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FROM maven:3-jdk-11 AS builder
COPY MetFragLib/ /MetFragRelaunched/MetFragLib/
COPY MetFragCommandLine/ /MetFragRelaunched/MetFragCommandLine/
COPY MetFragR/ /MetFragRelaunched/MetFragR/
COPY MetFragTools/ /MetFragRelaunched/MetFragTools/
COPY MetFragRest/ /MetFragRelaunched/MetFragRest/
COPY MetFragWeb/ /MetFragRelaunched/MetFragWeb/
COPY pom.xml /MetFragRelaunched/
RUN printf '# local database file folder \n\
LocalDatabasesFolderForWeb = /vol/file_databases' > /MetFragRelaunched/MetFragWeb/src/main/webapp/resources/settings.properties
RUN mvn -Dhttps.protocols=TLSv1.2 -f MetFragRelaunched clean package -pl MetFragLib -pl MetFragWeb -am -DskipTests
FROM tomee:8.0.15
RUN set -eux; \
apt-get update; \
apt-get install -y --no-install-recommends \
zip \
; \
rm -rf /var/lib/apt/lists/*
# RUN wget -q -O- https://msbi.ipb-halle.de/~sneumann/file_databases.tgz | tar -C / -xzf -
RUN mkdir -p /vol/file_databases; cd /vol/file_databases && \
wget -q https://zenodo.org/records/3548461/files/NORMANSusDat_20Nov2019.csv && \
touch NORMANSusDat_20Nov2019.csv && \
wget -q https://zenodo.org/records/3364464/files/CompTox_07March19_SmokingMetaData.csv && \
touch CompTox_07March19_SmokingMetaData.csv && \
wget -q https://zenodo.org/records/6475906/files/CompTox_07March19_SelectMetaData.csv && \
touch CompTox_07March19_SelectMetaData.csv && \
wget -q https://zenodo.org/records/3472781/files/CompTox_07March19_WWMetaData.csv && \
touch CompTox_07March19_WWMetaData.csv && \
wget -q https://zenodo.org/records/3541624/files/Zebrafish_13Nov2019_Beta.csv && \
touch Zebrafish_13Nov2019_Beta.csv && \
wget -q https://zenodo.org/records/3735703/files/EColiMDB_11Nov2019.csv && \
touch EColiMDB_11Nov2019.csv && \
wget -q https://zenodo.org/records/3434579/files/YMDB2_17Sept2019.csv && \
touch YMDB2_17Sept2019.csv && \
wget -q https://zenodo.org/records/3403530/files/WormJam_10Sept19.csv && \
touch WormJam_10Sept19.csv && \
wget -q https://zenodo.org/records/3375500/files/HMDB4_23Aug19.csv && \
touch HMDB4_23Aug19.csv && \
wget -q https://zenodo.org/records/3564602/files/BloodExposomeDB_03Dec2019.csv && \
touch BloodExposomeDB_03Dec2019.csv
RUN cd /vol/file_databases && \
wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv && \
touch HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv && \
wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020.csv && \
touch HBM4EU_CECscreen_MF_1Jul2020.csv && \
wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_Patents_20220420.csv && \
touch OntoChem_PFAS_Patents_20220420.csv && \
wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_CORE_20220420.csv && \
touch OntoChem_PFAS_CORE_20220420.csv && \
wget -q https://zenodo.org/records/5336447/files/COCONUT4MetFrag_april.csv && \
touch COCONUT4MetFrag_april.csv && \
wget -q https://zenodo.org/records/8144127/files/LIPIDMAPS_20230712.csv && \
touch LIPIDMAPS_20230712.csv && \
wget -q https://zenodo.org/records/12908412/files/PubChem_OECDPFAS_largerPFASparts_20240726.csv && \
touch PubChem_OECDPFAS_largerPFASparts_20240726.csv && \
wget -q https://zenodo.org/records/13148840/files/NPAtlas_2024_03.csv && \
touch NPAtlas_2024_03.csv && \
wget -q https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024_MetFrag.csv && \
touch CyanoMetDB_V03_2024_MetFrag.csv && \
wget -q https://zenodo.org/records/14034886/files/PubChemLite_CCSbase_20241025.csv && \
touch PubChemLite_CCSbase_20241025.csv && \
wget -q https://zenodo.org/records/14246393/files/PubChemLite_exposomics_20241129.csv && \
touch PubChemLite_exposomics_20241129.csv
COPY --from=builder /MetFragRelaunched/MetFragWeb/target/MetFragWeb.war /usr/local/tomee/webapps/
RUN printf '#!/bin/sh \n\
if [ -f "/resources/settings.properties" ] \n\
then \n\
zip -u /usr/local/tomee/webapps/MetFragWeb.war /resources/settings.properties \n\
fi \n\
if ! [ -z ${WEBPREFIX} ] \n\
then \n\
mv /usr/local/tomee/webapps/MetFragWeb.war /usr/local/tomee/webapps/${WEBPREFIX}.war \n\
fi \n\
catalina.sh run' > /start.sh
CMD [ "sh", "/start.sh" ]