id: fed_migrate
type: string
outputs:
- - id: report
- outputSource: main_2/report
+ - id: report3
+ outputSource: main_2/report3
type: File
requirements:
InlineJavascriptRequirement: {}
valueFrom: '$(inputs.superuser_tokens[0])'
out:
- report
+ - report2
+ - report3
+ - r
run:
- arguments:
- - $(inputs.fed_migrate)
- - '--report'
- - report.csv
- class: CommandLineTool
+ class: Workflow
id: main_2_embed
inputs:
- - id: arvados_api_hosts
+ - id: ar
type:
items: string
type: array
- - id: superuser_tokens
+ - id: arvados_api_hosts
type:
items: string
type: array
- - id: ar
+ - id: superuser_tokens
type:
items: string
type: array
type: Any
outputs:
- id: report
- outputBinding:
- glob: report.csv
+ outputSource: main_2_embed_1/report
+ type: File
+ - id: report2
+ outputSource: main_2_embed_2/report2
+ type: File
+ - id: report3
+ outputSource: main_2_embed_3/report3
+ type: File
+ - id: r
+ outputSource: main_2_embed_4/r
type: File
requirements:
- class: EnvVarRequirement
envDef:
ARVADOS_API_HOST: $(inputs.host)
+ ARVADOS_API_HOST_INSECURE: '1'
ARVADOS_API_TOKEN: $(inputs.token)
+ steps:
+ - id: main_2_embed_1
+ in:
+ fed_migrate:
+ source: fed_migrate
+ host:
+ source: host
+ token:
+ source: token
+ out:
+ - report
+ run:
+ arguments:
+ - $(inputs.fed_migrate)
+ - '--report'
+ - report.csv
+ class: CommandLineTool
+ id: main_2_embed_1_embed
+ inputs:
+ - id: fed_migrate
+ type: string
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report
+ outputBinding:
+ glob: report.csv
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ - id: main_2_embed_2
+ in:
+ host:
+ source: host
+ report:
+ source: main_2_embed_1/report
+ token:
+ source: token
+ out:
+ - report2
+ run:
+ arguments:
+ - sed
+ - '-E'
+ - 's/,(case[1-8])2?,/,\1,/g'
+ class: CommandLineTool
+ id: main_2_embed_2_embed
+ inputs:
+ - id: report
+ type: File
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report2
+ outputBinding:
+ glob: report.csv
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ stdin: $(inputs.report.path)
+ stdout: report.csv
+ - id: main_2_embed_3
+ in:
+ fed_migrate:
+ source: fed_migrate
+ host:
+ source: host
+ report2:
+ source: main_2_embed_2/report2
+ token:
+ source: token
+ out:
+ - report3
+ run:
+ arguments:
+ - $(inputs.fed_migrate)
+ - '--migrate'
+ - $(inputs.report2)
+ class: CommandLineTool
+ id: main_2_embed_3_embed
+ inputs:
+ - id: report2
+ type: File
+ - id: fed_migrate
+ type: string
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ outputs:
+ - id: report3
+ outputBinding:
+ outputEval: $(inputs.report2)
+ type: File
+ requirements:
+ InlineJavascriptRequirement: {}
+ - id: main_2_embed_4
+ in:
+ arvados_api_hosts:
+ source: arvados_api_hosts
+ check:
+ default:
+ class: File
+ location: check.py
+ host:
+ source: host
+ report3:
+ source: main_2_embed_3/report3
+ superuser_tokens:
+ source: superuser_tokens
+ token:
+ source: token
+ out:
+ - r
+ run:
+ arguments:
+ - python
+ - $(inputs.check)
+ - _script
+ class: CommandLineTool
+ id: main_2_embed_4_embed
+ inputs:
+ - id: report3
+ type: File
+ - id: host
+ type: Any
+ - id: token
+ type: Any
+ - id: arvados_api_hosts
+ type:
+ items: string
+ type: array
+ - id: superuser_tokens
+ type:
+ items: string
+ type: array
+ - id: check
+ type: File
+ outputs:
+ - id: r
+ outputBinding:
+ outputEval: $(inputs.report3)
+ type: File
+ requirements:
+ InitialWorkDirRequirement:
+ listing:
+ - entry: |
+ {
+ "arvados_api_hosts": $(inputs.arvados_api_hosts),
+ "superuser_tokens": $(inputs.superuser_tokens)
+ }
+ entryname: _script
+ InlineJavascriptRequirement: {}
- arguments:
- arvbox
- cat
- - /var/lib/arvados/superuser_token
+ - /var/lib/arvados-arvbox/superuser_token
class: CommandLineTool
cwlVersion: v1.0
id: '#superuser_tok'
- default: arv-federation-migrate
id: fed_migrate
type: string
+ - id: arvbox_bin
+ type: File
+ - default: master
+ id: refspec
+ type: string
outputs:
- id: supertok
outputSource: main_2/supertok
items: string
type: array
- id: report
- outputSource: run_test_3/report
+ outputSource: run_test_3/report3
type: File
requirements:
InlineJavascriptRequirement: {}
type: string
- id: main_2
in:
+ arvbox_bin:
+ source: arvbox_bin
cluster_id:
source: arvados_cluster_ids
container:
source: arvados_api_hosts
logincluster:
source: main_1/logincluster
+ refspec:
+ source: refspec
out:
- supertok
run:
type: string
- id: logincluster
type: string
+ - id: arvbox_bin
+ type: File
+ - id: refspec
+ type: string
outputs:
- id: supertok
- outputSource: superuser_tok_3/superuser_token
+ outputSource: superuser_tok_2/superuser_token
type: string
requirements:
- - class: EnvVarRequirement
- envDef:
- ARVBOX_CONTAINER: $(inputs.container)
+ InlineJavascriptRequirement: {}
steps:
- id: main_2_embed_1
in:
- cluster_id:
- source: cluster_id
+ arvbox_bin:
+ source: arvbox_bin
container:
source: container
- logincluster:
- source: logincluster
- set_login:
- default:
- class: File
- location: set_login.py
+ host:
+ source: host
+ refspec:
+ source: refspec
out:
- - c
+ - d
run:
arguments:
- sh
inputs:
- id: container
type: string
- - id: cluster_id
- type: string
- - id: logincluster
+ - id: host
type: string
- - id: set_login
+ - id: arvbox_bin
type: File
+ - id: refspec
+ type: string
outputs:
- - id: c
+ - id: d
outputBinding:
outputEval: $(inputs.container)
type: string
requirements:
InitialWorkDirRequirement:
listing:
- - entry: >
- set -x
+ - entry: >+
+ set -xe
- docker cp
- $(inputs.container):/var/lib/arvados/cluster_config.yml.override
- .
+ export ARVBOX_CONTAINER="$(inputs.container)"
- chmod +w cluster_config.yml.override
+ $(inputs.arvbox_bin.path) pipe <<EOF
- python $(inputs.set_login.path)
- cluster_config.yml.override $(inputs.cluster_id)
- $(inputs.logincluster)
+ cd /usr/src/arvados
- docker cp cluster_config.yml.override
- $(inputs.container):/var/lib/arvados
- entryname: _script
- InlineJavascriptRequirement: {}
- - id: main_2_embed_2
- in:
- c:
- source: main_2_embed_1/c
- container:
- source: container
- host:
- source: host
- out:
- - d
- run:
- arguments:
- - sh
- - _script
- class: CommandLineTool
- id: main_2_embed_2_embed
- inputs:
- - id: container
- type: string
- - id: host
- type: string
- - id: c
- type: string
- outputs:
- - id: d
- outputBinding:
- outputEval: $(inputs.c)
- type: string
- requirements:
- InitialWorkDirRequirement:
- listing:
- - entry: >
- set -x
+ git fetch
+
+ git checkout -f $(inputs.refspec)
+
+ git pull
+
+ chown arvbox:arvbox -R .
+
+ EOF
+
+
+ $(inputs.arvbox_bin.path) hotreset
- arvbox hotreset
while ! curl --fail --insecure --silent
https://$(inputs.host)/discovery/v1/apis/arvados/v1/rest
>/dev/null ; do sleep 3 ; done
- export ARVADOS_API_HOST=$(inputs.host)
- export ARVADOS_API_TOKEN=\$(arvbox cat
- /var/lib/arvados/superuser_token)
+ ARVADOS_VIRTUAL_MACHINE_UUID=\$($(inputs.arvbox_bin.path)
+ cat /var/lib/arvados-arvbox/vm-uuid)
- export ARVADOS_API_HOST_INSECURE=1
+ ARVADOS_API_TOKEN=\$($(inputs.arvbox_bin.path) cat
+ /var/lib/arvados-arvbox/superuser_token)
- ARVADOS_VIRTUAL_MACHINE_UUID=\$(arvbox cat
- /var/lib/arvados/vm-uuid)
+ while ! curl --fail --insecure --silent -H
+ "Authorization: Bearer $ARVADOS_API_TOKEN"
+ https://$(inputs.host)/arvados/v1/virtual_machines/$ARVADOS_VIRTUAL_MACHINE_UUID
+ >/dev/null ; do sleep 3 ; done
- while ! python -c "import arvados ;
- arvados.api().virtual_machines().get(uuid='$ARVADOS_VIRTUAL_MACHINE_UUID').execute()"
- 2>/dev/null ; do sleep 3; done
entryname: _script
InlineJavascriptRequirement: {}
- - id: superuser_tok_3
+ - id: superuser_tok_2
in:
container:
source: container
d:
- source: main_2_embed_2/d
+ source: main_2_embed_1/d
out:
- superuser_token
run: '#superuser_tok'
superuser_tokens:
source: main_2/supertok
out:
- - report
+ - report3
run: '#run_test'
cwlVersion: v1.0
projects / arvados.git / blobdiff