initial refactoring to match SMaHT portal changes #1
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pipeline_utils/lib/yaml_parser.py
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| frmt_json[self.DESCRIPTION_SCHEMA] = self.description | ||
| frmt_json[self.STANDARD_FILE_EXTENSION_SCHEMA] = self.extension | ||
| frmt_json[self.VALID_ITEM_TYPES_SCHEMA] = getattr(self, self.FILE_TYPES_SCHEMA, ['FileReference', 'FileProcessed']) | ||
| frmt_json[self.EXTRAFILE_FORMATS_SCHEMA] = getattr(self, self.SECONDARY_FORMATS_SCHEMA, []) | ||
| # frmt_json[self.VALID_ITEM_TYPES_SCHEMA] = getattr(self, self.FILE_TYPES_SCHEMA, ['FileReference', 'FileProcessed']) |
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Doug wants to try and remove this, I did comment it out for now
| schema.PATTERN: 'FileReference|FileProcessed|FileSubmitted|FileFastq' | ||
| } | ||
| }, | ||
| # 'file_types': { |
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Was this removed? I still see it in the schema on Doug's branch?
| @@ -12,11 +12,15 @@ secondary_files: | |||
| status: uploading | |||
| uuid: 1936f246-22e1-45dc-bb5c-9cfd55537fe7 | |||
| accession: GAPFIXRDPDK5 | |||
| category: Sequencing Reads | |||
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You might want to make this an enum portal side so we can control these values, could get messy with time especially if we have these coming from external submitters
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I think that is the plan and is already an enum
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In this PR we are adding the necessary changes to accommodate the updated schemas and QC infrastructure for the SMaHT portal