feat: display seqvars query execution results in UI (#1952)

[holtgrewe]

[github-actions[bot]]

deps-report 🔍

Commit scanned: c0dad7d ℹ️ Python version 3.10 is used by your project but the latest version is 3.13.

Vulnerable dependencies

4 dependencies have vulnerabilities 😱

Dependency	Advisory	Versions impacted
djangorestframework (transitive)	Affected versions of the package djangorestframework are vulnerable to Cross-site Scripting (XSS) via the break_long_headers template filter due to improper input sanitization before splitting and joining with tags.	<3.15.2
jinja2 (transitive)	In Jinja2, the from_string function is prone to Server Side Template Injection (SSTI) where it takes the source parameter as a template object, renders it, and then returns it. The attacker can exploit it with INJECTION COMMANDS in a URI. NOTE: The maintainer and multiple third parties believe that this vulnerability isn't valid because users shouldn't use untrusted templates without sandboxing.	>=0
setuptools (transitive)	Affected versions of Setuptools allow for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system.	<70.0.0
sqlalchemy	Sqlalchemy 2.0.0b1 avoids leaking cleartext passwords to the open for careless uses of str(engine.URL()) in logs and prints. https://github.com/sqlalchemy/sqlalchemy/pull/8563	<2.0.0b1

Outdated dependencies

47 outdated dependencies found (including 19 outdated major versions)😢

Dependency	Installed version	Latest version
alabaster (transitive)	0.7.16	1.0.0
argon2-cffi (transitive)	21.3.0	23.1.0
billiard (transitive)	3.6.4.0	4.2.1
crispy-bootstrap4 (transitive)	2022.1	2024.10
django	3.2.25	5.1.2
django-model-utils (transitive)	4.3.1	5.0.0
django-rest-knox (transitive)	4.2.0	5.0.2
django-sodar-core	0.13.4	1.0.2
jsonschema-specifications (transitive)	2023.12.1	2024.10.1
markupsafe (transitive)	2.1.5	3.0.1
mistune (transitive)	2.0.5	3.0.2
packaging (transitive)	23.2	24.1
protobuf	3.20.3	5.28.2
setuptools (transitive)	67.6.1	75.1.0
sphinx (transitive)	6.2.1	8.0.2
sphinx-rtd-theme (transitive)	1.2.2	3.0.1
sqlalchemy	1.4.54	2.0.35
unidecode (transitive)	0.4.21	1.3.8
xmlschema (transitive)	2.5.1	3.4.2

Dependency	Installed version	Latest version
aiobotocore (transitive)	2.15.1	2.15.2
black	24.8.0	24.10.0
botocore (transitive)	1.35.23	1.35.37
celery (transitive)	5.2.7	5.4.0
charset-normalizer (transitive)	3.3.2	3.4.0
coverage (dev,transitive)	7.6.1	7.6.2
django-autocomplete-light (transitive)	3.9.4	3.11.0
django-crispy-forms (transitive)	2.0	2.3
django-db-file-storage (transitive)	0.5.5	0.5.6.1
django-debug-toolbar	4.3.0	4.4.6
django-environ (transitive)	0.10.0	0.11.2
django-iconify (transitive)	0.1.1	0.4
django-plugins-bihealth	0.4.0	0.5.2
django-postgres-copy	2.3.7	2.7.6
djangorestframework (transitive)	3.14.0	3.15.2
docutils (transitive)	0.18.1	0.21.2
drf-keyed-list-bihealth	0.1.1	0.2.1
faker	30.1.0	30.3.0
markdown (transitive)	3.4.1	3.7
mypy-protobuf (dev)	3.3.0	3.6.0
pydantic-core (transitive)	2.23.4	2.24.0
requests-http-signature	0.2.0	0.7.1
rules (transitive)	3.3	3.5
sentry-sdk	2.15.0	2.16.0
versioneer (transitive)	0.28	0.29
wheel (transitive)	0.40.0	0.44.0
xmltodict (transitive)	0.13.0	0.14.1
yarl (transitive)	1.13.1	1.14.0

_Logs

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 50.52632% with 47 lines in your changes missing coverage. Please review.

Project coverage is 91%. Comparing base (0f405f6) to head (c0dad7d). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
backend/seqvars/protos/output_pb2.py	0%	46 Missing :warning:
backend/seqvars/models/protobufs.py	66%	1 Missing :warning:

Additional details and impacted files

@@          Coverage Diff           @@
##            main   #1957    +/-   ##
======================================
- Coverage     91%     91%    -1%     
======================================
  Files        667     674     +7     
  Lines      37986   38407   +421     
======================================
+ Hits       34869   35066   +197     
- Misses      3117    3341   +224     

Files with missing lines	Coverage Δ
...mport/tests/snapshots/snap_test_models_executor.py	100% <100%> (+62%)	:arrow_up:
...staltmatcher/migrations/0003_auto_20241009_0639.py	100% <100%> (ø)
...kend/seqvars/migrations/0010_auto_20240905_1017.py	100% <100%> (ø)
backend/seqvars/models/base.py	96% <100%> (+<1%)	:arrow_up:
backend/seqvars/tasks.py	100% <100%> (ø)
...end/seqvars/tests/snapshots/snap_test_views_api.py	100% <ø> (ø)
backend/seqvars/tests/test_permissions_api.py	99% <ø> (ø)
backend/seqvars/tests/test_views_api.py	99% <ø> (ø)
backend/seqvars/urls.py	100% <ø> (ø)
backend/seqvars/views_api.py	83% <100%> (+<1%)	:arrow_up:
... and 2 more

... and 2 files with indirect coverage changes

[holtgrewe]

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[!CAUTION]

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The pull request is closed.

Walkthrough

The changes in this pull request encompass the addition of new files and updates to existing files related to genetic data handling, API modifications, and user interface components. New VCF files and a pedigree file have been introduced, along with updates to Django models and API endpoints to accommodate changes in data retrieval and pagination methods. Additionally, several Vue components have been created or modified to enhance the user experience and data presentation in the frontend.

Changes

File Path	Change Summary
backend/Case_1_exons.ped	New entries added representing family genetic information.
backend/external-copy-0.vcf	New VCF file created following VCF version 4.2 specification.
backend/ingested.vcf	New VCF file created following VCF version 4.4 specification.
backend/seqvars/migrations/0009_auto_20240905_1017.py	Model ordering options updated for three models and genome_release field changed to CharField.
backend/seqvars/models/base.py	Added ordering specifications for SeqvarsResultSet and SeqvarsResultRow models.
backend/seqvars/models/executors.py	Added print statement in run_worker method for logging command execution.
backend/seqvars/urls.py	Updated URL pattern for api/resultset endpoint to capture queryexecution identifier.
backend/seqvars/views_api.py	Modified pagination mechanism, project retrieval, and API schema parameters.
backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml	Significant updates to OpenAPI schema, replacing cursor-based pagination with page-based pagination.
backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi	New compressed index file for VCF added.
backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl	New YAML template file for genomic data representation.
backend/varfish/users/management/commands/data/Case_1_exons.ped	New pedigree file created containing family information.
backend/varfish/users/management/commands/initdev.py	Updated --data-case argument choices to include "Case_1_exons".
frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts	Adjusted infinite query options and pagination parameters.
frontend/ext/varfish-api/src/lib/schemas.gen.ts	Added new properties to existing schema definitions.
frontend/ext/varfish-api/src/lib/services.gen.ts	Updated API view function URLs to reflect new parameter names.
frontend/ext/varfish-api/src/lib/types.gen.ts	Added count?: number; property to multiple paginated response types.
frontend/src/cases/components/CaseListTable/CaseListTable.vue	Enhanced rendering of data table with a new template slot for item indices.
frontend/src/cases/queries/cases.ts	New query function useCaseRetrieveQuery added for retrieving case details.
frontend/src/seqvars/components/QueryEditor/QueryEditor.vue	Modified selectedQueryUuid to use defineModel for enhanced state management.
frontend/src/seqvars/components/QueryResults/CellGeneFlags.vue	New component introduced for displaying genetic variant information.
frontend/src/seqvars/components/QueryResults/QueryResults.vue	New component for displaying query results related to a specific case.
frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue	New component for displaying a results table for query results.
frontend/src/seqvars/components/QueryResults/types.ts	New interface PageInfo added for pagination aspects.
frontend/src/seqvars/queries/seqvarQueryExecution.ts	Added import for useQuery and updated method signatures.
frontend/src/seqvars/queries/seqvarResultRow.ts	New file introduced for handling seqvar result sets with query functionalities.
frontend/src/seqvars/queries/seqvarResultSet.ts	New file for querying seqvar result sets.
frontend/src/seqvars/views/SeqvarsQuery/SeqvarsQuery.vue	Enhanced functionality with new imports and computed properties for query results management.

Possibly related PRs

• #1957: This PR is related as it involves the backend/Case_1_exons.ped file, which is also modified in the main PR to include new data entries for family genetic information. Both PRs deal with the same file and context of genetic data representation.

Poem

🐇 In the garden of genes, we play,
New files sprout, bright as the day.
With queries and tables, we hop with delight,
Each change a new path, a wondrous sight.
Let's celebrate data, both old and new,
For in every byte, there's magic too! 🌼

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