Phenotips importer update and corresponding Migration Script #102
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…s throwing error now
…beyhond the bounds of its container.
…fixed a few things found in the process
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./etc/database/restore-database.sh rosalution-rosalution-db-1 /Users/jscherer/Downloads/rosalution-db-2023-07-06-1688674415.archive 
docker exec -it rosalution-rosalution-db-1 mongosh /tmp/fixtures/migrations/migrate-new-sections-phenotips-importer.js 
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There appears to be missing information for Clinical History the following Analyses: Screenshot provided by the Pull Request:
Screenshot from my review:
This has been resolved:
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JmScherer
approved these changes
Jul 7, 2023
fatimarabab
added a commit
that referenced
this pull request
Jul 7, 2023
…mages Attachments (#103) * wip to refactoring to supporting multiple sections in an analysis to add attachments * wip for analysis backend integration with the adding/updating/removing * debugging whats going on * got it working? * reduced the CSS footprint for the gene box component and the dom to be simpler * wip for consolidating the css * conslidated work that was here * wip for refactoring the backend * fixed frontend linting issues * Refactoring to make the emits work, starting work on the updating section image in the backend * Image edit update and removal working * Replaced the component back into the sectionbox and am chaining emits from sectionimage to sectionbox to analysis view * fixed removing an image, it now properly reacts to the image removed * Updated the backend analysis collection attach image to use field instead of dataset to fix image attachment * Updated the analysis image system tests, changed system-tests/e2e/attach_pedigree_image.cy.js to be attach_analysis_section_image.cy.js * Knocked out some system tests, working on the others. I think there's a bug, need to check * Working out some of the system tests, they won't work until the collapsible and empty content boxes are resolved * fixed collasping of the section boxes in annotationview and made preliminary changes to the system test for collapsing * Work in progress to resolve CSS and remove the force render * Fixed most of the linting for python * Refactored to not require the force re-render for frontend images * frontend css changes to make progress to editing case" git push * System tests passing * disabled duplicate code check * formatted backend code with yapf * Frontned unit tests updated along with additional console logging on frontend removed for debugging * Updated test_analysis_collection.py to reflect the new tests for the analysis section images. Also removed a few functions from analysis_collection.py pretaining to pedigree. Lastly, updated some text fixtures to more accurately reflect what the structure is * Fixed up the integration tests for the analysis_router.py * Linting * Removed some comments * Linting again * removed special coloring to help resolve cleaning up and consolidating the CSS * Phenotips importer update and corresponding Migration Script (#102) * Added new sections to analysis * Modified phenotips importer to show sections for multiple genes in analysis * progress in migration script * Fixed backend linting * Fixed up phenotips_importer.py and added a test * Added migration script to reconfigure analysis sections. Gene sections throwing error now * Updated the CSS for the section text so that it wraps and doesn't go beyhond the bounds of its container. * Updated gene sections to reconfigure where HPO terms are displayed * Removed duplicate Clinical History/HPO terms loop * added the pedigree image if it exists * Removed print statements and included pedgree image migration * added type to sections * Added images-dataset type for fields * script fix, verified can only run it once succesfully * Updated the base fixtures to use the new analysis system * Updated phenotips importer to have field names match header * backend linting fixes * Updated the system tests for the image attaching * Fixed the formatting that came up with yapf * Resovled the system tests * Added some logging to the script to be informative of the output and fixed a few things found in the process * Pushign up fix for the clinical history --------- Co-authored-by: James Scherer <jscherer@uab.edu> Co-authored-by: Angelina Elizabeth Uno-Antonison <ange.unoantonison@gmail.com> * Updating system test to match the miggrated fixtures --------- Co-authored-by: James Scherer <jscherer@uab.edu> Co-authored-by: Rabab Fatima <rfatima@uab.edu>
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Pull Request Details
Wrike Tickets - Update the phenotips importer to create new sections that are needed from presentations as of Spring 2023
As a clinical researcher, I need a place to enter information regarding each gene's molecular mechanism data per gene in a case
Changes made:
To Review:
Static Analysis by Reviewer
The migration script migrates the production installation works as intended/rendered correctly.
To check this run the following commands:
Download the archived production database to your local machine. See @SeriousHorncat for the URL to download it from Box.
Import the production database backup to Rosalution from the rosalution root directory
# ./etc/database/restore-database.sh <container name> <absolute-file-path-to-backup-archive> ./etc/database/restore-database.sh rosalution-rosalution-db-1 rosalution-db-2023-07-06-1688674415.archivedocker exec -it rosalution-rosalution-db-1 mongosh /tmp/fixtures/migrations/migrate-new-sections-phenotips-importer.jsCPAM0092
CPAM0099
CPAM0082
Existing Fixtures are updated correctly to verify the new sections are added correctly
CPAM0084
CPAM0002
All Github Actions checks have passed.