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Annotation rendering configuration new section updates #104

Merged
merged 15 commits into from
Jul 7, 2023
Merged

Annotation rendering configuration new section updates #104

merged 15 commits into from
Jul 7, 2023

Commits on Jul 7, 2023

  1. annotation rendering configuration frontend updates (#84) 

    * updated annotation configuration, updated unit tests, partially updated system tests

* updating the sidebar style to remained a fixed size, updated the logic for removing '_' from the anchors when displaying them

* fixed system test & made the anchors have consistent naming style

* added back the dataset data for each model

* lint fix

* unit test update

* removed file upload where not needed

* made requested PR changes, updating variant to hgvs_variant for attachment/genomic Type type, update styling to use variable set in main.css

* Update frontend/src/models/analyses.js

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: Alex Moss <kuthedk@users.noreply.github.com>

* Update frontend/src/models/analyses.js

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: Alex Moss <kuthedk@users.noreply.github.com>

* Update frontend/src/models/analyses.js

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: Alex Moss <kuthedk@users.noreply.github.com>

* Update case_annotation_section_anchors.cy.js

* Update frontend/src/models/analyses.js

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: Alex Moss <kuthedk@users.noreply.github.com>

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Signed-off-by: Alex Moss <kuthedk@users.noreply.github.com>
Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
    @kuthedk @SeriousHorncat
    kuthedk and SeriousHorncat committed Jul 7, 2023
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  2. Alliance genome models into new configuration (#88) 

    * Update Annotation Configuration to include new annotations from Alliance Genome (#81)
* Now fetching the proper alliance genomic identifiers, with the correct identifiers the models are now being pulled in as expected
* Create Animal Model Card to represent the animal models from Alliance Genome (#86)
* Adding scrolling to the cards
* Changed the model annotations to get a limit of 100 models, rather than 20 models. Updated the fixtures to contain ALL models
* Removed display: block, position: relative from card-base. Changed li margin-left to use variable. Removed the overflow-y from card-source
* Consolidated duplicate conditional code to determine if a section is empty and change the text color in AlliangeGenomeCard
* Updated the AllianceGenomeCard.spec.js toContain to be to.include
* Merged and updated for the new configuration to allign with the new datasets being introduced.

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Signed-off-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Co-authored-by: James Scherer <jscherer@uab.edu>
    @SeriousHorncat @JmScherer
    SeriousHorncat and JmScherer committed Jul 7, 2023
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  3. Migration script to update the data layer for the additional sections (… 

    …#89)

* Created migration script file to add additional annotation sections

* Migration script saving changes in database. Debugging comments removed

* Update etc/fixtures/migrations/migrate-additional-sections.js

Added suggestion to update section name to match configuration

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: Rabab Fatima <fr.rabab@gmail.com>

---------

Signed-off-by: Rabab Fatima <fr.rabab@gmail.com>
Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
    @fatimarabab @SeriousHorncat
    fatimarabab and SeriousHorncat committed Jul 7, 2023
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  4. Investigate why CPAM0084 breaks when re-running annotation from the a… 

    …pi docs (#91)

* Updated the fixtures for CPAM0084

* Updated python tests
    @JmScherer @SeriousHorncat
    JmScherer authored and SeriousHorncat committed Jul 7, 2023
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  5. As a Computational Biologist, I want to see the various summaries for… 

    … animal models in the relevant section so I can have all the information consolidated in one location (#92)

* Updated annotation configuration to have both automated and specificed alliance genome animal summaries, updated the fixtures to include both summaries and are accurate to the gene identifier, and updated the annotation rendering configuration to display the new annotations

* Updated the python tests to include the 4 extra annotations in the configuration

* updated the existing tests and removed the mongo ids from the imported fixtures

* updated the existing tests and removed the mongo ids from the imported fixtures

* Updated the Text Dataset in the Annotation components to display as unavailable if the value also has empty string

* Updated the fixtures for genomic unit collection

* Removed the mongoids from the genomic units collection initial seed
    @JmScherer @SeriousHorncat
    JmScherer authored and SeriousHorncat committed Jul 7, 2023
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  6. additional annottations

    @kuthedk @SeriousHorncat
    kuthedk authored and SeriousHorncat committed Jul 7, 2023
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  7. resolved unit test failures

    @SeriousHorncat
    SeriousHorncat committed Jul 7, 2023
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  8. Fixing the backend tests

    @JmScherer @SeriousHorncat
    JmScherer authored and SeriousHorncat committed Jul 7, 2023
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  9. Updated the integration tests for backend

    @JmScherer @SeriousHorncat
    JmScherer authored and SeriousHorncat committed Jul 7, 2023
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  10. As a Developer, provide a way to remove all automatic annotations fro… 

    …m analyses, so they can be re-annotated with the correct information (#99)

* Adding the remove annotation and annotation queueing scripts

* Adding documentation and run feedback

* Updated the analysis annotation script to give relevant output

* Fixed the annotation config that broke annotation

* Linting should be passing

* Removed debugging print statements

* Added a note to the annotate-all-existing-analyses.sh that it may need to be run more than once

* Removed a space
    @JmScherer @SeriousHorncat
    JmScherer authored and SeriousHorncat committed Jul 7, 2023
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  11. Updated the the annotation configuration to uitilize the tag dataset … 

    …to visualize the HPO terms
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    SeriousHorncat committed Jul 7, 2023
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  12. Fixed the unit test failing due to the addition of the tag datasets c… 

    …omponent
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    SeriousHorncat committed Jul 7, 2023
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  13. fixed the mised merge issue

    @SeriousHorncat
    SeriousHorncat committed Jul 7, 2023
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  14. pushing up system test changes

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    SeriousHorncat committed Jul 7, 2023
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  15. Skipping the 'should allow the user to navigate the analysis via the … 

    …logo, header, and section anchor links' for now until we fix it
    @JmScherer
    JmScherer committed Jul 7, 2023
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