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Bring sarif-extract-tables up to date with sarif-extract-scans
This commit is contained in:
Michael Hohn
committed by
=Michael Hohn
=Michael Hohn
parent
da7d669eb9
commit
ef00559408
@@ -1,24 +1,29 @@
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#!/usr/bin/env python
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""" Extract data from sarif files in table form.
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"""Extract data from sarif files in table form.
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These particular table joins create tables matching the content of
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./sarif-results-summary
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Return tables providing the `problem`, `path-problem` and `relatedLocations`
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information.
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The table joins for `problem`, `path-problem` and `relatedLocations` create tables
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matching the content of ./sarif-results-summary.
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The `artifacts`, `codeflows`, `relatedLocations` and `rules` tables provide the
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remaining information from the sarif file; see
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../notes/typegraph-multi-with-tables.pdf for details.
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The `problem` and `path-problem` entries provide that information; the
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`relatedLocations` table provides the details when multiple results are present
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for either.
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"""
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import argparse
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import json
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import pathlib
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from dataclasses import dataclass
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from sarif_cli import signature, signature_single
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from sarif_cli import typegraph
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import sys
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from sarif_cli import snowflake_id
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import argparse
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import dataclasses as dc
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import json
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import pandas as pd
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import pathlib
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import sarif_cli.table_joins as tj
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import sys
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#
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# Start processing
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@@ -61,6 +66,83 @@ typegraph.destructure(tgraph, signature_single.start_node_2022_02_01, sarif_stru
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#
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typegraph.attach_tables(tgraph)
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#
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# Dataframe / table collection
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#
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@dataclass
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class BaseTables:
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artifacts : pd.DataFrame
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codeflows : pd.DataFrame
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kind_pathproblem : pd.DataFrame
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kind_problem : pd.DataFrame
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relatedLocations : pd.DataFrame
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rules : pd.DataFrame
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def __init__(self): pass
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bt = BaseTables()
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#
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# Add dataframes
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#
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sf_2683 = tj.joins_for_sf_2683(tgraph)
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af_0350_location = tj.joins_for_af_0350_location(tgraph)
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bt.artifacts = tj.joins_for_artifacts(tgraph)
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bt.codeflows = tj.joins_for_codeflows(tgraph, sf_2683)
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bt.kind_pathproblem = tj.joins_for_path_problem(tgraph, af_0350_location)
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bt.kind_problem = tj.joins_for_problem(tgraph, af_0350_location)
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bt.relatedLocations = tj.joins_for_relatedLocations(tgraph, sf_2683)
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bt.rules = tj.joins_for_rules(tgraph)
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#
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# Replace the remaining internal ids with snowflake ids
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#
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flakegen = snowflake_id.Snowflake(0)
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columns_to_reindex = {
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# template from {field.name : [''] for field in dc.fields(bt)}
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'artifacts': ['artifacts_id'],
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'codeflows': ['codeflow_id'],
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'kind_pathproblem': ['results_array_id', 'codeFlows_id'],
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'kind_problem': ['results_array_id'],
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'relatedLocations': ['struct_id'],
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'rules': ['rules_array_id']}
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_id_to_flake = {}
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def _get_flake(id):
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flake = _id_to_flake.get(id, -1)
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if flake == -1:
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flake = flakegen.next()
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_id_to_flake[id] = flake
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return flake
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for field in dc.fields(bt):
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table_name = field.name
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table = getattr(bt, field.name)
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# Turn all snowflake columns into uint64 and reset indexing to 0..len(table)
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newtable = table.astype(
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{ colname : 'uint64'
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for colname in columns_to_reindex[table_name]}
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).reset_index(drop=True)
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# Swap ids for flakes
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for colname in columns_to_reindex[table_name]:
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for i in range(0, len(newtable)):
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newtable.loc[i, colname] = _get_flake(newtable.loc[i, colname])
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# Replace the table
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setattr(bt, field.name, newtable)
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#
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# Write output
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#
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p = pathlib.Path(args.outdir)
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p.mkdir(exist_ok=True)
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def write(path, frame):
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with p.joinpath(path + ".csv").open(mode='wb') as fh:
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frame.to_csv(fh, index=False)
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for field in dc.fields(bt):
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table = getattr(bt, field.name)
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write(field.name, table)
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# TODO:
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"""
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Reproduce the
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@@ -105,161 +187,3 @@ Using ../notes/typegraph.pdf, we find these:
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|------------+----------+---------+-------------------+-------------------+------------|
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"""
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#
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# Access convenience functions
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#
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sf = lambda num: tgraph.dataframes['Struct' + str(num)]
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af = lambda num: tgraph.dataframes['Array' + str(num)]
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#
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# Form the message dataframe via joins
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#
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d1 = (
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sf(4055)
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.merge(af('0350'), how="left", left_on='locations', right_on='array_id', validate="1:m")
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.drop(columns=['locations', 'array_id', 'value_index', 'type_at_index'])
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.merge(sf(2683), how="left", left_on='id_or_value_at_index', right_on='struct_id',
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suffixes=("_4055", "_2683"), validate="1:m")
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.drop(columns=['struct_id_2683', 'id_or_value_at_index'])
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.merge(sf(4963), how="left", left_on='physicalLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'physicalLocation'])
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.merge(sf(6299), how="left", left_on='region', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'region'])
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.merge(sf(2685), how="left", left_on='artifactLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'artifactLocation'])
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.merge(sf(2774), how="left", left_on='message_4055', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'message_4055'])
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.merge(sf(2774), how="left", left_on='message_2683', right_on='struct_id',
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suffixes=("_4055", "_2683"), validate="1:m")
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)
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#
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# As expected from the above note
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#
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# Note that this IGNORES the path
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# - .results > .[] > .relatedLocations > .[] > .physicalLocation > .text
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#
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# we have no text entries that table:
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#
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# In [88]: d1[d1.text_2683 != '']
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# Out[88]:
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# Empty DataFrame
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#
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# Reproduce ALL `file:line:col:line:col: message` entries as a table
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#
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d2 = (d1[['struct_id_4055', 'uri', 'startLine', 'startColumn', 'endLine', 'endColumn', 'text_4055']]
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.rename({'text_4055': 'message'}, axis='columns'))
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#
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# Form the codeFlows dataframe
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#
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dco1 = (
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sf(9699)
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.merge(af(9799), how="left", left_on='codeFlows', right_on='array_id', validate="1:m")
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.drop(columns=['struct_id', 'codeFlows', 'array_id', 'type_at_index'])
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#
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.merge(sf(7122), how="left", left_on='id_or_value_at_index', right_on='struct_id', validate="1:m")
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.drop(columns=['id_or_value_at_index', 'struct_id'])
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#
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.merge(af(1597), how="left", left_on='threadFlows', right_on='array_id',
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suffixes=("_codeFlow_9799", "_threadFlows_1597"), validate="1:m")
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.drop(columns=['threadFlows', 'array_id', 'type_at_index'])
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#
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.merge(sf(4194), how="left", left_on='id_or_value_at_index', right_on='struct_id',
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suffixes=("_9699", "_4194"), validate="1:m")
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.drop(columns=['id_or_value_at_index', 'struct_id'])
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#
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.merge(af(1075), how="left", left_on='locations_4194', right_on='array_id', validate="1:m")
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.drop(columns=['locations_4194', 'array_id', 'type_at_index'])
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.rename(columns={"value_index": "value_index_locations_1075"})
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#
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.merge(sf('0987'), how="left", left_on='id_or_value_at_index', right_on='struct_id', validate="1:m")
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.drop(columns=['id_or_value_at_index', 'struct_id'])
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#
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.merge(sf(2683), how="left", left_on='location', right_on='struct_id',
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suffixes=("_9699", "_2683"), validate="1:m")
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.drop(columns=['location', 'struct_id'])
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#
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# The below is similar to dr1
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#
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.merge(sf(4963), how="left", left_on='physicalLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'physicalLocation'])
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#
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.merge(sf(6299), how="left", left_on='region', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'region'])
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#
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.merge(sf(2685), how="left", left_on='artifactLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'artifactLocation'])
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#
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.merge(sf(2774), how="left", left_on='message_2683', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'message_2683'])
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)
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# Keep columns of interest
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dco2 = (dco1[['uri',
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'startLine', 'startColumn', 'endLine', 'endColumn',
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'text',
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'ruleIndex', 'value_index_codeFlow_9799',
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'value_index_threadFlows_1597', 'value_index_locations_1075',
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]]
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.rename({'text': 'message',
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'value_index_codeFlow_9799': 'idx_codeFlow',
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'value_index_threadFlows_1597': 'idx_threadFlows',
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'value_index_locations_1075': 'idx_locations'}, axis='columns'))
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# Remove dummy locations previously injected by signature.fillsig
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dco3 = dco2[dco2.uri != 'scli-dyys dummy value']
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#
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# Form the relatedLocation dataframe via joins, starting from the union of
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# relatedLocations from `kind problem` (sf(4055)) and `kind path-problem`
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# (sf(9699)). This is only sligthly different from d1: left_on=relatedLocations,
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# and no left_on='message_4055'
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#
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dr1 = (
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pd.concat([sf(4055)[['relatedLocations', 'struct_id']], sf(9699)[['relatedLocations', 'struct_id']]])
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.merge(af('0350'), how="left", left_on='relatedLocations', right_on='array_id', validate="1:m")
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.drop(columns=['relatedLocations', 'array_id', 'value_index', 'type_at_index'])
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#
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.merge(sf(2683), how="left", left_on='id_or_value_at_index', right_on='struct_id',
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suffixes=("_4055_9699", "_2683"), validate="1:m")
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.drop(columns=['struct_id_2683', 'id_or_value_at_index'])
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#
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.merge(sf(4963), how="left", left_on='physicalLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'physicalLocation'])
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#
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.merge(sf(6299), how="left", left_on='region', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'region'])
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#
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.merge(sf(2685), how="left", left_on='artifactLocation', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'artifactLocation'])
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#
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.merge(sf(2774), how="left", left_on='message', right_on='struct_id', validate="1:m")
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.drop(columns=['struct_id', 'message'])
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)
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# Keep columns of interest
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dr2 = (dr1[['struct_id_4055_9699', 'uri', 'startLine', 'startColumn', 'endLine', 'endColumn', 'text']]
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.rename({'text': 'message', 'struct_id_4055_9699': 'struct_id'}, axis='columns'))
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# Remove dummy locations previously injected by signature.fillsig
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dr3 = dr2[dr2.uri != 'scli-dyys dummy value']
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#
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# Write output
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#
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if args.output_format == 'csv':
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p = pathlib.Path(args.outdir)
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p.mkdir(exist_ok=True)
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with p.joinpath('problem.csv').open(mode='wb') as problem:
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d2.to_csv(problem, index_label='index')
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with p.joinpath('path-problem.csv').open(mode='wb') as path_problem:
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dco3.to_csv(path_problem, index_label='index')
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with p.joinpath('relatedLocations.csv').open(mode='wb') as relo:
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dr3.to_csv(relo, index_label='index')
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else:
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sys.stderr.write("unknown output format")
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sys.exit(1)
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@@ -4,5 +4,6 @@
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# nothing on stdout/stderr
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#
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( cd ../data/treeio/2021-12-09 && sarif-extract-tables results.sarif test-tables )
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( cd ../data/treeio/2022-02-25 && sarif-extract-tables results.sarif test-tables )
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( cd ../data/treeio && sarif-extract-multi multi-sarif-01.json test-multi-table )
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( cd ../data/treeio && sarif-extract-scans scan-spec-0.json test-scan )
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