull request
GPL-714-2 As a user I would still like to process the destination plate if there is a partial failure (Lighthouse) #203
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pjvv
pjvv previously approved these changes Dec 2, 2020
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Lots of good stuff here Chris.

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@Chris-Friend @pjvv
Update lighthouse/config/defaults.py
3cf8db8 
Co-authored-by: Philip Jansen van Vuuren <31003728+pjvv@users.noreply.github.com>
Christopher Friend and others added 18 commits December 3, 2020 09:20
Update error message
8bebb8c
Use Dict[str, Any] for sample types
9a7f03f
Do case-invariant "Positive" string comparisons
f1f917e
Use set comprehension
4781e7a
@Chris-Friend @pjvv
Update lighthouse/helpers/plates.py
d613c39 
Co-authored-by: Philip Jansen van Vuuren <31003728+pjvv@users.noreply.github.com>
@Chris-Friend @pjvv
Update lighthouse/helpers/plates.py
4a355ab 
Co-authored-by: Philip Jansen van Vuuren <31003728+pjvv@users.noreply.github.com>
Merge branch 'GPL-714-partial-destinations' of github.com:sanger/ligh…
ce0a62d 
…thouse into GPL-714-partial-destinations
Simplify if conditions
755b4ee
Don't declare local variable to then just return it
75221c1
Another if condition change
22c8a17
Simplify string formatting
5cf374e
Update logging and messages returned for failed DART connection/no sa…
687a250 
…mples found in DART
Start adding SS constants
8effa7f
Add FIELD_SS_SUPPLIER_NAME constant
0252a0b
Add FIELD_SS_PHENOTYPE constant
cb1c3d3
Add FIELD_SS_CONTROL and CONTROL_TYPE constants
dfb1b2c
Add FIELD_SS_UUID constant
026c8b3
Add FIELD_SS_BARCODE and COORDINATE constants
fa5d974
@Chris-Friend
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@pjvv I've only extracted constants out for SequenceScape sample fields. This is a good start, but I don't intend to do any more in this PR (I could also extract out constants for the messages sent to the event warehouse)

@Chris-Friend Chris-Friend merged commit fd827c0 into develop Dec 3, 2020
@Chris-Friend Chris-Friend deleted the GPL-714-partial-destinations branch December 3, 2020 12:06
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@pjvv pjvv pjvv approved these changes

@alexperrin1 alexperrin1 Awaiting requested review from alexperrin1

@emrojo emrojo Awaiting requested review from emrojo

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@Chris-Friend @pjvv @harrietc52