Update Dockerfile to java 17 and tomee 10

ipb-halle · Oct 24, 2024 · 2bd0391 · 2bd0391
1 parent 8312f5a
commit 2bd0391
Showing 1 changed file with 34 additions and 39 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM maven:3-jdk-11 AS builder
+FROM maven:3.8-eclipse-temurin-17 AS builder
 
 COPY MetFragLib/ /MetFragRelaunched/MetFragLib/
 COPY MetFragCommandLine/ /MetFragRelaunched/MetFragCommandLine/
@@ -13,68 +13,63 @@ LocalDatabasesFolderForWeb = /vol/file_databases' > /MetFragRelaunched/MetFragWe
 
 RUN mvn -Dhttps.protocols=TLSv1.2 -f MetFragRelaunched clean package -pl MetFragLib -pl MetFragWeb -am -DskipTests
 
+FROM alpine:latest as downloader
 
-FROM tomee:10
-
-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 && \
+    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 && \
+    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 && \
+    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 && \
+    touch OntoChem_PFAS_CORE_20220420.csv && \
 	wget -q https://zenodo.org/records/5336447/files/COCONUT4MetFrag_april.csv && \
-        touch COCONUT4MetFrag_april.csv && \
+    touch COCONUT4MetFrag_april.csv && \
 	wget -q https://zenodo.org/records/8144127/files/LIPIDMAPS_20230712.csv && \
-        touch 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 && \
+    touch PubChem_OECDPFAS_largerPFASparts_20240726.csv && \
 	wget -q https://zenodo.org/records/13148840/files/NPAtlas_2024_03.csv && \
-        touch 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 && \
+    touch CyanoMetDB_V03_2024_MetFrag.csv && \
 	wget -q https://zenodo.org/records/13641886/files/PubChemLite_CCSbase_20240830.csv && \
-        touch PubChemLite_CCSbase_20240830.csv && \
+    touch PubChemLite_CCSbase_20240830.csv && \
 	wget -q https://zenodo.org/records/13848602/files/PubChemLite_exposomics_20240927.csv && \
-        touch PubChemLite_exposomics_20240927.csv
+    touch PubChemLite_exposomics_20240927.csv
+
+
+FROM tomee:10
 
 COPY --from=builder /MetFragRelaunched/MetFragWeb/target/MetFragWeb.war /usr/local/tomee/webapps/
+COPY --from=downloader /vol/file_databases/ /vol/file_databases/
 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\  
+	jar uf /usr/local/tomee/webapps/MetFragWeb.war /resources/settings.properties \n\
 fi \n\
 if ! [ -z ${WEBPREFIX} ] \n\
 then \n\