[ARVADOS] updated: 1.2.0-447-g3fd34f1f7
Git user
git at public.curoverse.com
Tue Nov 27 14:18:46 EST 2018
Summary of changes:
.licenseignore | 1 +
doc/_config.yml | 1 +
doc/_includes/_federated_cwl.liquid | 1 +
doc/_includes/_shards_yml.liquid | 1 +
doc/api/methods.html.textile.liquid | 6 +-
.../methods/container_requests.html.textile.liquid | 2 +-
doc/index.html.liquid | 2 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 23 ++
doc/user/cwl/cwl-run-options.html.textile.liquid | 57 +++--
doc/user/cwl/federated-workflow.odg | Bin 0 -> 12089 bytes
doc/user/cwl/federated-workflow.svg | 239 +++++++++++++++++++++
.../cwl/federated-workflows.html.textile.liquid | 57 +++++
.../cases => doc/user/cwl/federated}/cat.cwl | 0
doc/user/cwl/federated/federated.cwl | 87 ++++++++
doc/user/cwl/federated/file-on-clsr1.dat | 1 +
doc/user/cwl/federated/file-on-clsr2.dat | 1 +
doc/user/cwl/federated/file-on-clsr3.dat | 1 +
.../cases => doc/user/cwl/federated}/md5sum.cwl | 2 +-
doc/user/cwl/federated/shards.yml | 18 ++
doc/user/index.html.textile.liquid | 7 +-
.../tutorials/intro-crunch.html.textile.liquid | 1 -
.../tutorial-keep-get.html.textile.liquid | 13 ++
sdk/cwl/arvados_cwl/__init__.py | 7 +-
23 files changed, 499 insertions(+), 29 deletions(-)
create mode 120000 doc/_includes/_federated_cwl.liquid
create mode 120000 doc/_includes/_shards_yml.liquid
create mode 100644 doc/user/cwl/federated-workflow.odg
create mode 100644 doc/user/cwl/federated-workflow.svg
create mode 100644 doc/user/cwl/federated-workflows.html.textile.liquid
copy {sdk/cwl/tests/federation/cases => doc/user/cwl/federated}/cat.cwl (100%)
create mode 100644 doc/user/cwl/federated/federated.cwl
create mode 100644 doc/user/cwl/federated/file-on-clsr1.dat
create mode 100644 doc/user/cwl/federated/file-on-clsr2.dat
create mode 100644 doc/user/cwl/federated/file-on-clsr3.dat
copy {sdk/cwl/tests/federation/cases => doc/user/cwl/federated}/md5sum.cwl (98%)
create mode 100644 doc/user/cwl/federated/shards.yml
via 3fd34f1f780ed70d98afe5eaf8a655b60e0c0abd (commit)
via f24e1c6ca8d5636c1c747200dc87a0077b445707 (commit)
via fdd933cb69ea44d6c705b47be62f0f985eff742c (commit)
via 17311124babf9222a0205520b97adacbd7fef16b (commit)
via 601bf8bbefecb146651bac1306bf2464f0105b15 (commit)
via 8ec9c69eab7b914c0ea6d71dc8648f9a1f1c8255 (commit)
via c290df61bac294cd76d35b506a20bb9e76919f0e (commit)
via ca677782adf5d9334eb98b696359505d7ee8ef9f (commit)
via 90d69e2c02044c9d6effa9b2d52ca37b479c0c0d (commit)
via 267477f569cd2632ea14d6fdd467760c669fc087 (commit)
from efaa4cc24be924ade579dd16ec08f53a45e24d7b (commit)
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commit 3fd34f1f780ed70d98afe5eaf8a655b60e0c0abd
Merge: efaa4cc24 f24e1c6ca
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Nov 27 14:18:31 2018 -0500
Merge branch '14440-fed-user-doc' refs #14440
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
commit f24e1c6ca8d5636c1c747200dc87a0077b445707
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Tue Nov 27 14:14:54 2018 -0500
14440: Fix formatting of cwl-run-options table.
Also expand help text of --on-error option a bit.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/doc/user/cwl/cwl-run-options.html.textile.liquid b/doc/user/cwl/cwl-run-options.html.textile.liquid
index 2929a1cae..a7a634f37 100644
--- a/doc/user/cwl/cwl-run-options.html.textile.liquid
+++ b/doc/user/cwl/cwl-run-options.html.textile.liquid
@@ -24,7 +24,7 @@ table(table table-bordered table-condensed).
|_. Option |_. Description |
|==--basedir== BASEDIR| Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
|==--eval-timeout EVAL_TIMEOUT==|Time to wait for a Javascript expression to evaluate before giving an error, default 20s.|
-|==--print-dot==| Print workflow visualization in graphviz format and exit
+|==--print-dot==| Print workflow visualization in graphviz format and exit|
|==--version==| Print version and exit|
|==--validate==| Validate CWL document only.|
|==--verbose==| Default logging|
@@ -48,14 +48,14 @@ table(table table-bordered table-condensed).
|==--log-timestamps==| Prefix logging lines with timestamp|
|==--no-log-timestamps==| No timestamp on logging lines|
|==--api== {jobs,containers}|Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.|
-|==compute-checksum==| Compute checksum of contents while collecting outputs|
-|==submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)
-|==submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner job|
-|==always-submit-runner==|When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool|
-|==--submit-request-uuid== UUID|Update and commit to supplied container request instead of creating a new one (containers API only).
-|==--submit-runner-cluster== CLUSTER_ID|Submit workflow runner to a remote cluster (containers API only)
-|==--name NAME==|Name to use for workflow execution instance.
-|==--on-error== {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default is 'continue'.
+|==--compute-checksum==| Compute checksum of contents while collecting outputs|
+|==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
+|==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner job|
+|==--always-submit-runner==|When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool|
+|==--submit-request-uuid== UUID|Update and commit to supplied container request instead of creating a new one (containers API only).|
+|==--submit-runner-cluster== CLUSTER_ID|Submit workflow runner to a remote cluster (containers API only)|
+|==--name NAME==|Name to use for workflow execution instance.|
+|==--on-error== {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or 'continue' (may submit other steps that are not downstream from the error). Default is 'stop'.|
|==--enable-dev==|Enable loading and running development versions of CWL spec.|
|==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving workflow output to Keep.|
|==--intermediate-output-ttl== N|If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).|
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 7b2731ea9..c0915c06b 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -163,9 +163,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
help="Name to use for workflow execution instance.",
default=None)
- parser.add_argument("--on-error", type=str,
- help="Desired workflow behavior when a step fails. One of 'stop' or 'continue'. "
- "Default is 'continue'.", default="continue", choices=("stop", "continue"))
+ parser.add_argument("--on-error",
+ help="Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or "
+ "'continue' (may submit other steps that are not downstream from the error). Default is 'stop'.",
+ default="stop", choices=("stop", "continue"))
parser.add_argument("--enable-dev", action="store_true",
help="Enable loading and running development versions "
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