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metabolight-importer-pipeline.txt
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metabolight-importer-pipeline.txt
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ALTER TABLE BATCH_JOB_EXECUTION_PARAMS CHANGE COLUMN STRING_VAL STRING_VAL VARCHAR(10000);
ALTER TABLE TASK_EXECUTION_PARAMS CHANGE COLUMN TASK_PARAM TASK_PARAM VARCHAR(10000);
task.composed-task-runner=docker:omicsdi/composedtaskrunner-task:2.1.0.RELEASE
task.composed-task-runner.metadata=maven://org.springframework.cloud.task.app:composedtaskrunner-task:jar:metadata:2.1.0.RELEASE
task.ddi-download-ftpfiles=docker:omicsdi/ddi-download-ftpfiles:latest
task.ddi-generated-xml-validator=docker:omicsdi/ddi-generated-xml-validator:latest
task.ddi-source-splitter=docker:omicsdi/ddi-source-splitter:latest
task.ddi-dataset-importer=docker:omicsdi/ddi-dataset-importer:latest
task.ddi-dataset-annotation=docker:omicsdi/ddi-dataset-annotation:latest
task.ddi-dataset-enrichment=docker:omicsdi/ddi-dataset-enrichment:latest
task.ddi-dataset-file-retriever=docker:omicsdi/ddi-dataset-file-retriever:latest
metabolight-importer:
definition:
ddi-download-ftpfiles && ddi-generated-xml-validator && ddi-source-splitter && ddi-dataset-importer && ddi-dataset-annotation && ddi-dataset-enrichment && ddi-dataset-file-retriever
args:
parameters:
app.metabolight-importer.ddi-download-ftpfiles.ftp.server=ftp.ebi.ac.uk
app.metabolight-importer.ddi-download-ftpfiles.ftp.pattern=eb-eye_metabolights_studies.xml
app.metabolight-importer.ddi-download-ftpfiles.ftp.source_dir=/pub/databases/metabolights/eb-eye
app.metabolight-importer.ddi-download-ftpfiles.ftp.target_dir=data/metabolight
app.metabolight-importer.ddi-generated-xml-validator.validator.directory=data/metabolight
app.metabolight-importer.ddi-generated-xml-validator.validator.report_file_path=output/metabolight/report.validation.file.csv
app.metabolight-importer.ddi-source-splitter.splitter.input_directory=data/metabolight
app.metabolight-importer.ddi-source-splitter.splitter.output_directory=output/metabolight/data
app.metabolight-importer.ddi-source-splitter.splitter.file_prefix=METABOLIGHT_EBEYE
app.metabolight-importer.ddi-source-splitter.splitter.number_entries=10
app.metabolight-importer.ddi-source-splitter.splitter.original_prefix=.xml
app.metabolight-importer.ddi-dataset-importer.importer.database_name=MetaboLights
app.metabolight-importer.ddi-dataset-importer.importer.input_directory=output/metabolight/data
app.metabolight-importer.ddi-dataset-annotation.annotation.database_name=MetaboLights
app.metabolight-importer.ddi-dataset-enrichment.enrichment.database_name=MetaboLights
app.metabolight-importer.ddi-dataset-file-retriever.file-retriever.database_name=MetaboLights