#1412 Nucleotide splitting for V3000 molfile SCSR (#1420)

epam · Dec 6, 2023 · 745389d · 745389d
1 parent 7c571fb
commit 745389d
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diff --git a/.ci/docker/buildpack-arm64/Dockerfile b/.ci/docker/buildpack-arm64/Dockerfile
@@ -1,11 +1,11 @@
-FROM ubuntu:16.04
-
+FROM ubuntu:20.04
 RUN apt update && \
     apt upgrade -y && \
     apt install -y --no-install-recommends \
         apt-transport-https \
         curl \
         software-properties-common \
+        gpg-agent \
         lsb-release \
         && \
     export UBUNTU_VERSION=$(lsb_release -cs) && \
@@ -21,23 +21,23 @@ RUN apt update && \
     # Install tools required for building Indigo
     apt install -y --no-install-recommends \
         cmake \
-        g++-5-aarch64-linux-gnu \
+        g++-10-aarch64-linux-gnu \
         git \
         libfontconfig1-dev:arm64 \
         libfreetype6-dev:arm64 \
         make \
         qemu-user-static
 
-ENV CC=aarch64-linux-gnu-gcc-5
-ENV CXX=aarch64-linux-gnu-g++-5
+ENV CC=aarch64-linux-gnu-gcc-10
+ENV CXX=aarch64-linux-gnu-g++-10
 ENV INDIGO_QEMU_BINARY=qemu-aarch64-static
 ENV ASAN_OPTIONS=alloc_dealloc_mismatch=0
 RUN echo $'leak:libfontconfig\nleak:libc\n' >> /opt/external.supp
 ENV LSAN_OPTIONS=suppressions=/opt/external.supp
 
 RUN cmake --version && \
-    aarch64-linux-gnu-gcc-5 --version && \
-    aarch64-linux-gnu-g++-5 --version && \
+    aarch64-linux-gnu-gcc-10 --version && \
+    aarch64-linux-gnu-g++-10 --version && \
     git --version && \
     make --version
 

diff --git a/.ci/docker/indigo-tester/Dockerfile b/.ci/docker/indigo-tester/Dockerfile
@@ -64,8 +64,8 @@ RUN set -eux && \
     ln -fs /opt/ironpython/net${DOTNET_VERSION}/ipy.sh /opt/ironpython/ipy && \
     rm IronPython.${IRONPYTHON_VERSION}.zip && \
     # Python 3 packages
-    python3 -m pip install --upgrade pip && \
-    python3 -m pip install --upgrade setuptools wheel twine && \
+    python3 -m pip install wheel && \
+    apt install -y python3-pip python3-setuptools twine && \
     apt autoremove -y
 
 COPY ./ /indigo
@@ -74,22 +74,22 @@ RUN cd /indigo && \
     cd build && \
     cmake .. && \
     cmake --build . --target indigo-python --config Release -- -j $(nproc) && \
-    python3 -m pip install ../dist/*.whl
+    python3 -m pip install ../dist/*.whl --break-system-packages
 
-COPY /api/http/requirements.txt ./api_requirements.txt
-COPY /api/http/requirements_dev.txt ./api_requirements_dev.txt
-COPY /utils/indigo-service/backend/service/requirements.txt ./service_requirements.txt
-COPY /utils/indigo-service/backend/service/requirements.dev.txt ./service_requirements_dev.txt
+COPY ./api/http/requirements.txt ./api_requirements.txt
+COPY ./api/http/requirements_dev.txt ./api_requirements_dev.txt
+COPY ./utils/indigo-service/backend/service/requirements.txt ./service_requirements.txt
+COPY ./utils/indigo-service/backend/service/requirements.dev.txt ./service_requirements_dev.txt
 
 RUN python3 -m pip install  \
       -r api_requirements.txt  \
       -r api_requirements_dev.txt  \
       -r service_requirements.txt  \
-      -r service_requirements_dev.txt && \
+      -r service_requirements_dev.txt --break-system-packages && \
     rm ./api_requirements.txt ./api_requirements_dev.txt ./service_requirements.txt ./service_requirements_dev.txt
 
-COPY /bingo/bingo-elastic/python/ ./bingo-elastic
-RUN cd ./bingo-elastic && python3 -m pip install -e . && cd .. && rm -rf ./bingo-elastic
+COPY ./bingo/bingo-elastic/python/ ./bingo-elastic
+RUN cd ./bingo-elastic && python3 -m pip install -e . --break-system-packages && cd .. && rm -rf ./bingo-elastic
 
 ENV JAVA_HOME=/opt/jdk
 ENV PATH=${PATH}:${JAVA_HOME}/bin:/opt/jython/bin:/opt/maven/bin:/opt/ironpython

diff --git a/api/c/tests/unit/tests/formats.cpp b/api/c/tests/unit/tests/formats.cpp
@@ -179,7 +179,7 @@ TEST_F(IndigoApiFormatsTest, loadAssert)
 
 TEST_F(IndigoApiFormatsTest, fromBuffer)
 {
-    const byte mStr[] = "[CX4H3][#6]";
+    const uint8_t mStr[] = "[CX4H3][#6]";
     const int buffSize = sizeof(mStr);
 
     try
@@ -190,11 +190,11 @@ TEST_F(IndigoApiFormatsTest, fromBuffer)
         EXPECT_EQ(2, indigoCountAtoms(obj));
         EXPECT_EQ(1, indigoCountBonds(obj));
 
-        const byte react2[] = "C1CC[NH:2]CC1.C1CC[S:1]CC1>>C1CC2CC[S:2]CC2C[NH:1]1";
+        const uint8_t react2[] = "C1CC[NH:2]CC1.C1CC[S:1]CC1>>C1CC2CC[S:2]CC2C[NH:1]1";
         obj = indigoLoadStructureFromBuffer(react2, sizeof(react2), "");
         EXPECT_EQ(3, indigoCountMolecules(obj));
 
-        const byte react[] = "C[12CH2:1]C(CCCC)[CH]CCCCCCC>>C[13CH2:1]C(CCCC)[C]CCCCCCCC |^1:7,^4:22|";
+        const uint8_t react[] = "C[12CH2:1]C(CCCC)[CH]CCCCCCC>>C[13CH2:1]C(CCCC)[C]CCCCCCCC |^1:7,^4:22|";
         obj = indigoLoadStructureFromBuffer(react, sizeof(react), "query");
         EXPECT_EQ(2, indigoCountMolecules(obj));
     }

diff --git a/api/tests/integration/ref/formats/ket_to_mol.py.out b/api/tests/integration/ref/formats/ket_to_mol.py.out
@@ -1,5 +1,6 @@
 *** KET to MOL ***
 accl_no_class.ket:SUCCEED
+acgt_1412.ket:SUCCEED
 anacyclamide.ket:SUCCEED
 chem.ket:SUCCEED
 conj_no_class.ket:SUCCEED
@@ -10,6 +11,7 @@ dcysteine.ket:SUCCEED
 dna_mod.ket:SUCCEED
 dthymine.ket:SUCCEED
 fmoc.ket:SUCCEED
+mon_long_id.ket:SUCCEED
 pepchem.ket:SUCCEED
 peptides.ket:SUCCEED
 query_explicit_val.ket:SUCCEED

diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out
@@ -2,7 +2,9 @@
 1032-quadra.ket:SUCCEED
 1046-imp_hydrogen.ket:SUCCEED
 SgroupDifferent.ket:SUCCEED
+acgt_1412.ket:SUCCEED
 anacyclamide.ket:SUCCEED
+apamine.ket:SUCCEED
 atropisomer.ket:SUCCEED
 chem.ket:SUCCEED
 conjugate.ket:SUCCEED

diff --git a/api/tests/integration/tests/formats/ket_to_mol.py b/api/tests/integration/tests/formats/ket_to_mol.py
@@ -42,6 +42,8 @@ def find_diff(a, b):
     "accl_no_class",
     "conj_no_class",
     "query_explicit_val",
+    "mon_long_id",
+    "acgt_1412",
 ]
 
 files.sort()

diff --git a/api/tests/integration/tests/formats/mol_to_ket.py b/api/tests/integration/tests/formats/mol_to_ket.py
@@ -42,6 +42,8 @@ def find_diff(a, b):
     "peptides",
     "fmoc",
     "anacyclamide",
+    "acgt_1412",
+    "apamine",
 ]
 
 files.sort()