import re
from numpy import average, median, sum, round
from collections import Counter
# General comment - this would be so much easier to do with a DB!
# TODO - hook, directly or indirectly, into the ticket system. Could pull from owl_map.
results = glob1("../mapping_tables/results/", "*_RCV_*.tsv")
stats = tab(key_column = "RCV_ID", headers = ['RCV_ID', 'RCV_name',
'Auto sufficient', 'Manual only',
'Auto only', 'Manual blacklist',
'Auto blacklist', 'pattern']) # Should really load as rcd to enforce key column uniqueness
owl_map = rcd(path = "../mapping_tables/", file_name = "owl_map.tsv", key_column = 'RCV_ID' )
total_sufficient_maps = 0
# Lists for doing basic statistical analysis of results
# Sure this could be done more elegantly with list comps on tab, but still...
Auto_sufficient = []
Manual_only = []
Auto_only = []
Auto_blacklist = []
Manual_blacklist = []
mapping_table = rcd(path = "../mapping_tables/", file_name = "owl_map.tsv", key_column = "RCV_ID")
# TODO: Add code to generate full mapping table. This can be derived from results tables + ticket info without a further reasoner run.
## Spec: Include combined manual & auto mappings that are not blacklists from results files for while a ticket exists with label: mapping_complete.
# Rather scrappy, Perlish procedural code for generating mappings. Annoyingly monolithic: Have to run all mappings or none.
"""Reads owl_map and uses it to automatically populate RCV classes.
Compares these to manual mappings. Prints a results summary and results tables.
Ontology to use must be specified as argv[1] when runnning this script."""
from mapping_tools import (map_obj, load_ont, mappingTabs)
from tsv2pdm import tab, rcd
go = load_ont(sys.argv[1])
manMap = tab('../mapping_tables/',
'manual_mapping.tsv') # No key row. Stored as list of dicts.
owlMap = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID') # dict of dicts.
RCV = rcd('../mapping_tables/', 'RocheCV_def.tsv', 'RCV_ID') # dict of dicts.
mapping_tabs = mappingTabs(manMap.tab, owlMap.rowColDict, RCV.rowColDict, go)
# ...Hmmm - would give much more flexibility if passed objects rather than data structures.
manMap_updated = open('../mapping_tables/manual_mapping.tsv', "w")
manMap_updated.write(manMap.print_tab(sort_keys=('RCV_ID', )))
manMap_updated.close()
RCV_id_name = {} # Residual perlishness ?
for row in manMap.tab:
RCV_id_name[row['RCV_ID']] = row['RCV_NAME']
report_path = '../mapping_tables/results/'
#!/usr/bin/env python
import re
from github_tools import issueConn
from tsv2pdm import rcd, tab
import glob
import warnings
"""Generates a set of proforma tickets using owl_map.tsv
for entries in which the pattern field does not begin with a '?'
and for which there is not currently ticket following the standard name pattern.
Writes ticket number and state back to owl_map;
If mapping complete, updates RCV master file to record mapping_complete = 1
"""
ic = issueConn('GO-ROCHE-COLLAB', 'Roche_CV_mapping', 'dosumis')
owlMap = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID') # dict of dicts.
RCV = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID')
for RCV_id, rd in owlMap.rowColDict.items():
if not re.match("\?.*", rd['Applied pattern']):
ticket_name = "Review %s %s" % (rd['RCV_NAME'], RCV_id)
issue = ''
issues = ic.ticket_exists(ticket_name, ['Mapping_review'])
if not issues:
issue = ic.create_standard_review_ticket(RCV_id, rd['RCV_NAME'])
elif len(issues) > 1:
warnings.warn(
"Multiple tickets exist with the name '%s' and the label 'Mapping_review'."
% ticket_name)
continue
else:
from collections import Counter
# General comment - this would be so much easier to do with a DB!
# TODO - hook, directly or indirectly, into the ticket system. Could pull from owl_map.
results = glob1("../mapping_tables/results/", "*_RCV_*.tsv")
stats = tab(key_column="RCV_ID",
headers=[
'RCV_ID', 'RCV_name', 'Auto sufficient', 'Manual only',
'Auto only', 'Manual blacklist', 'Auto blacklist', 'pattern'
]) # Should really load as rcd to enforce key column uniqueness
owl_map = rcd(path="../mapping_tables/",
file_name="owl_map.tsv",
key_column='RCV_ID')
total_sufficient_maps = 0
# Lists for doing basic statistical analysis of results
# Sure this could be done more elegantly with list comps on tab, but still...
Auto_sufficient = []
Manual_only = []
Auto_only = []
Auto_blacklist = []
Manual_blacklist = []
mapping_table = rcd(path="../mapping_tables/",
file_name="owl_map.tsv",
import re
from github_tools import issueConn
from tsv2pdm import rcd, tab
import glob
import warnings
"""Generates a set of proforma tickets using owl_map.tsv
for entries in which the pattern field does not begin with a '?'
and for which there is not currently ticket following the standard name pattern.
Writes ticket number and state back to owl_map;
If mapping complete, updates RCV master file to record mapping_complete = 1
"""
ic = issueConn('GO-ROCHE-COLLAB', 'Roche_CV_mapping', 'dosumis')
owlMap = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID') # dict of dicts.
RCV = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID')
for RCV_id, rd in owlMap.rowColDict.items():
if not re.match("\?.*", rd['Applied pattern']):
ticket_name = "Review %s %s" % (rd['RCV_NAME'], RCV_id)
issue = ''
issues = ic.ticket_exists(ticket_name, ['Mapping_review'])
if not issues:
issue = ic.create_standard_review_ticket(RCV_id, rd['RCV_NAME'])
elif len(issues) > 1:
warnings.warn("Multiple tickets exist with the name '%s' and the label 'Mapping_review'." % ticket_name)
continue
else:
issue = issues[0]
if issue['state'] == 'closed':
# Rather scrappy, Perlish procedural code for generating mappings. Annoyingly monolithic: Have to run all mappings or none.
"""Reads owl_map and uses it to automatically populate RCV classes.
Compares these to manual mappings. Prints a results summary and results tables.
Ontology to use must be specified as argv[1] when runnning this script."""
from mapping_tools import (map_obj, load_ont, mappingTabs)
from tsv2pdm import tab, rcd
go = load_ont(sys.argv[1])
manMap = tab('../mapping_tables/', 'manual_mapping.tsv') # No key row. Stored as list of dicts.
owlMap = rcd('../mapping_tables/', 'owl_map.tsv', 'RCV_ID') # dict of dicts.
RCV = rcd('../mapping_tables/', 'RocheCV_def.tsv', 'RCV_ID') # dict of dicts.
mapping_tabs = mappingTabs(manMap.tab, owlMap.rowColDict, RCV.rowColDict, go)
# ...Hmmm - would give much more flexibility if passed objects rather than data structures.
manMap_updated = open('../mapping_tables/manual_mapping.tsv', "w")
manMap_updated.write(manMap.print_tab(sort_keys=('RCV_ID',)))
manMap_updated.close()
RCV_id_name = {} # Residual perlishness ?
for row in manMap.tab:
RCV_id_name[row['RCV_ID']]=row['RCV_NAME']
report_path = '../mapping_tables/results/'