"superuser_tokens": $(inputs.superuser_tokens)
}
>>>
- return arvados_api_hosts as ar
+ return arvados_api_hosts as ar
}
- run tool(arvados_api_hosts, superuser_tokens, ar,
- fed_migrate,
- host=$(inputs.arvados_api_hosts[0]),
- token=$(inputs.superuser_tokens[0])) {
+ run workflow(ar, arvados_api_hosts, superuser_tokens,
+ fed_migrate,
+ host=$(inputs.arvados_api_hosts[0]),
+ token=$(inputs.superuser_tokens[0])) {
requirements {
EnvVarRequirement {
envDef: {
ARVADOS_API_HOST: "$(inputs.host)",
- ARVADOS_API_TOKEN: "$(inputs.token)"
+ ARVADOS_API_TOKEN: "$(inputs.token)",
+ ARVADOS_API_HOST_INSECURE: "1"
}
}
}
- $(inputs.fed_migrate) --report report.csv
- return File("report.csv") as report
+
+ run tool(fed_migrate, host, token) {
+ $(inputs.fed_migrate) --report report.csv
+ return File("report.csv") as report
+ }
+
+ run tool(report, host, token) {
+ sed -E 's/,(case[1-8])2?,/,\\1,/g' < $(inputs.report.path) > report.csv
+ return File("report.csv") as report2
+ }
+
+ run tool(report2, fed_migrate, host, token) {
+ $(inputs.fed_migrate) --migrate $(inputs.report2)
+ return report2 as report3
+ }
+
+ run tool(report3, host, token, arvados_api_hosts, superuser_tokens, check=File("check.py")) {
+ python $(inputs.check) <<<
+{
+ "arvados_api_hosts": $(inputs.arvados_api_hosts),
+ "superuser_tokens": $(inputs.superuser_tokens)
+}
+>>>
+ return report3 as r
+ }
}
- return report
+ return report3
}
\ No newline at end of file