From 90a554a622476300d32ce6271f927be1802e7f98 Mon Sep 17 00:00:00 2001 From: Douglas Rioux Date: Tue, 26 Jul 2022 13:38:24 -0400 Subject: [PATCH] Remove FileFormats --- portal_objects/file_format.json | 219 -------------------------------- 1 file changed, 219 deletions(-) delete mode 100644 portal_objects/file_format.json diff --git a/portal_objects/file_format.json b/portal_objects/file_format.json deleted file mode 100644 index 766a879..0000000 --- a/portal_objects/file_format.json +++ /dev/null @@ -1,219 +0,0 @@ -[ - { - "status": "shared", - "project": "PROJECT_UUID", - "description": "plain text format", - "file_format": "txt", - "institution": "INSTITUTION_UUID", - "valid_item_types": [ - "FileProcessed", - "FileReference" - ], - "standard_file_extension": "txt", - "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3" - }, - { - "file_format": "tsv_gz_tbi", - "standard_file_extension": "tsv.gz.tbi", - "description": "tabix index file of tab-separate values (tsv), compressed", - "uuid": "829ed303-e427-4d9a-a217-be75ad11317e", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference", "FileProcessed"] - }, - { - "file_format": "tsv_gz", - "standard_file_extension": "tsv.gz", - "description": "tab-separate values (tsv), compressed", - "uuid": "11ca3783-db6e-430e-997b-9cf0ca275814", - "extrafile_formats": [ - "829ed303-e427-4d9a-a217-be75ad11317e" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference", "FileProcessed"] - }, - { - "file_format": "ann", - "standard_file_extension": "ann", - "description": "extra file of a bwt file", - "uuid": "106199e5-5a85-4817-9a55-7b31698e1fda", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "amb", - "standard_file_extension": "amb", - "description": "extra file of a bwt file", - "uuid": "8db70ed6-0121-4fe1-a72e-d91dc5aa6cd3", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "pac", - "standard_file_extension": "pac", - "description": "extra file of a bwt file", - "uuid": "7373ca48-0b3e-467b-967a-80870846f89b", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "sa", - "standard_file_extension": "sa", - "description": "extra file of a bwt file", - "uuid": "11f2fc36-9a65-4d60-9365-d8ff241df4f7", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "alt", - "standard_file_extension": "alt", - "description": "extra file of a bwt file", - "uuid": "9ed3e9f9-fee2-47e3-bbe3-c63a52f8d3b8", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "bwt", - "standard_file_extension": "bwt", - "description": "BWA genome index, untarred, uncompressed", - "uuid": "813b0001-5f3f-4e28-9203-4cdf261e19c4", - "extrafile_formats": [ - "106199e5-5a85-4817-9a55-7b31698e1fda", - "8db70ed6-0121-4fe1-a72e-d91dc5aa6cd3", - "7373ca48-0b3e-467b-967a-80870846f89b", - "11f2fc36-9a65-4d60-9365-d8ff241df4f7", - "9ed3e9f9-fee2-47e3-bbe3-c63a52f8d3b8" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "dict", - "standard_file_extension": "dict", - "description": "extra file of genome reference fasta", - "uuid": "4ed9f7e0-2b2f-4aca-9533-a0a652b43442", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "fa_fai", - "standard_file_extension": "fa.fai", - "description": "extra file of genome reference fasta", - "uuid": "fb728bb4-bc56-46d5-8df5-a05562826b9a", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "fa", - "standard_file_extension": "fa", - "description": "genome reference fasta", - "uuid": "5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", - "extrafile_formats": [ - "4ed9f7e0-2b2f-4aca-9533-a0a652b43442", - "fb728bb4-bc56-46d5-8df5-a05562826b9a" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference"] - }, - { - "file_format": "vcf_idx", - "standard_file_extension": "vcf.idx", - "description": "GATK/IGV-index of vcf, uncompressed", - "uuid": "ec96f95a-cf13-4633-ab0d-c4a5138bbe0b", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileProcessed", "FileReference"] - }, - { - "file_format": "vcf", - "standard_file_extension": "vcf", - "description": "vcf, uncompressed", - "uuid": "fcc2647d-301b-4888-8d9d-83ea4270309c", - "extrafile_formats": [ - "ec96f95a-cf13-4633-ab0d-c4a5138bbe0b" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileProcessed", "FileReference"] - }, - { - "file_format": "vcf_gz_tbi", - "standard_file_extension": "vcf.gz.tbi", - "description": "tabix index file of vcf, compressed", - "uuid": "f84f1922-7f4e-4afc-922f-bec620969bf1", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference", "FileProcessed"] - }, - { - "file_format": "vcf_gz", - "standard_file_extension": "vcf.gz", - "description": "vcf, compressed", - "uuid": "1b8f525f-aecb-4211-9ae5-a2c998b05599", - "extrafile_formats": [ - "f84f1922-7f4e-4afc-922f-bec620969bf1" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileReference", "FileProcessed"] - }, - { - "file_format": "bai", - "standard_file_extension": "bam.bai", - "description": "bam index format", - "uuid": "d13d06c1-218e-4f61-aaf0-91f226248b3c", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileProcessed"] - }, - { - "file_format": "bam", - "standard_file_extension": "bam", - "description": "this format is used for aligned reads", - "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", - "extrafile_formats": [ - "d13d06c1-218e-4f61-aaf0-91f226248b3c" - ], - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileProcessed"] - }, - { - "file_format": "fastq", - "standard_file_extension": "fastq.gz", - "other_allowed_extensions": ["fq.gz"], - "description": "this format is used for short read sequence data - more information can be found here https://www.ncbi.nlm.nih.gov/sra/docs/submitformats/#fastq-files", - "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", - "project": "PROJECT_UUID", - "institution": "INSTITUTION_UUID", - "status": "shared", - "valid_item_types": ["FileFastq", "FileProcessed"] - } -]