import os
import bam
# Define output paths
output_1 = os.path.join(bam.SRCDIR, "files", "out_sequential.sam")
output_2 = os.path.join(bam.SRCDIR, "files", "out_pairwise.sam")
# Run test with these paths
bam.exec_sql_file("sam_export.sql", {
'OUTPUT_1': output_1,
'OUTPUT_2': output_2
})
# And remove our garbage
os.remove(output_1)
os.remove(output_2)
import bam
bam.exec_sql_file("bam_loader_repos.sql", {'PWD': bam.SRCDIR})
import bam
bam.exec_sql_file("mergetable.sql", {'PWD': bam.SRCDIR})
import sys
import re
import bam
# This script drops the files with file IDs [5,12]
# Unfortunately, this functionality is not that clever yet and we have to
# provide the dbschema to the drop function
# To do that, we first get the dbschemas from the database and we create a mapping
# of file id to dbschema that we can pass to the bam.exec_sql_file function
# Run select query to get file info from files table
c = bam.new_client()
c.stdin.write("SELECT file_id, dbschema FROM bam.files;")
out, err = c.communicate()
# Parse this outcome into a dictionary {DBSCHEMA_file_id -> dbschema}
p = re.compile('^\s*\[\s*(\d+)\s*,\s*(\d)\s*\]\s*$', re.MULTILINE) # Parses raw DB output
mapping = {}
for match in p.finditer(out):
mapping['DBSCHEMA_'+match.group(1)] = match.group(2)
# And now we can execute the SQL
bam.exec_sql_file("drop_last_files.sql", mapping)
import os
import bam
# Define output paths
output_1 = os.path.join(bam.SRCDIR, "files", "out_sequential.sam")
output_2 = os.path.join(bam.SRCDIR, "files", "out_pairwise.sam")
# Run test with these paths
bam.exec_sql_file("sam_export.sql", {'OUTPUT_1': output_1, 'OUTPUT_2': output_2})
# And remove our garbage
os.remove(output_1)
os.remove(output_2)
