From 4a05b5946a5a21a47c29ac87a7c23d51674728bd Mon Sep 17 00:00:00 2001
From: intrigus <intrigus@users.noreply.github.com>
Date: Wed, 13 May 2020 20:31:42 +0200
Subject: [PATCH] Integrate rdkit with oss-fuzz (#3747)

---
 projects/rdkit/Dockerfile   | 44 +++++++++++++++++++++++++++++++++++++
 projects/rdkit/build.sh     | 34 ++++++++++++++++++++++++++++
 projects/rdkit/project.yaml |  8 +++++++
 3 files changed, 86 insertions(+)
 create mode 100644 projects/rdkit/Dockerfile
 create mode 100755 projects/rdkit/build.sh
 create mode 100644 projects/rdkit/project.yaml

diff --git a/projects/rdkit/Dockerfile b/projects/rdkit/Dockerfile
new file mode 100644
index 000000000..bb2fee3b9
--- /dev/null
+++ b/projects/rdkit/Dockerfile
@@ -0,0 +1,44 @@
+# Copyright 2017 Google Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+################################################################################
+
+FROM gcr.io/oss-fuzz-base/base-builder
+MAINTAINER greg.landrum@gmail.com
+RUN apt-get update && apt-get install -y make wget cmake \
+  libeigen3-dev python3 libpython3-all-dev \
+  zlib1g-dev \
+  libbz2-dev
+
+# Install latest cmake
+RUN wget --quiet https://github.com/Kitware/CMake/releases/download/v3.14.5/cmake-3.14.5-Linux-x86_64.sh; \
+    chmod +x cmake-3.14.5-Linux-x86_64.sh; \
+    ./cmake-3.14.5-Linux-x86_64.sh --skip-license --prefix="/usr/local"
+
+# We're building `rdkit` using clang, but the boost package is built using gcc.
+# For whatever reason, linking would fail.
+# (Mismatch between libstdc++ and libc++ maybe?)
+# It works if we build `rdkit` using gcc or build boost using clang instead.
+# We've opted for building boost using clang.
+WORKDIR /src
+RUN wget --quiet https://sourceforge.net/projects/boost/files/boost/1.69.0/boost_1_69_0.tar.bz2
+RUN tar xjf boost_1_69_0.tar.bz2
+WORKDIR /src/boost_1_69_0
+RUN ./bootstrap.sh --with-toolset=clang --with-libraries=serialization,system,iostreams,regex
+RUN ./b2 -q -j2 toolset=clang cxxflags="-fPIC $CXXFLAGS $CXXFLAGS_EXTRA" link=static install
+
+WORKDIR /src
+RUN git clone --depth 1 https://github.com/rdkit/rdkit.git rdkit
+WORKDIR rdkit
+COPY build.sh $SRC/
diff --git a/projects/rdkit/build.sh b/projects/rdkit/build.sh
new file mode 100755
index 000000000..d7999d2fb
--- /dev/null
+++ b/projects/rdkit/build.sh
@@ -0,0 +1,34 @@
+#!/bin/bash -eu
+# Copyright 2017 Google Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+################################################################################
+
+mkdir -p build && cd build
+cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DLIB_FUZZING_ENGINE=${LIB_FUZZING_ENGINE} -DRDK_BUILD_FUZZ_TARGETS=ON -DRDK_INSTALL_STATIC_LIBS=ON -DBoost_USE_STATIC_LIBS=ON ..
+make -j$(nproc)
+make install
+
+# Leave build directory
+cd ..
+
+# Copy the fuzzer executables, zip-ed corpora, options and dictionary files to $OUT
+find . -type f -name '*_fuzzer' -exec cp -v '{}' $OUT ';'
+find . -type f -name '*_fuzzer.dict' -exec cp -v '{}' $OUT ';'
+#find . -type f -name '*_fuzzer.options' -exec cp -v '{}' $OUT ';'
+corpora=$(find . -type d -name "*_fuzzer")
+for corpus in $corpora; do
+	corpus_basename=$(basename $corpus)
+	zip -j $OUT/${corpus_basename}_seed_corpus.zip ${corpus}/*
+done
diff --git a/projects/rdkit/project.yaml b/projects/rdkit/project.yaml
new file mode 100644
index 000000000..ef82b3899
--- /dev/null
+++ b/projects/rdkit/project.yaml
@@ -0,0 +1,8 @@
+homepage: "https://github.com/rdkit/rdkit"
+language: c++
+primary_contact: "greg.landrum@gmail.com"
+sanitizers:
+  - address
+  - undefined
+architectures:
+  - x86_64