Feature/update helix filters operator #428
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allanbolipata
commented
Jul 1, 2020
| @@ -11,7 +11,9 @@ def get_project_id(request_id): | |||
| def generate_sample_data_content(files, pipeline_name, pipeline_github, pipeline_version): | |||
| result = "SAMPLE_ID\tREQUEST_ID\tPROJECT_ID\tPATIENT_ID\tCOLLAB_ID\tSAMPLE_TYPE\tGENE_PANEL\tONCOTREE_CODE\tSAMPLE_CLASS\tSPECIMEN_PRESERVATION_TYPE\tSEX\tTISSUE_SITE\tIGO_ID\tPIPELINE_NAME\tPIPELINE_GITHUB_LINK\tPIPELINE_VERSION\n" | |||
| ret_str = 'metadata__sampleId' | |||
| query = Q(file__path__in=files) & Q(file__file_group_id=settings.IMPORT_FILE_GROUP) | |||
| query = Q(file__file_group_id=settings.IMPORT_FILE_GROUP) | |||
| query |= Q(file__file_group__slug="origin-unknown") | |||
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This assumes the file, if found, are structured the same way as in the LIMS filegroup.
This is needed because I suspect non-LIMS data sources will go through Helix Filters, requiring data clinical files.
nikhil
approved these changes
Jul 1, 2020
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Helix filters operator updated to work with most recent version
Added new resources
known_fusions_filter.txtandoncotree.json, which is used by the oncotree data handler if it can't get an internet connection to query oncotree directly.