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Feature/llm xml context #101

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5b5287b
Merge pull request #97 from AutoFiC/dev
inyeongjang Oct 12, 2025
c64f657
feat: XML generator & schema + LLM/SAST module updates
Oct 17, 2025
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190 changes: 190 additions & 0 deletions custom_context.xsd
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Original file line number Diff line number Diff line change
@@ -0,0 +1,190 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- =============================================================================
AutoFiC Team-Atlanta Style CUSTOM_CONTEXT XSD (v1.1)
============================================================================= -->
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
targetNamespace="urn:autofic:custom-context"
xmlns="urn:autofic:custom-context"
elementFormDefault="qualified"
attributeFormDefault="unqualified">

<xsd:element name="CUSTOM_CONTEXT">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="META" type="MetaType"/>
<xsd:element name="VULNERABILITY" type="VulnType" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="version" type="xsd:string" use="required"/>
<xsd:attribute ref="xsi:schemaLocation" use="optional"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"/>
</xsd:complexType>
</xsd:element>

<xsd:complexType name="MetaType">
<xsd:attribute name="generatedAt" type="xsd:string" use="required"/>
<xsd:attribute name="tool" type="xsd:string" use="required"/>
<xsd:attribute name="count" type="xsd:nonNegativeInteger" use="required"/>
</xsd:complexType>

<xsd:complexType name="VulnType">
<xsd:sequence>
<xsd:element name="FILE" type="FileType"/>
<xsd:element name="RANGE" type="RangeType"/>
<xsd:element name="SEVERITY" type="SeverityType"/>
<xsd:element name="MESSAGE" type="MessageType"/>
<xsd:element name="SNIPPET" type="CDataString"/>

<xsd:element name="BIT" type="BitType"/>

<xsd:element name="CLASSES" type="ClassesType" minOccurs="0"/>
<xsd:element name="WEAKNESSES" type="WeaknessesType" minOccurs="0"/>
<xsd:element name="REFERENCES" type="ReferencesType" minOccurs="0"/>
<xsd:element name="SOURCE" type="SourceType" minOccurs="0"/>
<xsd:element name="EVIDENCE" type="EvidenceType" minOccurs="0"/>
<xsd:element name="PRECONDITIONS" type="StringListType" minOccurs="0"/>
<xsd:element name="ENV" type="EnvType" minOccurs="0"/>
<xsd:element name="MITIGATION" type="MitigationType" minOccurs="0"/>
<xsd:element name="TRACKING" type="TrackingType" minOccurs="0"/>
<xsd:element name="CONTEXT" type="ContextType" minOccurs="0"/>
</xsd:sequence>
<xsd:attribute name="id" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="FileType">
<xsd:attribute name="path" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="RangeType">
<xsd:attribute name="start" type="xsd:positiveInteger" use="required"/>
<xsd:attribute name="end" type="xsd:positiveInteger" use="required"/>
</xsd:complexType>

<xsd:complexType name="SeverityType">
<xsd:attribute name="overall" type="xsd:string" use="required"/>
<xsd:attribute name="bit" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="MessageType" mixed="true">
<xsd:sequence minOccurs="0">
<xsd:element name="MESSAGES" type="StringListType" minOccurs="0"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="BitType">
<xsd:sequence>
<xsd:element name="TRIGGER" type="CDataString"/>
<xsd:element name="STEPS" type="StepsType"/>
<xsd:element name="REPRODUCTION" type="CDataString"/>
<xsd:element name="BIT_SEVERITY" type="xsd:string"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="StepsType">
<xsd:sequence>
<xsd:element name="STEP" type="xsd:string" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="ClassesType">
<xsd:sequence>
<xsd:element name="CLASS" type="xsd:string" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="WeaknessesType">
<xsd:sequence>
<xsd:element name="CWE" type="CweType" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="CweType">
<xsd:attribute name="id" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="ReferencesType">
<xsd:sequence>
<xsd:element name="REF" type="RefType" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="RefType">
<xsd:attribute name="href" type="xsd:anyURI" use="required"/>
</xsd:complexType>

<xsd:complexType name="SourceType">
<xsd:attribute name="tool" type="xsd:string" use="optional"/>
<xsd:attribute name="id" type="xsd:string" use="optional"/>
<xsd:attribute name="helpUri" type="xsd:anyURI" use="optional"/>
</xsd:complexType>

<xsd:complexType name="EvidenceType">
<xsd:sequence>
<xsd:element name="SINK" type="PointType" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="SOURCE" type="PointType" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="FLOW" type="xsd:string" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="PointType">
<xsd:attribute name="line" type="xsd:positiveInteger" use="optional"/>
<xsd:attribute name="symbol" type="xsd:string" use="optional"/>
<xsd:attribute name="taint" type="xsd:string" use="optional"/>
</xsd:complexType>

<xsd:complexType name="StringListType">
<xsd:sequence>
<xsd:element name="ITEM" type="xsd:string" minOccurs="1" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="EnvType">
<xsd:sequence>
<xsd:element name="RUNTIME" type="RuntimeType" minOccurs="0"/>
<xsd:element name="DEPENDENCY" type="DependencyType" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="RuntimeType">
<xsd:attribute name="node" type="xsd:string" use="optional"/>
<xsd:attribute name="os" type="xsd:string" use="optional"/>
</xsd:complexType>

<xsd:complexType name="DependencyType">
<xsd:attribute name="name" type="xsd:string" use="required"/>
<xsd:attribute name="version" type="xsd:string" use="optional"/>
</xsd:complexType>

<xsd:complexType name="MitigationType">
<xsd:sequence>
<xsd:element name="SUMMARY" type="xsd:string" minOccurs="1"/>
<xsd:element name="CODE_HINT" type="CDataString" minOccurs="0"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="TrackingType">
<xsd:sequence>
<xsd:element name="ISSUE" type="IssueType" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="COMMIT" type="CommitType" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>

<xsd:complexType name="IssueType">
<xsd:attribute name="key" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="CommitType">
<xsd:attribute name="hash" type="xsd:string" use="required"/>
</xsd:complexType>

<xsd:complexType name="ContextType">
<xsd:attribute name="before" type="xsd:nonNegativeInteger" use="required"/>
<xsd:attribute name="after" type="xsd:nonNegativeInteger" use="required"/>
</xsd:complexType>

<xsd:complexType name="CDataString" mixed="true">
<xsd:simpleContent>
<xsd:extension base="xsd:string"/>
</xsd:simpleContent>
</xsd:complexType>

</xsd:schema>
135 changes: 111 additions & 24 deletions src/autofic_core/cli.py
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@@ -1,35 +1,122 @@
from __future__ import annotations

from pathlib import Path
from typing import Optional

import click
from autofic_core.app import AutoFiCApp

SAST_TOOL_CHOICES = ['semgrep', 'codeql', 'snykcode']
from autofic_core.pipeline import AutoFiCPipeline


@click.command()
@click.option('--explain', is_flag=True, help="Print AutoFiC usage guide.")
@click.option('--repo', required=False, help="Target GitHub repository URL to analyze (required).")
@click.option('--save-dir', required=False, default="artifacts/downloaded_repo", help="Directory to save analysis results.")
def _echo_cfg(repo_url, save_dir, sast_tool, run_llm, llm_retry, run_patch, run_pr, xsd_path):
click.echo("AutoFiC - launching pipeline with the following options:\n")
click.echo(f" Repo URL : {repo_url}")
click.echo(f" Save dir : {save_dir}")
click.echo(f" SAST tool : {sast_tool}")
click.echo(f" LLM enabled : {run_llm} (retry={llm_retry})")
click.echo(f" Patch enabled : {run_patch}")
click.echo(f" PR enabled : {run_pr}")
click.echo(f" XSD path : {xsd_path if xsd_path else '(none)'}")
click.echo("")


@click.command(context_settings=dict(help_option_names=["-h", "--help"]))
@click.option(
"--repo",
"repo_url",
required=True,
help="Target GitHub repository URL. e.g., https://github.com/org/project",
)
@click.option(
"--save-dir",
type=click.Path(path_type=Path, file_okay=False, dir_okay=True, writable=True),
default=Path("./artifacts"),
show_default=True,
help="Directory to store outputs (snippets, XML, LLM responses, patches).",
)
@click.option(
'--sast',
type=click.Choice(SAST_TOOL_CHOICES, case_sensitive=False),
required=False,
help='Select SAST tool to use (choose one of: semgrep, codeql, snykcode).'
"--sast",
"sast_tool",
type=click.Choice(["semgrep", "codeql", "snykcode"], case_sensitive=False),
default="semgrep",
show_default=True,
help="Choose SAST tool (legacy style): --sast <semgrep|codeql|snykcode>.",
)
@click.option('--llm', is_flag=True, help="Run LLM to fix vulnerable code and save responses.")
@click.option('--llm-retry', is_flag=True, help="Re-run LLM for final verification and fixes.")
@click.option('--patch', is_flag=True, help="Generate diffs and apply patches using git.")
@click.option('--pr', is_flag=True, help="Automatically create a pull request.")
@click.option(
"--llm/--no-llm",
"run_llm",
default=True,
show_default=True,
help="Run LLM stage after SAST & XML.",
)
@click.option(
"--retry",
"llm_retry",
is_flag=True,
default=False,
help="Use retry directories (retry_llm/retry_parsed/retry_patch).",
)
@click.option(
"--patch/--no-patch",
"run_patch",
default=True,
show_default=True,
help="Generate unified diffs and attempt to apply patches.",
)
@click.option(
"--pr/--no-pr",
"run_pr",
default=False,
show_default=True,
help="(Reserved) Create a PR automatically. (Not wired in this CLI)",
)
@click.option(
"--xsd",
"xsd_path",
type=click.Path(path_type=Path, exists=True, dir_okay=False),
default=None,
help="Path to custom_context.xsd for XML validation (optional). If omitted, CLI will look for ./custom_context.xsd.",
)
def main(
repo_url: str,
save_dir: Path,
sast_tool: str,
run_llm: bool,
llm_retry: bool,
run_patch: bool,
run_pr: bool,
xsd_path: Optional[Path],
) -> None:
"""
AutoFiC — run pipeline end-to-end (legacy CLI).

Examples:
python -m autofic_core.cli --repo https://github.com/org/project --sast semgrep
python -m autofic_core.cli --repo https://github.com/org/project --sast codeql --no-llm
"""
# Normalize paths
save_dir = save_dir.expanduser().resolve()

# Default XSD at project root (optional)
if xsd_path is None:
local_xsd = Path("custom_context.xsd").resolve()
if local_xsd.exists():
xsd_path = local_xsd

def main(explain, repo, save_dir, sast, llm, llm_retry, patch, pr):
app = AutoFiCApp(
explain=explain,
repo=repo,
_echo_cfg(repo_url, save_dir, sast_tool, run_llm, llm_retry, run_patch, run_pr, xsd_path)

pipe = AutoFiCPipeline(
repo_url=repo_url,
save_dir=save_dir,
sast=sast,
llm=llm,
sast=True,
sast_tool=sast_tool.lower(),
llm=run_llm,
llm_retry=llm_retry,
patch=patch,
pr=pr
patch=run_patch,
pr=run_pr,
)
app.run()
pipe.run()


if __name__ == "__main__":
main()
main()
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