Files that changed from the base of the PR and between 0f405f6 and 40bc415.

• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz is excluded by !**/*.gz

• backend/Case_1_exons.ped (1 hunks)
• backend/external-copy-0.vcf (1 hunks)
• backend/ingested.vcf (1 hunks)
• backend/seqvars/migrations/0009_auto_20240905_1017.py (1 hunks)
• backend/seqvars/models/base.py (3 hunks)
• backend/seqvars/models/executors.py (1 hunks)
• backend/seqvars/urls.py (1 hunks)
• backend/seqvars/views_api.py (5 hunks)
• backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml (19 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi (1 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl (1 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.ped (1 hunks)
• backend/varfish/users/management/commands/initdev.py (1 hunks)
• frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts (22 hunks)
• frontend/ext/varfish-api/src/lib/schemas.gen.ts (16 hunks)
• frontend/ext/varfish-api/src/lib/services.gen.ts (1 hunks)
• frontend/ext/varfish-api/src/lib/types.gen.ts (19 hunks)
• frontend/src/cases/components/CaseListTable/CaseListTable.vue (1 hunks)
• frontend/src/cases/queries/cases.ts (1 hunks)
• frontend/src/seqvars/components/QueryEditor/QueryEditor.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/CellGeneFlags.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/QueryResults.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/types.ts (1 hunks)
• frontend/src/seqvars/queries/seqvarQueryExecution.ts (6 hunks)
• frontend/src/seqvars/queries/seqvarResultRow.ts (1 hunks)
• frontend/src/seqvars/queries/seqvarResultSet.ts (1 hunks)
• frontend/src/seqvars/views/SeqvarsQuery/SeqvarsQuery.vue (4 hunks)

• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi
• backend/varfish/users/management/commands/data/Case_1_exons.ped

frontend/src/seqvars/components/QueryResults/types.ts (1)

1-7: LGTM: Well-structured interface for pagination

The PageInfo interface is well-designed with clear and consistent naming conventions. It provides a good foundation for handling pagination in the application.

backend/Case_1_exons.ped (1)

1-3: LGTM! The pedigree file structure is correct.

The file follows the standard pedigree file format used in genetic studies. Each line correctly represents a family member with the required attributes: Family ID, Individual ID, Father ID, Mother ID, Sex, and Affected Status. The relationships and attributes are consistent across the three entries.

backend/seqvars/migrations/0009_auto_20240905_1017.py (4)

13-16: LGTM: Ordering change for seqvarsqueryexecutionbackgroundjob

The change to order seqvarsqueryexecutionbackgroundjob by descending primary key (-pk) is appropriate. This will ensure that the most recently created background jobs appear first in queries by default, which is often desirable for displaying job lists or in admin interfaces.

---

17-20: LGTM: Logical ordering for seqvarsresultrow

The new ordering for seqvarsresultrow (["chrom_no", "pos", "ref_allele", "alt_allele"]) is well-chosen. This ordering will:

1. Group variants by chromosome
2. Sort variants by position within each chromosome
3. Further sort by reference and alternate alleles

This is a standard and efficient way to organize genetic variant data, facilitating easier data analysis and visualization.

---

21-24: LGTM: Chronological ordering for seqvarsresultset

The change to order seqvarsresultset by descending date created (-date_created) is appropriate. This ensures that:

1. The most recent result sets appear first in queries by default.
2. Users can easily access the latest results.
3. It aligns with common user expectations of seeing the newest data first.

This ordering is particularly useful for displaying result sets in user interfaces or when retrieving the latest analysis results.

---

1-32: LGTM: Well-structured migration improving model organization and data integrity

This migration file makes several beneficial changes:

1. Improves ordering for three models, enhancing query efficiency and user experience.
2. Restricts the genome_release field to valid options, ensuring data integrity.

These changes will positively impact data organization, query performance, and prevent invalid data entry. The migration is well-structured and follows Django best practices.

backend/seqvars/urls.py (1)

84-87: LGTM! Verify related code for consistency.

The URL pattern change from (?P<query>[0-9a-f-]+) to (?P<queryexecution>[0-9a-f-]+) looks good. This update improves the API's semantics by explicitly referring to a query execution rather than just a query.

To ensure consistency across the codebase, please verify that corresponding changes have been made in the related view, serializer, and any other components that interact with this endpoint. Run the following script to check for potential inconsistencies:

This script will help identify any potential inconsistencies or areas that might need updating due to this URL pattern change.

frontend/src/cases/queries/cases.ts (1)

Line range hint 96-115: Well-integrated with existing code structure.

The new useCaseRetrieveQuery function is well-integrated with the existing code structure. It follows the same patterns as the other query functions in the file, using the same imports and similar configuration. This consistency makes the code more maintainable and easier to understand.

frontend/src/cases/components/CaseListTable/CaseListTable.vue (1)

Line range hint 1-234: Summary: Good enhancement to the CaseListTable component

The changes in this file successfully add an index column to the case list table, enhancing the user interface and partially meeting the PR objectives. The implementation is correct, consistent with existing code, and follows Vue.js best practices.

Key points:

1. The new index column provides a clear reference for each row in the table.
2. The changes are minimal and don't affect the existing functionality.
3. The implementation is well-integrated with the v-data-table-server component.

Overall, this is a solid improvement to the component that will enhance the user experience when viewing the case list.

backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl (4)

Line range hint 2-26: LGTM: Family section structure

The structure of the family section is well-organized and consistent, providing a clear representation of the proband's information.

---

Line range hint 42-58: LGTM: Diseases and metadata sections

The structure of the diseases and metaData sections is well-organized. The use of a YAML anchor for metadata promotes reusability across the document.

---

Line range hint 135-157: LGTM: Pedigree section

The pedigree section is well-structured and uses template variables appropriately for customization. The family relationships are clearly defined.

---

Line range hint 158-171: LGTM: Final files section

The final files section is well-structured and uses template variables appropriately for customization. The genomebuild attribute is correctly set to "grch37", which is consistent with the filename.

backend/ingested.vcf (1)

1-17: LGTM: File format and INFO fields are well-defined.

The VCF file format and INFO fields are correctly specified. The inclusion of gnomAD (exomes, genomes, mtDNA) and HelixMtDb data provides comprehensive allele frequency information. The ANN field for functional annotations follows the standard format.

backend/seqvars/models/base.py (2)

2376-2378: LGTM: Appropriate ordering added to SeqvarsResultSet

The addition of the Meta class with ordering = ["-date_created"] is a good practice. This ensures that the most recent results are displayed first when querying SeqvarsResultSet objects.

---

2420-2422: LGTM: Appropriate ordering added to SeqvarsResultRow

The addition of the Meta class with ordering = ["chrom_no", "pos", "ref_allele", "alt_allele"] is well-thought-out. This ordering ensures that the result rows are sorted in a genomically meaningful way: first by chromosome number, then by position, and finally by reference and alternative alleles.

frontend/ext/varfish-api/src/lib/services.gen.ts (3)

Line range hint 1671-1681: Verify impact on frontend components

The changes to both seqvarsApiResultsetList and seqvarsApiResultsetRetrieve functions may have a broader impact on the frontend components that interact with result sets.

To ensure a smooth transition, please run the following command to identify all files that import and use these functions:

#!/bin/bash
# Find all files that import and use seqvarsApiResultsetList or seqvarsApiResultsetRetrieve
rg "import.*\{.*(?:seqvarsApiResultsetList|seqvarsApiResultsetRetrieve).*\}.*from.*services\.gen" --type ts -A 10

Review the output and update any component logic that may be affected by this change, such as how query executions are handled or how result sets are fetched and displayed.

---

Line range hint 1679-1681: Update URL parameter from query to queryexecution

The URL path for seqvarsApiResultsetRetrieve has been updated to use queryexecution instead of query. This change is consistent with the modification made to seqvarsApiResultsetList.

Please verify that all frontend code calling this function has been updated to provide the queryexecution parameter instead of query. Run the following command to check for any remaining usage of the old parameter:

✅ Verification successful

Verification Successful: No remaining query parameter usages found in seqvarsApiResultsetRetrieve calls.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for any remaining usage of 'query' parameter in seqvarsApiResultsetRetrieve calls
rg "seqvarsApiResultsetRetrieve\s*\(\s*\{[^}]*query\s*:" --type ts

Length of output: 7200

---

1671-1673: Update URL parameter from query to queryexecution

The URL path for seqvarsApiResultsetList has been updated to use queryexecution instead of query. This change aligns with the backend API modifications.

Please ensure that all frontend code calling this function has been updated to provide the queryexecution parameter instead of query. Run the following command to check for any remaining usage of the old parameter:

frontend/ext/varfish-api/src/lib/types.gen.ts (5)

1022-1025: LGTM: Addition of count property to PaginatedSeqvarsPredefinedQueryList

The addition of the optional count property to the PaginatedSeqvarsPredefinedQueryList type is a good improvement. This will allow clients to know the total number of items available, which is useful for pagination controls.

---

1029-1032: LGTM: Addition of count property to PaginatedSeqvarsQueryExecutionList

The change to PaginatedSeqvarsQueryExecutionList is consistent with the previous change, adding an optional count property. This maintains consistency across paginated types.

---

1036-1039: LGTM: Addition of count property to PaginatedSeqvarsQueryList

The addition of the count property to PaginatedSeqvarsQueryList follows the same pattern as the previous changes. This consistency is good for maintaining a uniform API structure.

---

1043-1046: LGTM: Consistent addition of count property to multiple paginated types

The changes to the following types are consistent with the previous modifications:

• PaginatedSeqvarsQueryPresetsClinvarList
• PaginatedSeqvarsQueryPresetsColumnsList
• PaginatedSeqvarsQueryPresetsConsequenceList
• PaginatedSeqvarsQueryPresetsFrequencyList
• PaginatedSeqvarsQueryPresetsLocusList
• PaginatedSeqvarsQueryPresetsPhenotypePrioList
• PaginatedSeqvarsQueryPresetsQualityList
• PaginatedSeqvarsQueryPresetsSetList
• PaginatedSeqvarsQueryPresetsSetVersionList
• PaginatedSeqvarsQueryPresetsVariantPrioList
• PaginatedSeqvarsQuerySettingsList
• PaginatedSeqvarsResultRowList
• PaginatedSeqvarsResultSetList

Each type now includes an optional count property. This consistent approach across all paginated types is excellent for maintaining a uniform API structure and improving the client's ability to handle pagination.

Also applies to: 1050-1053, 1057-1060, 1064-1067, 1071-1074, 1078-1081, 1085-1088, 1092-1095, 1099-1102, 1106-1109, 1113-1116, 1120-1123, 1127-1130

---

1022-1130: Summary: Improved pagination support across multiple types

The changes in this file consistently add an optional count property to various paginated response types. This enhancement will allow clients to access the total count of items in a paginated list, which is crucial for implementing effective pagination controls and improving the overall user experience.

The modifications are uniform across all affected types, maintaining consistency in the API structure. This update represents a positive improvement in the API's functionality without introducing any apparent issues or inconsistencies.

frontend/ext/varfish-api/src/lib/schemas.gen.ts (16)

2934-2937: New property added to paginated response schemas

A count property has been added to the PaginatedSeqvarsPredefinedQueryList schema. This addition is consistent with the changes mentioned in the AI-generated summary. The count property will provide the total number of items in the list, which is a useful feature for pagination.

Also applies to: 2940-2942, 2946-2948

---

2962-2965: Consistent addition of count property

The count property has also been added to the PaginatedSeqvarsQueryExecutionList schema. This change is consistent with the previous addition and follows the same pattern.

Also applies to: 2968-2970, 2974-2976

---

2990-2993: Continued consistency in schema updates

The count property has been added to the PaginatedSeqvarsQueryList schema as well. This maintains consistency across the paginated response schemas.

Also applies to: 2996-2998, 3002-3004

---

3018-3021: Uniform updates to paginated schemas

The PaginatedSeqvarsQueryPresetsClinvarList schema has also been updated with the count property. This change continues the pattern of updates across paginated response schemas.

Also applies to: 3024-3026, 3030-3032

---

3046-3049: Consistent schema updates

The PaginatedSeqvarsQueryPresetsColumnsList schema has been updated with the count property, maintaining consistency with the other changes.

Also applies to: 3052-3054, 3058-3060

---

3074-3077: Uniform addition of count property

The PaginatedSeqvarsQueryPresetsConsequenceList schema has been updated with the count property, following the same pattern as the previous changes.

Also applies to: 3080-3082, 3086-3088

---

3102-3105: Consistent schema updates continue

The PaginatedSeqvarsQueryPresetsFrequencyList schema has also been updated with the count property, maintaining the consistency of the changes.

Also applies to: 3108-3110, 3114-3116

---

3130-3133: Uniform updates to paginated schemas

The PaginatedSeqvarsQueryPresetsLocusList schema has been updated with the count property, following the same pattern as the previous changes.

Also applies to: 3136-3138, 3142-3144

---

3158-3161: Consistent addition of count property

The PaginatedSeqvarsQueryPresetsPhenotypePrioList schema has been updated with the count property, maintaining consistency with the other changes.

Also applies to: 3164-3166, 3170-3172

---

3186-3189: Uniform schema updates

The PaginatedSeqvarsQueryPresetsQualityList schema has been updated with the count property, following the same pattern as the previous changes.

Also applies to: 3192-3194, 3198-3200

---

3214-3217: Consistent schema updates continue

The PaginatedSeqvarsQueryPresetsSetList schema has also been updated with the count property, maintaining the consistency of the changes.

Also applies to: 3220-3222, 3226-3228

---

3242-3245: Uniform updates to paginated schemas

The PaginatedSeqvarsQueryPresetsSetVersionList schema has been updated with the count property, following the same pattern as the previous changes.

Also applies to: 3248-3250, 3254-3256

---

3270-3273: Consistent addition of count property

The PaginatedSeqvarsQueryPresetsVariantPrioList schema has been updated with the count property, maintaining consistency with the other changes.

Also applies to: 3276-3278, 3282-3284

---

3298-3301: Uniform schema updates

The PaginatedSeqvarsQuerySettingsList schema has been updated with the count property, following the same pattern as the previous changes.

Also applies to: 3304-3306, 3310-3312

---

3326-3329: Consistent schema updates continue

The PaginatedSeqvarsResultRowList schema has also been updated with the count property, maintaining the consistency of the changes.

Also applies to: 3332-3334, 3338-3340

---

3354-3357: Final uniform update to paginated schemas

The PaginatedSeqvarsResultSetList schema has been updated with the count property, following the same pattern as all the previous changes.

These consistent updates across all paginated response schemas will improve the API's functionality by providing a standardized way to access the total count of items in each list. This information is crucial for implementing proper pagination in the frontend.

Also applies to: 3360-3362, 3366-3368

frontend/src/seqvars/queries/seqvarResultSet.ts (1)

85-87: Avoid using @ts-ignore and resolve the TypeScript issue

This issue also occurs here. Please address it as mentioned in the previous comment.

frontend/src/seqvars/queries/seqvarQueryExecution.ts (3)

8-8: Importing useQuery is appropriate.

The addition of useQuery to the imports from @tanstack/vue-query is necessary for the new query functions.

---

36-39: Inclusion of queryExecution parameter improves function flexibility.

Adding the queryExecution parameter to the invalidateSeqvarQueryExecutionKeys function allows for selective invalidation of specific query execution caches. This change aligns the function's parameters with its internal usage and enhances its utility.

---

123-123: Ensure consistent use of client in API options.

Adding client to the seqvarsApiQueryexecutionListOptions ensures that the correct API client is used for the requests. This change enhances consistency and correctness in API calls.

frontend/src/seqvars/views/SeqvarsQuery/SeqvarsQuery.vue (4)

16-16: Import of QueryResults Component

The QueryResults component is correctly imported, enabling its usage within this file.

---

74-88: Proper Management of Query Selection State

The reactive references selectedQueryUuidRef and openQueryUuids, along with the computed property selectedQueryUuid, are well-defined. The computed property effectively manages the selected query UUID and ensures that the openQueryUuids array is updated when a new query is selected.

---

197-198: Binding Query Selection Props to QueryEditor Component

The use of v-model to bind selectedQueryUuid and openQueryUuids to the QueryEditor component ensures two-way data binding and keeps the state synchronized between components.

---

211-231: Integration and Conditional Rendering of QueryResults Component

The conditional rendering using v-if and v-else correctly handles the loading state with v-skeleton-loader and displays the QueryResults component once the data is available. The bindings of selectedQueryUuid and openQueryUuids to QueryResults ensure consistent state management across the application.

frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue (1)

1-425: Overall Implementation Looks Good

The component is well-structured and follows Vue and TypeScript best practices. Reactive properties, computed properties, and watchers are used appropriately. The template is logically organized, and the use of slots and teleports enhances flexibility.

backend/seqvars/views_api.py (3)

8-8: Import Statement Update is Correct

The import of OpenApiParameter from drf_spectacular.utils is appropriate, as it's used later for enhancing the API schema documentation.

---

92-96: Project Retrieval Logic for queryexecution is Sound

The added condition in the get_project function correctly handles the retrieval of the project associated with a queryexecution UUID. This enhances the function's capability to determine the project context in more scenarios.

---

590-590: Filtering Adjustment in SeqvarsResultSetViewSet is Appropriate

Changing the filter to use queryexecution__sodar_uuid aligns with the updated data model and simplifies the query. This should efficiently retrieve the relevant result sets based on the provided queryexecution UUID.

frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts (1)

68-71: Verify the necessity of commenting out the body parameter

The body parameter merging logic in the infinite query options has been commented out. Since you're transitioning from cursor-based to page-based pagination, please confirm that the API endpoints function correctly without the body parameter and that all necessary data is passed via query parameters.

Files that changed from the base of the PR and between 40bc415 and 1195ef1.

• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz is excluded by !**/*.gz

• backend/cases_import/tests/snapshots/snap_test_models_executor.py (1 hunks)
• backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py (1 hunks)
• backend/protos/seqvars/protos/output.proto (1 hunks)
• backend/seqvars/migrations/0010_auto_20240905_1017.py (1 hunks)
• backend/seqvars/models/base.py (5 hunks)
• backend/seqvars/models/protobufs.py (3 hunks)
• backend/seqvars/protos/output_pb2.py (2 hunks)
• backend/seqvars/protos/output_pb2.pyi (2 hunks)
• backend/seqvars/tasks.py (1 hunks)
• backend/seqvars/tests/snapshots/snap_test_views_api.py (1 hunks)
• backend/seqvars/tests/test_permissions_api.py (2 hunks)
• backend/seqvars/tests/test_views_api.py (21 hunks)
• backend/seqvars/urls.py (1 hunks)
• backend/seqvars/views_api.py (6 hunks)
• backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml (22 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi (1 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl (1 hunks)
• backend/varfish/users/management/commands/data/Case_1_exons.ped (1 hunks)
• backend/varfish/users/management/commands/initdev.py (1 hunks)
• frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts (24 hunks)
• frontend/ext/varfish-api/src/lib/schemas.gen.ts (20 hunks)
• frontend/ext/varfish-api/src/lib/services.gen.ts (3 hunks)
• frontend/ext/varfish-api/src/lib/types.gen.ts (25 hunks)
• frontend/src/cases/components/CaseListTable/CaseListTable.vue (1 hunks)
• frontend/src/cases/queries/cases.ts (1 hunks)
• frontend/src/seqvars/components/QueryEditor/QueryEditor.vue (3 hunks)
• frontend/src/seqvars/components/QueryResults/CellGeneFlags.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/ClingenDosage.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/QueryResults.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue (1 hunks)
• frontend/src/seqvars/components/QueryResults/types.ts (1 hunks)
• frontend/src/seqvars/queries/seqvarQuery.ts (1 hunks)
• frontend/src/seqvars/queries/seqvarQueryExecution.ts (6 hunks)
• frontend/src/seqvars/queries/seqvarResultRow.ts (1 hunks)
• frontend/src/seqvars/queries/seqvarResultSet.ts (1 hunks)
• frontend/src/seqvars/views/SeqvarsQuery/SeqvarsQuery.vue (4 hunks)
• utils/docker/Dockerfile (1 hunks)

• frontend/ext/varfish-api/src/lib/services.gen.ts

• backend/seqvars/urls.py
• backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi
• backend/varfish/users/management/commands/data/Case_1_exons.ped
• backend/varfish/users/management/commands/initdev.py
• frontend/src/cases/components/CaseListTable/CaseListTable.vue
• frontend/src/cases/queries/cases.ts
• frontend/src/seqvars/components/QueryResults/types.ts
• frontend/src/seqvars/queries/seqvarResultSet.ts
• frontend/src/seqvars/views/SeqvarsQuery/SeqvarsQuery.vue

backend/seqvars/tasks.py (1)

2-10: LGTM! Approve the refactoring changes.

The changes look good and improve the code organization:

1. The import statement now correctly reflects the new location of the run_seqvarsqueryexecutionbackgroundjob function in seqvars.models.executors, which is more appropriate for sequence variant related functionality.
2. The task function maintains its signature, ensuring backward compatibility.
3. The function body now delegates the execution to the imported module, which is a good practice for separation of concerns.

To ensure a smooth transition, let's verify that there are no remaining references to the old import path:

✅ Verification successful

Import path update verified successfully.

• No remaining references to cases_import.models.run_seqvarsqueryexecutionbackgroundjob.
• All references now use seqvars.models.executors.run_seqvarsqueryexecutionbackgroundjob in backend/seqvars/tasks.py.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any remaining references to the old import path

# Test: Search for references to 'cases_import.models' related to 'run_seqvarsqueryexecutionbackgroundjob'
# Expect: No results, as all references should have been updated
rg --type python 'from cases_import.models import.*run_seqvarsqueryexecutionbackgroundjob'
rg --type python 'cases_import.models.*run_seqvarsqueryexecutionbackgroundjob'

# Test: Confirm the new import is used consistently
# Expect: References to the new import path
rg --type python 'from seqvars.models import executors'
rg --type python 'executors.run_seqvarsqueryexecutionbackgroundjob'

Length of output: 423

---

Script:

#!/bin/bash
# Description: Check for any remaining references to the old import path with corrected file type

# Test: Search for references to 'cases_import.models' related to 'run_seqvarsqueryexecutionbackgroundjob'
# Expect: No results, as all references should have been updated
rg --type py 'from cases_import.models import.*run_seqvarsqueryexecutionbackgroundjob'
rg --type py 'cases_import.models.*run_seqvarsqueryexecutionbackgroundjob'

# Test: Confirm the new import is used consistently
# Expect: References to the new import path
rg --type py 'from seqvars.models import executors'
rg --type py 'executors.run_seqvarsqueryexecutionbackgroundjob'

Length of output: 431

backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py (3)

1-10: LGTM: Migration class and dependencies are correctly defined.

The migration file is properly generated by Django 3.2.25, and the dependency on the previous migration "0002_smallvariantquerypediascores" is correctly specified. This ensures that migrations are applied in the correct order, maintaining database schema consistency.

---

20-26: LGTM: Consistent change to BigAutoField for smallvariantquerypediascores.

The modification of the id field to BigAutoField for smallvariantquerypediascores is consistent with the previous change and follows good practices for handling potentially large datasets.

Please verify that this change doesn't affect existing data. Run the following script to check for any potential issues:

This script will help you ensure that the change to BigAutoField doesn't cause any conflicts with existing data.

---

13-19: LGTM: Appropriate change to BigAutoField for smallvariantquerygestaltmatcherscores.

The modification of the id field to BigAutoField is a good practice, especially if you anticipate a large number of records. This change ensures that you won't run out of unique identifiers in the future.

Please verify that this change doesn't affect existing data. Run the following script to check for any potential issues:

This script will help you ensure that the change to BigAutoField doesn't cause any conflicts with existing data.

backend/seqvars/migrations/0010_auto_20240905_1017.py (4)

13-16: LGTM: Appropriate ordering for background jobs.

The change to order seqvarsqueryexecutionbackgroundjob by -pk is a good practice. It ensures that the most recent jobs (assuming pk correlates with creation time) appear first in querysets, which is typically desired for background job models.

---

17-20: Excellent: Logical ordering for genetic variant data.

The ordering ["chrom_no", "pos", "ref_allele", "alt_allele"] for seqvarsresultrow is ideal for genetic variant data. It ensures that results are consistently sorted by chromosome number, position, and then alleles, which is crucial for accurate analysis and presentation of genetic data.

---

21-24: LGTM: Appropriate ordering for result sets.

Ordering seqvarsresultset by -date_created is a good choice. It ensures that the most recent result sets appear first in querysets, which is typically what users expect when viewing sets of results.

---

1-32: Overall: Well-structured migration with logical changes.

This migration file makes several important improvements to the model structure:

1. Appropriate ordering for background jobs, result rows, and result sets.
2. Proper definition of the genome_release field with valid choices.

These changes will enhance data organization and query efficiency. The migration is well-structured and follows Django best practices. Consider the suggestion about using enumerations for genome releases in future development to further improve code quality and maintainability.

frontend/src/seqvars/queries/seqvarResultRow.ts (3)

1-14: LGTM: Imports and type definition are appropriate.

The imports from '@tanstack/vue-query' and '@varfish-org/varfish-api' are correctly used, and the custom type 'OrderDir' is well-defined for its purpose.

---

86-123: LGTM: Function implementation is correct.

The useSeqvarResultRowRetrieveQueries function is well-implemented:

1. The use of useQueries is appropriate for handling multiple queries.
2. The enabled condition correctly uses toValue(resultRowUuids)?.length for transparent access into refs or getters.
3. The combine function effectively filters out undefined data and tracks the pending state.

Good job on implementing this complex query function!

---

56-84: ⚠️ Potential issue

Address TypeScript issues and correct parameter description.

1. The @ts-ignore comments indicate underlying type issues. Consider resolving these to maintain type safety:

   • Lines 76-79: Investigate why TypeScript is flagging errors for the resultset and seqvarresultrow paths.

2. In the function's JSDoc comment, correct the parameter description for resultRowUuid:

   • Current: "UUID of the seqvar result row to load."
   • Suggested: "UUID of the specific seqvar result row to retrieve."

This change will provide a more precise description of the parameter's purpose.

frontend/src/seqvars/queries/seqvarQueryExecution.ts (4)

8-8: LGTM: New import added for enhanced functionality.

The addition of useQuery import from '@tanstack/vue-query' is appropriate for the new useSeqvarQueryExecutionListQuery function introduced in this file.

---

36-39: LGTM: Improved naming consistency.

The parameter name change from queryexecution to queryExecution and the corresponding type definition update enhance code consistency and adhere to camelCase naming conventions.

---

84-107: LGTM: New query function implemented correctly.

The new useSeqvarQueryExecutionListQuery function is well-implemented:

• It correctly uses useQuery for fetching seqvar query executions.
• The enabled option ensures the query only runs when seqvarQueryUuid is available.
• The staleTime setting helps in managing cache invalidation.

Note: The @ts-ignore comment is present and necessary due to the composable function potentially being used in different contexts, as per the previous discussion.

---

Line range hint 111-123: LGTM: Improved documentation and consistent client usage.

The changes in useSeqvarQueryExecutionListQueries function are appropriate:

• The updated documentation provides better clarity on the function's purpose and parameters.
• Adding client to seqvarsApiQueryexecutionListOptions ensures consistent API call handling across the module.

backend/cases_import/tests/snapshots/snap_test_models_executor.py (4)

36-65: Well-structured snapshot for external files in sequence variant tests.

The snapshot for ImportCreateWithSeqvarsVcfTest::test_run external files is well-organized and contains all necessary information for testing. It correctly includes both the VCF file and its index, with appropriate file attributes, checksums, and identifier mappings. The use of the file:// scheme for paths is suitable for local file testing.

---

100-129: Consistent snapshot structure for structural variant external files.

The snapshot for ImportCreateWithStrucvarsVcfTest::test_run external files maintains the same well-organized structure as the sequence variant snapshot. The only difference is the correct use of "variant_type": "strucvars", which appropriately distinguishes it from the sequence variant test. This consistency in structure between different variant types is a good practice and suggests effective code reuse.

---

131-162: Consistent snapshot structure for structural variant internal files.

The snapshot for ImportCreateWithStrucvarsVcfTest::test_run internal files maintains the same well-organized structure as the sequence variant internal files snapshot. The correct use of "variant_type": "strucvars" appropriately distinguishes it from the sequence variant test.

As mentioned in the previous comment for sequence variants, please verify:

1. The intentional use of None for checksums.
2. The expected empty file_attributes and identifier_map for ingested files.

This consistency in structure between different variant types is a good practice and suggests effective code reuse.

---

35-162: Summary: Well-structured and consistent snapshots for variant import tests

The new snapshots for both ImportCreateWithSeqvarsVcfTest and ImportCreateWithStrucvarsVcfTest are well-structured and consistent. They appropriately capture the expected state for external and internal files in the import process. The use of UUIDs for internal file paths and the consistent structure between sequence and structural variant tests are commendable.

Key points:

1. Excellent consistency between sequence and structural variant test snapshots.
2. Appropriate use of variant_type to distinguish between test cases.
3. Well-organized file attributes and paths for both external and internal files.

As mentioned in previous comments, please verify the intentional use of None for checksums and empty attributes for ingested files in both test cases.

Overall, these snapshots provide a solid foundation for testing the variant import functionality.

frontend/src/seqvars/components/QueryResults/CellGeneFlags.vue (1)

1-228: Overall, well-implemented component with minor improvements suggested

The CellGeneFlags component is well-structured and effectively displays genetic variant information. It makes good use of Vue 3 features and follows best practices for conditional rendering and prop management. The use of AbbrHint components for tooltips enhances user experience.

A few minor improvements have been suggested in previous comments, including:

1. Adding a type annotation to the moiIncludes function
2. Fixing typos in hint messages
3. Updating chip labels for consistency
4. Considering an alternative approach for fallback rendering

Implementing these suggestions will further improve the component's quality and maintainability.

backend/protos/seqvars/protos/output.proto (1)

Line range hint 1-194: Overall, the changes enhance the protocol buffer definition.

The addition of the ModeOfInheritance enum and the mode_of_inheritances field to the GeneRelatedPhenotypes message are well-implemented. These changes improve the representation of genetic inheritance patterns in the protocol buffer, which is crucial for accurate genetic data handling.

The suggestions provided are minor and focus on improving documentation. Implementation of these suggestions would further enhance the clarity and maintainability of the code.

frontend/src/seqvars/components/QueryResults/QueryResultsTable.vue (3)

1-15: LGTM: Imports and component setup

The import statements and component setup are well-organized and appropriate for the component's functionality. The use of TypeScript and the Composition API is a good choice for maintaining type safety and code organization.

---

318-328: Correct implementation of watcher callback

The watcher for error handling is correctly implemented. As per the previous learning, the use of (value: Ref<boolean>) as the callback parameter type in the watch function is correct for this specific use case.

watch(
  () => resultRowListRes.isError,
  (value: Ref<boolean>) => {
    if (value.value) {
      // ... error handling logic
    }
  },
)

This implementation aligns with the expected behavior and maintains type safety.

---

1-430: Overall: Well-implemented and feature-rich component

This QueryResultsTable component is well-structured and effectively implements a complex data table for displaying query results. Key strengths include:

1. Proper use of TypeScript and the Composition API for type safety and code organization.
2. Dynamic header generation based on the case object, providing flexibility.
3. Efficient data fetching with pagination, sorting, and debounced updates.
4. Custom cell renderings for complex data presentation.
5. Flexible pagination controls with teleport functionality.

While there are a few minor areas for potential improvement (as noted in previous comments), the overall implementation is solid and should serve its purpose well.

backend/seqvars/protos/output_pb2.py (3)

Line range hint 21-98: Changes in serialized positions are consistent with the summary.

The updates to the serialized start and end positions for various message types and enums are consistent with the AI-generated summary. These changes reflect a reorganization of the generated code structure, which is expected when the underlying .proto file is modified.

---

33-34: New enum ModeOfInheritance added successfully.

The new enum ModeOfInheritance has been properly integrated into the generated code. This addition aligns with the AI-generated summary and expands the capabilities of the protocol buffer definition.

---

Line range hint 1-98: Overall, the changes in this generated file look good.

The updates to the serialized positions and the addition of the new ModeOfInheritance enum are consistent with the expected changes. The file appears to be correctly generated based on modifications to the underlying .proto file. The only suggestion is a minor readability improvement for the condition checking _USE_C_DESCRIPTORS.

frontend/src/seqvars/components/QueryEditor/QueryEditor.vue (7)

62-63: New prop openQueryUuids added

The addition of the openQueryUuids prop allows the component to track currently opened queries. This can be useful for managing the state of multiple queries across the application.

Also applies to: 76-76

---

91-91: Improved two-way binding for selectedQueryUuid

The change from a reactive reference to defineModel for selectedQueryUuid enhances the two-way binding capability of the component. This allows for better synchronization of the selected query UUID between parent and child components.

---

Line range hint 171-180: Improved label generation in createQuery function

The label generation mechanism in the createQuery function has been optimized. The new implementation prevents duplicate labels more efficiently by using a single loop and incrementing the counter outside the loop. This change improves the performance and reliability of creating new queries.

---

Line range hint 345-376: Refactored revertQueryToPresets function for better maintainability

The revertQueryToPresets function has been refactored to use helper functions queryWithGenotypePresets and queryWithGroupPresets. This change improves code readability and maintainability by breaking down the logic into smaller, reusable functions. It also ensures consistent handling of different types of presets.

---

Line range hint 395-408: Simplified updateGenotypeToPresets function

The updateGenotypeToPresets function has been simplified and now uses the queryWithGenotypePresets helper function. This change improves readability and ensures consistent handling of genotype presets across the component. The function is now more focused and easier to maintain.

---

Line range hint 458-463: Refined event handling in QueryList component

The event handling for updating the selected query UUID has been improved. The new implementation uses an inline arrow function, which is more concise and easier to read. This change enhances the maintainability of the component.

---

Line range hint 1-738: Overall improvement in code quality and maintainability

The changes made to this component demonstrate a significant improvement in code quality, maintainability, and performance. Key improvements include:

1. Better state management with the use of defineModel for selectedQueryUuid.
2. Improved query creation and preset reversion logic with the use of helper functions.
3. Refined event handling in the template section.
4. Addition of the openQueryUuids prop for better query state tracking.

These changes contribute to a more robust and efficient implementation of the QueryEditor component.

backend/seqvars/models/protobufs.py (1)

794-801: LGTM! The changes integrate well with the existing code.

The update to _phenotypes_from_protobuf function correctly incorporates the new mode of inheritance functionality. The use of map() with the new _mode_of_inheritance_from_protobuf function is an efficient way to convert the list of mode_of_inheritances.

backend/seqvars/tests/snapshots/snap_test_views_api.py (2)

Line range hint 40-359: Unchanged snapshot looks good.

The "TestQueryPresetsFactoryDefaultsViewSet::test_retrieve 1" snapshot remains unchanged, which is expected as the modification was only for the list view. The detailed structure of the preset provides comprehensive coverage for testing the retrieve endpoint.

---

Line range hint 1-359: Summary: API response structure improved with count field

The changes in this file enhance the API response structure for the list view by adding a "count" field. This improvement likely supports pagination or provides better metadata about the response. The retrieve view snapshot remains unchanged, maintaining its comprehensive test coverage.

Key points:

1. The new "count" field accurately reflects the number of items in the results.
2. The change is isolated to the list view, as expected.
3. The detailed structure of the retrieve view continues to provide thorough test coverage.

These changes appear to be part of a larger effort to improve the API's functionality and should integrate well with the existing codebase.

backend/seqvars/tests/test_permissions_api.py (3)

2284-2287: LGTM: Updated URL kwargs in test_retrieve method

The change from 'query' to 'queryexecution' in the URL kwargs for the test_retrieve method is consistent with the update in the test_list method. This ensures that the test suite accurately reflects the new API structure.

---

Line range hint 2314-2357: Consider reviewing TestResultRowViewSet for consistency

While no changes were made to the TestResultRowViewSet class in this diff, it's worth reviewing to ensure consistency with the updates made to the TestResultSetViewSet class. Specifically, check if any URL kwargs need to be updated from 'query' to 'queryexecution' or if any other adjustments are necessary to align with the new API structure.

Let's check if there are any occurrences of 'query' in the URL kwargs for this class:

#!/bin/bash
# Search for 'query' in URL kwargs within the TestResultRowViewSet class
rg --type python 'class TestResultRowViewSet.*?kwargs=\{.*"query":' -U

---

2264-2266: LGTM: Updated URL kwargs in test_list method

The change from 'query' to 'queryexecution' in the URL kwargs is consistent with the updated API structure. This modification better represents the relationship between queries, their executions, and the resulting sets.

To ensure consistency across the codebase, let's check if similar changes are needed elsewhere:

✅ Verification successful

LGTM: No additional occurrences of 'query' found in URL kwargs.

All relevant URL kwargs have been updated consistently across the codebase.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for other occurrences of 'query' in URL kwargs that might need updating
rg --type python 'kwargs=\{.*"query":' -g '!test_permissions_api.py'

Length of output: 197

---

Script:

#!/bin/bash
# Search for other occurrences of 'query' in URL kwargs that might need updating
rg 'kwargs\s*=\s*\{.*"query":' -g '*.py' -g '!backend/seqvars/tests/test_permissions_api.py'

Length of output: 94

backend/seqvars/models/base.py (6)

2058-2067: New enum SeqvarsModeOfInheritance added

This new enum represents different modes of inheritance for gene annotations. It includes common inheritance patterns such as autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked, and mitochondrial.

The enum is well-defined and covers the main inheritance patterns. This addition will improve the clarity and consistency of inheritance mode representation in the codebase.

---

2068-2077: Updated GeneRelatedPhenotypesPydantic class

The GeneRelatedPhenotypesPydantic class has been updated to include a new field:

mode_of_inheritances: list[SeqvarsModeOfInheritance] = []

This change allows for storing multiple modes of inheritance for a gene, which is appropriate as some genes can be associated with multiple inheritance patterns. The use of the newly defined SeqvarsModeOfInheritance enum ensures consistency in the data representation.

---

2389-2391: Added ordering to SeqvarsResultSet model

A Meta class has been added to the SeqvarsResultSet model:

class Meta:
    ordering = ["-date_created"]

This change ensures that SeqvarsResultSet instances will be ordered by their creation date in descending order by default. This is a good practice for maintaining a consistent order and typically showing the most recent results first.

---

2433-2435: Added ordering to SeqvarsResultRow model

A Meta class has been added to the SeqvarsResultRow model:

class Meta:
    ordering = ["chrom_no", "pos", "ref_allele", "alt_allele"]

This ordering ensures that SeqvarsResultRow instances will be sorted by chromosome number, position, reference allele, and alternative allele. This is a logical order for genomic variants and will help in presenting the data in a consistent and meaningful way.

---

2501-2502: Added ordering to SeqvarsQueryExecutionBackgroundJob model

A Meta class has been added to the SeqvarsQueryExecutionBackgroundJob model:

class Meta:
    ordering = ["-pk"]

This ordering ensures that SeqvarsQueryExecutionBackgroundJob instances will be sorted by their primary key in descending order. This typically means that the most recently created jobs will appear first, which is often desirable for background job management.

---

Line range hint 2058-2502: Overall assessment of changes

The changes in this file enhance the structure and functionality of the seqvars models:

1. The new SeqvarsModeOfInheritance enum provides a standardized way to represent inheritance patterns.
2. The GeneRelatedPhenotypesPydantic class now supports multiple modes of inheritance for a gene.
3. Ordering has been added to SeqvarsResultSet, SeqvarsResultRow, and SeqvarsQueryExecutionBackgroundJob models, ensuring consistent data presentation.

These changes improve the organization of the code and add useful functionality for handling genetic inheritance patterns. The additions are well-integrated with the existing code structure.

frontend/ext/varfish-api/src/lib/schemas.gen.ts (9)

Line range hint 1-1: LGTM: Auto-generated file header

The comment at the top of the file correctly indicates that this is an auto-generated file. This is good practice for generated code.

---

2493-2500: Verify the structure of the constraints property

The constraints property has also been modified. Ensure this change is intended and consistent with the overall schema design.

#!/bin/bash
# Check for other occurrences of GeneRelatedConstraintsPydantic
ast-grep --lang typescript --pattern 'GeneRelatedConstraintsPydantic'

---

2473-2480: Verify the structure of the consequences property

Similar to the identity property, the consequences property has been modified. Ensure this change is intended and consistent across the codebase.

#!/bin/bash
# Check for other occurrences of GeneRelatedConsequencesPydantic
ast-grep --lang typescript --pattern 'GeneRelatedConsequencesPydantic'

---

2614-2621: New property mode_of_inheritances added

A new property mode_of_inheritances has been added to the GeneRelatedPhenotypesPydantic type. Verify that this addition is intentional and that it's being used correctly in the rest of the codebase.

#!/bin/bash
# Check for usage of mode_of_inheritances
ast-grep --lang typescript --pattern 'mode_of_inheritances'

---

2483-2490: Verify the structure of the phenotypes property

The phenotypes property has been modified in a similar manner. Confirm that this change is intentional and consistent with other related types.

#!/bin/bash
# Check for other occurrences of GeneRelatedPhenotypesPydantic
ast-grep --lang typescript --pattern 'GeneRelatedPhenotypesPydantic'

---

6133-6138: New enum SeqvarsModeOfInheritance added

A new enum SeqvarsModeOfInheritance has been added. This seems to be related to the new mode_of_inheritances property. Verify that this enum is being used correctly throughout the codebase.

#!/bin/bash
# Check for usage of SeqvarsModeOfInheritance
ast-grep --lang typescript --pattern 'SeqvarsModeOfInheritance'

---

2970-2973: New count property added to paginated responses

A count property has been added to various paginated response types. This is a good addition as it provides information about the total number of items. Ensure this change is consistent across all paginated response types.

#!/bin/bash
# Check for consistency of count property in paginated responses
ast-grep --lang typescript --pattern 'type: '\''object'\'',
    properties: {
        count: {
            type: '\''integer'\'',
            example: 123
        },'

Also applies to: 2976-2978, 2982-2984

---

9795-9797: Default value added to recessive_mode property

A default value of 'disabled' has been added to the recessive_mode property in SeqvarsQuerySettingsGenotypePydantic. Ensure this default value is appropriate and consistent with the backend implementation.

#!/bin/bash
# Check for other occurrences of recessive_mode
ast-grep --lang typescript --pattern 'recessive_mode'

---

2463-2470: Verify the structure of the identity property

The identity property in the GeneRelatedAnnotationPydantic type has been modified. Please ensure that this change is intentional and consistent with the expected schema.

backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml (11)

2399-2404: Consistent implementation of pagination change

The change from cursor to page parameter has been consistently applied here as well. This is in line with the overall pagination mechanism update.

---

2642-2647: Pagination change applied to query execution endpoint

The pagination change has been correctly implemented for the query execution endpoint, maintaining consistency with other endpoints.

---

2735-2740: Consistent pagination implementation across multiple endpoints

The pagination change from cursor to page has been consistently applied across multiple endpoints, including:

• Query presets for ClinVar
• Query presets for columns
• Query presets for consequences
• Query presets factory defaults
• Query presets for locus
• Query presets for phenotype prioritization
• Query presets for quality
• Query presets set
• Query presets set version
• Query presets for variant prioritization
• Query settings

This consistent implementation ensures a uniform API behavior across different endpoints.

Also applies to: 2942-2947, 3149-3154, 3359-3364, 3625-3630, 3832-3837, 4039-4044, 4246-4251, 4495-4500, 4741-4746, 4948-4953

---

7423-7437: Nullable fields added to GeneRelatedAnnotationPydantic

The GeneRelatedAnnotationPydantic schema now includes nullable fields for identity, consequences, phenotypes, and constraints. This change allows for more flexible data representation, accommodating cases where some of this information might be missing.

---

7508-7513: Default empty list for mode_of_inheritances

A default empty list has been added for the mode_of_inheritances field in the GeneRelatedPhenotypesPydantic schema. This is a good practice as it ensures that the field always has a valid value, even when no specific modes of inheritance are specified.

---

7775-7787: Consistent implementation of pagination in response schemas

The pagination response schemas have been updated to include a count field, which provides the total number of results available. This change has been consistently applied across multiple paginated response schemas, including:

• PaginatedSeqvarsPredefinedQueryList
• PaginatedSeqvarsQueryExecutionList
• PaginatedSeqvarsQueryList
• PaginatedSeqvarsQueryPresetsClinvarList
• PaginatedSeqvarsQueryPresetsColumnsList
• PaginatedSeqvarsQueryPresetsConsequenceList
• PaginatedSeqvarsQueryPresetsFrequencyList
• PaginatedSeqvarsQueryPresetsLocusList
• PaginatedSeqvarsQueryPresetsPhenotypePrioList
• PaginatedSeqvarsQueryPresetsQualityList
• PaginatedSeqvarsQueryPresetsSetList
• PaginatedSeqvarsQueryPresetsSetVersionList
• PaginatedSeqvarsQueryPresetsVariantPrioList
• PaginatedSeqvarsQuerySettingsList
• PaginatedSeqvarsResultRowList
• PaginatedSeqvarsResultSetList

This consistent implementation improves the API's usability by providing important metadata about the query results.

Also applies to: 7795-7807, 7815-7827, 7835-7847, 7855-7867, 7875-7887, 7895-7907, 7915-7927, 7935-7947, 7955-7967, 7975-7987, 7995-8007, 8015-8027, 8035-8047, 8055-8067, 8075-8087

---

10116-10126: New enumeration for SeqvarsModeOfInheritance

A new enumeration SeqvarsModeOfInheritance has been added to represent different modes of inheritance for gene annotations. This addition provides a standardized way to represent inheritance patterns, which is crucial for genetic analysis and interpretation.

---

Line range hint 1-11273: Overall assessment of API schema changes

The changes to the VarFish API schema demonstrate a significant improvement in pagination mechanisms and data representation. Key points include:

1. Consistent update from cursor-based to page-based pagination across multiple endpoints.
2. Addition of a count field in paginated response schemas, providing valuable metadata about query results.
3. Introduction of new parameters (e.g., order_by, order_dir) to enhance query capabilities.
4. Improved flexibility in data representation with nullable fields and default values.
5. New enumerations (e.g., SeqvarsModeOfInheritance) for standardized representation of genetic concepts.

These changes collectively enhance the API's consistency, usability, and flexibility. The modifications appear to be well-implemented and should improve the overall developer experience when working with the VarFish API.

---

5224-5242: Updated parameter name in result set endpoints

The parameter name has been changed from query to queryexecution in the result set endpoints. This change appears to be more descriptive and aligns better with the endpoint's purpose.

Let's verify this change has been applied consistently:

#!/bin/bash
# Check for the parameter name change in result set endpoints
echo "Checking for 'queryexecution' parameter in result set endpoints:"
sed -n '/\/seqvars\/api\/resultset/,/responses:/p' backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml | grep -E "queryexecution"

Also applies to: 5260-5284

---

2192-2197: Pagination parameter updated from cursor to page

The pagination mechanism has been changed from cursor-based to page-based pagination. This change is consistent with the AI-generated summary and appears to be implemented correctly.

To ensure this change has been applied consistently across all relevant endpoints, let's run the following verification:

---

5155-5168: New parameters added to result row endpoint

New parameters order_by and order_dir have been added to the /seqvars/api/resultrow/{resultset}/ endpoint. This addition enhances the query capabilities for result rows, allowing for more flexible sorting options.

Let's verify that these new parameters are properly documented:

✅ Verification successful

New parameters order_by and order_dir are properly documented

The new parameters order_by and order_dir have been successfully documented in the /seqvars/api/resultrow/{resultset}/ endpoint within backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check for the new parameters in the result row endpoint
echo "Checking for new parameters in result row endpoint:"
sed -n '/\/seqvars\/api\/resultrow\/{resultset}\/:$/,/responses:/p' backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml | grep -E "order_by|order_dir"

Length of output: 539

---

Script:

#!/bin/bash
# Corrected script to check for the new parameters in the result row endpoint
echo "Checking for new parameters 'order_by' and 'order_dir' in the result row endpoint:"
sed -n '/\/seqvars\/api\/resultrow\/{resultset}\/:$/,/responses:/p' backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml | grep -E "order_by|order_dir"

Length of output: 399

frontend/src/seqvars/components/QueryResults/ClingenDosage.vue (1)

57-64: Verify the scoring values for 'recessive' and 'unlikely'

The scores for 'recessive' and 'unlikely' are set to 30 and 40, respectively, while other scores range from 0 to 3. This might cause confusion when displaying the scores. Please verify if these values are intentional or consider aligning them for consistency.

utils/docker/Dockerfile (1)

142-142: Confirm compatibility with varfish-server-worker version 0.14.0

The COPY instruction now references varfish-server-worker version 0.14.0. Please ensure that this version is fully compatible with the existing application and that any necessary changes have been made to accommodate updates or changes in the worker's behavior or APIs.

To verify compatibility, consider reviewing the release notes or changelogs for varfish-server-worker 0.14.0 for any breaking changes or important updates that might affect the application.

frontend/src/seqvars/queries/seqvarQuery.ts (1)

88-88: ⚠️ Potential issue

Use explicit typing to eliminate the @ts-ignore comment.

The use of @ts-ignore suppresses TypeScript errors and can mask potential issues. Instead of ignoring the error, consider defining the correct type for lastPage so that TypeScript recognizes the next property. This will enhance type safety and maintain code quality.

Apply this diff to specify the type of lastPage:

- // @ts-ignore // https://github.com/hey-api/openapi-ts/issues/653#issuecomment-2314847011
  getNextPageParam: (lastPage) => lastPage.next,
+ getNextPageParam: (lastPage: YourResponseType) => lastPage.next,

Replace YourResponseType with the appropriate type that includes the next property. This approach addresses the TypeScript error without suppressing it.

⛔ Skipped due to learnings

Learnt from: holtgrewe
PR: varfish-org/varfish-server#1957
File: frontend/src/seqvars/queries/seqvarQueryExecution.ts:84-107
Timestamp: 2024-10-09T06:55:05.311Z
Learning: In the function `useSeqvarQueryExecutionListQuery` within `frontend/src/seqvars/queries/seqvarQueryExecution.ts`, the `@ts-ignore` comment is necessary because the composable function might be used in different contexts, and removing it may not be appropriate.

backend/seqvars/protos/output_pb2.pyi (4)

81-84: Definition of _ModeOfInheritance is correct

The _ModeOfInheritance class is properly defined with ValueType and the type alias V.

---

85-104: Enumeration _ModeOfInheritanceEnumTypeWrapper and constants are appropriately defined

The enum wrapper _ModeOfInheritanceEnumTypeWrapper and the enumeration constants for modes of inheritance are correctly implemented.

---

105-107: ModeOfInheritance class is accurately inherited

The ModeOfInheritance class correctly inherits from _ModeOfInheritance with the appropriate metaclass.

---

108-122: Global constants for ModeOfInheritance are correctly declared

All global variables representing different modes of inheritance are properly assigned and documented.

backend/seqvars/tests/test_views_api.py (16)

113-116: Ensure pagination fields are correctly tested in TestQueryPresetsSetViewSet

The addition of "count", "next", "previous", and "results" fields in the response verification ensures that the pagination is properly validated in the test_list method.

---

270-273: Ensure pagination fields are correctly tested in TestQueryPresetsSetVersionViewSet

Including the pagination fields in the response enhances the verification of the pagination functionality in the test_list method.

---

420-423: Ensure pagination fields are correctly tested in TestQueryPresetsQualityViewSet

Validating the pagination fields in the response ensures comprehensive testing of the list endpoint's pagination.

---

557-560: Ensure pagination fields are correctly tested in TestQueryPresetsConsequenceViewSet

Adding the pagination fields to the expected response improves the accuracy of the pagination tests in the test_list method.

---

694-697: Ensure pagination fields are correctly tested in TestQueryPresetsFrequencyViewSet

The inclusion of pagination fields in the response verification strengthens the testing of the pagination feature.

---

831-834: Ensure pagination fields are correctly tested in TestQueryPresetsLocusViewSet

Verifying the pagination fields in the response confirms that the pagination is implemented correctly in the test_list method.

---

968-971: Ensure pagination fields are correctly tested in TestQueryPresetsPhenotypePrioViewSet

Including "count", "next", "previous", and "results" in the response enhances the validation of pagination in the list endpoint.

---

1105-1108: Ensure pagination fields are correctly tested in TestQueryPresetsVariantPrioViewSet

Adding pagination fields to the response verification ensures that the pagination functionality is thoroughly tested.

---

1242-1245: Ensure pagination fields are correctly tested in TestQueryPresetsColumnsViewSet

Validating the pagination fields in the response improves the test coverage for the list endpoint's pagination.

---

1379-1382: Ensure pagination fields are correctly tested in TestQueryPresetsClinvarViewSet

Including pagination fields in the response ensures accurate testing of the pagination feature in the test_list method.

---

1516-1519: Ensure pagination fields are correctly tested in PredefinedQueryViewSet

Verifying the presence of pagination fields in the response strengthens the pagination tests for the list endpoint.

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1649-1652: Ensure pagination fields are correctly tested in TestQuerySettingsViewSet

Adding the pagination fields to the expected response enhances the validation of the list endpoint's pagination.

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1826-1829: Ensure pagination fields are correctly tested in TestQueryViewSet

Including "count", "next", "previous", and "results" in the response verification confirms proper pagination implementation.

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2110-2113: Ensure pagination fields are correctly tested in TestQueryExecutionViewSet

Adding pagination fields to the response checks improves the thoroughness of the pagination tests.

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2213-2216: Ensure pagination fields are correctly tested in TestResultSetViewSet

Including the pagination fields in the response verification enhances the testing of the list endpoint's pagination functionality.

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2287-2290: Ensure pagination fields are correctly tested in TestResultRowViewSet

Validating the pagination fields in the response confirms that pagination is properly implemented in the test_list method.

frontend/ext/varfish-api/src/lib/types.gen.ts (4)

884-887: Ensure proper handling of nullable properties in GeneRelatedAnnotationPydantic

The properties identity, consequences, phenotypes, and constraints in GeneRelatedAnnotationPydantic are now nullable. Please verify that any code consuming this type correctly handles cases where these properties may be null to prevent potential null reference errors.

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916-916: Addition of mode_of_inheritances property is appropriate

The new property mode_of_inheritances has been added to GeneRelatedPhenotypesPydantic. This enhancement aligns with the need to represent multiple modes of inheritance and appears correctly implemented.

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2036-2039: New SeqvarsModeOfInheritance type enhances type safety

The addition of the SeqvarsModeOfInheritance type enumerates various modes of inheritance, improving type safety and clarity in code that deals with genetic annotations.

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2933-2933: Verify handling of optional recessive_mode in SeqvarsQuerySettingsGenotypePydantic

The recessive_mode property in SeqvarsQuerySettingsGenotypePydantic is now optional. Please ensure that all usages of this type account for recessive_mode potentially being undefined to avoid unintended behavior.

frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts (2)

5-6: Code Import and Declarations Look Good

The updated imports and function declarations correctly reflect the necessary changes.

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68-71: Confirm the Impact of Commenting Out 'body' Parameter Handling

The 'body' parameter merging is commented out in multiple infinite query options functions. Please verify that this change is intentional and does not affect API calls relying on the 'body' parameter.

Run the following script to check for any API calls that require the 'body' parameter in infinite query options:

backend/seqvars/views_api.py (2)

8-8: Import OpenAPI utilities for schema enhancements

The import of OpenApiParameter and extend_schema from drf_spectacular.utils is correctly added to support OpenAPI schema enhancements.

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14-14: Changed pagination strategy to PageNumberPagination

The switch from CursorPagination to PageNumberPagination by importing PageNumberPagination and updating the StandardPagination class reflects a change in pagination strategy.

Please ensure that this change does not adversely affect existing API clients that might rely on cursor-based pagination. Confirm that all endpoints and clients are compatible with page-number-based pagination.

Also applies to: 64-66