Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Gpl 745 sample and plate UUID #158

Merged
merged 26 commits into from
Nov 24, 2020
Merged

Gpl 745 sample and plate UUID #158

merged 26 commits into from
Nov 24, 2020

Conversation

Chris-Friend
Copy link
Contributor

Closes #156

Changes proposed in this pull request:

  • Add lh_sample_uuid to each sample. Store in mongo, MLWH and DART
  • Store all newly uploaded source plates in new mongo source_plates collection, unique on barcode with the added implementation logic that source plates with the same barcode must have the same lab id
  • Assign new/existing lh_source_plate_uuids to each sample, or reject sample if source plate not unique (above point). Store lh_source_plate_uuids in MLWH and mongo

Christopher Friend added 24 commits November 18, 2020 13:08
Add new mongo/mlwh/dart lh sample uuid fields
ceefe82
Add lh_sample_uuid entry to the mongo samples collection
e46242e
On mapping the mongo to mlwh entries, include the lh_sample_uuid
18e46ba
On mapping the mongo to dart entries, include the lh_sample_uuid
84d4fa0
Ensure we use the string representation of the UUID
0aed28f
Ensure correct types are used in tests
1a0c9d5
Update sql queries to include lh_sample_uuid column
56d054c
Add source plates collection constants
bc20df9
Create the source_plates collection on running main. Add (failing) tests
4a4128e
Use correct field name for a source plate's barcode
e8ab349
Add new error types
13c81ac
Add missing documentation
9dfb77f
Reformat files
3282b73
Use unique plate barcodes in the test files
9c537cb
Update tests to expect correct source plates
32860f7
Add new test to check for source plate barcode duplicated across labs…
1e71f2e 
… error messages
Update failing tests following changes to test data
57d0b06
Initial implementation of adding source plates, and adding uuids to s…
e285ec5 
…amples
Add file processing source plate update tests
ae30533
Address code quality issues
27f25a7
Add MLWH lh source plate uuid constant
4625a2b
Map the source plate uuid property from mongo doc to MLWH entry
3891348
Update mlwh insert to include lh_source_plate_uuid column value
a99519f
Update test database setup to include lh_source_plate_uuid column
3e765eb
@codecov
Copy link

codecov bot commented Nov 19, 2020 •
edited
Loading

Codecov Report

Merging #158 (a89c2f1) into develop (cafcb4f) will increase coverage by 0.50%.
The diff coverage is 100.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #158      +/-   ##
===========================================
+ Coverage    90.23%   90.73%   +0.50%     
===========================================
  Files           13       13              
  Lines         1219     1285      +66     
  Branches       142      148       +6     
===========================================
+ Hits          1100     1166      +66     
  Misses          91       91              
  Partials        28       28
Impacted Files Coverage Δ
crawler/sql_queries.py 100.00% <ø> (ø)
crawler/constants.py 100.00% <100.00%> (ø)
crawler/file_processing.py 85.92% <100.00%> (+1.09%) ⬆️
crawler/helpers.py 96.71% <100.00%> (+0.15%) ⬆️
crawler/main.py 83.33% <100.00%> (+1.70%) ⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update cafcb4f...a89c2f1. Read the comment docs.

harrietc52
harrietc52 previously approved these changes Nov 23, 2020
View reviewed changes
Copy link
Contributor

@harrietc52 harrietc52 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks great, some minor comments 👍

crawler/file_processing.py Show resolved Hide resolved
crawler/main.py Outdated Show resolved Hide resolved
tests/test_main.py Show resolved Hide resolved
tests/test_main.py Show resolved Hide resolved
@Chris-Friend
Copy link
Contributor Author

@harrietc52 just replied to some of your comments. Let me know what you think

@Chris-Friend Chris-Friend mentioned this pull request Nov 23, 2020
Closed
9 tasks
@Chris-Friend
Copy link
Contributor Author

@harrietc52 do you mind approving so I don't have to force merge without approval?

harrietc52
harrietc52 approved these changes Nov 24, 2020
View reviewed changes
Copy link
Contributor

@harrietc52 harrietc52 left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@Chris-Friend sorry missed your comments yesterday. Agree with your tests comments, me and Andrew were discussing a wider refactor of crawler for this reason. Merge away.

crawler/file_processing.py Show resolved Hide resolved
@Chris-Friend Chris-Friend merged commit 4e4ce8d into develop Nov 24, 2020
@Chris-Friend Chris-Friend deleted the GPL-745-sample-and-plate-uuid branch November 24, 2020 10:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@harrietc52 harrietc52 harrietc52 approved these changes

@andrewsparkes andrewsparkes Awaiting requested review from andrewsparkes

@emrojo emrojo Awaiting requested review from emrojo

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

GPL-745 Add sample and plate uuids to lighthouse cherrypicking - Crawler
2 participants
@Chris-Friend @harrietc52