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Author	SHA1	Message	Date
george-hall-ucl	19caa6cb80	Sorry -- forgot to lint	2023-08-08 16:04:03 +01:00
george-hall-ucl	56bd079024	Save gene sets without cell annotations ... This fixes a bug whereby new gene_sets csv files created without accompanying cell-level annotations could not be detected by the filecrawler.	2023-08-08 15:49:57 +01:00
george-hall-ucl	81c8ce4219	#81 Add support for gene sets ... This adds the flag `GATEWAY_ENABLE_GENE_SETS` to enable support for gene sets. To simplify implementation, activating this flag also activates `GATEWAY_ENABLE_ANNOTATIONS`. The gene sets are saved in a file that has the same name as the annotations `csv` but with `_gene_sets` appended to the file name (before the extension). This file is hidden in filecrawler, and the gene sets are loaded when the associated annotations file is loaded. If the annotations file is missing, then an Exception is raised. I have updated one unit test to make it expect `--disable-gene-sets-save` in the default case (i.e. if `GATEWAY_ENABLE_ANNOTATIONS = 0`). All units tests pass. I have updated the README to document `GATEWAY_ENABLE_GENE_SETS`.	2023-07-06 07:59:12 -06:00