Hidden analyses not found when uploading to scout #502
Comments
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@diitaz93 assigned to reproduce the bug |
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In TB: on case Then running command Output is: In TB: on case Then: command Output: |
UPDATE:The request sent from cg to Trailblazer is based on this: f"analyses?case_id={case_id}&status[]={AnalysisStatus.COMPLETED}&limit=1"In Trailblazer, the response is parsed into this model: class AnalysesRequest(BaseModel):
workflow: str = ""
search: str | None = None
page_size: int = Field(alias="pageSize", default=250)
page: int = 1
sort_field: AnalysisSortField = Field(alias="sortField", default=AnalysisSortField.STARTED_AT)
sort_order: SortOrder = Field(alias="sortOrder", default=SortOrder.DESC)
status: list[TrailblazerStatus] = []
priority: list[TrailblazerPriority] = []
type: list[TrailblazerTypes] = []
has_comment: bool | None = Field(alias="hasComment", default=None)
order_id: int | None = Field(alias="orderId", default=None)
case_id: str | None = None
delivered: bool | None = None
include_hidden: bool | None = Field(alias="includeHidden", default=None)This request is used to parse the TB database using: def _filter_analyses(self, request: AnalysesRequest) -> Query:
filters: list[AnalysisFilter] = [
AnalysisFilter.BY_WORKFLOW,
AnalysisFilter.BY_HAS_COMMENT,
AnalysisFilter.BY_ORDER_ID,
AnalysisFilter.BY_PRIORITIES,
AnalysisFilter.BY_STATUSES,
AnalysisFilter.BY_TYPES,
AnalysisFilter.BY_CASE_ID,
AnalysisFilter.BY_SEARCH_TERM,
AnalysisFilter.BY_IS_VISIBLE,
AnalysisFilter.BY_DELIVERED,
AnalysisFilter.SORTING,
]
show_hidden = bool(request.search) or request.include_hidden
return apply_analysis_filter(
filter_functions=filters,
analyses=self.get_query(Analysis),
has_comment=request.has_comment,
order_id=request.order_id,
priorities=request.priority,
statuses=request.status,
types=request.type,
case_id=request.case_id,
workflow=request.workflow,
search_term=request.search,
show_hidden=show_hidden,
sort_field=request.sort_field,
sort_order=request.sort_order,
delivered=request.delivered,
)Which assigns |
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Description
Originates from https://github.com/Clinical-Genomics/bug-reports/issues/15
Development case
petmakotried to be uploaded usingcg upload -r -c petmakobut got the error:Trailblazer (Cigrid) showed that the analysis was there.
As the analysis was for development (cust000), it was by default hidden in Trailblazer. When the analysis was manually set to "unhidden" the command worked as expected.
Steps to reproduce
Using taxprofiler development case
petmako, run:The same bug is expected for any development case
Expected behaviour
That development analyses can be uploaded without manually setting them as "unhidden" in trailblazer
Additional context
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