bioproject-db-gap-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.ddi-file-downloader=docker:omicsdi/ddi-file-downloader:latest
task.ddi-bioproject-genxml=docker:omicsdi/ddi-bioproject-genxml: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

ddi-dbgap-importer: 
definition: 
    ddi-file-downloader && ddi-source-splitter && ddi-bioproject-genxml && ddi-generated-xml-validator && ddi-dataset-importer && ddi-dataset-annotation && ddi-dataset-enrichment && ddi-dataset-file-retriever
args:

parameters:
app.ddi-dbgap-importer.ddi-file-downloader.downloader.originalFileURL=ftp://ftp.ncbi.nlm.nih.gov/bioproject/bioproject.xml
app.ddi-dbgap-importer.ddi-file-downloader.downloader.targetFileName=data/dbgap/bioproject.xml
app.ddi-dbgap-importer.ddi-source-splitter.splitter.input_directory=data/dbgap
app.ddi-dbgap-importer.ddi-source-splitter.splitter.output_directory=output/dbgap/data
app.ddi-dbgap-importer.ddi-source-splitter.splitter.file_prefix=DBGAP_EBYE
app.ddi-dbgap-importer.ddi-source-splitter.splitter.databaseElement=None
app.ddi-dbgap-importer.ddi-source-splitter.splitter.entriesElement=PackageSet
app.ddi-dbgap-importer.ddi-source-splitter.splitter.entryElement=Package
app.ddi-dbgap-importer.ddi-source-splitter.splitter.filters=db="dbGaP"
app.ddi-dbgap-importer.ddi-source-splitter.splitter.original_prefix=bioproject.xml
app.ddi-dbgap-importer.ddi-bioproject-genxml.bioprojectxml.input_folder=output/dbgap/data
app.ddi-dbgap-importer.ddi-bioproject-genxml.bioprojectxml.output_folder=output/dbgap/preprocess
app.ddi-dbgap-importer.ddi-bioproject-genxml.bioprojectxml.intermediate_folder=intermediate/dbgap
app.ddi-dbgap-importer.ddi-bioproject-genxml.bioprojectxml.database=dbGaP
app.ddi-dbgap-importer.ddi-bioproject-genxml.bioprojectxml.prefix=DBGAP-
app.ddi-dbgap-importer.ddi-generated-xml-validator.validator.directory=output/dbgap/preprocess
app.ddi-dbgap-importer.ddi-generated-xml-validator.validator.report_file_path=output/dbgap/report.validation.file.csv
app.ddi-dbgap-importer.ddi-dataset-importer.importer.database_name=dbGaP
app.ddi-dbgap-importer.ddi-dataset-importer.importer.input_directory=output/dbgap/preprocess
app.ddi-dbgap-importer.ddi-dataset-annotation.annotation.database_name=dbGaP
app.ddi-dbgap-importer.ddi-dataset-enrichment.enrichment.database_name=dbGaP
app.ddi-dbgap-importer.ddi-dataset-file-retriever.file-retriever.database_name=dbGaP