[ARVADOS] updated: e502060ffe4f68d33e2cca8f8d7544ce40d53eb7
Git user
git at public.curoverse.com
Mon Jan 30 16:29:37 EST 2017
Summary of changes:
.../app/views/work_units/_show_child.html.erb | 2 +-
.../app/views/work_units/_show_component.html.erb | 2 +-
build/build.list | 34 +--
build/package-build-dockerfiles/Makefile | 6 +-
.../{ubuntu1204 => ubuntu1604}/Dockerfile | 10 +-
.../{ubuntu1204 => ubuntu1604}/Dockerfile | 11 +-
.../ubuntu1604/etc-apt-preferences.d-arvados | 3 +
build/package-testing/deb-common-test-packages.sh | 2 +-
...ages-debian7.sh => test-packages-ubuntu1604.sh} | 0
build/run-build-packages-one-target.sh | 5 +-
build/run-build-packages.sh | 3 +
doc/_includes/_navbar_top.liquid | 2 +-
doc/api/methods.html.textile.liquid | 2 +
doc/sdk/cli/reference.html.textile.liquid | 13 +-
doc/user/index.html.textile.liquid | 2 +-
sdk/cli/bin/crunch-job | 10 +
sdk/cwl/arvados_cwl/__init__.py | 87 ++++--
sdk/cwl/arvados_cwl/arvcontainer.py | 38 ++-
sdk/cwl/arvados_cwl/arvdocker.py | 2 +
sdk/cwl/arvados_cwl/arvjob.py | 35 ++-
sdk/cwl/arvados_cwl/arvworkflow.py | 57 ++--
sdk/cwl/arvados_cwl/done.py | 35 ++-
sdk/cwl/arvados_cwl/fsaccess.py | 31 +-
sdk/cwl/arvados_cwl/pathmapper.py | 8 +-
sdk/cwl/arvados_cwl/runner.py | 180 ++++++++----
sdk/cwl/setup.py | 4 +-
sdk/cwl/tests/test_job.py | 17 +-
sdk/cwl/tests/test_submit.py | 245 ++++++++++------
sdk/cwl/tests/wf/expect_arvworkflow.cwl | 22 +-
sdk/cwl/tests/wf/expect_packed.cwl | 4 +-
sdk/cwl/tests/wf/scatter2_subwf.cwl | 116 +++++---
.../wf/{expect_packed.cwl => submit_wf_packed.cwl} | 8 +-
sdk/go/arvados/resource_list.go | 2 +
sdk/go/keepclient/block_cache.go | 104 +++++++
sdk/go/keepclient/collectionreader.go | 321 ++++++++-------------
sdk/go/keepclient/collectionreader_test.go | 48 ++-
sdk/go/keepclient/keepclient.go | 9 +
sdk/python/arvados/arvfile.py | 7 +-
sdk/python/arvados/commands/put.py | 2 +-
.../api/app/controllers/application_controller.rb | 15 +-
.../controllers/arvados/v1/schema_controller.rb | 10 +-
.../api/config/initializers/noop_deep_munge.rb | 9 +
.../api/test/functional/arvados/v1/query_test.rb | 29 ++
services/api/test/integration/noop_deep_munge.rb | 35 +++
services/crunch-run/crunchrun.go | 2 +-
services/crunch-run/crunchrun_test.go | 14 +-
services/keep-balance/balance_run_test.go | 4 +-
services/keep-balance/collection.go | 75 +++--
services/keep-balance/collection_test.go | 57 ++++
services/keep-web/handler.go | 52 +---
services/keep-web/handler_test.go | 43 ---
services/keep-web/ranges_test.go | 90 ++++++
52 files changed, 1246 insertions(+), 678 deletions(-)
copy build/package-build-dockerfiles/{ubuntu1204 => ubuntu1604}/Dockerfile (72%)
copy build/package-test-dockerfiles/{ubuntu1204 => ubuntu1604}/Dockerfile (55%)
create mode 100644 build/package-test-dockerfiles/ubuntu1604/etc-apt-preferences.d-arvados
rename build/package-testing/{test-packages-debian7.sh => test-packages-ubuntu1604.sh} (100%)
copy sdk/cwl/tests/wf/{expect_packed.cwl => submit_wf_packed.cwl} (53%)
create mode 100644 sdk/go/keepclient/block_cache.go
create mode 100644 services/api/config/initializers/noop_deep_munge.rb
create mode 100644 services/api/test/integration/noop_deep_munge.rb
create mode 100644 services/keep-balance/collection_test.go
create mode 100644 services/keep-web/ranges_test.go
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit e502060ffe4f68d33e2cca8f8d7544ce40d53eb7
Merge: dcf5452 d6579d9
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Jan 30 18:29:10 2017 -0300
10813: Merge branch 'master' into 10813-arv-put-six-threads
commit dcf5452fb14c7025feff04b3003ff68c9f4ec630
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Jan 30 18:26:35 2017 -0300
10813: Added only_committed argument to ArvFile.manifest_text() method to maintain consistency with its counterpart from Collection class.
diff --git a/sdk/python/arvados/arvfile.py b/sdk/python/arvados/arvfile.py
index 8446fb6..edeb910 100644
--- a/sdk/python/arvados/arvfile.py
+++ b/sdk/python/arvados/arvfile.py
@@ -1070,12 +1070,15 @@ class ArvadosFile(object):
return 0
@synchronized
- def manifest_text(self, stream_name=".", portable_locators=False, normalize=False):
+ def manifest_text(self, stream_name=".", portable_locators=False,
+ normalize=False, only_committed=False):
buf = ""
filestream = []
for segment in self.segments:
loc = segment.locator
- if loc.startswith("bufferblock"):
+ if self.parent._my_block_manager().is_bufferblock(loc):
+ if only_committed:
+ continue
loc = self._bufferblocks[loc].calculate_locator()
if portable_locators:
loc = KeepLocator(loc).stripped()
commit 4f485c1318130c61d81f6553460d5eb063f100cb
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Mon Jan 30 18:25:34 2017 -0300
10813: Removed unnecessary argument
diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index d57b2b7..5b46ba7 100644
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -520,7 +520,7 @@ class ArvPutUploadJob(object):
manifest = self._local_collection.manifest_text()
else:
# Get the manifest text without comitting pending blocks
- manifest = self._local_collection.manifest_text(".", strip=False,
+ manifest = self._local_collection.manifest_text(strip=False,
normalize=False,
only_committed=True)
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