peptide-atlas-orig-importer-pipeline.txt

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.pep-atlas-xml-generator=docker:omicsdi/pep-atlas-xml-generator: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

pepatlas-orig-importer: 
definition: 
    pep-atlas-xml-generator && ddi-source-splitter && ddi-generated-xml-validator && ddi-dataset-importer && ddi-dataset-annotation && ddi-dataset-enrichment && ddi-dataset-file-retriever
args:

parameters:
app.pepatlas-orig-importer.pep-atlas-xml-generator.pep-atlas.output_dir=data/pepatlas-orig
app.pepatlas-orig-importer.ddi-source-splitter.splitter.input_directory=data/pepatlas-orig
app.pepatlas-orig-importer.ddi-source-splitter.splitter.output_directory=output/pepatlas-orig/data
app.pepatlas-orig-importer.ddi-source-splitter.splitter.file_prefix=PEPATLAS_ORIG_EBEYE
app.pepatlas-orig-importer.ddi-generated-xml-validator.validator.directory=output/pepatlas-orig/data
app.pepatlas-orig-importer.ddi-generated-xml-validator.validator.report_file_path=output/pepatlas-orig/report.validation.file.csv
app.pepatlas-orig-importer.ddi-dataset-importer.importer.database_name=PeptideAtlas
app.pepatlas-orig-importer.ddi-dataset-importer.importer.input_directory=output/pepatlas-orig/data
app.pepatlas-orig-importer.ddi-dataset-annotation.annotation.database_name=PeptideAtlas
app.pepatlas-orig-importer.ddi-dataset-enrichment.enrichment.database_name=PeptideAtlas
app.pepatlas-orig-importer.ddi-dataset-file-retriever.file-retriever.database_name=PeptideAtlas