-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbiomodels-importer-pipeline.txt
36 lines (32 loc) · 2.46 KB
/
biomodels-importer-pipeline.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
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
biomodels-importer:
definition:
ddi-download-ftpfiles && ddi-source-splitter && ddi-generated-xml-validator && ddi-dataset-importer && ddi-dataset-annotation && ddi-dataset-enrichment && ddi-dataset-file-retriever
args:
parameters:
app.biomodels-importer.ddi-download-ftpfiles.ftp.server=ftp.ebi.ac.uk
app.biomodels-importer.ddi-download-ftpfiles.ftp.pattern=OmicsDIEntries
app.biomodels-importer.ddi-download-ftpfiles.ftp.source_dir=/ebi/ftp/pub/databases/biomodels/omicsdi/BioModelsOmicsDIExport
app.biomodels-importer.ddi-download-ftpfiles.ftp.target_dir=data/biomodels
app.biomodels-importer.ddi-source-splitter.splitter.input_directory=data/biomodels
app.biomodels-importer.ddi-source-splitter.splitter.output_directory=output/biomodels/data
app.biomodels-importer.ddi-source-splitter.splitter.file_prefix=BIOMODELS_EBEYE
app.biomodels-importer.ddi-source-splitter.splitter.number_entries=10
app.biomodels-importer.ddi-source-splitter.splitter.original_prefix=.xml
app.biomodels-importer.ddi-generated-xml-validator.validator.directory=output/biomodels/data
app.biomodels-importer.ddi-generated-xml-validator.validator.report_file_path=output/biomodels/report.validation.file.csv
app.biomodels-importer.ddi-dataset-importer.importer.database_name=BioModels
app.biomodels-importer.ddi-dataset-importer.importer.input_directory=output/biomodels/data
app.biomodels-importer.ddi-dataset-annotation.annotation.database_name=BioModels
app.biomodels-importer.ddi-dataset-enrichment.enrichment.database_name=BioModels
app.biomodels-importer.ddi-dataset-file-retriever.file-retriever.database_name=BioModels