URGENT: two of the bdb databases does not download with action #45
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@tabbassidaloii, can you help out here? What is the status of these files? @marvinm2, the JSON files have fields to indicate compatibility. I think we should add there the "tested with Docker" option, and just exclude these two files from that for now. |
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@marvinm2 both Ec_Derby_Ensembl_91 and Mx_Derby_Ensembl_85.bridge are on Zenodo (https://zenodo.org/record/3667670 and https://zenodo.org/record/5638771/, respectively), and the links are correctly provided in gene.json file. I just tried and both are working. |
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I experience these issues when starting the service |
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Are these files valid? They do not have QC notes |
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For $ bash qc.sh ~/Downloads/Ec_Derby_Ensembl_91.bridge ~/Downloads/Ec_Derby_Ensembl_91.bridge
INFO: old database is Ensembl 91 (build: 20180509)
INFO: new database is Ensembl 91 (build: 20180509)
INFO: Number of ids in T (GeneOntology): 3660 (unchanged)
INFO: Number of ids in En (Ensembl): 4140 (unchanged)
INFO: Number of ids in S (UniProtKB): 8241 (unchanged)
INFO: Attribute provided: Type
INFO: Attribute provided: Description
INFO: Attribute provided: Symbol
INFO: Attribute provided: Chromosome
INFO: new size is 12 Mb (changed +0.0%)
INFO: OLD database has a total number of identifiers of 16041
INFO: OLD database has a total number of mappings of 31933
INFO: OLD database has Schema Version is less than 4, and we cannot calculate Primary and Secondary identifier counts
INFO: NEW database has a total number of identifiers of 16041
INFO: NEW database has a total number of mappings of 31933
INFO: NEW database has Schema Version is less than 4, and we cannot calculate Primary and Secondary identifier counts
ERROR: 4140/4140 (100%) ids do not match expected pattern for Ensembl
ERROR: expected pattern is '^ENS[A-Z]*[FPTG]\d{11}$'
ERROR: aberrant ids are e.g. 'b4471', 'b1227', 'b4470', 'b1223', 'b1224', 'b1225', 'b1226', 'b1220', 'b1221', 'b1222'
ERROR: 4103/8241 (49%) ids do not match expected pattern for UniProtKB
ERROR: expected pattern is '^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$'
ERROR: aberrant ids are e.g. 'UPI000012FD85', 'UPI000012FD86', 'UPI0000168087', 'UPI000012FD87', 'UPI00003B25FD', 'UPI000012FD88', 'UPI000016825D', 'UPI000012FD89', 'UPI000012FD90', 'UPI0001505B8D'And $ bash qc.sh ~/Downloads/Mx_Derby_Ensembl_85.bridge ~/Downloads/Mx_Derby_Ensembl_85.bridge
INFO: old database is Ensembl 1 (build: 20161018)
INFO: new database is Ensembl 1 (build: 20161018)
INFO: Number of ids in T (GeneOntology): 2106 (unchanged)
INFO: Number of ids in En (Ensembl): 4018 (unchanged)
INFO: Number of ids in S (UniProtKB): 7955 (unchanged)
INFO: Attribute provided: Type
INFO: Attribute provided: Description
INFO: Attribute provided: Symbol
INFO: Attribute provided: Chromosome
INFO: new size is 11 Mb (changed +0.0%)
INFO: OLD database has a total number of identifiers of 14079
INFO: OLD database has a total number of mappings of 26457
INFO: OLD database has Schema Version is less than 4, and we cannot calculate Primary and Secondary identifier counts
INFO: NEW database has a total number of identifiers of 14079
INFO: NEW database has a total number of mappings of 26457
INFO: NEW database has Schema Version is less than 4, and we cannot calculate Primary and Secondary identifier counts
ERROR: 4018/4018 (100%) ids do not match expected pattern for Ensembl
ERROR: expected pattern is '^ENS[A-Z]*[FPTG]\d{11}$'
ERROR: aberrant ids are e.g. 'Rv0753c', 'Rv1176c', 'Rv3716c', 'Rv2919c', 'Rv2918c', 'Rv1103c', 'Rv2349c', 'Rv2129c', 'Rv3432c', 'Rv3047c'
ERROR: 3978/7955 (50%) ids do not match expected pattern for UniProtKB
ERROR: expected pattern is '^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$'
ERROR: aberrant ids are e.g. 'UPI00000D0FEC', 'UPI000012B714', 'UPI00000C1538', 'UPI00001650EB', 'UPI000012B72A', 'UPI000016527E', 'UPI000013944B', 'UPI00001652CE', 'UPI00000D4FCB', 'UPI00000D1117' |
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@marvinm2, I also not the |
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From the gene.json file (https://data.bridgedb.org/gene.json), the following two .bridge files do not download:
Because of this, the Docker image does not work.
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