def copy_gpad(nex_session): dstDir = "curation/literature/" gpad_file = "gp_association.559292_sgd.gpad.gz" for x in nex_session.query(Filedbentity).filter( Filedbentity.previous_file_name.like( 'gp_association.559292_sgd_%.gz')).filter( Filedbentity.dbentity_status == 'Active').all(): if x.s3_url is None: continue urlParam = x.s3_url.split('/') filename = urlParam[4].split('?')[0] srcFile = urlParam[3] + '/' + filename ## copy to archive dstFile = dstDir + "archive/" + filename print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile) ## copy to current directory dstFile = dstDir + gpad_file print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile)
def copy_gff(nex_session): dstDir = "curation/chromosomal_feature/archive/" for x in nex_session.query(Filedbentity).filter( Filedbentity.previous_file_name.like( 'saccharomyces_cerevisiae.%.gff.gz')).all(): if '.2019' in x.s3_url or '.2020' in x.s3_url: urlParam = x.s3_url.split('/') srcFile = urlParam[3] + '/' + urlParam[4].split('?')[0] dstFile = dstDir + urlParam[4].split('?')[0] print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile)
def copy_gaf(nex_session): dstDir = "curation/literature/archive/" for x in nex_session.query(Filedbentity).filter( Filedbentity.previous_file_name.like( 'gene_association.sgd.%.gz')).all(): if x.s3_url is not None: urlParam = x.s3_url.split('/') srcFile = urlParam[3] + '/' + urlParam[4].split('?')[0] dstFile = dstDir + urlParam[4].split('?')[0] print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile)
def copy_gff(nex_session): ## current directory dstDir = "curation/chromosomal_feature/" gff_file = "saccharomyces_cerevisiae.gff.gz" for x in nex_session.query(Filedbentity).filter( Filedbentity.previous_file_name.like( 'saccharomyces_cerevisiae.%.gff.gz')).filter( Filedbentity.dbentity_status == 'Active').all(): if x.s3_url is None: continue urlParam = x.s3_url.split('/') filename = urlParam[4].split('?')[0] srcFile = urlParam[3] + '/' + filename ## copy to archive dstFile = dstDir + "archive/" + filename print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile) ## copy to current directory dstFile = dstDir + gff_file print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET2, dstFile) ## copy to latest directory dstFile = "latest/" + gff_file print(x.dbentity_status, srcFile, dstFile) boto3_copy_file(S3_BUCKET, srcFile, S3_BUCKET, dstFile)