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Download file databases in multiple steps, to identify failure
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Lines changed: 42 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -15,50 +15,49 @@ RUN --mount=type=cache,target=/root/.m2 mvn -f MetFragRelaunched clean package -
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FROM alpine:latest AS downloader
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RUN mkdir -p /vol/file_databases; cd /vol/file_databases && \
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wget -q https://zenodo.org/records/3548461/files/NORMANSusDat_20Nov2019.csv && \
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touch NORMANSusDat_20Nov2019.csv && \
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wget -q https://zenodo.org/records/3364464/files/CompTox_07March19_SmokingMetaData.csv && \
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touch CompTox_07March19_SmokingMetaData.csv && \
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wget -q https://zenodo.org/records/6475906/files/CompTox_07March19_SelectMetaData.csv && \
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touch CompTox_07March19_SelectMetaData.csv && \
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wget -q https://zenodo.org/records/3472781/files/CompTox_07March19_WWMetaData.csv && \
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touch CompTox_07March19_WWMetaData.csv && \
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wget -q https://zenodo.org/records/14561114/files/Zebrafish_Metabolites_20241220.csv && \
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touch Zebrafish_Metabolites_20241220.csv && \
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wget -q https://zenodo.org/records/3735703/files/EColiMDB_11Nov2019.csv && \
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touch EColiMDB_11Nov2019.csv && \
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wget -q https://zenodo.org/records/3434579/files/YMDB2_17Sept2019.csv && \
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touch YMDB2_17Sept2019.csv && \
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wget -q https://zenodo.org/records/3403530/files/WormJam_10Sept19.csv && \
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touch WormJam_10Sept19.csv && \
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wget -q https://zenodo.org/records/3375500/files/HMDB4_23Aug19.csv && \
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touch HMDB4_23Aug19.csv && \
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wget -q https://zenodo.org/records/3564602/files/BloodExposomeDB_03Dec2019.csv && \
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RUN mkdir -p /vol/file_databases
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WORKDIR /vol/file_databases
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RUN wget -q https://zenodo.org/records/3548461/files/NORMANSusDat_20Nov2019.csv && \
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touch NORMANSusDat_20Nov2019.csv
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RUN wget -q https://zenodo.org/records/3364464/files/CompTox_07March19_SmokingMetaData.csv && \
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touch CompTox_07March19_SmokingMetaData.csv
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RUN wget -q https://zenodo.org/records/6475906/files/CompTox_07March19_SelectMetaData.csv && \
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touch CompTox_07March19_SelectMetaData.csv
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RUN wget -q https://zenodo.org/records/3472781/files/CompTox_07March19_WWMetaData.csv && \
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touch CompTox_07March19_WWMetaData.csv
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RUN wget -q https://zenodo.org/records/14561114/files/Zebrafish_Metabolites_20241220.csv && \
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touch Zebrafish_Metabolites_20241220.csv
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RUN wget -q https://zenodo.org/records/3735703/files/EColiMDB_11Nov2019.csv && \
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touch EColiMDB_11Nov2019.csv
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RUN wget -q https://zenodo.org/records/3434579/files/YMDB2_17Sept2019.csv && \
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touch YMDB2_17Sept2019.csv
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RUN wget -q https://zenodo.org/records/3403530/files/WormJam_10Sept19.csv && \
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touch WormJam_10Sept19.csv
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RUN wget -q https://zenodo.org/records/3375500/files/HMDB4_23Aug19.csv && \
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touch HMDB4_23Aug19.csv
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RUN wget -q https://zenodo.org/records/3564602/files/BloodExposomeDB_03Dec2019.csv && \
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touch BloodExposomeDB_03Dec2019.csv
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RUN cd /vol/file_databases && \
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wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv && \
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touch HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv && \
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wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020.csv && \
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touch HBM4EU_CECscreen_MF_1Jul2020.csv && \
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wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_Patents_20220420.csv && \
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touch OntoChem_PFAS_Patents_20220420.csv && \
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wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_CORE_20220420.csv && \
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touch OntoChem_PFAS_CORE_20220420.csv && \
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wget -q https://zenodo.org/records/5336447/files/COCONUT4MetFrag_april.csv && \
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touch COCONUT4MetFrag_april.csv && \
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wget -q https://zenodo.org/records/8144127/files/LIPIDMAPS_20230712.csv && \
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touch LIPIDMAPS_20230712.csv && \
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wget -q https://zenodo.org/records/14738325/files/PubChem_OECDPFAS_largerPFASparts_20250125.csv && \
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touch PubChem_OECDPFAS_largerPFASparts_20250125.csv && \
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wget -q https://zenodo.org/records/13148840/files/NPAtlas_2024_03.csv && \
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touch NPAtlas_2024_03.csv && \
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wget -q https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024_MetFrag.csv && \
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touch CyanoMetDB_V03_2024_MetFrag.csv && \
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wget -q https://zenodo.org/records/17775114/files/PubChemLite_CCSbase_20251128.csv && \
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touch PubChemLite_CCSbase_20251128.csv && \
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wget -q https://zenodo.org/records/17751750/files/PubChemLite_exposomics_20251128.csv && \
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RUN wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv && \
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touch HBM4EU_CECscreen_MF_1Jul2020_plusTPs.csv
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RUN wget -q https://zenodo.org/records/3957497/files/HBM4EU_CECscreen_MF_1Jul2020.csv && \
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touch HBM4EU_CECscreen_MF_1Jul2020.csv
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RUN wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_Patents_20220420.csv && \
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touch OntoChem_PFAS_Patents_20220420.csv
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RUN wget -q https://zenodo.org/records/6474542/files/OntoChem_PFAS_CORE_20220420.csv && \
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touch OntoChem_PFAS_CORE_20220420.csv
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RUN wget -q https://zenodo.org/records/5336447/files/COCONUT4MetFrag_april.csv && \
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touch COCONUT4MetFrag_april.csv
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RUN wget -q https://zenodo.org/records/8144127/files/LIPIDMAPS_20230712.csv && \
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touch LIPIDMAPS_20230712.csv
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RUN wget -q https://zenodo.org/records/14738325/files/PubChem_OECDPFAS_largerPFASparts_20250125.csv && \
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touch PubChem_OECDPFAS_largerPFASparts_20250125.csv
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RUN wget -q https://zenodo.org/records/13148840/files/NPAtlas_2024_03.csv && \
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touch NPAtlas_2024_03.csv
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RUN wget -q https://zenodo.org/records/13854577/files/CyanoMetDB_V03_2024_MetFrag.csv && \
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touch CyanoMetDB_V03_2024_MetFrag.csv
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RUN wget -q https://zenodo.org/records/17775114/files/PubChemLite_CCSbase_20251128.csv && \
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touch PubChemLite_CCSbase_20251128.csv
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RUN wget -q https://zenodo.org/records/17751750/files/PubChemLite_exposomics_20251128.csv && \
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touch PubChemLite_exposomics_20251128.csv
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FROM tomee:10-jre21-Temurin-microprofile

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