Add program model demo (#17)

* add program model uv

* add tool to common

* remove oss fuzz tool

* add docker

* implement build base image

* fix ret check

* add builder for subimage

* remove old tool

* hack to avoid dupped kzip files

* fixes... need to work out LD hack

* fix find

* justfile for building kythe

* update dockerfile

* add upload tool

* update protobuf

* move into compose

* fix merge invocation

* fix up invoc

* bump kythe

* reformat

* format

* format

* remove unused

* add lint and change version

* fixes

* exclude

* fix formatting:

* dev deps

* add dep

* exclude gen

* fix

.github/workflows/lint.yml

@@ -40,3 +40,7 @@ jobs:
       - name: Run ruff on fuzzer
         run: uv run ruff format --check && uv run ruff check
         working-directory: fuzzer
+
+      - name: Run ruff on program-model
+        run: uv run ruff format --check && uv run ruff check
+        working-directory: program-model

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "program-model/aixcc-kythe"]
+	path = program-model/aixcc-kythe
+	url = git@github.com:trailofbits/aixcc-kythe.git

common/src/buttercup/common/oss_fuzz_tool.py

@@ -0,0 +1,64 @@
+from dataclasses import dataclass
+from buttercup.common.queues import BuildConfiguration
+import subprocess
+import os
+from typing import Optional
+
+
+@dataclass
+class Conf:
+    oss_fuzz_path: str
+    python_path: str
+    allow_pull: bool
+    base_image_url: str
+
+
+class OSSFuzzTool:
+    def __init__(self, conf: Conf):
+        self._conf = conf
+        self._helper_path = os.path.join(self._conf.oss_fuzz_path, "infra/helper.py")
+
+    @staticmethod
+    def add_optional_arg(lst: list, flag: str, arg: str):
+        if arg is not None:
+            lst.append(flag)
+            lst.append(arg)
+
+    def build_fuzzer_command(self, cmd: str, fuzz_conf: BuildConfiguration):
+        args = [self._conf.python_path, self._helper_path, cmd]
+
+        OSSFuzzTool.add_optional_arg(args, "--engine", fuzz_conf.engine)
+        OSSFuzzTool.add_optional_arg(args, "--sanitizer", fuzz_conf.sanitizer)
+        args.append(fuzz_conf.project_id)
+        return args
+
+    def check_fuzzer_runs(self, fuzz_conf: BuildConfiguration):
+        args = self.build_fuzzer_command("check_build", fuzz_conf)
+        ret = subprocess.run(args)
+        return ret.returncode == 0
+
+    def build_base_image(self, package_conf: str) -> Optional[str]:
+        args = [self._conf.python_path, self._helper_path, "build_image"]
+
+        if self._conf.allow_pull:
+            args.append("--pull")
+        else:
+            args.append("--no-pull")
+
+        args.append(package_conf)
+        ret = subprocess.run(args)
+        if ret.returncode == 0:
+            return f"{self._conf.base_image_url}/{package_conf}"
+        else:
+            return None
+
+    def build_fuzzer(self, fuzz_conf: BuildConfiguration):
+        args = self.build_fuzzer_command("build_fuzzers", fuzz_conf)
+        ret = subprocess.run(args)
+        return ret.returncode == 0
+
+    def build_fuzzer_with_cache(self, fuzz_conf: BuildConfiguration):
+        if not self.check_fuzzer_runs(fuzz_conf):
+            return self.build_fuzzer(fuzz_conf)
+
+        return True

compose.yaml

@@ -30,6 +30,12 @@ services:
       interval: 1s
       timeout: 3s
       retries: 5
+
+  graphdb:
+    image: janusgraph/janusgraph:1.2.0-20250113-082101.7f6ffcf
+    restart: always
+    ports:
+      - '127.0.0.1:8182:8182'
   
   stimulate-fuzzer-test:
     build:
@@ -54,6 +60,25 @@ services:
       redis:
         condition: service_healthy
 
+  indexer-run:
+    image: program-model-image
+    command: -m buttercup.program_model.indexer.oss_fuzz_indexer --scriptdir /app/scripts --url ws://graphdb:8182/gremlin --allow_pull --oss_fuzz_dir /crs_scratch/ossfuzz --base_image_url gcr.io/oss-fuzz --package_name libpng --wdir /crs_scratch/ --kythe_dir /app/kythe-v0.0.67 --python /app/.venv/bin/python
+    build:
+      context: ./
+      dockerfile: ./program-model/upload_worker.Dockerfile
+    volumes:
+      - ./crs_scratch:/crs_scratch
+    environment:
+      # These values will be modified automatically at competition time
+      - DOCKER_HOST=tcp://dind:2375
+    restart: no
+    depends_on:
+      redis:
+        condition: service_healthy
+      dind:
+        condition: service_started
+      graphdb:
+        condition: service_started
   build-bot:
     command: ["buttercup-fuzzer-builder", "--wdir", "/crs_scratch", "--redis_url", "redis://redis:6379"]
     build:

fuzzer/src/buttercup/fuzzing_infra/builder.py

@@ -1,8 +1,6 @@
 import argparse
-import subprocess
-import os
-from dataclasses import dataclass
 from buttercup.common.queues import BuildConfiguration
+from buttercup.common.oss_fuzz_tool import OSSFuzzTool, Conf
 # General idea for fuzzer arch:
 # build out a build and a run entrypoint, fuzzer is checkpointed as a configuration after a build
 # build is in shared mount for all fuzzer pods.
@@ -12,48 +10,6 @@ from buttercup.common.queues import BuildConfiguration
 # build might be possible with just helper.py but may want to share with clusterfuzz to make engine options line up
 
 
-@dataclass
-class Conf:
-    oss_fuzz_path: str
-    python_path: str
-
-
-class OSSFuzzTool:
-    def __init__(self, conf: Conf):
-        self._conf = conf
-        self._helper_path = os.path.join(self._conf.oss_fuzz_path, "infra/helper.py")
-
-    @staticmethod
-    def add_optional_arg(lst: list, flag: str, arg: str):
-        if arg is not None:
-            lst.append(flag)
-            lst.append(arg)
-
-    def build_fuzzer_command(self, cmd: str, fuzz_conf: BuildConfiguration):
-        args = [self._conf.python_path, self._helper_path, cmd]
-
-        OSSFuzzTool.add_optional_arg(args, "--engine", fuzz_conf.engine)
-        OSSFuzzTool.add_optional_arg(args, "--sanitizer", fuzz_conf.sanitizer)
-        args.append(fuzz_conf.project_id)
-        return args
-
-    def check_fuzzer_runs(self, fuzz_conf: BuildConfiguration):
-        args = self.build_fuzzer_command("check_build", fuzz_conf)
-        ret = subprocess.run(args)
-        return ret.returncode == 0
-
-    def build_fuzzer(self, fuzz_conf: BuildConfiguration):
-        args = self.build_fuzzer_command("build_fuzzers", fuzz_conf)
-        ret = subprocess.run(args)
-        return ret.returncode == 0
-
-    def build_fuzzer_with_cache(self, fuzz_conf: BuildConfiguration):
-        if not self.check_fuzzer_runs(fuzz_conf):
-            return self.build_fuzzer(fuzz_conf)
-
-        return True
-
-
 def main():
     prsr = argparse.ArgumentParser("Fuzzing Infra")
     prsr.add_argument("target")

fuzzer/src/buttercup/fuzzing_infra/builder_bot.py

@@ -1,4 +1,5 @@
-from buttercup.fuzzing_infra.builder import OSSFuzzTool, Conf, BuildConfiguration
+from buttercup.common.queues import BuildConfiguration
+from buttercup.common.oss_fuzz_tool import OSSFuzzTool, Conf
 from redis import Redis
 import argparse
 import tempfile

justfile

@@ -0,0 +1,23 @@
+BUILDER_IMAGE_NAME := "kythe_builder"
+
+build-kythe-builder:
+    docker build -t {{BUILDER_IMAGE_NAME}} -f ./program-model/kythe_builder/Dockerfile .
+
+build-kythe-tar-gz: build-kythe-builder
+    docker run -v {{justfile_directory()}}/program-model/scripts/gzs/:/out {{BUILDER_IMAGE_NAME}}
+
+
+download-kythe:
+    #!/usr/bin/env bash
+    set -euxo pipefail
+    if [[ ! -f "program-model/scripts/gzs/kythe-v0.0.67.tar.gz" ]] 
+    then
+        curl -o program-model/scripts/gzs/kythe-v0.0.67.tar.gz https://github.com/trailofbits/aixcc-kythe/releases/download/v0.0.2/kythe-v0.0.67.tar.gz
+    fi
+
+build-indexer-image: 
+    docker build -t indexer -f ./program-model/upload_worker.Dockerfile  .
+
+
+run-indexer: download-kythe
+    docker compose --profile=development up --build indexer-run

program-model/.gitignore

@@ -0,0 +1,5 @@
+scripts/gzs
+*.pyc
+program_model/data/kythe/proto
+program_model/services/kythe/proto
+kythe_builder/build_out

program-model/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "kythe"]
+	path = kythe
+	url = git@github.com:kythe/kythe.git

program-model/README.md

@@ -0,0 +1,53 @@
+# Program Model
+
+This is a demo project that shows how to index an oss-fuzz project (reliablyish) with kythe and upload the results in a graph db
+
+The components are listed and discussed below:
+
+## kythe_builder
+
+This is a docker image responsible for building kythe within the base-clang image. This should be built first and produces a tar.gz of kythe that can be injected in oss-fuzz docker images.
+
+## scripts
+
+These scripts are used to create a Docker image that is dervived from a project builder e.g. gcr.io/oss-fuzz/libpng.
+
+The Dockerfile is parameterized over the base image used. So one can build an oss-fuzz project with kythe as follows:
+* use oss-fuzz helper.py to build the project 
+* build the scripts/Dockerfile with the project as the base 
+
+`cd scripts && docker build --build-arg BASE_IMAGE=gcr.io/oss-fuzz/libpng .` 
+Then you should be able to run compile as normal for an oss-fuzz image and generate kzips (indexed versions of the object files).
+
+## kythe
+
+Once you have a kzip for each compilation action then you need to merge these to a global kzip using 
+`kythe/tools/kzip merge --output $KYTHE_OUTPUT_DIRECTORY/merged.kzip $KYTHE_OUTPUT_DIRECTORY/*.kzip`
+
+Once you have a bunch of kzips you need to index these with the cxx_indexer in kythe. 
+
+e.g.
+
+`kythe/indexers/cxx_indexer --ignore_unimplemented <merged.kzip>`
+
+This produces a stream of protobuf on stdout. Specifically each protobuf record is an entry described in this spec [text](https://kythe.io/docs/kythe-storage.html#_entry)
+
+## program_model
+
+This pyhon script specifically program_model/indexer/entries_into_db.py reads the protobuf entries from kythe and uploads them to JanusGraph. 
+
+This is invoked (after entering poetry shell) with 
+`python program_model/indexer/entries_into_db --url <janus_graph_url>`
+
+janus graph can be run via docker with 
+
+`docker run janusgraph/janusgraph`
+
+The url can be determined with  
+
+```
+docker inspect \
+  -f '{{range.NetworkSettings.Networks}}{{.IPAddress}}{{end}}' <janus container>
+```
+
+this will get you the ip, then the url is `ws://<IP address>:8182/gremlin`

program-model/build_protobuf.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+protoc -Iaixcc-kythe/ --python_out=./src/buttercup/program_model/data --pyi_out=./src/buttercup/program_model/data aixcc-kythe/kythe/proto/storage.proto

program-model/kythe_builder/Dockerfile

@@ -0,0 +1,17 @@
+FROM gcr.io/oss-fuzz-base/base-clang
+
+ENV KYTHE_VERSION=v0.0.67
+RUN apt update && apt -y install bison flex uuid-dev asciidoc graphviz source-highlight
+RUN apt -y install git
+COPY program-model/aixcc-kythe /kythe
+RUN apt install apt-transport-https curl gnupg -y
+RUN curl -fsSL https://bazel.build/bazel-release.pub.gpg | gpg --dearmor >bazel-archive-keyring.gpg
+RUN mv bazel-archive-keyring.gpg /usr/share/keyrings
+RUN echo "deb [arch=amd64 signed-by=/usr/share/keyrings/bazel-archive-keyring.gpg] https://storage.googleapis.com/bazel-apt stable jdk1.8" | tee /etc/apt/sources.list.d/bazel.list
+RUN apt update && apt -y install bazel-7.1.0 build-essential
+
+COPY program-model/kythe_builder/entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+WORKDIR /kythe
+
+ENTRYPOINT ["/entrypoint.sh"]

program-model/kythe_builder/entrypoint.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -euxo pipefail
+
+cp -r ./ $OUT/kythe 
+pushd $OUT/kythe 
+bazel-7.1.0 build //kythe/release --sandbox_debug
+cp bazel-bin/kythe/release/kythe-v0.0.67.tar.gz ./

program-model/pyproject.toml

@@ -0,0 +1,33 @@
+[project]
+name = "program-model"
+version = "0.1.0"
+description = ""
+authors = [
+    {name = "Trail of Bits",email = "opensource@trailofbits"}
+]
+requires-python = ">=3.9,<3.11"
+dependencies = [
+    "gremlinpython==3.7.3",
+    "common",
+    "protobuf (>=3.20, <=3.20.3)",
+]
+
+[tool.uv.sources]
+common = { path = "../common", editable = true }
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/buttercup"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+
+[tool.ruff]
+extend-exclude = ["aixcc-kythe", "src/buttercup/program_model/data/kythe/proto/"]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.4",
+    "ruff>=0.9.2",
+]

program-model/scripts/Dockerfile

@@ -0,0 +1,20 @@
+ARG BASE_IMAGE=myorg/myapp:latest
+FROM $BASE_IMAGE
+ARG KYTHE_VERSION=v0.0.67
+ARG KYTHE_TAR=gzs/kythe-v0.0.67.tar.gz
+
+COPY ./ccwrapper.sh $SRC/ccwrapper.sh
+COPY ./cxxwrapper.sh $SRC/cxxwrapper.sh
+RUN chmod +x $SRC/ccwrapper.sh &&  chmod +x $SRC/cxxwrapper.sh
+
+ENV FUZZING_LANGUAGE=c++
+
+ENV ORIG_CXX=$CXX
+ENV ORIG_CC=$CC
+ENV CXX=$SRC/cxxwrapper.sh
+ENV CCC=$SRC/cxxwrapper.sh
+ENV CC=$SRC/ccwrapper.sh
+
+ADD $KYTHE_TAR $SRC/kythe
+#RUN tar -xvf $SRC/kythe-release.tar.gz -C $SRC 
+ENV KYTHE_RELEASE_DIR=$SRC/kythe/kythe-$KYTHE_VERSION

program-model/scripts/ccwrapper.sh

@@ -0,0 +1,17 @@
+# cxx_wrapper.sh
+#!/bin/bash -e
+
+set -euxo pipefail
+
+echo "Called with $@"
+echo "done"
+
+KYTHE_OUTPUT_DIRECTORY_ORIG=$KYTHE_OUTPUT_DIRECTORY
+KYTHE_OUTPUT_DIRECTORY=$(mktemp -d -t kythe_output_XXXXXXXXXXXXXXX)
+mkdir -p $KYTHE_OUTPUT_DIRECTORY
+KYTHE_OUTPUT_DIRECTORY=$KYTHE_OUTPUT_DIRECTORY $KYTHE_RELEASE_DIR/extractors/cxx_extractor "$@" & pid=$!
+$ORIG_CC  "$@"
+wait "$pid"
+
+for X in $KYTHE_OUTPUT_DIRECTORY/*.kzip; do [[ -e $X ]] && mv "$X" $KYTHE_OUTPUT_DIRECTORY_ORIG/; done
+rm -r $KYTHE_OUTPUT_DIRECTORY

program-model/scripts/cxxwrapper.sh

@@ -0,0 +1,9 @@
+# cxx_wrapper.sh
+#!/bin/bash -e
+
+# TODO(Ian): we need to share the code from ccwrapper.sh that moves kzip files between temp and original directories
+echo "Called with $@"
+echo "done"
+$KYTHE_RELEASE_DIR/extractors/cxx_extractor "$@" & pid=$!
+$ORIG_CXX "$@"
+wait "$pid"

program-model/src/buttercup/program_model/data/kythe/proto/storage_pb2.py

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# source: kythe/proto/storage.proto
+"""Generated protocol buffer code."""
+
+from google.protobuf.internal import builder as _builder
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import descriptor_pool as _descriptor_pool
+from google.protobuf import symbol_database as _symbol_database
+# @@protoc_insertion_point(imports)
+
+_sym_db = _symbol_database.Default()
+
+
+DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(
+    b'\n\x19kythe/proto/storage.proto\x12\x0bkythe.proto"X\n\x05VName\x12\x11\n\tsignature\x18\x01 \x01(\t\x12\x0e\n\x06\x63orpus\x18\x02 \x01(\t\x12\x0c\n\x04root\x18\x03 \x01(\t\x12\x0c\n\x04path\x18\x04 \x01(\t\x12\x10\n\x08language\x18\x05 \x01(\t"\\\n\tVNameMask\x12\x11\n\tsignature\x18\x01 \x01(\x08\x12\x0e\n\x06\x63orpus\x18\x02 \x01(\x08\x12\x0c\n\x04root\x18\x03 \x01(\x08\x12\x0c\n\x04path\x18\x04 \x01(\x08\x12\x10\n\x08language\x18\x05 \x01(\x08"\x89\x01\n\x05\x45ntry\x12"\n\x06source\x18\x01 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x11\n\tedge_kind\x18\x02 \x01(\t\x12"\n\x06target\x18\x03 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x11\n\tfact_name\x18\x04 \x01(\t\x12\x12\n\nfact_value\x18\x05 \x01(\x0c".\n\x07\x45ntries\x12#\n\x07\x65ntries\x18\x01 \x03(\x0b\x32\x12.kythe.proto.Entry"D\n\x0bReadRequest\x12"\n\x06source\x18\x01 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x11\n\tedge_kind\x18\x02 \x01(\t"\xcc\x01\n\x0cWriteRequest\x12"\n\x06source\x18\x01 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x30\n\x06update\x18\x02 \x03(\x0b\x32 .kythe.proto.WriteRequest.Update\x1a\x66\n\x06Update\x12\x11\n\tedge_kind\x18\x01 \x01(\t\x12"\n\x06target\x18\x02 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x11\n\tfact_name\x18\x03 \x01(\t\x12\x12\n\nfact_value\x18\x04 \x01(\x0c"\x0c\n\nWriteReply"Y\n\x0bScanRequest\x12"\n\x06target\x18\x01 \x01(\x0b\x32\x12.kythe.proto.VName\x12\x11\n\tedge_kind\x18\x02 \x01(\t\x12\x13\n\x0b\x66\x61\x63t_prefix\x18\x03 \x01(\t"-\n\x0c\x43ountRequest\x12\r\n\x05index\x18\x01 \x01(\x03\x12\x0e\n\x06shards\x18\x02 \x01(\x03"\x1d\n\nCountReply\x12\x0f\n\x07\x65ntries\x18\x01 \x01(\x03"-\n\x0cShardRequest\x12\r\n\x05index\x18\x01 \x01(\x03\x12\x0e\n\x06shards\x18\x02 \x01(\x03"N\n\x10VNameRewriteRule\x12\x0f\n\x07pattern\x18\x01 \x01(\t\x12)\n\x06v_name\x18\x02 \x01(\x0b\x32\x12.kythe.proto.VNameR\x05vname"@\n\x11VNameRewriteRules\x12+\n\x04rule\x18\x01 \x03(\x0b\x32\x1d.kythe.proto.VNameRewriteRuleBH\n\x1f\x63om.google.devtools.kythe.protoZ%kythe.io/kythe/proto/storage_go_protob\x06proto3'
+)
+
+_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, globals())
+_builder.BuildTopDescriptorsAndMessages(
+    DESCRIPTOR, "kythe.proto.storage_pb2", globals()
+)
+if _descriptor._USE_C_DESCRIPTORS == False:
+    DESCRIPTOR._options = None
+    DESCRIPTOR._serialized_options = (
+        b"\n\037com.google.devtools.kythe.protoZ%kythe.io/kythe/proto/storage_go_proto"
+    )
+    _VNAME._serialized_start = 42
+    _VNAME._serialized_end = 130
+    _VNAMEMASK._serialized_start = 132
+    _VNAMEMASK._serialized_end = 224
+    _ENTRY._serialized_start = 227
+    _ENTRY._serialized_end = 364
+    _ENTRIES._serialized_start = 366
+    _ENTRIES._serialized_end = 412
+    _READREQUEST._serialized_start = 414
+    _READREQUEST._serialized_end = 482
+    _WRITEREQUEST._serialized_start = 485
+    _WRITEREQUEST._serialized_end = 689
+    _WRITEREQUEST_UPDATE._serialized_start = 587
+    _WRITEREQUEST_UPDATE._serialized_end = 689
+    _WRITEREPLY._serialized_start = 691
+    _WRITEREPLY._serialized_end = 703
+    _SCANREQUEST._serialized_start = 705
+    _SCANREQUEST._serialized_end = 794
+    _COUNTREQUEST._serialized_start = 796
+    _COUNTREQUEST._serialized_end = 841
+    _COUNTREPLY._serialized_start = 843
+    _COUNTREPLY._serialized_end = 872
+    _SHARDREQUEST._serialized_start = 874
+    _SHARDREQUEST._serialized_end = 919
+    _VNAMEREWRITERULE._serialized_start = 921
+    _VNAMEREWRITERULE._serialized_end = 999
+    _VNAMEREWRITERULES._serialized_start = 1001
+    _VNAMEREWRITERULES._serialized_end = 1065
+# @@protoc_insertion_point(module_scope)

program-model/src/buttercup/program_model/data/kythe/proto/storage_pb2.pyi

@@ -0,0 +1,190 @@
+from google.protobuf.internal import containers as _containers
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from typing import (
+    ClassVar as _ClassVar,
+    Iterable as _Iterable,
+    Mapping as _Mapping,
+    Optional as _Optional,
+    Union as _Union,
+)
+
+DESCRIPTOR: _descriptor.FileDescriptor
+
+class CountReply(_message.Message):
+    __slots__ = ["entries"]
+    ENTRIES_FIELD_NUMBER: _ClassVar[int]
+    entries: int
+    def __init__(self, entries: _Optional[int] = ...) -> None: ...
+
+class CountRequest(_message.Message):
+    __slots__ = ["index", "shards"]
+    INDEX_FIELD_NUMBER: _ClassVar[int]
+    SHARDS_FIELD_NUMBER: _ClassVar[int]
+    index: int
+    shards: int
+    def __init__(
+        self, index: _Optional[int] = ..., shards: _Optional[int] = ...
+    ) -> None: ...
+
+class Entries(_message.Message):
+    __slots__ = ["entries"]
+    ENTRIES_FIELD_NUMBER: _ClassVar[int]
+    entries: _containers.RepeatedCompositeFieldContainer[Entry]
+    def __init__(
+        self, entries: _Optional[_Iterable[_Union[Entry, _Mapping]]] = ...
+    ) -> None: ...
+
+class Entry(_message.Message):
+    __slots__ = ["edge_kind", "fact_name", "fact_value", "source", "target"]
+    EDGE_KIND_FIELD_NUMBER: _ClassVar[int]
+    FACT_NAME_FIELD_NUMBER: _ClassVar[int]
+    FACT_VALUE_FIELD_NUMBER: _ClassVar[int]
+    SOURCE_FIELD_NUMBER: _ClassVar[int]
+    TARGET_FIELD_NUMBER: _ClassVar[int]
+    edge_kind: str
+    fact_name: str
+    fact_value: bytes
+    source: VName
+    target: VName
+    def __init__(
+        self,
+        source: _Optional[_Union[VName, _Mapping]] = ...,
+        edge_kind: _Optional[str] = ...,
+        target: _Optional[_Union[VName, _Mapping]] = ...,
+        fact_name: _Optional[str] = ...,
+        fact_value: _Optional[bytes] = ...,
+    ) -> None: ...
+
+class ReadRequest(_message.Message):
+    __slots__ = ["edge_kind", "source"]
+    EDGE_KIND_FIELD_NUMBER: _ClassVar[int]
+    SOURCE_FIELD_NUMBER: _ClassVar[int]
+    edge_kind: str
+    source: VName
+    def __init__(
+        self,
+        source: _Optional[_Union[VName, _Mapping]] = ...,
+        edge_kind: _Optional[str] = ...,
+    ) -> None: ...
+
+class ScanRequest(_message.Message):
+    __slots__ = ["edge_kind", "fact_prefix", "target"]
+    EDGE_KIND_FIELD_NUMBER: _ClassVar[int]
+    FACT_PREFIX_FIELD_NUMBER: _ClassVar[int]
+    TARGET_FIELD_NUMBER: _ClassVar[int]
+    edge_kind: str
+    fact_prefix: str
+    target: VName
+    def __init__(
+        self,
+        target: _Optional[_Union[VName, _Mapping]] = ...,
+        edge_kind: _Optional[str] = ...,
+        fact_prefix: _Optional[str] = ...,
+    ) -> None: ...
+
+class ShardRequest(_message.Message):
+    __slots__ = ["index", "shards"]
+    INDEX_FIELD_NUMBER: _ClassVar[int]
+    SHARDS_FIELD_NUMBER: _ClassVar[int]
+    index: int
+    shards: int
+    def __init__(
+        self, index: _Optional[int] = ..., shards: _Optional[int] = ...
+    ) -> None: ...
+
+class VName(_message.Message):
+    __slots__ = ["corpus", "language", "path", "root", "signature"]
+    CORPUS_FIELD_NUMBER: _ClassVar[int]
+    LANGUAGE_FIELD_NUMBER: _ClassVar[int]
+    PATH_FIELD_NUMBER: _ClassVar[int]
+    ROOT_FIELD_NUMBER: _ClassVar[int]
+    SIGNATURE_FIELD_NUMBER: _ClassVar[int]
+    corpus: str
+    language: str
+    path: str
+    root: str
+    signature: str
+    def __init__(
+        self,
+        signature: _Optional[str] = ...,
+        corpus: _Optional[str] = ...,
+        root: _Optional[str] = ...,
+        path: _Optional[str] = ...,
+        language: _Optional[str] = ...,
+    ) -> None: ...
+
+class VNameMask(_message.Message):
+    __slots__ = ["corpus", "language", "path", "root", "signature"]
+    CORPUS_FIELD_NUMBER: _ClassVar[int]
+    LANGUAGE_FIELD_NUMBER: _ClassVar[int]
+    PATH_FIELD_NUMBER: _ClassVar[int]
+    ROOT_FIELD_NUMBER: _ClassVar[int]
+    SIGNATURE_FIELD_NUMBER: _ClassVar[int]
+    corpus: bool
+    language: bool
+    path: bool
+    root: bool
+    signature: bool
+    def __init__(
+        self,
+        signature: bool = ...,
+        corpus: bool = ...,
+        root: bool = ...,
+        path: bool = ...,
+        language: bool = ...,
+    ) -> None: ...
+
+class VNameRewriteRule(_message.Message):
+    __slots__ = ["pattern", "v_name"]
+    PATTERN_FIELD_NUMBER: _ClassVar[int]
+    V_NAME_FIELD_NUMBER: _ClassVar[int]
+    pattern: str
+    v_name: VName
+    def __init__(
+        self,
+        pattern: _Optional[str] = ...,
+        v_name: _Optional[_Union[VName, _Mapping]] = ...,
+    ) -> None: ...
+
+class VNameRewriteRules(_message.Message):
+    __slots__ = ["rule"]
+    RULE_FIELD_NUMBER: _ClassVar[int]
+    rule: _containers.RepeatedCompositeFieldContainer[VNameRewriteRule]
+    def __init__(
+        self, rule: _Optional[_Iterable[_Union[VNameRewriteRule, _Mapping]]] = ...
+    ) -> None: ...
+
+class WriteReply(_message.Message):
+    __slots__ = []
+    def __init__(self) -> None: ...
+
+class WriteRequest(_message.Message):
+    __slots__ = ["source", "update"]
+    class Update(_message.Message):
+        __slots__ = ["edge_kind", "fact_name", "fact_value", "target"]
+        EDGE_KIND_FIELD_NUMBER: _ClassVar[int]
+        FACT_NAME_FIELD_NUMBER: _ClassVar[int]
+        FACT_VALUE_FIELD_NUMBER: _ClassVar[int]
+        TARGET_FIELD_NUMBER: _ClassVar[int]
+        edge_kind: str
+        fact_name: str
+        fact_value: bytes
+        target: VName
+        def __init__(
+            self,
+            edge_kind: _Optional[str] = ...,
+            target: _Optional[_Union[VName, _Mapping]] = ...,
+            fact_name: _Optional[str] = ...,
+            fact_value: _Optional[bytes] = ...,
+        ) -> None: ...
+
+    SOURCE_FIELD_NUMBER: _ClassVar[int]
+    UPDATE_FIELD_NUMBER: _ClassVar[int]
+    source: VName
+    update: _containers.RepeatedCompositeFieldContainer[WriteRequest.Update]
+    def __init__(
+        self,
+        source: _Optional[_Union[VName, _Mapping]] = ...,
+        update: _Optional[_Iterable[_Union[WriteRequest.Update, _Mapping]]] = ...,
+    ) -> None: ...

program-model/src/buttercup/program_model/data/kythe/proto/storage_service_pb2.py

@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+# Generated by the protocol buffer compiler.  DO NOT EDIT!
+# NO CHECKED-IN PROTOBUF GENCODE
+# source: kythe/proto/storage_service.proto
+# Protobuf Python Version: 5.28.1
+"""Generated protocol buffer code."""
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import descriptor_pool as _descriptor_pool
+from google.protobuf import runtime_version as _runtime_version
+from google.protobuf import symbol_database as _symbol_database
+from google.protobuf.internal import builder as _builder
+
+_runtime_version.ValidateProtobufRuntimeVersion(
+    _runtime_version.Domain.PUBLIC, 5, 28, 1, "", "kythe/proto/storage_service.proto"
+)
+# @@protoc_insertion_point(imports)
+
+_sym_db = _symbol_database.Default()
+
+
+DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(
+    b'\n!kythe/proto/storage_service.proto\x12\x0bkythe.proto\x1a\x19kythe/proto/storage.proto2\xbf\x01\n\nGraphStore\x12\x38\n\x04Read\x12\x18.kythe.proto.ReadRequest\x1a\x12.kythe.proto.Entry"\x00\x30\x01\x12\x38\n\x04Scan\x12\x18.kythe.proto.ScanRequest\x1a\x12.kythe.proto.Entry"\x00\x30\x01\x12=\n\x05Write\x12\x19.kythe.proto.WriteRequest\x1a\x17.kythe.proto.WriteReply"\x00\x32\x8e\x01\n\x11ShardedGraphStore\x12=\n\x05\x43ount\x12\x19.kythe.proto.CountRequest\x1a\x17.kythe.proto.CountReply"\x00\x12:\n\x05Shard\x12\x19.kythe.proto.ShardRequest\x1a\x12.kythe.proto.Entry"\x00\x30\x01\x42P\n\x1f\x63om.google.devtools.kythe.protoZ-kythe.io/kythe/proto/storage_service_go_protob\x06proto3'
+)
+
+_globals = globals()
+_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals)
+_builder.BuildTopDescriptorsAndMessages(
+    DESCRIPTOR, "kythe.proto.storage_service_pb2", _globals
+)
+if not _descriptor._USE_C_DESCRIPTORS:
+    _globals["DESCRIPTOR"]._loaded_options = None
+    _globals[
+        "DESCRIPTOR"
+    ]._serialized_options = b"\n\037com.google.devtools.kythe.protoZ-kythe.io/kythe/proto/storage_service_go_proto"
+    _globals["_GRAPHSTORE"]._serialized_start = 78
+    _globals["_GRAPHSTORE"]._serialized_end = 269
+    _globals["_SHARDEDGRAPHSTORE"]._serialized_start = 272
+    _globals["_SHARDEDGRAPHSTORE"]._serialized_end = 414
+# @@protoc_insertion_point(module_scope)

program-model/src/buttercup/program_model/data/kythe/proto/storage_service_pb2.pyi

@@ -0,0 +1,3 @@
+from google.protobuf import descriptor as _descriptor
+
+DESCRIPTOR: _descriptor.FileDescriptor

program-model/src/buttercup/program_model/indexer/entries_into_db.py

@@ -0,0 +1,110 @@
+from buttercup.program_model.data.kythe.proto.storage_pb2 import Entry, VName
+from buttercup.program_model.utils.varint import decode_stream
+from typing import Generator
+from io import BytesIO
+from gremlin_python.structure.graph import Graph, GraphTraversalSource
+from gremlin_python.driver.driver_remote_connection import DriverRemoteConnection
+from dataclasses import dataclass
+import urllib
+from gremlin_python.structure.graph import Vertex
+import sys
+import argparse
+
+
+@dataclass(frozen=True, repr=False)
+class KytheURI:
+    signature: str
+    corpus: str
+    root: str
+    path: str
+    language: str
+
+    def __str__(self):
+        lst = [self.signature, self.corpus, self.root, self.path, self.language]
+        uristr = "/".join([urllib.parse.quote(x, safe="") for x in lst])
+        return uristr
+
+    @staticmethod
+    def from_vname(vn: VName):
+        return KytheURI(
+            signature=vn.signature,
+            corpus=vn.corpus,
+            root=vn.root,
+            path=vn.path,
+            language=vn.language,
+        )
+
+
+def is_edge(ent: Entry) -> bool:
+    return ent.edge_kind != ""
+
+
+def convert_node(trv: GraphTraversalSource, nd: VName) -> Vertex:
+    ur = KytheURI.from_vname(nd)
+    s = str(ur)
+    print(s)
+    maybe_nd = next(trv.V().has_label(s), None)
+    if maybe_nd is not None:
+        return maybe_nd
+
+    return trv.add_v(str(ur)).next()
+
+
+class JanusStorage:
+    def __init__(self, url: str):
+        self.connection = DriverRemoteConnection(url, traversal_source="g")
+        self.graph = Graph()
+        self.g = self.graph.traversal().with_remote(self.connection)
+        next(self.g.V().has_label("x"), None)
+
+    def process_stream(self, _project_name: str, fl: BytesIO):
+        next(self.g.V().has_label("x"), None)
+        tx = self.g.tx()
+        trv = tx.begin()
+        for ent in iterate_over_entries(fl):
+            next(trv.V().has_label("x"), None)
+            if is_edge(ent):
+                n1 = convert_node(trv, ent.source)
+                n2 = convert_node(trv, ent.target)
+                trv.add_e().from_(n1).to(n2).property(
+                    "edge_kind", ent.edge_kind
+                ).iterate()
+            else:
+                n1 = convert_node(trv, ent.source)
+                trv.V().has_id(n1.id).property(
+                    ent.fact_name, ent.fact_value.decode()
+                ).iterate()
+        tx.commit()
+
+
+def iterate_over_entries(fl: BytesIO) -> Generator[Entry, None, None]:
+    try:
+        sz = decode_stream(fl)
+        bts = bytes()
+        while len(bts) < sz:
+            rd = fl.read(sz - len(bts))
+            if len(rd) <= 0:
+                return None
+            bts += rd
+        ent = Entry()
+        ent.ParseFromString(bts)
+        yield ent
+    except EOFError:
+        return None
+    except Exception:
+        # TODO(Ian) should catch decode errors
+        return None
+
+
+def main():
+    prsr = argparse.ArgumentParser("Entry Upload to Janus")
+    prsr.add_argument("--url", required=True)
+    args = prsr.parse_args()
+
+    storage = JanusStorage(args.url)
+    with sys.stdin.buffer as f:
+        storage.process_stream("", f)
+
+
+if __name__ == "__main__":
+    main()

program-model/src/buttercup/program_model/indexer/oss_fuzz_indexer.py

@@ -0,0 +1,155 @@
+import argparse
+import uuid
+import subprocess
+from dataclasses import dataclass
+from buttercup.common import oss_fuzz_tool
+from buttercup.common.oss_fuzz_tool import OSSFuzzTool
+from buttercup.program_model.indexer.entries_into_db import JanusStorage
+
+import os
+
+
+@dataclass
+class IndexTarget:
+    oss_fuzz_dir: str
+    package_name: str
+
+
+@dataclass
+class Conf:
+    scriptdir: str
+    url: str
+    python: str
+    allow_pull: bool
+    base_image_url: str
+    wdir: str
+
+
+class Indexer:
+    def __init__(self, conf: Conf):
+        self.conf = conf
+
+    def build_image(self, idx_target: IndexTarget):
+        fzz_tool = OSSFuzzTool(
+            oss_fuzz_tool.Conf(
+                idx_target.oss_fuzz_dir,
+                self.conf.python,
+                self.conf.allow_pull,
+                self.conf.base_image_url,
+            )
+        )
+        base_image_name = fzz_tool.build_base_image(idx_target.package_name)
+        print(base_image_name)
+        if base_image_name is None:
+            return None
+
+        buildid = str(uuid.uuid4())
+        emitted_image = f"kyther_indexer_image_{idx_target.package_name}_{buildid}"
+        wdir = f"{self.conf.scriptdir}"
+        command = [
+            "docker",
+            "build",
+            "-t",
+            emitted_image,
+            "--build-arg",
+            f"BASE_IMAGE={base_image_name}",
+            ".",
+        ]
+        subprocess.run(command, check=True, cwd=wdir)
+        # TODO(Ian): do more forgiving error handling
+        return emitted_image
+
+    def index_target(self, idx_target: IndexTarget):
+        emitted_image = self.build_image(idx_target)
+        if emitted_image is None:
+            return None
+
+        indexuid = str(uuid.uuid4())
+        output_dir = f"{self.conf.wdir}/output_{indexuid}"
+        os.makedirs(output_dir, exist_ok=True)
+        # TODO(Ian): we need to figure out how to make ccwrapper.sh not break LD detection
+        command = [
+            "docker",
+            "run",
+            "-v",
+            f"{output_dir}:/kythe_out",
+            "-e",
+            "LD=ld",
+            "-e",
+            "KYTHE_OUTPUT_DIRECTORY=/kythe_out",
+            emitted_image,
+            "compile",
+        ]
+        # TODO(Ian): we probably shouldnt keep around indexing images for disk space reasons
+        subprocess.run(command, check=True)
+        return output_dir
+
+
+@dataclass
+class KytheConf:
+    kythe_dir: str
+
+
+class KytheTool:
+    def __init__(self, conf: KytheConf):
+        self.conf = conf
+
+    def merge_kythe_output(self, input_dir: str, output_kzip: str):
+        merge_path = os.path.join(self.conf.kythe_dir, "tools/kzip")
+
+        total = []
+        for fl in os.listdir(input_dir):
+            if fl.endswith(".kzip"):
+                total.append(os.path.join(input_dir, fl))
+
+        command = [merge_path, "merge", "--output", output_kzip] + total
+        subprocess.run(command, check=True)
+        return True
+
+    def cxx_index(self, input_kzip: str, output_bin: str):
+        indexer_path = os.path.join(self.conf.kythe_dir, "indexers/cxx_indexer")
+        command = [indexer_path, "-i", input_kzip, "-o", output_bin]
+        subprocess.run(command, check=True)
+        return True
+
+
+def main():
+    prsr = argparse.ArgumentParser("oss fuzz builder")
+    prsr.add_argument("--scriptdir", required=True)
+    prsr.add_argument("--url", required=True)
+    prsr.add_argument("--python", default="python")
+    prsr.add_argument("--allow_pull", action="store_true", default=False)
+    prsr.add_argument("--base_image_url", required=True)
+    prsr.add_argument("--oss_fuzz_dir", required=True)
+    prsr.add_argument("--package_name", required=True)
+    prsr.add_argument("--wdir", required=True)
+    prsr.add_argument("--kythe_dir", required=True)
+    args = prsr.parse_args()
+
+    conf = Conf(
+        args.scriptdir,
+        args.url,
+        args.python,
+        args.allow_pull,
+        args.base_image_url,
+        args.wdir,
+    )
+    indexer = Indexer(conf)
+    output_dir = indexer.index_target(IndexTarget(args.oss_fuzz_dir, args.package_name))
+    if output_dir is None:
+        print("Failed to index target")
+        return
+    print(output_dir)
+    output_id = str(uuid.uuid4())
+    ktool = KytheTool(KytheConf(args.kythe_dir))
+    merged_kzip = os.path.join(args.wdir, f"kythe_output_merge_{output_id}.kzip")
+    ktool.merge_kythe_output(output_dir, merged_kzip)
+    cxx_bin = os.path.join(args.wdir, f"kythe_output_cxx_{output_id}.bin")
+    ktool.cxx_index(merged_kzip, cxx_bin)
+
+    with open(cxx_bin, "rb") as f:
+        JanusStorage(args.url).process_stream(args.package_name, f)
+
+
+if __name__ == "__main__":
+    main()

program-model/src/buttercup/program_model/services/kythe/proto/storage_pb2_grpc.py

@@ -0,0 +1,27 @@
+# Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
+"""Client and server classes corresponding to protobuf-defined services."""
+
+import grpc
+
+
+GRPC_GENERATED_VERSION = "1.68.1"
+GRPC_VERSION = grpc.__version__
+_version_not_supported = False
+
+try:
+    from grpc._utilities import first_version_is_lower
+
+    _version_not_supported = first_version_is_lower(
+        GRPC_VERSION, GRPC_GENERATED_VERSION
+    )
+except ImportError:
+    _version_not_supported = True
+
+if _version_not_supported:
+    raise RuntimeError(
+        f"The grpc package installed is at version {GRPC_VERSION},"
+        + " but the generated code in kythe/proto/storage_pb2_grpc.py depends on"
+        + f" grpcio>={GRPC_GENERATED_VERSION}."
+        + f" Please upgrade your grpc module to grpcio>={GRPC_GENERATED_VERSION}"
+        + f" or downgrade your generated code using grpcio-tools<={GRPC_VERSION}."
+    )

program-model/src/buttercup/program_model/test.py

@@ -0,0 +1,3 @@
+import kuzu
+
+kuzu.Database()

program-model/src/buttercup/program_model/utils/varint.py

@@ -0,0 +1,61 @@
+"""Varint encoder/decoder
+varint from https://github.com/fmoo/python-varint/blob/master/varint.py
+"""
+
+from io import BytesIO
+
+
+import sys
+
+if sys.version > "3":
+
+    def _byte(b):
+        return bytes((b,))
+else:
+
+    def _byte(b):
+        return chr(b)
+
+
+def encode(number):
+    """Pack `number` into varint bytes"""
+    buf = b""
+    while True:
+        towrite = number & 0x7F
+        number >>= 7
+        if number:
+            buf += _byte(towrite | 0x80)
+        else:
+            buf += _byte(towrite)
+            break
+    return buf
+
+
+def decode_stream(stream):
+    """Read a varint from `stream`"""
+    shift = 0
+    result = 0
+    while True:
+        i = _read_one(stream)
+        result |= (i & 0x7F) << shift
+        shift += 7
+        if not (i & 0x80):
+            break
+
+    return result
+
+
+def decode_bytes(buf):
+    """Read a varint from from `buf` bytes"""
+    return decode_stream(BytesIO(buf))
+
+
+def _read_one(stream):
+    """Read a byte from the file (as an integer)
+
+    raises EOFError if the stream ends while reading bytes.
+    """
+    c = stream.read(1)
+    if c == b"":
+        raise EOFError("Unexpected EOF while reading bytes")
+    return ord(c)

program-model/upload_worker.Dockerfile

@@ -0,0 +1,46 @@
+ARG BASE_IMAGE=ubuntu:20.04@sha256:4a45212e9518f35983a976eead0de5eecc555a2f047134e9dd2cfc589076a00d
+
+FROM $BASE_IMAGE AS base
+RUN apt-get update && apt-get install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update && apt-get install -y python3.10 curl
+RUN curl -fsSL https://get.docker.com | sh
+
+FROM base AS builder
+COPY --from=ghcr.io/astral-sh/uv:0.5.20 /uv /uvx /bin/
+
+ENV UV_LINK_MODE=copy \
+    UV_COMPILE_BYTECODE=1 \
+    UV_PYTHON_DOWNLOADS=never \
+    UV_PYTHON=python3.10
+
+WORKDIR /app
+
+RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=common/uv.lock,target=/common/uv.lock \
+    --mount=type=bind,source=common/pyproject.toml,target=/common/pyproject.toml \
+    --mount=type=bind,source=common/README.md,target=/common/README.md \    
+    --mount=type=bind,source=program-model/uv.lock,target=uv.lock \
+    --mount=type=bind,source=program-model/pyproject.toml,target=pyproject.toml \
+    uv sync --frozen --no-install-project --no-editable
+
+ADD ./common /common
+
+COPY program-model/src /app/src
+COPY program-model/pyproject.toml /app/pyproject.toml
+COPY program-model/uv.lock /app/uv.lock
+COPY program-model/scripts /app/scripts
+
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --frozen --no-editable
+
+
+FROM base AS runtime
+WORKDIR /app
+
+COPY --from=builder --chown=app:app /app/scripts /app/scripts
+RUN tar -xvf /app/scripts/gzs/kythe-v0.0.67.tar.gz
+COPY --from=builder --chown=app:app /app/.venv /app/.venv
+
+
+ENTRYPOINT ["/app/.venv/bin/python"]

program-model/uv.lock

@@ -0,0 +1,494 @@
+version = 1
+requires-python = ">=3.9, <3.11"
+
+[[package]]
+name = "aenum"
+version = "3.1.15"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d0/f8/33e75863394f42e429bb553e05fda7c59763f0fd6848de847a25b3fbccf6/aenum-3.1.15.tar.gz", hash = "sha256:8cbd76cd18c4f870ff39b24284d3ea028fbe8731a58df3aa581e434c575b9559", size = 134730 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d0/fa/ca0c66b388624ba9dbbf35aab3a9f326bfdf5e56a7237fe8f1b600da6864/aenum-3.1.15-py3-none-any.whl", hash = "sha256:e0dfaeea4c2bd362144b87377e2c61d91958c5ed0b4daf89cb6f45ae23af6288", size = 137633 },
+]
+
+[[package]]
+name = "aiohappyeyeballs"
+version = "2.4.4"
+source = { registry = "https://pypi.org/simple" }
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