@unreadable_inputs_present
end
+ def cancel
+ @object.cancel
+ if params[:return_to]
+ redirect_to params[:return_to]
+ else
+ redirect_to @object
+ end
+ end
+
protected
def for_comparison v
if v.is_a? Hash or v.is_a? Array
link.destroy
end
- # If this object has the 'trash_at' attribute, then simply mark it
- # as trash.
- if item.attributes.include?("trash_at")
- item.update_attributes trash_at: Time.now
+ if item.class == Collection
+ # Use delete API on collections
+ item.destroy
@removed_uuids << item.uuid
elsif item.owner_uuid == @object.uuid
# Object is owned by this project. Remove it from the project by
end
def cancel
- arvados_api_client.api "jobs/#{self.uuid}/", "cancel", {}
+ arvados_api_client.api "jobs/#{self.uuid}/", "cancel", {"cascade" => true}
end
def self.queue_size
state_label.in? ["Queued", "Running"]
end
+ def confirm_cancellation
+ "All unfinished child jobs and pipelines will also be canceled, even if they are being used in another job or pipeline. Are you sure you want to cancel this job?"
+ end
+
def uri
uuid = get(:uuid)
"/jobs/#{uuid}"
PipelineInstanceWorkUnit.new(self, label || self.name, self.uuid)
end
+ def cancel
+ arvados_api_client.api "pipeline_instances/#{self.uuid}/", "cancel", {"cascade" => true}
+ end
+
private
def components_map
# returns true if this work unit can be canceled
end
+ def confirm_cancellation
+ # returns true if this work unit wants to use a confirmation for cancellation
+ end
+
def uri
# returns the uri for this work unit
end
<div class="panel-heading">
<span class="panel-title">Used in pipelines</span>
</div>
- <div class="panel-body">
+ <div class="panel-body used-in-pipelines">
<% pi = PipelineInstance.order("created_at desc").filter([["components", "like", "%#{@object.uuid}%"]]) %>
<% pi.each do |pipeline| %>
<% end %>
<% end %>
</div>
+
+ <div class="panel-heading">
+ <span class="panel-title">Used in jobs</span>
+ </div>
+
+ <% jobs = Job.order("created_at desc").filter([["components", "like", "%#{@object.uuid}%"]]).limit(10) %>
+ <%
+ too_many_message = ""
+ if jobs.items_available > jobs.results.size
+ too_many_message = (jobs.items_available - jobs.results.size).to_s + ' more jobs are not listed.'
+ end
+ %>
+ <div class="panel-body used-in-jobs">
+ <% if too_many_message != "" %>
+ <p><i><%= too_many_message %></i></p>
+ <% end %>
+ <% jobs.each do |j| %>
+ <% j.components.each do |k, v| %>
+ <% if v == @object.uuid %>
+ <div>
+ <b><%= k %></b>
+ component of
+ <%= link_to_if_arvados_object j, friendly_name: true %>
+ created at
+ <%= render_localized_date(j.created_at) %>.
+ </div>
+ <% end %>
+ <% end %>
+ <% end %>
+ </div>
</div>
<% end %>
<% else %>
<% if @object.state.in? ['RunningOnClient', 'RunningOnServer'] %>
- <%= link_to(url_for('pipeline_instance[state]' => 'Paused'),
+ <%= link_to(cancel_pipeline_instance_path,
class: 'btn btn-primary run-pipeline-button',
title: 'Pause this pipeline',
- method: :patch
+ data: {confirm: 'All unfinished child jobs will be canceled, even if they are being used in another job or pipeline. Are you sure you want to pause this pipeline?'},
+ method: :post
) do %>
<i class="fa fa-fw fa-pause"></i> Pause
<% end %>
<div class="col-md-4">
<% if wu.is_paused? %>
<p>
- This <%= wu.title %> is paused. Children that are already running
- will continue to run, but no new processes will be submitted.
+ This <%= wu.title %> is paused. Children that were running
+ were cancelled and no new processes will be submitted.
</p>
<% end %>
</div>
<div class="col-md-2">
<% if wu.can_cancel? and @object.editable? %>
+ <% confirm = if wu.confirm_cancellation then {confirm: wu.confirm_cancellation} else {} end %>
<%= form_tag "#{wu.uri}/cancel", remote: true, style: "display:inline; padding-left: 1em" do |f| %>
<%= hidden_field_tag :return_to, url_for(@object) %>
- <%= button_tag "Cancel", {class: 'btn btn-xs btn-warning', id: "cancel-obj-button"} %>
+ <%= button_tag "Cancel", {class: 'btn btn-xs btn-warning', id: "cancel-obj-button", data: confirm} %>
<% end %>
<% end %>
</div>
get 'choose', on: :collection
end
resources :pipeline_instances do
+ post 'cancel', :on => :member
get 'compare', on: :collection
post 'copy', on: :member
end
get :index, {}, session_for(:active)
assert_response :success
end
+
+ test "job page lists pipelines and jobs in which it is used" do
+ get(:show,
+ {id: api_fixture('jobs')['completed_job_in_publicly_accessible_project']['uuid']},
+ session_for(:active))
+ assert_response :success
+
+ assert_select "div.used-in-pipelines" do
+ assert_select "a[href=/pipeline_instances/zzzzz-d1hrv-n68vc490mloy4fi]"
+ end
+
+ assert_select "div.used-in-jobs" do
+ assert_select "a[href=/jobs/zzzzz-8i9sb-with2components]"
+ end
+ end
end
end
[
- ['jobs', 'running_job_with_components', true],
- ['pipeline_instances', 'components_is_jobspec', false],
+ ['jobs', 'running_job_with_components', true, true],
+ ['pipeline_instances', 'components_is_jobspec', true, true],
['containers', 'running', false],
['container_requests', 'running', true],
- ].each do |type, fixture, cancelable|
+ ].each do |type, fixture, cancelable, confirm_cancellation|
test "cancel button for #{type}/#{fixture}" do
if cancelable
need_selenium 'to cancel'
visit page_with_token "active", "/#{type}/#{obj['uuid']}"
assert_text 'created_at'
-
if cancelable
assert_text 'priority: 1' if type.include?('container')
- assert_selector 'button', text: 'Cancel'
- first('a,button', text: 'Cancel').click
+ if type.include?('pipeline')
+ assert_selector 'a', text: 'Pause'
+ first('a,link', text: 'Pause').click
+ else
+ assert_selector 'button', text: 'Cancel'
+ first('a,button', text: 'Cancel').click
+ end
+ if confirm_cancellation
+ alert = page.driver.browser.switch_to.alert
+ alert.accept
+ end
wait_for_ajax
end
- assert_text 'priority: 0' if cancelable and type.include?('container')
+
+ if type.include?('pipeline')
+ assert_selector 'a', text: 'Resume'
+ assert_no_selector 'a', text: 'Pause'
+ elsif type.include?('job')
+ assert_text 'Cancelled'
+ assert_text 'Paused' # this job has a pipeline child which was also cancelled
+ assert_no_selector 'button', text: 'Cancel'
+ elsif cancelable
+ assert_text 'priority: 0'
+ end
end
end
"kind":"json",
"content":{"foo":"bar"}
}</pre>|
+
+h2(#pre-populate-output). Pre-populate output using Mount points
+
+When a container's output_path is a tmp mount backed by local disk, this output directory can be pre-populated with content from existing collections. This content can be specified by mounting collections at mount points that are subdirectories of output_path. Certain restrictions apply:
+
+1. Only mount points of kind @collection@ are supported.
+
+2. Mount points underneath output_path must not use @"writable":true@. If any of them are set as @writable@, the API will refuse to create/update the container request, and crunch-run will fail the container.
+
+3. If any such mount points are configured as @exclude_from_output":true@, they will be excluded from the output.
+
+If any process in the container tries to modify, remove, or rename these mount points or anything underneath them, the operation will fail and the container output and the underlying collections used to pre-populate are unaffected.
+
+h3. Example mount point configurations
+
+All the below examples are based on this collection:
+<pre><code>
+portable_data_hash cdfbe2e823222d26483d52e5089d553c+175
+
+manifest_text: ./alice 03032680d3fa0561ef4f85071140861e+13+A04e9d06459cda00aa997565bd78001061cf5bffb@58ab593d 0:13:hello.txt\n./bob d820b9df970e1b498e7723c50b107e1b+11+A42d162a60210479d1cfaf9fbb98d494ac6322ae6@58ab593d 0:11:hello.txt\n./carol cf72b172ff969250ae14a893a6745440+13+A476a2fd39e14e9c03af3076bd17e3612c075ff66@58ab593d 0:13:hello.txt\n
+</code></pre>
+
+table(table table-bordered table-condensed).
+|{width:40%}. *Mount point*|{width:30%}. *Description*|{width:30%}. *Resulting collection manifest text*|
+|<pre><code>"mounts": {
+ "/tmp/foo": {
+ "kind": "collection",
+ "portable_data_hash": "cdfbe2...+175"
+ },
+},
+"output_path": "/tmp"
+</code></pre>|No path specified and hence the entire collection will be mounted.|./*foo/*alice 030326... 0:13:hello.txt\n
+./*foo/*bob d820b9... 0:11:hello.txt\n
+./*foo/*carol cf72b1... 0:13:hello.txt\n
+*Note:* Here the "." in streams is replaced with *foo*.|
+|<pre><code>"mounts": {
+ "/tmp/foo/bar": {
+ "kind": "collection",
+ "portable_data_hash": "cdfbe2...+175"
+ "path": "alice"
+ },
+},
+"output_path": "/tmp"
+</code></pre>|Specified path refers to the subdirectory *alice* in the collection.|./*foo/bar* 030326... 0:13:hello.txt\n
+*Note:* only the manifest text segment for the subdirectory *alice* is included after replacing the subdirectory *alice* with *foo/bar*.|
+|<pre><code>"mounts": {
+ "/tmp/foo/bar": {
+ "kind": "collection",
+ "portable_data_hash": "cdfbe2...+175"
+ "path": "alice/hello.txt"
+ },
+},
+"output_path": "/tmp"
+</code></pre>|Specified path refers to the file *hello.txt* in the *alice* subdirectory|./*foo* 030326... 0:13:*bar*\n
+*Note:* Here the subdirectory *alice* is replaced with *foo* and the filename *hello.txt* from this subdirectory is replaced with *bar*.|
|environment|hash|Environment variables and values that should be set in the container environment (@docker run --env@). This augments and (when conflicts exist) overrides environment variables given in the image's Dockerfile.||
|cwd|string|Initial working directory, given as an absolute path (in the container) or a path relative to the WORKDIR given in the image's Dockerfile.|Required.|
|command|array of strings|Command to execute in the container.|Required. e.g., @["echo","hello"]@|
-|output_path|string|Path to a directory or file inside the container that should be preserved as container's output when it finishes. This path must be, or be inside, one of the mount targets. For best performance, point output_path to a writable collection mount.|Required.|
+|output_path|string|Path to a directory or file inside the container that should be preserved as container's output when it finishes. This path must be, or be inside, one of the mount targets. For best performance, point output_path to a writable collection mount. Also, see "Pre-populate output using Mount points":#pre-populate-output for details regarding optional output pre-population using mount points.|Required.|
|priority|integer|Higher value means spend more resources on this container_request, i.e., go ahead of other queued containers, bring up more nodes etc.|Priority 0 means a container should not be run on behalf of this request. Clients are expected to submit container requests with zero priority in order to preview the container that will be used to satisfy it. Priority can be null if and only if state!="Committed".|
|expires_at|datetime|After this time, priority is considered to be zero.|Not yet implemented.|
|use_existing|boolean|If possible, use an existing (non-failed) container to satisfy the request instead of creating a new one.|Default is true|
from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver
from .perf import Perf
-from .pathmapper import FinalOutputPathMapper
+from .pathmapper import NoFollowPathMapper
from ._version import __version__
from cwltool.pack import pack
def check_features(self, obj):
if isinstance(obj, dict):
- if obj.get("class") == "InitialWorkDirRequirement":
- if self.work_api == "containers":
- raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
if obj.get("writable"):
raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
if obj.get("class") == "CommandLineTool":
adjustDirObjs(outputObj, capture)
adjustFileObjs(outputObj, capture)
- generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
+ generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
final = arvados.collection.Collection(api_client=self.api,
keep_client=self.keep_client,
from . import done
from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
from .fsaccess import CollectionFetcher
+from .pathmapper import NoFollowPathMapper
+from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
class ArvadosContainer(object):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
dirs = set()
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if tp == "Directory" and '/' not in p[6:]:
+ pdh, p, tp = self.pathmapper.mapper(f)
+ if tp == "Directory" and '/' not in pdh:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh[5:]
}
- dirs.add(p[6:])
+ dirs.add(pdh)
+
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if p[6:].split("/")[0] not in dirs:
+ res, p, tp = self.pathmapper.mapper(f)
+ if res.startswith("keep:"):
+ res = res[5:]
+ elif res.startswith("/keep/"):
+ res = res[6:]
+ else:
+ continue
+ sp = res.split("/", 1)
+ pdh = sp[0]
+ if pdh not in dirs:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh
}
-
- if self.generatefiles["listing"]:
- raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
+ if len(sp) == 2:
+ mounts[p]["path"] = sp[1]
+
+ with Perf(metrics, "generatefiles %s" % self.name):
+ if self.generatefiles["listing"]:
+ vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
+
+ with Perf(metrics, "createfiles %s" % self.name):
+ for f, p in generatemapper.items():
+ if not p.target:
+ pass
+ elif p.type in ("File", "Directory"):
+ source, path = self.arvrunner.fs_access.get_collection(p.resolved)
+ vwd.copy(path, p.target, source_collection=source)
+ elif p.type == "CreateFile":
+ with vwd.open(p.target, "w") as n:
+ n.write(p.resolved.encode("utf-8"))
+
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
+
+ for f, p in generatemapper.items():
+ if not p.target:
+ continue
+ mountpoint = "%s/%s" % (self.outdir, p.target)
+ mounts[mountpoint] = {"kind": "collection",
+ "portable_data_hash": vwd.portable_data_hash(),
+ "path": p.target}
container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
- runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
+ runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"] * 2**20
partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
if partition_req:
from .arvdocker import arv_docker_get_image
from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing, upload_workflow_collection
-from .pathmapper import InitialWorkDirPathMapper
+from .pathmapper import VwdPathMapper
from .perf import Perf
from . import done
from ._version import __version__
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
script_parameters["task.vwd"] = {}
- generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
- separateDirs=False)
+ generatemapper = VwdPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
with Perf(metrics, "createfiles %s" % self.name):
for f, p in generatemapper.items():
with vwd.open(p.target, "w") as n:
n.write(p.resolved.encode("utf-8"))
- with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ if vwd:
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
for f, p in generatemapper.items():
if p.type == "File":
elif not crunchstat_re.match(l):
logt.append(l)
- if len(mergelogs) > 1:
+ if containersapi:
keys = mergelogs.keys()
loglines = []
while True:
self.collections = {}
def get_collection(self, path):
- p = path.split("/")
- if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
- pdh = p[0][5:]
+ sp = path.split("/", 1)
+ p = sp[0]
+ if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]):
+ pdh = p[5:]
if pdh not in self.collections:
self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
keep_client=self.keep_client)
- return (self.collections[pdh], "/".join(p[1:]))
+ return (self.collections[pdh], sp[1] if len(sp) == 2 else None)
else:
return (None, path)
self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
-class InitialWorkDirPathMapper(StagingPathMapper):
+class VwdPathMapper(StagingPathMapper):
def setup(self, referenced_files, basedir):
# type: (List[Any], unicode) -> None
self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type)
-class FinalOutputPathMapper(StagingPathMapper):
+class NoFollowPathMapper(StagingPathMapper):
_follow_dirs = False
def setup(self, referenced_files, basedir):
# type: (List[Any], unicode) -> None
# Note that arvados/build/run-build-packages.sh looks at this
# file to determine what version of cwltool and schema-salad to build.
install_requires=[
- 'cwltool==1.0.20170119234115',
- 'schema-salad==2.2.20170126160727',
+ 'cwltool==1.0.20170213175853',
+ 'schema-salad==2.2.20170208112505',
'ruamel.yaml==0.13.7',
'arvados-python-client>=0.1.20170112173420',
'setuptools'
pip_install \$(ls -r dist/arvados-cwl-runner-*.tar.gz | head -n1)
fi
+pip install cwltest
+
mkdir -p /tmp/cwltest
cd /tmp/cwltest
if ! test -d common-workflow-language ; then
'runtime_constraints': {
'vcpus': 3,
'ram': 3145728000,
- 'keep_cache_ram': 512,
+ 'keep_cache_ram': 536870912,
'API': True
},
'use_existing': True,
for key in call_body:
self.assertEqual(call_body_expected.get(key), call_body.get(key))
+
+ # The test passes some fields in builder.resources
+ # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
+ @mock.patch("arvados.commands.keepdocker.list_images_in_arv")
+ @mock.patch("arvados.collection.Collection")
+ def test_initial_work_dir(self, collection_mock, keepdocker):
+ arv_docker_clear_cache()
+ runner = mock.MagicMock()
+ runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
+ runner.ignore_docker_for_reuse = False
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
+
+ keepdocker.return_value = [("zzzzz-4zz18-zzzzzzzzzzzzzz3", "")]
+ runner.api.collections().get().execute.return_value = {
+ "portable_data_hash": "99999999999999999999999999999993+99"}
+
+ sourcemock = mock.MagicMock()
+ def get_collection_mock(p):
+ if "/" in p:
+ return (sourcemock, p.split("/", 1)[1])
+ else:
+ return (sourcemock, "")
+ runner.fs_access.get_collection.side_effect = get_collection_mock
+
+ vwdmock = mock.MagicMock()
+ collection_mock.return_value = vwdmock
+ vwdmock.portable_data_hash.return_value = "99999999999999999999999999999996+99"
+
+ tool = cmap({
+ "inputs": [],
+ "outputs": [],
+ "hints": [{
+ "class": "InitialWorkDirRequirement",
+ "listing": [{
+ "class": "File",
+ "basename": "foo",
+ "location": "keep:99999999999999999999999999999995+99/bar"
+ },
+ {
+ "class": "Directory",
+ "basename": "foo2",
+ "location": "keep:99999999999999999999999999999995+99"
+ },
+ {
+ "class": "File",
+ "basename": "filename",
+ "location": "keep:99999999999999999999999999999995+99/baz/filename"
+ },
+ {
+ "class": "Directory",
+ "basename": "subdir",
+ "location": "keep:99999999999999999999999999999995+99/subdir"
+ } ]
+ }],
+ "baseCommand": "ls"
+ })
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
+ avsc_names=avsc_names, make_fs_access=make_fs_access,
+ loader=Loader({}))
+ arvtool.formatgraph = None
+ for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_initial_work_dir",
+ make_fs_access=make_fs_access, tmpdir="/tmp"):
+ j.run()
+
+ call_args, call_kwargs = runner.api.container_requests().create.call_args
+
+ vwdmock.copy.assert_has_calls([mock.call('bar', 'foo', source_collection=sourcemock)])
+ vwdmock.copy.assert_has_calls([mock.call('', 'foo2', source_collection=sourcemock)])
+ vwdmock.copy.assert_has_calls([mock.call('baz/filename', 'filename', source_collection=sourcemock)])
+ vwdmock.copy.assert_has_calls([mock.call('subdir', 'subdir', source_collection=sourcemock)])
+
+ call_body_expected = {
+ 'environment': {
+ 'HOME': '/var/spool/cwl',
+ 'TMPDIR': '/tmp'
+ },
+ 'name': 'test_initial_work_dir',
+ 'runtime_constraints': {
+ 'vcpus': 1,
+ 'ram': 1073741824
+ },
+ 'use_existing': True,
+ 'priority': 1,
+ 'mounts': {
+ '/var/spool/cwl': {'kind': 'tmp'},
+ '/var/spool/cwl/foo': {
+ 'kind': 'collection',
+ 'path': 'foo',
+ 'portable_data_hash': '99999999999999999999999999999996+99'
+ },
+ '/var/spool/cwl/foo2': {
+ 'kind': 'collection',
+ 'path': 'foo2',
+ 'portable_data_hash': '99999999999999999999999999999996+99'
+ },
+ '/var/spool/cwl/filename': {
+ 'kind': 'collection',
+ 'path': 'filename',
+ 'portable_data_hash': '99999999999999999999999999999996+99'
+ },
+ '/var/spool/cwl/subdir': {
+ 'kind': 'collection',
+ 'path': 'subdir',
+ 'portable_data_hash': '99999999999999999999999999999996+99'
+ }
+ },
+ 'state': 'Committed',
+ 'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
+ 'output_path': '/var/spool/cwl',
+ 'container_image': '99999999999999999999999999999993+99',
+ 'command': ['ls'],
+ 'cwd': '/var/spool/cwl',
+ 'scheduling_parameters': {
+ },
+ 'properties': {}
+ }
+
+ call_body = call_kwargs.get('body', None)
+ self.assertNotEqual(None, call_body)
+ for key in call_body:
+ self.assertEqual(call_body_expected.get(key), call_body.get(key))
+
@mock.patch("arvados.collection.Collection")
def test_done(self, col):
api = mock.MagicMock()
'class': 'Directory'
},
'cwl:tool':
- '4db32e8a15aa48ea084b2f38108f406d+60/workflow.cwl#main'
+ '99999999999999999999999999999994+99/workflow.cwl#main'
},
'repository': 'arvados',
'script_version': 'master',
'listing': [
{'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
]}},
- 'cwl:tool': '4db32e8a15aa48ea084b2f38108f406d+60/workflow.cwl#main',
+ 'cwl:tool': '99999999999999999999999999999994+99/workflow.cwl#main',
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
expect_pipeline["name"] = "hello job 123"
stubs.api.pipeline_instances().create.assert_called_with(
- body=expect_pipeline)
+ body=JsonDiffMatcher(expect_pipeline))
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
},
'script_parameters': {
'cwl:tool':
- '00e281847a33e1c0df93161d70a6fc5d+60/workflow.cwl#main',
+ '99999999999999999999999999999992+99/workflow.cwl#main',
'optionalFloatInput': None,
'fileInput': {
'type': 'File',
params = expect_template[
"components"]["inputs_test.cwl"]["script_parameters"]
params["fileInput"]["value"] = '99999999999999999999999999999992+99/blorp.txt'
+ params["cwl:tool"] = '99999999999999999999999999999994+99/workflow.cwl#main'
params["floatInput"]["value"] = 1.234
params["boolInput"]["value"] = True
import (
"bufio"
"fmt"
+ "git.curoverse.com/arvados.git/sdk/go/blockdigest"
"strings"
"time"
-
- "git.curoverse.com/arvados.git/sdk/go/manifest"
)
// Collection is an arvados#collection resource.
return nil, fmt.Errorf("Invalid stream (<3 tokens): %q", line)
}
for _, token := range tokens[1:] {
- if !manifest.LocatorPattern.MatchString(token) {
+ if !blockdigest.LocatorPattern.MatchString(token) {
// FIXME: ensure it's a file token
break
}
// Mount is special behavior to attach to a filesystem path or device.
type Mount struct {
- Kind string `json:"kind"`
- Writable bool `json:"writable"`
- PortableDataHash string `json:"portable_data_hash"`
- UUID string `json:"uuid"`
- DeviceType string `json:"device_type"`
- Path string `json:"path"`
- Content interface{} `json:"content"`
+ Kind string `json:"kind"`
+ Writable bool `json:"writable"`
+ PortableDataHash string `json:"portable_data_hash"`
+ UUID string `json:"uuid"`
+ DeviceType string `json:"device_type"`
+ Path string `json:"path"`
+ Content interface{} `json:"content"`
+ ExcludeFromOutput bool `json:"exclude_from_output"`
}
// RuntimeConstraints specify a container's compute resources (RAM,
-// Framework for monitoring the Arvados container Queue, Locks container
-// records, and runs goroutine callbacks which implement execution and
-// monitoring of the containers.
+// Package dispatch is a helper library for building Arvados container
+// dispatchers.
package dispatch
import (
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "context"
+ "fmt"
"log"
"sync"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
)
const (
Cancelled = arvados.ContainerStateCancelled
)
-// Dispatcher holds the state of the dispatcher
type Dispatcher struct {
- // The Arvados client
Arv *arvadosclient.ArvadosClient
- // When a new queued container appears and is either already owned by
- // this dispatcher or is successfully locked, the dispatcher will call
- // go RunContainer(). The RunContainer() goroutine gets a channel over
- // which it will receive updates to the container state. The
- // RunContainer() goroutine should only assume status updates come when
- // the container record changes on the API server; if it needs to
- // monitor the job submission to the underlying slurm/grid engine/etc
- // queue it should spin up its own polling goroutines. When the
- // channel is closed, that means the container is no longer being
- // handled by this dispatcher and the goroutine should terminate. The
- // goroutine is responsible for draining the 'status' channel, failure
- // to do so may deadlock the dispatcher.
- RunContainer func(*Dispatcher, arvados.Container, chan arvados.Container)
-
- // Amount of time to wait between polling for updates.
+ // Queue polling frequency
PollPeriod time.Duration
- // Minimum time between two attempts to run the same container
+ // Time to wait between successive attempts to run the same container
MinRetryPeriod time.Duration
- mineMutex sync.Mutex
- mineMap map[string]chan arvados.Container
- Auth arvados.APIClientAuthorization
+ // Func that implements the container lifecycle. Must be set
+ // to a non-nil DispatchFunc before calling Run().
+ RunContainer DispatchFunc
+ auth arvados.APIClientAuthorization
+ mtx sync.Mutex
+ trackers map[string]*runTracker
throttle throttle
-
- stop chan struct{}
-}
-
-// Goroutine-safely add/remove uuid to the set of "my" containers, i.e., ones
-// for which this process is actively starting/monitoring. Returns channel to
-// be used to send container status updates.
-func (dispatcher *Dispatcher) setMine(uuid string) chan arvados.Container {
- dispatcher.mineMutex.Lock()
- defer dispatcher.mineMutex.Unlock()
- if ch, ok := dispatcher.mineMap[uuid]; ok {
- return ch
- }
-
- ch := make(chan arvados.Container)
- dispatcher.mineMap[uuid] = ch
- return ch
-}
-
-// Release a container which is no longer being monitored.
-func (dispatcher *Dispatcher) notMine(uuid string) {
- dispatcher.mineMutex.Lock()
- defer dispatcher.mineMutex.Unlock()
- if ch, ok := dispatcher.mineMap[uuid]; ok {
- close(ch)
- delete(dispatcher.mineMap, uuid)
- }
}
-// checkMine returns true if there is a channel for updates associated
-// with container c. If update is true, also send the container record on
-// the channel.
-func (dispatcher *Dispatcher) checkMine(c arvados.Container, update bool) bool {
- dispatcher.mineMutex.Lock()
- defer dispatcher.mineMutex.Unlock()
- ch, ok := dispatcher.mineMap[c.UUID]
- if ok {
- if update {
- ch <- c
- }
- return true
- }
- return false
-}
-
-func (dispatcher *Dispatcher) getContainers(params arvadosclient.Dict, touched map[string]bool) {
- var containers arvados.ContainerList
- err := dispatcher.Arv.List("containers", params, &containers)
+// A DispatchFunc executes a container (if the container record is
+// Locked) or resume monitoring an already-running container, and wait
+// until that container exits.
+//
+// While the container runs, the DispatchFunc should listen for
+// updated container records on the provided channel. When the channel
+// closes, the DispatchFunc should stop the container if it's still
+// running, and return.
+//
+// The DispatchFunc should not return until the container is finished.
+type DispatchFunc func(*Dispatcher, arvados.Container, <-chan arvados.Container)
+
+// Run watches the API server's queue for containers that are either
+// ready to run and available to lock, or are already locked by this
+// dispatcher's token. When a new one appears, Run calls RunContainer
+// in a new goroutine.
+func (d *Dispatcher) Run(ctx context.Context) error {
+ err := d.Arv.Call("GET", "api_client_authorizations", "", "current", nil, &d.auth)
if err != nil {
- log.Printf("Error getting list of containers: %q", err)
- return
- }
-
- if containers.ItemsAvailable > len(containers.Items) {
- // TODO: support paging
- log.Printf("Warning! %d containers are available but only received %d, paged requests are not yet supported, some containers may be ignored.",
- containers.ItemsAvailable,
- len(containers.Items))
- }
- for _, container := range containers.Items {
- touched[container.UUID] = true
- dispatcher.handleUpdate(container)
+ return fmt.Errorf("error getting my token UUID: %v", err)
}
-}
-func (dispatcher *Dispatcher) pollContainers(stop chan struct{}) {
- ticker := time.NewTicker(dispatcher.PollPeriod)
- defer ticker.Stop()
+ d.throttle.hold = d.MinRetryPeriod
- paramsQ := arvadosclient.Dict{
- "filters": [][]interface{}{{"state", "=", "Queued"}, {"priority", ">", "0"}},
- "order": []string{"priority desc"},
- "limit": "1000"}
- paramsP := arvadosclient.Dict{
- "filters": [][]interface{}{{"locked_by_uuid", "=", dispatcher.Auth.UUID}},
- "limit": "1000"}
+ poll := time.NewTicker(d.PollPeriod)
+ defer poll.Stop()
for {
- touched := make(map[string]bool)
- dispatcher.getContainers(paramsQ, touched)
- dispatcher.getContainers(paramsP, touched)
- dispatcher.mineMutex.Lock()
- var monitored []string
- for k := range dispatcher.mineMap {
- if _, ok := touched[k]; !ok {
- monitored = append(monitored, k)
- }
- }
- dispatcher.mineMutex.Unlock()
- if monitored != nil {
- dispatcher.getContainers(arvadosclient.Dict{
- "filters": [][]interface{}{{"uuid", "in", monitored}}}, touched)
- }
+ tracked := d.trackedUUIDs()
+ d.checkForUpdates([][]interface{}{
+ {"uuid", "in", tracked}})
+ d.checkForUpdates([][]interface{}{
+ {"locked_by_uuid", "=", d.auth.UUID},
+ {"uuid", "not in", tracked}})
+ d.checkForUpdates([][]interface{}{
+ {"state", "=", Queued},
+ {"priority", ">", "0"},
+ {"uuid", "not in", tracked}})
select {
- case <-ticker.C:
- case <-stop:
- return
+ case <-poll.C:
+ continue
+ case <-ctx.Done():
+ return ctx.Err()
}
}
}
-func (dispatcher *Dispatcher) handleUpdate(container arvados.Container) {
- if container.State == Queued && dispatcher.checkMine(container, false) {
- // If we previously started the job, something failed, and it
- // was re-queued, this dispatcher might still be monitoring it.
- // Stop the existing monitor, then try to lock and run it
- // again.
- dispatcher.notMine(container.UUID)
+func (d *Dispatcher) trackedUUIDs() []string {
+ d.mtx.Lock()
+ defer d.mtx.Unlock()
+ if len(d.trackers) == 0 {
+ // API bug: ["uuid", "not in", []] does not work as
+ // expected, but this does:
+ return []string{"this-uuid-does-not-exist"}
}
-
- if container.LockedByUUID != dispatcher.Auth.UUID && container.State != Queued {
- // If container is Complete, Cancelled, or Queued, LockedByUUID
- // will be nil. If the container was formerly Locked, moved
- // back to Queued and then locked by another dispatcher,
- // LockedByUUID will be different. In either case, we want
- // to stop monitoring it.
- log.Printf("Container %v now in state %q with locked_by_uuid %q", container.UUID, container.State, container.LockedByUUID)
- dispatcher.notMine(container.UUID)
- return
+ uuids := make([]string, 0, len(d.trackers))
+ for x := range d.trackers {
+ uuids = append(uuids, x)
}
+ return uuids
+}
- if dispatcher.checkMine(container, true) {
- // Already monitored, sent status update
- return
- }
+// Start a runner in a new goroutine, and send the initial container
+// record to its updates channel.
+func (d *Dispatcher) start(c arvados.Container) *runTracker {
+ tracker := &runTracker{updates: make(chan arvados.Container, 1)}
+ tracker.updates <- c
+ go func() {
+ d.RunContainer(d, c, tracker.updates)
+
+ d.mtx.Lock()
+ delete(d.trackers, c.UUID)
+ d.mtx.Unlock()
+ }()
+ return tracker
+}
- if container.State == Queued && container.Priority > 0 {
- if !dispatcher.throttle.Check(container.UUID) {
+func (d *Dispatcher) checkForUpdates(filters [][]interface{}) {
+ params := arvadosclient.Dict{
+ "filters": filters,
+ "order": []string{"priority desc"}}
+
+ var list arvados.ContainerList
+ for offset, more := 0, true; more; offset += len(list.Items) {
+ params["offset"] = offset
+ err := d.Arv.List("containers", params, &list)
+ if err != nil {
+ log.Printf("Error getting list of containers: %q", err)
return
}
- // Try to take the lock
- if err := dispatcher.Lock(container.UUID); err != nil {
- return
- }
- container.State = Locked
+ more = list.ItemsAvailable > len(list.Items)
+ d.checkListForUpdates(list.Items)
}
+}
- if container.State == Locked || container.State == Running {
- // Not currently monitored but in Locked or Running state and
- // owned by this dispatcher, so start monitoring.
- go dispatcher.RunContainer(dispatcher, container, dispatcher.setMine(container.UUID))
+func (d *Dispatcher) checkListForUpdates(containers []arvados.Container) {
+ d.mtx.Lock()
+ defer d.mtx.Unlock()
+ if d.trackers == nil {
+ d.trackers = make(map[string]*runTracker)
+ }
+
+ for _, c := range containers {
+ tracker, alreadyTracking := d.trackers[c.UUID]
+ if c.LockedByUUID != "" && c.LockedByUUID != d.auth.UUID {
+ log.Printf("debug: ignoring %s locked by %s", c.UUID, c.LockedByUUID)
+ } else if alreadyTracking {
+ switch c.State {
+ case Queued:
+ tracker.close()
+ case Locked, Running:
+ tracker.update(c)
+ case Cancelled, Complete:
+ tracker.close()
+ }
+ } else {
+ switch c.State {
+ case Queued:
+ if !d.throttle.Check(c.UUID) {
+ break
+ }
+ err := d.lock(c.UUID)
+ if err != nil {
+ log.Printf("debug: error locking container %s: %s", c.UUID, err)
+ break
+ }
+ c.State = Locked
+ d.trackers[c.UUID] = d.start(c)
+ case Locked, Running:
+ if !d.throttle.Check(c.UUID) {
+ break
+ }
+ d.trackers[c.UUID] = d.start(c)
+ case Cancelled, Complete:
+ tracker.close()
+ }
+ }
}
}
// UpdateState makes an API call to change the state of a container.
-func (dispatcher *Dispatcher) UpdateState(uuid string, newState arvados.ContainerState) error {
- err := dispatcher.Arv.Update("containers", uuid,
+func (d *Dispatcher) UpdateState(uuid string, state arvados.ContainerState) error {
+ err := d.Arv.Update("containers", uuid,
arvadosclient.Dict{
- "container": arvadosclient.Dict{"state": newState}},
- nil)
+ "container": arvadosclient.Dict{"state": state},
+ }, nil)
if err != nil {
- log.Printf("Error updating container %s to state %q: %q", uuid, newState, err)
+ log.Printf("Error updating container %s to state %q: %s", uuid, state, err)
}
return err
}
// Lock makes the lock API call which updates the state of a container to Locked.
-func (dispatcher *Dispatcher) Lock(uuid string) error {
- err := dispatcher.Arv.Call("POST", "containers", uuid, "lock", nil, nil)
- if err != nil {
- log.Printf("Error locking container %s: %q", uuid, err)
- }
- return err
+func (d *Dispatcher) lock(uuid string) error {
+ return d.Arv.Call("POST", "containers", uuid, "lock", nil, nil)
}
// Unlock makes the unlock API call which updates the state of a container to Queued.
-func (dispatcher *Dispatcher) Unlock(uuid string) error {
- err := dispatcher.Arv.Call("POST", "containers", uuid, "unlock", nil, nil)
- if err != nil {
- log.Printf("Error unlocking container %s: %q", uuid, err)
- }
- return err
+func (d *Dispatcher) Unlock(uuid string) error {
+ return d.Arv.Call("POST", "containers", uuid, "unlock", nil, nil)
}
-// Stop causes Run to return after the current polling cycle.
-func (dispatcher *Dispatcher) Stop() {
- if dispatcher.stop == nil {
- // already stopped
- return
+type runTracker struct {
+ closing bool
+ updates chan arvados.Container
+}
+
+func (tracker *runTracker) close() {
+ if !tracker.closing {
+ close(tracker.updates)
}
- close(dispatcher.stop)
- dispatcher.stop = nil
+ tracker.closing = true
}
-// Run runs the main loop of the dispatcher.
-func (dispatcher *Dispatcher) Run() (err error) {
- err = dispatcher.Arv.Call("GET", "api_client_authorizations", "", "current", nil, &dispatcher.Auth)
- if err != nil {
- log.Printf("Error getting my token UUID: %v", err)
+func (tracker *runTracker) update(c arvados.Container) {
+ if tracker.closing {
return
}
-
- dispatcher.mineMap = make(map[string]chan arvados.Container)
- dispatcher.stop = make(chan struct{})
- dispatcher.throttle.hold = dispatcher.MinRetryPeriod
- dispatcher.pollContainers(dispatcher.stop)
- return nil
+ select {
+ case <-tracker.updates:
+ log.Printf("debug: runner is handling updates slowly, discarded previous update for %s", c.UUID)
+ default:
+ }
+ tracker.updates <- c
}
// parameter when retrieving the collection record).
var ErrNoManifest = errors.New("Collection has no manifest")
-// CollectionFileReader returns a Reader that reads file content from
-// a collection. The filename must be given relative to the root of
-// the collection, without a leading "./".
+// CollectionFileReader returns a Reader that reads content from a single file
+// in the collection. The filename must be relative to the root of the
+// collection. A leading prefix of "/" or "./" in the filename is ignored.
func (kc *KeepClient) CollectionFileReader(collection map[string]interface{}, filename string) (Reader, error) {
mText, ok := collection["manifest_text"].(string)
if !ok {
for _, testCase := range []rdrTest{
{mt: mt, f: "zzzz", want: os.ErrNotExist},
{mt: mt, f: "frob", want: os.ErrNotExist},
- {mt: mt, f: "/segmented/frob", want: os.ErrNotExist},
- {mt: mt, f: "./segmented/frob", want: os.ErrNotExist},
- {mt: mt, f: "/f", want: os.ErrNotExist},
- {mt: mt, f: "./f", want: os.ErrNotExist},
- {mt: mt, f: "foo bar//baz", want: os.ErrNotExist},
+ {mt: mt, f: "/segmented/frob", want: "frob"},
+ {mt: mt, f: "./segmented/frob", want: "frob"},
+ {mt: mt, f: "/f", want: "f"},
+ {mt: mt, f: "./f", want: "f"},
+ {mt: mt, f: "foo bar//baz", want: "foo"},
{mt: mt, f: "foo/zero", want: ""},
{mt: mt, f: "zero@0", want: ""},
{mt: mt, f: "zero@1", want: ""},
"errors"
"fmt"
"git.curoverse.com/arvados.git/sdk/go/blockdigest"
+ "path"
"regexp"
+ "sort"
"strconv"
"strings"
)
var ErrInvalidToken = errors.New("Invalid token")
-var LocatorPattern = regexp.MustCompile(
- "^[0-9a-fA-F]{32}\\+[0-9]+(\\+[A-Z][A-Za-z0-9@_-]+)*$")
-
type Manifest struct {
Text string
Err error
Hints []string
}
-type DataSegment struct {
- BlockLocator
- Locator string
- StreamOffset uint64
-}
-
// FileSegment is a portion of a file that is contained within a
// single block.
type FileSegment struct {
type ManifestStream struct {
StreamName string
Blocks []string
+ blockOffsets []uint64
FileStreamSegments []FileStreamSegment
Err error
}
+// Array of segments referencing file content
+type segmentedFile []FileSegment
+
+// Map of files to list of file segments referencing file content
+type segmentedStream map[string]segmentedFile
+
+// Map of streams
+type segmentedManifest map[string]segmentedStream
+
var escapeSeq = regexp.MustCompile(`\\([0-9]{3}|\\)`)
func unescapeSeq(seq string) string {
return string([]byte{byte(i)})
}
+func EscapeName(s string) string {
+ raw := []byte(s)
+ escaped := make([]byte, 0, len(s))
+ for _, c := range raw {
+ if c <= 32 {
+ oct := fmt.Sprintf("\\%03o", c)
+ escaped = append(escaped, []byte(oct)...)
+ } else {
+ escaped = append(escaped, c)
+ }
+ }
+ return string(escaped)
+}
+
func UnescapeName(s string) string {
return escapeSeq.ReplaceAllStringFunc(s, unescapeSeq)
}
func ParseBlockLocator(s string) (b BlockLocator, err error) {
- if !LocatorPattern.MatchString(s) {
+ if !blockdigest.LocatorPattern.MatchString(s) {
err = fmt.Errorf("String \"%s\" does not match BlockLocator pattern "+
"\"%s\".",
s,
- LocatorPattern.String())
+ blockdigest.LocatorPattern.String())
} else {
tokens := strings.Split(s, "+")
var blockSize int64
}
func (s *ManifestStream) FileSegmentIterByName(filepath string) <-chan *FileSegment {
- ch := make(chan *FileSegment)
+ ch := make(chan *FileSegment, 64)
go func() {
s.sendFileSegmentIterByName(filepath, ch)
close(ch)
return ch
}
+func firstBlock(offsets []uint64, range_start uint64) int {
+ // range_start/block_start is the inclusive lower bound
+ // range_end/block_end is the exclusive upper bound
+
+ hi := len(offsets) - 1
+ var lo int
+ i := ((hi + lo) / 2)
+ block_start := offsets[i]
+ block_end := offsets[i+1]
+
+ // perform a binary search for the first block
+ // assumes that all of the blocks are contiguous, so range_start is guaranteed
+ // to either fall into the range of a block or be outside the block range entirely
+ for !(range_start >= block_start && range_start < block_end) {
+ fmt.Println(i, block_start, block_end)
+ if lo == i {
+ // must be out of range, fail
+ return -1
+ }
+ if range_start > block_start {
+ lo = i
+ } else {
+ hi = i
+ }
+ i = ((hi + lo) / 2)
+ block_start = offsets[i]
+ block_end = offsets[i+1]
+ }
+ return i
+}
+
func (s *ManifestStream) sendFileSegmentIterByName(filepath string, ch chan<- *FileSegment) {
- blockLens := make([]int, 0, len(s.Blocks))
// This is what streamName+"/"+fileName will look like:
- target := "./" + filepath
+ target := fixStreamName(filepath)
for _, fTok := range s.FileStreamSegments {
wantPos := fTok.SegPos
wantLen := fTok.SegLen
ch <- &FileSegment{Locator: "d41d8cd98f00b204e9800998ecf8427e+0", Offset: 0, Len: 0}
continue
}
- // Linear search for blocks containing data for this
- // file
- var blockPos uint64 = 0 // position of block in stream
- for i, loc := range s.Blocks {
+
+ // Binary search to determine first block in the stream
+ i := firstBlock(s.blockOffsets, wantPos)
+ if i == -1 {
+ // Shouldn't happen, file segments are checked in parseManifestStream
+ panic(fmt.Sprintf("File segment %v extends past end of stream", fTok))
+ }
+ for ; i < len(s.Blocks); i++ {
+ blockPos := s.blockOffsets[i]
+ blockEnd := s.blockOffsets[i+1]
+ if blockEnd <= wantPos {
+ // Shouldn't happen, FirstBlock() should start
+ // us on the right block, so if this triggers
+ // that means there is a bug.
+ panic(fmt.Sprintf("Block end %v comes before start of file segment %v", blockEnd, wantPos))
+ }
if blockPos >= wantPos+wantLen {
+ // current block comes after current file span
break
}
- if len(blockLens) <= i {
- blockLens = blockLens[:i+1]
- b, err := ParseBlockLocator(loc)
- if err != nil {
- // Unparseable locator -> unusable
- // stream.
- ch <- nil
- return
- }
- blockLens[i] = b.Size
- }
- blockLen := uint64(blockLens[i])
- if blockPos+blockLen <= wantPos {
- blockPos += blockLen
- continue
- }
+
fseg := FileSegment{
- Locator: loc,
+ Locator: s.Blocks[i],
Offset: 0,
- Len: blockLens[i],
+ Len: int(blockEnd - blockPos),
}
if blockPos < wantPos {
fseg.Offset = int(wantPos - blockPos)
fseg.Len -= fseg.Offset
}
- if blockPos+blockLen > wantPos+wantLen {
+ if blockEnd > wantPos+wantLen {
fseg.Len = int(wantPos+wantLen-blockPos) - fseg.Offset
}
ch <- &fseg
- blockPos += blockLen
}
}
}
return
}
+ m.blockOffsets = make([]uint64, len(m.Blocks)+1)
+ var streamoffset uint64
+ for i, b := range m.Blocks {
+ bl, err := ParseBlockLocator(b)
+ if err != nil {
+ m.Err = err
+ return
+ }
+ m.blockOffsets[i] = streamoffset
+ streamoffset += uint64(bl.Size)
+ }
+ m.blockOffsets[len(m.Blocks)] = streamoffset
+
if len(fileTokens) == 0 {
m.Err = fmt.Errorf("No file tokens found")
return
m.Err = fmt.Errorf("Invalid file token: %s", ft)
break
}
+ if pft.SegPos+pft.SegLen > streamoffset {
+ m.Err = fmt.Errorf("File segment %s extends past end of stream %d", ft, streamoffset)
+ break
+ }
m.FileStreamSegments = append(m.FileStreamSegments, pft)
}
return
}
+func fixStreamName(sn string) string {
+ sn = path.Clean(sn)
+ if strings.HasPrefix(sn, "/") {
+ sn = "." + sn
+ } else if sn != "." {
+ sn = "./" + sn
+ }
+ return sn
+}
+
+func splitPath(srcpath string) (streamname, filename string) {
+ pathIdx := strings.LastIndex(srcpath, "/")
+ if pathIdx >= 0 {
+ streamname = srcpath[0:pathIdx]
+ filename = srcpath[pathIdx+1:]
+ } else {
+ streamname = srcpath
+ filename = ""
+ }
+ return
+}
+
+func (m *Manifest) segment() (*segmentedManifest, error) {
+ files := make(segmentedManifest)
+
+ for stream := range m.StreamIter() {
+ if stream.Err != nil {
+ // Stream has an error
+ return nil, stream.Err
+ }
+ currentStreamfiles := make(map[string]bool)
+ for _, f := range stream.FileStreamSegments {
+ sn := stream.StreamName
+ if strings.HasSuffix(sn, "/") {
+ sn = sn[0 : len(sn)-1]
+ }
+ path := sn + "/" + f.Name
+ streamname, filename := splitPath(path)
+ if files[streamname] == nil {
+ files[streamname] = make(segmentedStream)
+ }
+ if !currentStreamfiles[path] {
+ segs := files[streamname][filename]
+ for seg := range stream.FileSegmentIterByName(path) {
+ if seg.Len > 0 {
+ segs = append(segs, *seg)
+ }
+ }
+ files[streamname][filename] = segs
+ currentStreamfiles[path] = true
+ }
+ }
+ }
+
+ return &files, nil
+}
+
+func (stream segmentedStream) normalizedText(name string) string {
+ var sortedfiles []string
+ for k, _ := range stream {
+ sortedfiles = append(sortedfiles, k)
+ }
+ sort.Strings(sortedfiles)
+
+ stream_tokens := []string{EscapeName(name)}
+
+ blocks := make(map[blockdigest.BlockDigest]int64)
+ var streamoffset int64
+
+ // Go through each file and add each referenced block exactly once.
+ for _, streamfile := range sortedfiles {
+ for _, segment := range stream[streamfile] {
+ b, _ := ParseBlockLocator(segment.Locator)
+ if _, ok := blocks[b.Digest]; !ok {
+ stream_tokens = append(stream_tokens, segment.Locator)
+ blocks[b.Digest] = streamoffset
+ streamoffset += int64(b.Size)
+ }
+ }
+ }
+
+ if len(stream_tokens) == 1 {
+ stream_tokens = append(stream_tokens, "d41d8cd98f00b204e9800998ecf8427e+0")
+ }
+
+ for _, streamfile := range sortedfiles {
+ // Add in file segments
+ span_start := int64(-1)
+ span_end := int64(0)
+ fout := EscapeName(streamfile)
+ for _, segment := range stream[streamfile] {
+ // Collapse adjacent segments
+ b, _ := ParseBlockLocator(segment.Locator)
+ streamoffset = blocks[b.Digest] + int64(segment.Offset)
+ if span_start == -1 {
+ span_start = streamoffset
+ span_end = streamoffset + int64(segment.Len)
+ } else {
+ if streamoffset == span_end {
+ span_end += int64(segment.Len)
+ } else {
+ stream_tokens = append(stream_tokens, fmt.Sprintf("%d:%d:%s", span_start, span_end-span_start, fout))
+ span_start = streamoffset
+ span_end = streamoffset + int64(segment.Len)
+ }
+ }
+ }
+
+ if span_start != -1 {
+ stream_tokens = append(stream_tokens, fmt.Sprintf("%d:%d:%s", span_start, span_end-span_start, fout))
+ }
+
+ if len(stream[streamfile]) == 0 {
+ stream_tokens = append(stream_tokens, fmt.Sprintf("0:0:%s", fout))
+ }
+ }
+
+ return strings.Join(stream_tokens, " ") + "\n"
+}
+
+func (m segmentedManifest) manifestTextForPath(srcpath, relocate string) string {
+ srcpath = fixStreamName(srcpath)
+
+ var suffix string
+ if strings.HasSuffix(relocate, "/") {
+ suffix = "/"
+ }
+ relocate = fixStreamName(relocate) + suffix
+
+ streamname, filename := splitPath(srcpath)
+
+ if stream, ok := m[streamname]; ok {
+ // check if it refers to a single file in a stream
+ filesegs, okfile := stream[filename]
+ if okfile {
+ newstream := make(segmentedStream)
+ relocate_stream, relocate_filename := splitPath(relocate)
+ if relocate_filename == "" {
+ relocate_filename = filename
+ }
+ newstream[relocate_filename] = filesegs
+ return newstream.normalizedText(relocate_stream)
+ }
+ }
+
+ // Going to extract multiple streams
+ prefix := srcpath + "/"
+
+ if strings.HasSuffix(relocate, "/") {
+ relocate = relocate[0 : len(relocate)-1]
+ }
+
+ var sortedstreams []string
+ for k, _ := range m {
+ sortedstreams = append(sortedstreams, k)
+ }
+ sort.Strings(sortedstreams)
+
+ manifest := ""
+ for _, k := range sortedstreams {
+ if strings.HasPrefix(k, prefix) || k == srcpath {
+ manifest += m[k].normalizedText(relocate + k[len(srcpath):])
+ }
+ }
+ return manifest
+}
+
+// Extract extracts some or all of the manifest and returns the extracted
+// portion as a normalized manifest. This is a swiss army knife function that
+// can be several ways:
+//
+// If 'srcpath' and 'relocate' are '.' it simply returns an equivalent manifest
+// in normalized form.
+//
+// Extract(".", ".") // return entire normalized manfest text
+//
+// If 'srcpath' points to a single file, it will return manifest text for just that file.
+// The value of "relocate" is can be used to rename the file or set the file stream.
+//
+// Extract("./foo", ".") // extract file "foo" and put it in stream "."
+// Extract("./foo", "./bar") // extract file "foo", rename it to "bar" in stream "."
+// Extract("./foo", "./bar/") // extract file "foo", rename it to "./bar/foo"
+// Extract("./foo", "./bar/baz") // extract file "foo", rename it to "./bar/baz")
+//
+// Otherwise it will return the manifest text for all streams with the prefix in "srcpath" and place
+// them under the path in "relocate".
+//
+// Extract("./stream", ".") // extract "./stream" to "." and "./stream/subdir" to "./subdir")
+// Extract("./stream", "./bar") // extract "./stream" to "./bar" and "./stream/subdir" to "./bar/subdir")
+func (m Manifest) Extract(srcpath, relocate string) (ret Manifest) {
+ segmented, err := m.segment()
+ if err != nil {
+ ret.Err = err
+ return
+ }
+ ret.Text = segmented.manifestTextForPath(srcpath, relocate)
+ return
+}
+
func (m *Manifest) StreamIter() <-chan ManifestStream {
ch := make(chan ManifestStream)
go func(input string) {
}
func (m *Manifest) FileSegmentIterByName(filepath string) <-chan *FileSegment {
- ch := make(chan *FileSegment)
+ ch := make(chan *FileSegment, 64)
+ filepath = fixStreamName(filepath)
go func() {
for stream := range m.StreamIter() {
- if !strings.HasPrefix("./"+filepath, stream.StreamName+"/") {
+ if !strings.HasPrefix(filepath, stream.StreamName+"/") {
continue
}
stream.sendFileSegmentIterByName(filepath, ch)
package manifest
import (
+ "fmt"
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
+ "git.curoverse.com/arvados.git/sdk/go/blockdigest"
"io/ioutil"
"reflect"
"regexp"
"runtime"
"testing"
-
- "git.curoverse.com/arvados.git/sdk/go/arvadostest"
- "git.curoverse.com/arvados.git/sdk/go/blockdigest"
)
func getStackTrace() string {
firstStream,
ManifestStream{StreamName: ".",
Blocks: []string{"b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c"},
- FileStreamSegments: []FileStreamSegment{{0, 15893477, "chr10_band0_s0_e3000000.fj"}}})
+ FileStreamSegments: []FileStreamSegment{{0, 15693477, "chr10_band0_s0_e3000000.fj"}}})
received, ok := <-streamIter
if ok {
}
}
}
+
+func TestNormalizeManifest(t *testing.T) {
+ m1 := Manifest{Text: `. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+`}
+ expectEqual(t, m1.Extract(".", ".").Text,
+ `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt
+`)
+
+ m2 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+`}
+ expectEqual(t, m2.Extract(".", ".").Text, m2.Text)
+
+ m3 := Manifest{Text: `. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt
+. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt
+. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt
+`}
+ expectEqual(t, m3.Extract(".", ".").Text, `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt
+`)
+ expectEqual(t, m3.Extract("/md5sum.txt", "/wiggle.txt").Text, `. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:wiggle.txt
+`)
+
+ m4 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`}
+
+ expectEqual(t, m4.Extract(".", ".").Text,
+ `./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+`)
+
+ expectEqual(t, m4.Extract("./foo", ".").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
+ expectEqual(t, m4.Extract("./foo", "./baz").Text, "./baz 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
+ expectEqual(t, m4.Extract("./foo/bar", ".").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
+ expectEqual(t, m4.Extract("./foo/bar", "./baz").Text, ". 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:baz 67108864:3:baz\n")
+ expectEqual(t, m4.Extract("./foo/bar", "./quux/").Text, "./quux 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar\n")
+ expectEqual(t, m4.Extract("./foo/bar", "./quux/baz").Text, "./quux 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:baz 67108864:3:baz\n")
+ expectEqual(t, m4.Extract(".", ".").Text, `./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+`)
+ expectEqual(t, m4.Extract(".", "./zip").Text, `./zip/foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar
+./zip/zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+`)
+
+ expectEqual(t, m4.Extract("foo/.//bar/../../zzz/", "/waz/").Text, `./waz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+`)
+
+ m5 := Manifest{Text: `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar
+`}
+ expectEqual(t, m5.Extract(".", ".").Text,
+ `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+`)
+
+ m8 := Manifest{Text: `./a\040b\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\040world.txt
+`}
+ expectEqual(t, m8.Extract(".", ".").Text, m8.Text)
+
+ m9 := Manifest{Text: ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:10:one 20:10:two 10:10:one 30:10:two\n"}
+ expectEqual(t, m9.Extract("", "").Text, ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:20:one 20:20:two\n")
+
+ m10 := Manifest{Text: ". acbd18db4cc2f85cedef654fccc4a4d8+40 0:10:one 20:10:two 10:10:one 30:10:two\n"}
+ expectEqual(t, m10.Extract("./two", "./three").Text, ". acbd18db4cc2f85cedef654fccc4a4d8+40 20:20:three\n")
+
+ m11 := Manifest{Text: arvadostest.PathologicalManifest}
+ expectEqual(t, m11.Extract(".", ".").Text, `. acbd18db4cc2f85cedef654fccc4a4d8+3 37b51d194a7513e45b56f6524f2d51f2+3 73feffa4b7f6bb68e44cf984c85f6e88+3+Z+K@xyzzy 0:1:f 1:4:ooba 5:1:r 5:4:rbaz 0:0:zero@0 0:0:zero@1 0:0:zero@4 0:0:zero@9
+./foo acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo 0:3:foo 0:0:zero
+./foo\040bar acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:baz 0:3:baz\040waz
+./overlapReverse acbd18db4cc2f85cedef654fccc4a4d8+3 2:1:o 2:1:ofoo 0:3:ofoo 1:2:oo
+./segmented acbd18db4cc2f85cedef654fccc4a4d8+3 37b51d194a7513e45b56f6524f2d51f2+3 0:1:frob 5:1:frob 1:1:frob 3:1:frob 1:2:oof 0:1:oof
+`)
+
+ m12 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz
+./foo/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`}
+
+ expectEqual(t, m12.Extract("./foo", ".").Text, `. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+./baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`)
+ expectEqual(t, m12.Extract("./foo", "./blub").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`)
+ expectEqual(t, m12.Extract("./foo", "./blub/").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`)
+ expectEqual(t, m12.Extract("./foo/", "./blub/").Text, `./blub 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+./blub/baz 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar
+`)
+
+ m13 := Manifest{Text: `foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3:bar
+`}
+
+ expectEqual(t, m13.Extract(".", ".").Text, ``)
+ expectEqual(t, m13.Extract(".", ".").Err.Error(), "Invalid stream name: foo")
+
+ m14 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 67108863:3:bar
+`}
+
+ expectEqual(t, m14.Extract(".", ".").Text, ``)
+ expectEqual(t, m14.Extract(".", ".").Err.Error(), "File segment 67108863:3:bar extends past end of stream 67108864")
+
+ m15 := Manifest{Text: `./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:3bar
+`}
+
+ expectEqual(t, m15.Extract(".", ".").Text, ``)
+ expectEqual(t, m15.Extract(".", ".").Err.Error(), "Invalid file token: 0:3bar")
+}
+
+func TestFirstBlock(t *testing.T) {
+ fmt.Println("ZZZ")
+ expectEqual(t, firstBlock([]uint64{1, 2, 3, 4}, 3), 2)
+ expectEqual(t, firstBlock([]uint64{1, 2, 3, 4, 5, 6}, 4), 3)
+}
-. b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c 109cd35b4d3f83266b63fb46c6943454+6770629+Ed0c0561b669237162996223b813b811d248ff9b0@5441920c 1455890e7b56831edff40738856e4194+15962669+Ec298b770d14205b5185d0e2b016ddd940c745446@5441920c 8c87f1c69c6f302c8c05e7d0e740d233+16342794+Ec432f4c24e63b840c1f12976b9edf396d70b8f67@5441920c 451cfce8c67bf92b67b5c6190d45d4f5+5067634+E406821d6ceb1d16ec638e66b7603c69f3482d895@5441920c f963d174978dc966910be6240e8602c7+4264756+E00241238e18635fdb583dd0c6d6561b672996467@5441920c 33be2d8cdd100eec6e842f644556d031+16665404+E6c773004b8296523014b9d23ed066ec72387485e@5441920c 6db13c2df6342b52d72df469c065b675+13536792+E6011e6057857f68d9b1b486571f239614b0707be@5441920c fb7ccc93e86187c519f6716c26474cb3+13714429+Ec4677bfcbe8689621d1b2d4f1bdce5b52f379f98@5441920c 972f24d216684646dfb9e266b7166f63+44743112+E1706fe89133bcd3625cc88de1035681c2d179770@5441920c 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13278407184:22764188:chr8_band30_s106200000_e110500000.fj 13301171372:8501850:chr8_band31_s110500000_e112100000.fj 13309673222:30459907:chr8_band32_s112100000_e117700000.fj 13340133129:7937153:chr8_band33_s117700000_e119200000.fj 13348070282:17300095:chr8_band34_s119200000_e122500000.fj 13365370377:25178211:chr8_band35_s122500000_e127300000.fj 13390548588:22053170:chr8_band36_s127300000_e131500000.fj 13412601758:26170716:chr8_band37_s131500000_e136400000.fj 13438772474:18915984:chr8_band38_s136400000_e139900000.fj 13457688458:33011109:chr8_band39_s139900000_e146364022.fj 13490699567:34615593:chr8_band3_s12700000_e19000000.fj 13525315160:22721686:chr8_band4_s19000000_e23300000.fj 13548036846:21858716:chr8_band5_s23300000_e27400000.fj 13569895562:7279298:chr8_band6_s27400000_e28800000.fj 13577174860:40036264:chr8_band7_s28800000_e36500000.fj 13617211124:9223086:chr8_band8_s36500000_e38300000.fj 13626434210:7285487:chr8_band9_s38300000_e39700000.fj 13633719697:11189873:chr9_band0_s0_e2200000.fj 13644909570:15398551:chr9_band10_s33200000_e36300000.fj 13660308121:10859291:chr9_band11_s36300000_e38400000.fj 13671167412:8098913:chr9_band12_s38400000_e41000000.fj 13679266325:7680539:chr9_band13_s41000000_e43600000.fj 13686946864:11204600:chr9_band14_s43600000_e47300000.fj 13698151464:54388:chr9_band15_s47300000_e49000000.fj 13698205852:3468752:chr9_band16_s49000000_e50700000.fj 13701674604:31370255:chr9_band17_s50700000_e65900000.fj 13733044859:8507254:chr9_band18_s65900000_e68700000.fj 13741552113:13175993:chr9_band19_s68700000_e72200000.fj 13754728106:12788834:chr9_band1_s2200000_e4600000.fj 13767516940:9460838:chr9_band20_s72200000_e74000000.fj 13776977778:27323515:chr9_band21_s74000000_e79200000.fj 13804301293:9840418:chr9_band22_s79200000_e81100000.fj 13814141711:15804284:chr9_band23_s81100000_e84100000.fj 13829945995:14087052:chr9_band24_s84100000_e86900000.fj 13844033047:17922209:chr9_band25_s86900000_e90400000.fj 13861955256:6951532:chr9_band26_s90400000_e91800000.fj 13868906788:10179374:chr9_band27_s91800000_e93900000.fj 13879086162:13769787:chr9_band28_s93900000_e96600000.fj 13892855949:13598284:chr9_band29_s96600000_e99300000.fj 13906454233:22891146:chr9_band2_s4600000_e9000000.fj 13929345379:16625559:chr9_band30_s99300000_e102600000.fj 13945970938:29592637:chr9_band31_s102600000_e108200000.fj 13975563575:16101070:chr9_band32_s108200000_e111300000.fj 13991664645:18810443:chr9_band33_s111300000_e114900000.fj 14010475088:14696084:chr9_band34_s114900000_e117700000.fj 14025171172:25738558:chr9_band35_s117700000_e122500000.fj 14050909730:17151669:chr9_band36_s122500000_e125800000.fj 14068061399:23282243:chr9_band37_s125800000_e130300000.fj 14091343642:15933520:chr9_band38_s130300000_e133500000.fj 14107277162:2539339:chr9_band39_s133500000_e134000000.fj 14109816501:28353605:chr9_band3_s9000000_e14200000.fj 14138170106:9895904:chr9_band40_s134000000_e135900000.fj 14148066010:7847526:chr9_band41_s135900000_e137400000.fj 14155913536:19420968:chr9_band42_s137400000_e141213431.fj 14175334504:12634378:chr9_band4_s14200000_e16600000.fj 14187968882:10157396:chr9_band5_s16600000_e18500000.fj 14198126278:7156443:chr9_band6_s18500000_e19900000.fj 14205282721:29952199:chr9_band7_s19900000_e25600000.fj 14235234920:12640911:chr9_band8_s25600000_e28000000.fj 14247875831:28005247:chr9_band9_s28000000_e33200000.fj 14275881078:61284:chrM_band0_s0_e16571.fj 14275942362:14544713:chrX_band0_s0_e4300000.fj 14290487075:24455427:chrX_band10_s37600000_e42400000.fj 14314942502:19979357:chrX_band11_s42400000_e46400000.fj 14334921859:15780934:chrX_band12_s46400000_e49800000.fj 14350702793:22068346:chrX_band13_s49800000_e54800000.fj 14372771139:15483950:chrX_band14_s54800000_e58100000.fj 14388255089:2245852:chrX_band15_s58100000_e60600000.fj 14390500941:8206011:chrX_band16_s60600000_e63000000.fj 14398706952:7456077:chrX_band17_s63000000_e64600000.fj 14406163029:15544112:chrX_band18_s64600000_e67800000.fj 14421707141:19435511:chrX_band19_s67800000_e71800000.fj 14441142652:8840055:chrX_band1_s4300000_e6000000.fj 14449982707:9325419:chrX_band20_s71800000_e73900000.fj 14459308126:9811498:chrX_band21_s73900000_e76000000.fj 14469119624:42415433:chrX_band22_s76000000_e84600000.fj 14511535057:8048575:chrX_band23_s84600000_e86200000.fj 14519583632:22647045:chrX_band24_s86200000_e91800000.fj 14542230677:7507452:chrX_band25_s91800000_e93500000.fj 14549738129:24532176:chrX_band26_s93500000_e98300000.fj 14574270305:20702445:chrX_band27_s98300000_e102600000.fj 14594972750:5393310:chrX_band28_s102600000_e103700000.fj 14600366060:25038697:chrX_band29_s103700000_e108700000.fj 14625404757:17528792:chrX_band2_s6000000_e9500000.fj 14642933549:39123936:chrX_band30_s108700000_e116500000.fj 14682057485:21530282:chrX_band31_s116500000_e120900000.fj 14703587767:39763257:chrX_band32_s120900000_e128700000.fj 14743351024:8637631:chrX_band33_s128700000_e130400000.fj 14751988655:16073438:chrX_band34_s130400000_e133600000.fj 14768062093:21768801:chrX_band35_s133600000_e138000000.fj 14789830894:11318859:chrX_band36_s138000000_e140300000.fj 14801149753:8828151:chrX_band37_s140300000_e142100000.fj
-. b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c 0:15893477:chr10_band0_s0_e3000000.fj
-
-
-
-
-
+. b746e3d2104645f2f64cd3cc69dd895d+15693477+E2866e643690156651c03d876e638e674dcd79475@5441920c 0:15693477:chr10_band0_s0_e3000000.fj
def portable_data_hash(self):
"""Get the portable data hash for this collection's manifest."""
- stripped = self.portable_manifest_text()
- return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+ if self._manifest_locator and self.committed():
+ # If the collection is already saved on the API server, and it's committed
+ # then return API server's PDH response.
+ return self._portable_data_hash
+ else:
+ stripped = self.portable_manifest_text()
+ return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
@synchronized
def subscribe(self, callback):
self.num_retries = num_retries if num_retries is not None else 0
self._manifest_locator = None
self._manifest_text = None
+ self._portable_data_hash = None
self._api_response = None
self._past_versions = set()
).execute(
num_retries=num_retries))
self._manifest_text = self._api_response["manifest_text"]
+ self._portable_data_hash = self._api_response["portable_data_hash"]
self.set_committed()
return self._manifest_text
text = self._api_response["manifest_text"]
self._manifest_locator = self._api_response["uuid"]
+ self._portable_data_hash = self._api_response["portable_data_hash"]
self._manifest_text = text
self.set_committed()
return self._my_collection().manifest_locator()
def portable_data_hash(self):
- return self._my_collection().portable_data_hash()
+ pdh = self._my_collection().portable_data_hash()
+ m = self._my_collection().stripped_manifest()
+ local_pdh = hashlib.md5(m).hexdigest() + '+' + str(len(m))
+ if pdh != local_pdh:
+ logger.warning("\n".join([
+ "arv-put: API server provided PDH differs from local manifest.",
+ " This should not happen; showing API server version."]))
+ return pdh
def manifest_text(self, stream_name=".", strip=False, normalize=False):
return self._my_collection().manifest_text(stream_name, strip, normalize)
"manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
+ "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
+ "portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
+ "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n",
+ "portable_data_hash":"c5c3af76565c8efb6a806546bcf073f3+88"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
"manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"})
+ "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
+ "portable_data_hash":"9132ca8e3f671c76103a38f5bc24328c+108"})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
"manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"})
+ "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n",
+ "portable_data_hash":"217665c6b713e1b78dfba7ebd42344db+156"})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"})
with Collection(api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "w+")
self.assertEqual(writer.size(), 0)
"manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
+ "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "portable_data_hash":"1b02aaa62528d28a5be41651cbb9d7c7+59"})
with Collection(api_client=api, keep_client=keep) as c:
self.assertIsNone(c.api_response())
writer = c.open("foo/bar/count.txt", "w+")
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"})
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
+ "portable_data_hash":"7a461a8c58601798f690f8b368ac4423+51"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "w+")
"manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
"replication_desired":None},
{"uuid":"zzzzz-4zz18-mockcollection0",
- "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"})
+ "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
+ "portable_data_hash":"71e7bb6c00d31fc2b4364199fd97be08+102"})
with Collection(api_client=api, keep_client=keep) as c:
w1 = c.open("count1.txt", "w")
w2 = c.open("count2.txt", "w")
def cancel
reload_object_before_update
- @object.update_attributes! state: Job::Cancelled
+ @object.cancel cascade: params[:cascade]
show
end
accept_attribute_as_json :components, Hash
accept_attribute_as_json :properties, Hash
accept_attribute_as_json :components_summary, Hash
+
+ def cancel
+ reload_object_before_update
+ @object.cancel cascade: params[:cascade]
+ show
+ end
end
end
end
+ def cancel(cascade: false, need_transaction: true)
+ if need_transaction
+ ActiveRecord::Base.transaction do
+ cancel(cascade: cascade, need_transaction: false)
+ end
+ return
+ end
+
+ if self.state.in?([Queued, Running])
+ self.state = Cancelled
+ self.save!
+ elsif self.state != Cancelled
+ raise InvalidStateTransitionError
+ end
+
+ return if !cascade
+
+ # cancel all children; they could be jobs or pipeline instances
+ children = self.components.andand.collect{|_, u| u}.compact
+
+ return if children.empty?
+
+ # cancel any child jobs
+ Job.where(uuid: children, state: [Queued, Running]).each do |job|
+ job.cancel(cascade: cascade, need_transaction: false)
+ end
+
+ # cancel any child pipelines
+ PipelineInstance.where(uuid: children, state: [PipelineInstance::RunningOnServer, PipelineInstance::RunningOnClient]).each do |pi|
+ pi.cancel(cascade: cascade, need_transaction: false)
+ end
+ end
+
protected
def self.sorted_hash_digest h
self.where("state = 'RunningOnServer'")
end
+ def cancel(cascade: false, need_transaction: true)
+ if need_transaction
+ ActiveRecord::Base.transaction do
+ cancel(cascade: cascade, need_transaction: false)
+ end
+ return
+ end
+
+ if self.state.in?([RunningOnServer, RunningOnClient])
+ self.state = Paused
+ self.save!
+ elsif self.state != Paused
+ raise InvalidStateTransitionError
+ end
+
+ return if !cascade
+
+ # cancel all child jobs
+ children = self.components.andand.collect{|_, c| c['job']}.compact.collect{|j| j['uuid']}.compact
+
+ return if children.empty?
+
+ Job.where(uuid: children, state: [Job::Queued, Job::Running]).each do |job|
+ job.cancel(cascade: cascade, need_transaction: false)
+ end
+ end
+
protected
def bootstrap_components
if pipeline_template and (!components or components.empty?)
resources :nodes do
post 'ping', on: :member
end
- resources :pipeline_instances
+ resources :pipeline_instances do
+ post 'cancel', on: :member
+ end
resources :pipeline_templates
resources :workflows
resources :repositories do
component1: zzzzz-8i9sb-jyq01m7in1jlofj
component2: zzzzz-d1hrv-partdonepipelin
script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+
+# This main level job is in running state with one job and one pipeline instance components
+running_job_with_components_at_level_1:
+ uuid: zzzzz-8i9sb-jobcomponentsl1
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+ components:
+ component1: zzzzz-8i9sb-jobcomponentsl2
+ component2: zzzzz-d1hrv-picomponentsl02
+
+# This running job, a child of level_1, has one child component
+running_job_with_components_at_level_2:
+ uuid: zzzzz-8i9sb-jobcomponentsl2
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+ components:
+ component1: zzzzz-8i9sb-job1atlevel3noc
+
+# The below two running jobs, children of level_2, have no child components
+running_job_1_with_components_at_level_3:
+ uuid: zzzzz-8i9sb-job1atlevel3noc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+
+running_job_2_with_components_at_level_3:
+ uuid: zzzzz-8i9sb-job2atlevel3noc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+
+# The two jobs below are so confused, they have circular relationship
+running_job_1_with_circular_component_relationship:
+ uuid: zzzzz-8i9sb-job1withcirculr
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+ components:
+ component1: zzzzz-8i9sb-job2withcirculr
+
+running_job_2_with_circular_component_relationship:
+ uuid: zzzzz-8i9sb-job2withcirculr
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ cancelled_at: ~
+ cancelled_by_user_uuid: ~
+ cancelled_by_client_uuid: ~
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ finished_at: ~
+ repository: active/foo
+ script: hash
+ script_version: 1de84a854e2b440dc53bf42f8548afa4c17da332
+ script_parameters_digest: 99914b932bd37a50b983c5e7c90ae93b
+ running: true
+ success: ~
+ output: ~
+ priority: 0
+ log: ~
+ is_locked_by_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ tasks_summary:
+ failed: 0
+ todo: 3
+ running: 1
+ done: 1
+ runtime_constraints: {}
+ state: Running
+ components:
+ component1: zzzzz-8i9sb-job1withcirculr
uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
log: zzzzz-4zz18-op4e2lbej01tcvu
+# This pipeline is a child of another running job and has it's own running children
+job_child_pipeline_with_components_at_level_2:
+ state: RunningOnServer
+ uuid: zzzzz-d1hrv-picomponentsl02
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ components:
+ foo:
+ script: foo
+ script_version: master
+ script_parameters: {}
+ job:
+ uuid: zzzzz-8i9sb-job1atlevel3noc
+ script_version: master
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ state: Running
+ tasks_summary:
+ failed: 0
+ todo: 0
+ running: 1
+ done: 1
+ bar:
+ script: bar
+ script_version: master
+ script_parameters: {}
+ job:
+ uuid: zzzzz-8i9sb-job2atlevel3noc
+ script_version: master
+ created_at: <%= 12.hour.ago.to_s(:db) %>
+ started_at: <%= 12.hour.ago.to_s(:db) %>
+ state: Running
+ tasks_summary:
+ failed: 0
+ todo: 1
+ running: 2
+ done: 3
+
# Test Helper trims the rest of the file
# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
assert_equal({}, assigns(:object).components)
end
+ [
+ true,
+ false
+ ].each do |cascade|
+ test "cancel a pipeline instance with cascade=#{cascade}" do
+ authorize_with :active
+ pi_uuid = pipeline_instances(:job_child_pipeline_with_components_at_level_2).uuid
+
+ post :cancel, {id: pi_uuid, cascade: cascade}
+ assert_response :success
+
+ pi = PipelineInstance.where(uuid: pi_uuid).first
+ assert_equal "Paused", pi.state
+
+ children = Job.where(uuid: ['zzzzz-8i9sb-job1atlevel3noc', 'zzzzz-8i9sb-job2atlevel3noc'])
+ children.each do |child|
+ assert_equal ("Cancelled" == child.state), cascade
+ end
+ end
+ end
end
update_all(output: 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+1')
assert_nil Job.find_reusable(example_attrs, {}, [], [users(:active)])
end
+
+ [
+ true,
+ false,
+ ].each do |cascade|
+ test "cancel job with cascade #{cascade}" do
+ job = Job.find_by_uuid jobs(:running_job_with_components_at_level_1).uuid
+ job.cancel cascade: cascade
+ assert_equal Job::Cancelled, job.state
+
+ descendents = ['zzzzz-8i9sb-jobcomponentsl2',
+ 'zzzzz-d1hrv-picomponentsl02',
+ 'zzzzz-8i9sb-job1atlevel3noc',
+ 'zzzzz-8i9sb-job2atlevel3noc']
+
+ jobs = Job.where(uuid: descendents)
+ jobs.each do |j|
+ assert_equal ('Cancelled' == j.state), cascade
+ end
+
+ pipelines = PipelineInstance.where(uuid: descendents)
+ pipelines.each do |pi|
+ assert_equal ('Paused' == pi.state), cascade
+ end
+ end
+ end
+
+ test 'cancelling a completed job raises error' do
+ job = Job.find_by_uuid jobs(:job_with_latest_version).uuid
+ assert job
+ assert_equal 'Complete', job.state
+
+ assert_raises(ArvadosModel::InvalidStateTransitionError) do
+ job.cancel
+ end
+ end
+
+ test 'cancelling a job with circular relationship with another does not result in an infinite loop' do
+ job = Job.find_by_uuid jobs(:running_job_2_with_circular_component_relationship).uuid
+
+ job.cancel cascade: true
+
+ assert_equal Job::Cancelled, job.state
+
+ child = Job.find_by_uuid job.components.collect{|_, uuid| uuid}[0]
+ assert_equal Job::Cancelled, child.state
+ end
end
// Dispatcher service for Crunch that runs containers locally.
import (
+ "context"
"flag"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/dispatch"
"log"
"os"
"os/exec"
"sync"
"syscall"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/dispatch"
)
func main() {
PollPeriod: time.Duration(*pollInterval) * time.Second,
}
- err = dispatcher.Run()
+ ctx, cancel := context.WithCancel(context.Background())
+ err = dispatcher.Run(ctx)
if err != nil {
return err
}
log.Printf("Received %s, shutting down", sig)
signal.Stop(c)
- dispatcher.Stop()
+ cancel()
runningCmdsMutex.Lock()
// Finished dispatching; interrupt any crunch jobs that are still running
// crunch-run terminates, mark the container as Cancelled.
func run(dispatcher *dispatch.Dispatcher,
container arvados.Container,
- status chan arvados.Container) {
+ status <-chan arvados.Container) {
uuid := container.UUID
if err != nil {
log.Printf("Error getting final container state: %v", err)
}
- if container.LockedByUUID == dispatcher.Auth.UUID &&
- (container.State == dispatch.Locked || container.State == dispatch.Running) {
+ if container.State == dispatch.Locked || container.State == dispatch.Running {
log.Printf("After %s process termination, container state for %v is %q. Updating it to %q",
*crunchRunCommand, container.State, uuid, dispatch.Cancelled)
dispatcher.UpdateState(uuid, dispatch.Cancelled)
import (
"bytes"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/arvadostest"
- "git.curoverse.com/arvados.git/sdk/go/dispatch"
- . "gopkg.in/check.v1"
+ "context"
"io"
"log"
"net/http"
"strings"
"testing"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
+ "git.curoverse.com/arvados.git/sdk/go/dispatch"
+ . "gopkg.in/check.v1"
)
// Gocheck boilerplate
echo := "echo"
crunchRunCommand = &echo
+ ctx, cancel := context.WithCancel(context.Background())
dispatcher := dispatch.Dispatcher{
Arv: arv,
PollPeriod: time.Second,
- RunContainer: func(dispatcher *dispatch.Dispatcher,
- container arvados.Container,
- status chan arvados.Container) {
- run(dispatcher, container, status)
- dispatcher.Stop()
+ RunContainer: func(d *dispatch.Dispatcher, c arvados.Container, s <-chan arvados.Container) {
+ run(d, c, s)
+ cancel()
},
}
return cmd.Start()
}
- err = dispatcher.Run()
- c.Assert(err, IsNil)
+ err = dispatcher.Run(ctx)
+ c.Assert(err, Equals, context.Canceled)
// Wait for all running crunch jobs to complete / terminate
waitGroup.Wait()
apiStubResponses["/arvados/v1/containers/zzzzz-dz642-xxxxxxxxxxxxxx1"] =
arvadostest.StubResponse{500, string(`{}`)}
- testWithServerStub(c, apiStubResponses, "echo", "Error locking container zzzzz-dz642-xxxxxxxxxxxxxx1")
+ testWithServerStub(c, apiStubResponses, "echo", "error locking container zzzzz-dz642-xxxxxxxxxxxxxx1")
}
func (s *MockArvadosServerSuite) Test_ContainerStillInRunningAfterRun(c *C) {
*crunchRunCommand = crunchCmd
+ ctx, cancel := context.WithCancel(context.Background())
dispatcher := dispatch.Dispatcher{
Arv: arv,
PollPeriod: time.Duration(1) * time.Second,
- RunContainer: func(dispatcher *dispatch.Dispatcher,
- container arvados.Container,
- status chan arvados.Container) {
- run(dispatcher, container, status)
- dispatcher.Stop()
+ RunContainer: func(d *dispatch.Dispatcher, c arvados.Container, s <-chan arvados.Container) {
+ run(d, c, s)
+ cancel()
},
}
for i := 0; i < 80 && !strings.Contains(buf.String(), expected); i++ {
time.Sleep(100 * time.Millisecond)
}
- dispatcher.Stop()
+ cancel()
}()
- err := dispatcher.Run()
- c.Assert(err, IsNil)
+ err := dispatcher.Run(ctx)
+ c.Assert(err, Equals, context.Canceled)
// Wait for all running crunch jobs to complete / terminate
waitGroup.Wait()
import (
"bytes"
+ "context"
"flag"
"fmt"
"log"
var (
theConfig Config
- sqCheck SqueueChecker
+ sqCheck = &SqueueChecker{}
)
const defaultConfigPath = "/etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml"
}
arv.Retries = 25
- sqCheck = SqueueChecker{Period: time.Duration(theConfig.PollPeriod)}
+ sqCheck = &SqueueChecker{Period: time.Duration(theConfig.PollPeriod)}
defer sqCheck.Stop()
- dispatcher := dispatch.Dispatcher{
+ dispatcher := &dispatch.Dispatcher{
Arv: arv,
RunContainer: run,
PollPeriod: time.Duration(theConfig.PollPeriod),
log.Printf("Error notifying init daemon: %v", err)
}
- return dispatcher.Run()
+ return dispatcher.Run(context.Background())
}
// sbatchCmd
sbatchArgs = append(sbatchArgs, fmt.Sprintf("--job-name=%s", container.UUID))
sbatchArgs = append(sbatchArgs, fmt.Sprintf("--mem-per-cpu=%d", int(memPerCPU)))
sbatchArgs = append(sbatchArgs, fmt.Sprintf("--cpus-per-task=%d", container.RuntimeConstraints.VCPUs))
- if container.SchedulingParameters.Partitions != nil {
+ if len(container.SchedulingParameters.Partitions) > 0 {
sbatchArgs = append(sbatchArgs, fmt.Sprintf("--partition=%s", strings.Join(container.SchedulingParameters.Partitions, ",")))
}
var scancelCmd = scancelFunc
// Submit job to slurm using sbatch.
-func submit(dispatcher *dispatch.Dispatcher,
- container arvados.Container, crunchRunCommand []string) (submitErr error) {
- defer func() {
- // If we didn't get as far as submitting a slurm job,
- // unlock the container and return it to the queue.
- if submitErr == nil {
- // OK, no cleanup needed
- return
- }
- dispatcher.Unlock(container.UUID)
- }()
-
+func submit(dispatcher *dispatch.Dispatcher, container arvados.Container, crunchRunCommand []string) error {
cmd := sbatchCmd(container)
// Send a tiny script on stdin to execute the crunch-run
log.Printf("exec sbatch %+q", cmd.Args)
err := cmd.Run()
+
switch err.(type) {
case nil:
log.Printf("sbatch succeeded: %q", strings.TrimSpace(stdout.String()))
return nil
+
case *exec.ExitError:
- return fmt.Errorf("sbatch %+q failed: %v (stderr: %q)", cmd.Args, err, stderr)
+ dispatcher.Unlock(container.UUID)
+ return fmt.Errorf("sbatch %+q failed: %v (stderr: %q)", cmd.Args, err, stderr.Bytes())
+
default:
+ dispatcher.Unlock(container.UUID)
return fmt.Errorf("exec failed: %v", err)
}
}
-// If the container is marked as Locked, check if it is already in the slurm
-// queue. If not, submit it.
-//
-// If the container is marked as Running, check if it is in the slurm queue.
-// If not, mark it as Cancelled.
-func monitorSubmitOrCancel(dispatcher *dispatch.Dispatcher, container arvados.Container, monitorDone *bool) {
- submitted := false
- for !*monitorDone {
- if sqCheck.HasUUID(container.UUID) {
- // Found in the queue, so continue monitoring
- submitted = true
- } else if container.State == dispatch.Locked && !submitted {
- // Not in queue but in Locked state and we haven't
- // submitted it yet, so submit it.
-
- log.Printf("About to submit queued container %v", container.UUID)
-
- if err := submit(dispatcher, container, theConfig.CrunchRunCommand); err != nil {
- log.Printf("Error submitting container %s to slurm: %v",
- container.UUID, err)
- // maybe sbatch is broken, put it back to queued
- dispatcher.Unlock(container.UUID)
- }
- submitted = true
- } else {
- // Not in queue and we are not going to submit it.
- // Refresh the container state. If it is
- // Complete/Cancelled, do nothing, if it is Locked then
- // release it back to the Queue, if it is Running then
- // clean up the record.
-
- var con arvados.Container
- err := dispatcher.Arv.Get("containers", container.UUID, nil, &con)
- if err != nil {
- log.Printf("Error getting final container state: %v", err)
- }
+// Submit a container to the slurm queue (or resume monitoring if it's
+// already in the queue). Cancel the slurm job if the container's
+// priority changes to zero or its state indicates it's no longer
+// running.
+func run(disp *dispatch.Dispatcher, ctr arvados.Container, status <-chan arvados.Container) {
+ ctx, cancel := context.WithCancel(context.Background())
+ defer cancel()
+
+ if ctr.State == dispatch.Locked && !sqCheck.HasUUID(ctr.UUID) {
+ log.Printf("Submitting container %s to slurm", ctr.UUID)
+ if err := submit(disp, ctr, theConfig.CrunchRunCommand); err != nil {
+ log.Printf("Error submitting container %s to slurm: %s", ctr.UUID, err)
+ disp.Unlock(ctr.UUID)
+ return
+ }
+ }
- switch con.State {
- case dispatch.Locked:
- log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.",
- container.UUID, con.State, dispatch.Queued)
- dispatcher.Unlock(container.UUID)
+ log.Printf("Start monitoring container %s", ctr.UUID)
+ defer log.Printf("Done monitoring container %s", ctr.UUID)
+
+ // If the container disappears from the slurm queue, there is
+ // no point in waiting for further dispatch updates: just
+ // clean up and return.
+ go func(uuid string) {
+ for ctx.Err() == nil && sqCheck.HasUUID(uuid) {
+ }
+ cancel()
+ }(ctr.UUID)
+
+ for {
+ select {
+ case <-ctx.Done():
+ // Disappeared from squeue
+ if err := disp.Arv.Get("containers", ctr.UUID, nil, &ctr); err != nil {
+ log.Printf("Error getting final container state for %s: %s", ctr.UUID, err)
+ }
+ switch ctr.State {
case dispatch.Running:
- st := dispatch.Cancelled
- log.Printf("Container %s in state %v but missing from slurm queue, changing to %v.",
- container.UUID, con.State, st)
- dispatcher.UpdateState(container.UUID, st)
- default:
- // Container state is Queued, Complete or Cancelled so stop monitoring it.
- return
+ disp.UpdateState(ctr.UUID, dispatch.Cancelled)
+ case dispatch.Locked:
+ disp.Unlock(ctr.UUID)
+ }
+ return
+ case updated, ok := <-status:
+ if !ok {
+ log.Printf("Dispatcher says container %s is done: cancel slurm job", ctr.UUID)
+ scancel(ctr)
+ } else if updated.Priority == 0 {
+ log.Printf("Container %s has state %q, priority %d: cancel slurm job", ctr.UUID, updated.State, updated.Priority)
+ scancel(ctr)
}
}
}
}
-// Run or monitor a container.
-//
-// Monitor status updates. If the priority changes to zero, cancel the
-// container using scancel.
-func run(dispatcher *dispatch.Dispatcher,
- container arvados.Container,
- status chan arvados.Container) {
-
- log.Printf("Monitoring container %v started", container.UUID)
- defer log.Printf("Monitoring container %v finished", container.UUID)
-
- monitorDone := false
- go monitorSubmitOrCancel(dispatcher, container, &monitorDone)
-
- for container = range status {
- if container.Priority == 0 && (container.State == dispatch.Locked || container.State == dispatch.Running) {
- log.Printf("Canceling container %s", container.UUID)
- // Mutex between squeue sync and running sbatch or scancel.
- sqCheck.L.Lock()
- cmd := scancelCmd(container)
- msg, err := cmd.CombinedOutput()
- sqCheck.L.Unlock()
-
- if err != nil {
- log.Printf("Error stopping container %s with %v %v: %v %v", container.UUID, cmd.Path, cmd.Args, err, string(msg))
- if sqCheck.HasUUID(container.UUID) {
- log.Printf("Container %s is still in squeue after scancel.", container.UUID)
- continue
- }
- }
+func scancel(ctr arvados.Container) {
+ sqCheck.L.Lock()
+ cmd := scancelCmd(ctr)
+ msg, err := cmd.CombinedOutput()
+ sqCheck.L.Unlock()
- // Ignore errors; if necessary, we'll try again next time
- dispatcher.UpdateState(container.UUID, dispatch.Cancelled)
- }
+ if err != nil {
+ log.Printf("%q %q: %s %q", cmd.Path, cmd.Args, err, msg)
+ time.Sleep(time.Second)
+ } else if sqCheck.HasUUID(ctr.UUID) {
+ log.Printf("container %s is still in squeue after scancel", ctr.UUID)
+ time.Sleep(time.Second)
}
- monitorDone = true
}
func readConfig(dst interface{}, path string) error {
import (
"bytes"
+ "context"
"fmt"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/arvadostest"
- "git.curoverse.com/arvados.git/sdk/go/dispatch"
"io"
"io/ioutil"
"log"
"testing"
"time"
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
+ "git.curoverse.com/arvados.git/sdk/go/dispatch"
. "gopkg.in/check.v1"
)
}
func (s *TestSuite) TestIntegrationNormal(c *C) {
- container := s.integrationTest(c, func() *exec.Cmd { return exec.Command("echo", "zzzzz-dz642-queuedcontainer") },
+ done := false
+ container := s.integrationTest(c,
+ func() *exec.Cmd {
+ if done {
+ return exec.Command("true")
+ } else {
+ return exec.Command("echo", "zzzzz-dz642-queuedcontainer")
+ }
+ },
[]string(nil),
func(dispatcher *dispatch.Dispatcher, container arvados.Container) {
dispatcher.UpdateState(container.UUID, dispatch.Running)
time.Sleep(3 * time.Second)
dispatcher.UpdateState(container.UUID, dispatch.Complete)
+ done = true
})
c.Check(container.State, Equals, arvados.ContainerStateComplete)
}
func (s *TestSuite) TestIntegrationCancel(c *C) {
-
- // Override sbatchCmd
+ var cmd *exec.Cmd
var scancelCmdLine []string
defer func(orig func(arvados.Container) *exec.Cmd) {
scancelCmd = orig
}(scancelCmd)
+ attempt := 0
scancelCmd = func(container arvados.Container) *exec.Cmd {
- scancelCmdLine = scancelFunc(container).Args
- return exec.Command("echo")
+ if attempt++; attempt == 1 {
+ return exec.Command("false")
+ } else {
+ scancelCmdLine = scancelFunc(container).Args
+ cmd = exec.Command("echo")
+ return cmd
+ }
}
container := s.integrationTest(c,
- func() *exec.Cmd { return exec.Command("echo", "zzzzz-dz642-queuedcontainer") },
+ func() *exec.Cmd {
+ if cmd != nil && cmd.ProcessState != nil {
+ return exec.Command("true")
+ } else {
+ return exec.Command("echo", "zzzzz-dz642-queuedcontainer")
+ }
+ },
[]string(nil),
func(dispatcher *dispatch.Dispatcher, container arvados.Container) {
dispatcher.UpdateState(container.UUID, dispatch.Running)
theConfig.CrunchRunCommand = []string{"echo"}
+ ctx, cancel := context.WithCancel(context.Background())
dispatcher := dispatch.Dispatcher{
Arv: arv,
PollPeriod: time.Duration(1) * time.Second,
- RunContainer: func(dispatcher *dispatch.Dispatcher,
- container arvados.Container,
- status chan arvados.Container) {
- go runContainer(dispatcher, container)
- run(dispatcher, container, status)
- dispatcher.Stop()
+ RunContainer: func(disp *dispatch.Dispatcher, ctr arvados.Container, status <-chan arvados.Container) {
+ go runContainer(disp, ctr)
+ run(disp, ctr, status)
+ cancel()
},
}
- sqCheck = SqueueChecker{Period: 500 * time.Millisecond}
+ sqCheck = &SqueueChecker{Period: 500 * time.Millisecond}
- err = dispatcher.Run()
- c.Assert(err, IsNil)
+ err = dispatcher.Run(ctx)
+ c.Assert(err, Equals, context.Canceled)
sqCheck.Stop()
theConfig.CrunchRunCommand = []string{crunchCmd}
+ ctx, cancel := context.WithCancel(context.Background())
dispatcher := dispatch.Dispatcher{
Arv: arv,
PollPeriod: time.Duration(1) * time.Second,
- RunContainer: func(dispatcher *dispatch.Dispatcher,
- container arvados.Container,
- status chan arvados.Container) {
+ RunContainer: func(disp *dispatch.Dispatcher, ctr arvados.Container, status <-chan arvados.Container) {
go func() {
time.Sleep(1 * time.Second)
- dispatcher.UpdateState(container.UUID, dispatch.Running)
- dispatcher.UpdateState(container.UUID, dispatch.Complete)
+ disp.UpdateState(ctr.UUID, dispatch.Running)
+ disp.UpdateState(ctr.UUID, dispatch.Complete)
}()
- run(dispatcher, container, status)
- dispatcher.Stop()
+ run(disp, ctr, status)
+ cancel()
},
}
for i := 0; i < 80 && !strings.Contains(buf.String(), expected); i++ {
time.Sleep(100 * time.Millisecond)
}
- dispatcher.Stop()
+ cancel()
}()
- err := dispatcher.Run()
- c.Assert(err, IsNil)
+ err := dispatcher.Run(ctx)
+ c.Assert(err, Equals, context.Canceled)
c.Check(buf.String(), Matches, `(?ms).*`+expected+`.*`)
}
"os/signal"
"path"
"path/filepath"
+ "sort"
"strings"
"sync"
"syscall"
return c, nil
}
+func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
+ if runner.ArvMountPoint == "" {
+ runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
+ }
+ return
+}
+
func (runner *ContainerRunner) SetupMounts() (err error) {
- runner.ArvMountPoint, err = runner.MkTempDir("", "keep")
+ err = runner.SetupArvMountPoint("keep")
if err != nil {
return fmt.Errorf("While creating keep mount temp dir: %v", err)
}
runner.Binds = nil
needCertMount := true
- for bind, mnt := range runner.Container.Mounts {
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
if bind == "stdout" {
// Is it a "file" mount kind?
if mnt.Kind != "file" {
return fmt.Errorf("Stdout path does not start with OutputPath: %s, %s", mnt.Path, prefix)
}
}
+
if bind == "/etc/arvados/ca-certificates.crt" {
needCertMount = false
}
+ if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
+ if mnt.Kind != "collection" {
+ return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind)
+ }
+ }
+
switch {
case mnt.Kind == "collection":
var src string
if mnt.Writable {
return fmt.Errorf("Can never write to a collection specified by portable data hash")
}
+ idx := strings.Index(mnt.PortableDataHash, "/")
+ if idx > 0 {
+ mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
+ mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
+ runner.Container.Mounts[bind] = mnt
+ }
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
+ if mnt.Path != "" && mnt.Path != "." {
+ if strings.HasPrefix(mnt.Path, "./") {
+ mnt.Path = mnt.Path[2:]
+ } else if strings.HasPrefix(mnt.Path, "/") {
+ mnt.Path = mnt.Path[1:]
+ }
+ src += "/" + mnt.Path
+ }
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp")
if mnt.Writable {
if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
+ } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
+ return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind)
}
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
} else {
manifestText = rec.ManifestText
}
+ // Pre-populate output from the configured mount points
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
+
+ bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
+
+ if bindSuffix == bind || len(bindSuffix) <= 0 {
+ // either does not start with OutputPath or is OutputPath itself
+ continue
+ }
+
+ if mnt.ExcludeFromOutput == true {
+ continue
+ }
+
+ // append to manifest_text
+ m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
+ if err != nil {
+ return err
+ }
+
+ manifestText = manifestText + m
+ }
+
+ // Save output
var response arvados.Collection
+ manifest := manifest.Manifest{Text: manifestText}
+ manifestText = manifest.Extract(".", ".").Text
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
"collection": arvadosclient.Dict{
return nil
}
+var outputCollections = make(map[string]arvados.Collection)
+
+// Fetch the collection for the mnt.PortableDataHash
+// Return the manifest_text fragment corresponding to the specified mnt.Path
+// after making any required updates.
+// Ex:
+// If mnt.Path is not specified,
+// return the entire manifest_text after replacing any "." with bindSuffix
+// If mnt.Path corresponds to one stream,
+// return the manifest_text for that stream after replacing that stream name with bindSuffix
+// Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
+// for that stream after replacing stream name with bindSuffix minus the last word
+// and the file name with last word of the bindSuffix
+// Allowed path examples:
+// "path":"/"
+// "path":"/subdir1"
+// "path":"/subdir1/subdir2"
+// "path":"/subdir/filename" etc
+func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
+ collection := outputCollections[mnt.PortableDataHash]
+ if collection.PortableDataHash == "" {
+ err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
+ if err != nil {
+ return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
+ }
+ outputCollections[mnt.PortableDataHash] = collection
+ }
+
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ return "", nil
+ }
+
+ mft := manifest.Manifest{Text: collection.ManifestText}
+ extracted := mft.Extract(mnt.Path, bindSuffix)
+ if extracted.Err != nil {
+ return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
+ }
+ return extracted.Text, nil
+}
+
func (runner *ContainerRunner) loadDiscoveryVars() {
tl, err := runner.ArvClient.Discovery("defaultTrashLifetime")
if err != nil {
Calls int
Content []arvadosclient.Dict
arvados.Container
- Logs map[string]*bytes.Buffer
- WasSetRunning bool
+ Logs map[string]*bytes.Buffer
sync.Mutex
+ WasSetRunning bool
}
type KeepTestClient struct {
var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
+var normalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt\n"
+var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
+
+var denormalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt 0:10:subdir1/file1_in_subdir1.txt 10:17:subdir1/file2_in_subdir1.txt\n"
+var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
+
var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
output.(*arvados.Collection).ManifestText = hwManifest
} else if uuid == otherPDH {
output.(*arvados.Collection).ManifestText = otherManifest
+ } else if uuid == normalizedWithSubdirsPDH {
+ output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
+ } else if uuid == denormalizedWithSubdirsPDH {
+ output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
}
}
if resourceType == "containers" {
// Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
// dress rehearsal of the Run() function, starting from a JSON container record.
-func FullRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner) {
+func FullRunHelper(c *C, record string, extraMounts []string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
rec := arvados.Container{}
err := json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
+ realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
+ c.Assert(err, IsNil)
+ defer os.RemoveAll(realTemp)
+
+ tempcount := 0
+ cr.MkTempDir = func(_ string, prefix string) (string, error) {
+ tempcount++
+ d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
+ err := os.Mkdir(d, os.ModePerm)
+ if err != nil && strings.Contains(err.Error(), ": file exists") {
+ // Test case must have pre-populated the tempdir
+ err = nil
+ }
+ return d, err
+ }
+
+ if extraMounts != nil && len(extraMounts) > 0 {
+ err := cr.SetupArvMountPoint("keep")
+ c.Check(err, IsNil)
+
+ for _, m := range extraMounts {
+ os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
+ }
+ }
+
err = cr.Run()
c.Check(err, IsNil)
c.Check(api.WasSetRunning, Equals, true)
}
func (s *TestSuite) TestFullRunHello(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["echo", "hello world"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, "hello world\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{}
}
func (s *TestSuite) TestCrunchstat(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
- }`, func(t *TestDockerClient) {
+ }`, nil, func(t *TestDockerClient) {
time.Sleep(time.Second)
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{}
}
func (s *TestSuite) TestFullRunStderr(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, "hello\n"))
t.logWriter.Write(dockerLog(2, "world\n"))
t.logWriter.Close()
}
func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
}
func (s *TestSuite) TestFullRunSetCwd(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
}
func (s *TestSuite) TestFullRunSetEnv(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = make(map[string]arvados.Mount)
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.OutputPath = "/tmp"
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = make(map[string]arvados.Mount)
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.OutputPath = "/tmp"
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/keeptmp": {Kind: "collection", Writable: true},
}
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
"/keepout": {Kind: "collection", Writable: true},
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.RuntimeConstraints.KeepCacheRAM = 512
cr.Container.Mounts = map[string]arvados.Mount{
"/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
{in: map[string]int{"foo": 123}, out: `{"foo":123}`},
} {
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/mnt/test.json": {Kind: "json", Content: test.in},
}
cr.CleanupDirs()
checkEmpty()
}
+
+ // Read-only mount points are allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "collection"},
+ }
+ cr.OutputPath = "/tmp"
+
+ os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
+
+ err := cr.SetupMounts()
+ c.Check(err, IsNil)
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
+ // Writable mount points are not allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "collection", Writable: true},
+ }
+ cr.OutputPath = "/tmp"
+
+ err := cr.SetupMounts()
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
+ // Only mount points of kind 'collection' are allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "json"},
+ }
+ cr.OutputPath = "/tmp"
+
+ err := cr.SetupMounts()
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
+ cr.CleanupDirs()
+ checkEmpty()
+ }
}
func (s *TestSuite) TestStdout(c *C) {
"runtime_constraints": {}
}`
- api, _ := FullRunHelper(c, helperRecord, func(t *TestDockerClient) {
+ api, _, _ := FullRunHelper(c, helperRecord, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
func (s *TestSuite) TestFullRunWithAPI(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {"API": true}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
func (s *TestSuite) TestFullRunSetOutput(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {"API": true}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
c.Check(api.CalledWith("container.state", "Complete"), NotNil)
c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
}
+
+func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo": {"kind": "collection",
+ "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
+ "exclude_from_output": true
+ },
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ t.finish <- dockerclient.WaitResult{ExitCode: 0}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
+}
+
+func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
+ "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
+ "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
+ "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
+ }
+
+ api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ t.finish <- dockerclient.WaitResult{ExitCode: 0}
+ })
+
+ c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
+./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
+./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
+./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ }
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ t.finish <- dockerclient.WaitResult{ExitCode: 0}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
+`)
+ }
+ }
+ }
+}
"""
# Reasons for a shutdown to be cancelled.
WINDOW_CLOSED = "shutdown window closed"
- NODE_BROKEN = "cloud failed to shut down broken node"
+ DESTROY_FAILED = "destroy_node failed"
def __init__(self, timer_actor, cloud_client, arvados_client, node_monitor,
cancellable=True, retry_wait=1, max_retry_wait=180):
self.success = success_flag
return super(ComputeNodeShutdownActor, self)._finished()
- def cancel_shutdown(self, reason):
+ def cancel_shutdown(self, reason, **kwargs):
self.cancel_reason = reason
self._logger.info("Shutdown cancelled: %s.", reason)
self._finished(success_flag=False)
return orig_func(self, *args, **kwargs)
except Exception as error:
self._logger.error("Actor error %s", error)
- self._later.cancel_shutdown("Unhandled exception %s" % error)
+ self._logger.debug("", exc_info=True)
+ self._later.cancel_shutdown("Unhandled exception %s" % error, try_resume=False)
return finish_wrapper
@_cancel_on_exception
- @RetryMixin._retry()
def shutdown_node(self):
+ if self.cancellable:
+ self._logger.info("Checking that node is still eligible for shutdown")
+ eligible, reason = self._monitor.shutdown_eligible().get()
+ if not eligible:
+ self.cancel_shutdown("No longer eligible for shut down because %s" % reason,
+ try_resume=True)
+ return
+
self._logger.info("Starting shutdown")
arv_node = self._arvados_node()
- if not self._cloud.destroy_node(self.cloud_node):
- if self._cloud.broken(self.cloud_node):
- self._later.cancel_shutdown(self.NODE_BROKEN)
- return
+ if self._cloud.destroy_node(self.cloud_node):
+ self._logger.info("Shutdown success")
+ if arv_node:
+ self._later.clean_arvados_node(arv_node)
else:
- # Force a retry.
- raise cloud_types.LibcloudError("destroy_node failed")
- self._logger.info("Shutdown success")
- if arv_node is None:
- self._finished(success_flag=True)
+ self._finished(success_flag=True)
else:
- self._later.clean_arvados_node(arv_node)
+ self.cancel_shutdown(self.DESTROY_FAILED, try_resume=False)
@ComputeNodeStateChangeBase._finish_on_exception
@RetryMixin._retry(config.ARVADOS_ERRORS)
):
super(ComputeNodeMonitorActor, self).__init__()
self._later = self.actor_ref.tell_proxy()
- self._last_log = None
self._shutdowns = shutdown_timer
self._cloud_node_fqdn = cloud_fqdn_func
self._timer = timer_actor
self.subscribers.add(subscriber)
def _debug(self, msg, *args):
- if msg == self._last_log:
- return
- self._last_log = msg
self._logger.debug(msg, *args)
def get_state(self):
if self.arvados_node is None:
return 'unpaired'
+ # This node is indicated as non-functioning by the cloud
+ if self._cloud.broken(self.cloud_node):
+ return 'down'
+
state = self.arvados_node['crunch_worker_state']
# If state information is not available because it is missing or the
self._later.issue_slurm_drain()
@RetryMixin._retry((subprocess.CalledProcessError,))
- def cancel_shutdown(self, reason):
+ def cancel_shutdown(self, reason, try_resume=True):
if self._nodename:
- if self._get_slurm_state(self._nodename) in self.SLURM_DRAIN_STATES:
+ if try_resume and self._get_slurm_state(self._nodename) in self.SLURM_DRAIN_STATES:
# Resume from "drng" or "drain"
self._set_node_state(self._nodename, 'RESUME')
else:
self._timer.schedule(time.time() + 10,
self._later.await_slurm_drain)
elif output in ("idle\n"):
- # Not in "drng" so cancel self.
- self.cancel_shutdown("slurm state is %s" % output.strip())
+ # Not in "drng" but idle, don't shut down
+ self.cancel_shutdown("slurm state is %s" % output.strip(), try_resume=False)
else:
# any other state.
self._later.shutdown_node()
def __init__(self):
self.nodes = {}
self.orphans = {}
- self._blacklist = set()
# Proxy the methods listed below to self.nodes.
def _proxy_method(name):
def add(self, record):
self.nodes[self.record_key(record)] = record
- def blacklist(self, key):
- self._blacklist.add(key)
-
def update_record(self, key, item):
setattr(self.nodes[key], self.RECORD_ATTR, item)
unseen = set(self.nodes.iterkeys())
for item in response:
key = self.item_key(item)
- if key in self._blacklist:
- continue
- elif key in unseen:
+ if key in unseen:
unseen.remove(key)
self.update_record(key, item)
else:
if hasattr(record.cloud_node, "_nodemanager_recently_booted"):
self.cloud_nodes.add(record)
else:
- record.actor.stop()
+ # Node disappeared from the cloud node list. Stop the monitor
+ # actor if necessary and forget about the node.
+ if record.actor:
+ try:
+ record.actor.stop()
+ except pykka.ActorDeadError:
+ pass
+ record.actor = None
record.cloud_node = None
def _register_arvados_node(self, key, arv_node):
def node_finished_shutdown(self, shutdown_actor):
try:
- cloud_node, success, cancel_reason = self._get_actor_attrs(
- shutdown_actor, 'cloud_node', 'success', 'cancel_reason')
+ cloud_node, success = self._get_actor_attrs(
+ shutdown_actor, 'cloud_node', 'success')
except pykka.ActorDeadError:
return
cloud_node_id = cloud_node.id
record = self.cloud_nodes[cloud_node_id]
shutdown_actor.stop()
+ record.shutdown_actor = None
+
if not success:
- if cancel_reason == self._node_shutdown.NODE_BROKEN:
- self.cloud_nodes.blacklist(cloud_node_id)
- record.shutdown_actor = None
- else:
- # If the node went from being booted to being shut down without ever
- # appearing in the cloud node list, it will have the
- # _nodemanager_recently_booted tag, so get rid of it so that the node
- # can be forgotten completely.
- if hasattr(self.cloud_nodes[cloud_node_id].cloud_node, "_nodemanager_recently_booted"):
- del self.cloud_nodes[cloud_node_id].cloud_node._nodemanager_recently_booted
+ return
+
+ # Shutdown was successful, so stop the monitor actor, otherwise it
+ # will keep offering the node as a candidate for shutdown.
+ record.actor.stop()
+ record.actor = None
+
+ # If the node went from being booted to being shut down without ever
+ # appearing in the cloud node list, it will have the
+ # _nodemanager_recently_booted tag, so get rid of it so that the node
+ # can be forgotten completely.
+ if hasattr(record.cloud_node, "_nodemanager_recently_booted"):
+ del record.cloud_node._nodemanager_recently_booted
def shutdown(self):
self._logger.info("Shutting down after signal.")
else:
self.fail("success flag {} is not {}".format(last_flag, expected))
+ def test_cancellable_shutdown(self, *mocks):
+ self.make_mocks(shutdown_open=True, arvados_node=testutil.arvados_node_mock(crunch_worker_state="busy"))
+ self.cloud_client.destroy_node.return_value = True
+ self.make_actor(cancellable=True)
+ self.check_success_flag(False)
+ self.assertFalse(self.cloud_client.destroy_node.called)
+
def test_uncancellable_shutdown(self, *mocks):
- self.make_mocks(shutdown_open=False)
- self.cloud_client.destroy_node.return_value = False
- self.make_actor(cancellable=False)
- self.check_success_flag(None, 0)
- self.shutdowns._set_state(True, 600)
+ self.make_mocks(shutdown_open=True, arvados_node=testutil.arvados_node_mock(crunch_worker_state="busy"))
self.cloud_client.destroy_node.return_value = True
- self.check_success_flag(True)
+ self.make_actor(cancellable=False)
+ self.check_success_flag(True, 2)
+ self.assertTrue(self.cloud_client.destroy_node.called)
def test_arvados_node_cleaned_after_shutdown(self, *mocks):
cloud_node = testutil.cloud_node_mock(62)
self.check_success_flag(True)
self.assertTrue(self.cloud_client.destroy_node.called)
- def test_shutdown_retries_when_cloud_fails(self):
- self.make_mocks()
- self.cloud_client.destroy_node.return_value = False
- self.make_actor(start_time=0)
- self.assertIsNone(self.shutdown_actor.success.get(self.TIMEOUT))
- self.cloud_client.destroy_node.return_value = True
- self.check_success_flag(True)
-
- def test_shutdown_cancelled_when_cloud_fails_on_broken_node(self):
+ def test_shutdown_cancelled_when_destroy_node_fails(self):
self.make_mocks(node_broken=True)
self.cloud_client.destroy_node.return_value = False
self.make_actor(start_time=0)
self.check_success_flag(False, 2)
self.assertEqual(1, self.cloud_client.destroy_node.call_count)
- self.assertEqual(self.ACTOR_CLASS.NODE_BROKEN,
+ self.assertEqual(self.ACTOR_CLASS.DESTROY_FAILED,
self.shutdown_actor.cancel_reason.get(self.TIMEOUT))
def test_late_subscribe(self):
proc_mock.return_value = 'drain\n'
super(SLURMComputeNodeShutdownActorTestCase,
self).test_arvados_node_cleaned_after_shutdown()
+
+ def test_cancellable_shutdown(self, proc_mock):
+ proc_mock.return_value = 'other\n'
+ super(SLURMComputeNodeShutdownActorTestCase,
+ self).test_cancellable_shutdown()
+
+ def test_uncancellable_shutdown(self, proc_mock):
+ proc_mock.return_value = 'other\n'
+ super(SLURMComputeNodeShutdownActorTestCase,
+ self).test_uncancellable_shutdown()
def test_node_found_after_timeout_has_fixed_size(self):
size = testutil.MockSize(4)
node_props = {'hardwareProfile': {'vmSize': size.id}}
- cloud_node = testutil.cloud_node_mock(
- size=None, tags={'arvados-class': 'test'}, properties=node_props)
+ cloud_node = testutil.cloud_node_mock(tags={'arvados-class': 'test'}, properties=node_props)
+ cloud_node.size = None
self.check_node_found_after_timeout_has_fixed_size(
size, cloud_node, {'tag_arvados-class': 'test'})
return mock_actor
def make_daemon(self, cloud_nodes=[], arvados_nodes=[], want_sizes=[],
- avail_sizes=[(testutil.MockSize(1), {"cores": 1})],
+ avail_sizes=None,
min_nodes=0, max_nodes=8,
shutdown_windows=[54, 5, 1],
max_total_price=None):
for name in ['cloud_nodes', 'arvados_nodes', 'server_wishlist']:
setattr(self, name + '_poller', mock.MagicMock(name=name + '_mock'))
+
+ if not avail_sizes:
+ if cloud_nodes or want_sizes:
+ avail_sizes=[(c.size, {"cores": int(c.id)}) for c in cloud_nodes] + [(s, {"cores": 1}) for s in want_sizes]
+ else:
+ avail_sizes=[(testutil.MockSize(1), {"cores": 1})]
+
self.arv_factory = mock.MagicMock(name='arvados_mock')
api_client = mock.MagicMock(name='api_client')
api_client.nodes().create().execute.side_effect = [testutil.arvados_node_mock(1),
self.cloud_updates = mock.MagicMock(name='updates_mock')
self.timer = testutil.MockTimer(deliver_immediately=False)
self.cloud_factory().node_id.side_effect = lambda node: node.id
+ self.cloud_factory().broken.return_value = False
self.node_setup = mock.MagicMock(name='setup_mock')
self.node_setup.start.side_effect = self.mock_node_start
def test_arvados_node_un_and_re_paired(self):
# We need to create the Arvados node mock after spinning up the daemon
# to make sure it's new enough to pair with the cloud node.
- self.make_daemon([testutil.cloud_node_mock(3)], arvados_nodes=None)
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(3)],
+ arvados_nodes=None)
arv_node = testutil.arvados_node_mock(3)
self.daemon.update_arvados_nodes([arv_node]).get(self.TIMEOUT)
self.check_monitors_arvados_nodes(arv_node)
def test_old_arvados_node_not_double_assigned(self):
arv_node = testutil.arvados_node_mock(3, age=9000)
size = testutil.MockSize(3)
- self.make_daemon(arvados_nodes=[arv_node], avail_sizes=[(size, {"cores":1})])
+ self.make_daemon(arvados_nodes=[arv_node],
+ avail_sizes=[(size, {"cores":1})])
self.daemon.update_server_wishlist([size]).get(self.TIMEOUT)
self.daemon.update_server_wishlist([size, size]).get(self.TIMEOUT)
self.stop_proxy(self.daemon)
self.assertIn(None, used_nodes)
def test_node_count_satisfied(self):
- self.make_daemon([testutil.cloud_node_mock()],
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(1)],
want_sizes=[testutil.MockSize(1)])
self.stop_proxy(self.daemon)
self.assertFalse(self.node_setup.start.called)
def test_dont_count_missing_as_busy(self):
size = testutil.MockSize(1)
- self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(1),
- testutil.cloud_node_mock(2)],
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(1, size=size),
+ testutil.cloud_node_mock(2, size=size)],
arvados_nodes=[testutil.arvados_node_mock(1),
- testutil.arvados_node_mock(2,
- last_ping_at='1970-01-01T01:02:03.04050607Z')],
+ testutil.arvados_node_mock(
+ 2,
+ last_ping_at='1970-01-01T01:02:03.04050607Z')],
want_sizes=[size, size])
self.stop_proxy(self.daemon)
self.assertTrue(self.node_setup.start.called)
def test_missing_counts_towards_max(self):
size = testutil.MockSize(1)
- self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(1),
- testutil.cloud_node_mock(2)],
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(1, size=size),
+ testutil.cloud_node_mock(2, size=size)],
arvados_nodes=[testutil.arvados_node_mock(1),
testutil.arvados_node_mock(2, last_ping_at='1970-01-01T01:02:03.04050607Z')],
want_sizes=[size, size],
def test_excess_counts_missing(self):
size = testutil.MockSize(1)
- cloud_nodes = [testutil.cloud_node_mock(1), testutil.cloud_node_mock(2)]
+ cloud_nodes = [testutil.cloud_node_mock(1, size=size), testutil.cloud_node_mock(2, size=size)]
self.make_daemon(cloud_nodes=cloud_nodes,
arvados_nodes=[testutil.arvados_node_mock(1),
testutil.arvados_node_mock(2, last_ping_at='1970-01-01T01:02:03.04050607Z')],
def test_missing_shutdown_not_excess(self):
size = testutil.MockSize(1)
- cloud_nodes = [testutil.cloud_node_mock(1), testutil.cloud_node_mock(2)]
+ cloud_nodes = [testutil.cloud_node_mock(1, size=size), testutil.cloud_node_mock(2, size=size)]
self.make_daemon(cloud_nodes=cloud_nodes,
arvados_nodes=[testutil.arvados_node_mock(1),
testutil.arvados_node_mock(2, last_ping_at='1970-01-01T01:02:03.04050607Z')],
for call in self.node_setup.start.call_args_list])
def test_no_new_node_when_ge_min_nodes_busy(self):
- cloud_nodes = [testutil.cloud_node_mock(n) for n in range(1, 4)]
+ size = testutil.MockSize(2)
+ cloud_nodes = [testutil.cloud_node_mock(n, size=size) for n in range(1, 4)]
arv_nodes = [testutil.arvados_node_mock(n, job_uuid=True)
for n in range(1, 4)]
self.make_daemon(cloud_nodes, arv_nodes, [], min_nodes=2)
self.assertEqual(0, self.node_setup.start.call_count)
def test_no_new_node_when_max_nodes_busy(self):
- self.make_daemon([testutil.cloud_node_mock(3)],
- [testutil.arvados_node_mock(3, job_uuid=True)],
- [testutil.MockSize(3)],
+ size = testutil.MockSize(3)
+ self.make_daemon(cloud_nodes=[testutil.cloud_node_mock(3)],
+ arvados_nodes=[testutil.arvados_node_mock(3, job_uuid=True)],
+ want_sizes=[size],
max_nodes=1)
self.stop_proxy(self.daemon)
self.assertFalse(self.node_setup.start.called)
def start_node_boot(self, cloud_node=None, arv_node=None, id_num=1):
if cloud_node is None:
cloud_node = testutil.cloud_node_mock(id_num)
+ id_num = int(cloud_node.id)
if arv_node is None:
arv_node = testutil.arvados_node_mock(id_num)
self.make_daemon(want_sizes=[testutil.MockSize(id_num)],
self.daemon.update_cloud_nodes([cloud_node])
self.monitor_list()[0].proxy().cloud_node_start_time = time.time()-1801
self.daemon.update_server_wishlist(
- [testutil.MockSize(1)]).get(self.TIMEOUT)
+ [testutil.MockSize(4)]).get(self.TIMEOUT)
self.stop_proxy(self.daemon)
self.assertEqual(2, self.node_setup.start.call_count)
self.assertTrue(self.node_shutdown.start.called)
def test_shutdown_declined_when_idle_and_job_queued(self):
- cloud_nodes = [testutil.cloud_node_mock(n) for n in [3, 4]]
+ size = testutil.MockSize(1)
+ cloud_nodes = [testutil.cloud_node_mock(n, size=size) for n in [3, 4]]
arv_nodes = [testutil.arvados_node_mock(3, job_uuid=True),
testutil.arvados_node_mock(4, job_uuid=None)]
- self.make_daemon(cloud_nodes, arv_nodes, [testutil.MockSize(1)])
+ self.make_daemon(cloud_nodes, arv_nodes, [size])
self.assertEqual(2, self.alive_monitor_count())
for mon_ref in self.monitor_list():
monitor = mon_ref.proxy()
self.daemon.node_finished_shutdown(self.last_shutdown).get(self.TIMEOUT)
self.assertEqual(0, self.alive_monitor_count())
- def test_broken_node_blackholed_after_cancelled_shutdown(self):
+ def test_broken_node_not_counted(self):
size = testutil.MockSize(8)
cloud_node = testutil.cloud_node_mock(8, size=size)
wishlist = [size]
shutdown_proxy = self.node_shutdown.start().proxy
shutdown_proxy().cloud_node.get.return_value = cloud_node
shutdown_proxy().success.get.return_value = False
- shutdown_proxy().cancel_reason.get.return_value = self.node_shutdown.NODE_BROKEN
+ self.cloud_factory().broken.return_value = True
self.daemon.update_server_wishlist([]).get(self.TIMEOUT)
self.daemon.node_can_shutdown(monitor).get(self.TIMEOUT)
self.daemon.node_finished_shutdown(shutdown_proxy()).get(self.TIMEOUT)
time.sleep(2)
return True
-class ActorUnhandledExceptionTest(unittest.TestCase):
+class ActorUnhandledExceptionTest(testutil.ActorTestMixin, unittest.TestCase):
def test_fatal_error(self):
for e in (MemoryError(), threading.ThreadError(), OSError(errno.ENOMEM, "")):
with mock.patch('os.kill') as kill_mock:
act.actor_ref.stop(block=True)
self.assertFalse(kill_mock.called)
-class WatchdogActorTest(unittest.TestCase):
+class WatchdogActorTest(testutil.ActorTestMixin, unittest.TestCase):
@mock.patch('os.kill')
def test_time_timout(self, kill_mock):
act = BogusActor.start(OSError(errno.ENOENT, ""))
self.monitor = self.TEST_CLASS.start(
self.client, self.timer, *args, **kwargs).proxy()
-def cloud_node_mock(node_num=99, size=MockSize(1), **extra):
+def cloud_node_mock(node_num=99, size=None, **extra):
+ if size is None:
+ size = MockSize(node_num)
node = mock.NonCallableMagicMock(
['id', 'name', 'state', 'public_ips', 'private_ips', 'driver', 'size',
'image', 'extra'],
package main
import (
+ "context"
"database/sql"
"strconv"
"strings"
pqListener *pq.Listener
queue chan *event
sinks map[*pgEventSink]bool
- setupOnce sync.Once
mtx sync.Mutex
- shutdown chan error
lastQDelay time.Duration
eventsIn uint64
eventsOut uint64
+
+ cancel func()
}
var _ debugStatuser = (*pgEventSource)(nil)
-func (ps *pgEventSource) setup() {
- ps.shutdown = make(chan error, 1)
- ps.sinks = make(map[*pgEventSink]bool)
+func (ps *pgEventSource) listenerProblem(et pq.ListenerEventType, err error) {
+ if et == pq.ListenerEventConnected {
+ logger(nil).Debug("pgEventSource connected")
+ return
+ }
+
+ // Until we have a mechanism for catching up on missed events,
+ // we cannot recover from a dropped connection without
+ // breaking our promises to clients.
+ logger(nil).
+ WithField("eventType", et).
+ WithError(err).
+ Error("listener problem")
+ ps.cancel()
+}
+
+// Run listens for event notifications on the "logs" channel and sends
+// them to all subscribers.
+func (ps *pgEventSource) Run() {
+ logger(nil).Debug("pgEventSource Run starting")
+ defer logger(nil).Debug("pgEventSource Run finished")
+
+ ctx, cancel := context.WithCancel(context.Background())
+ ps.cancel = cancel
+ defer cancel()
+
+ defer func() {
+ // Disconnect all clients
+ ps.mtx.Lock()
+ for sink := range ps.sinks {
+ close(sink.channel)
+ }
+ ps.sinks = nil
+ ps.mtx.Unlock()
+ }()
db, err := sql.Open("postgres", ps.DataSource)
if err != nil {
logger(nil).WithError(err).Fatal("sql.Open failed")
+ return
}
if err = db.Ping(); err != nil {
logger(nil).WithError(err).Fatal("db.Ping failed")
+ return
}
ps.db = db
- ps.pqListener = pq.NewListener(ps.DataSource, time.Second, time.Minute, func(ev pq.ListenerEventType, err error) {
- if err != nil {
- // Until we have a mechanism for catching up
- // on missed events, we cannot recover from a
- // dropped connection without breaking our
- // promises to clients.
- logger(nil).WithError(err).Error("listener problem")
- ps.shutdown <- err
- }
- })
+ ps.pqListener = pq.NewListener(ps.DataSource, time.Second, time.Minute, ps.listenerProblem)
err = ps.pqListener.Listen("logs")
if err != nil {
logger(nil).WithError(err).Fatal("pq Listen failed")
}
- logger(nil).Debug("pgEventSource listening")
+ defer ps.pqListener.Close()
+ logger(nil).Debug("pq Listen setup done")
- go ps.run()
-}
-
-func (ps *pgEventSource) run() {
ps.queue = make(chan *event, ps.QueueSize)
+ defer close(ps.queue)
go func() {
for e := range ps.queue {
defer ticker.Stop()
for {
select {
- case err, ok := <-ps.shutdown:
- if ok {
- logger(nil).WithError(err).Info("shutdown")
- }
- close(ps.queue)
+ case <-ctx.Done():
+ logger(nil).Debug("ctx done")
return
case <-ticker.C:
case pqEvent, ok := <-ps.pqListener.Notify:
if !ok {
- close(ps.queue)
+ logger(nil).Debug("pqListener Notify chan closed")
return
}
+ if pqEvent == nil {
+ // pq should call listenerProblem
+ // itself in addition to sending us a
+ // nil event, so this might be
+ // superfluous:
+ ps.listenerProblem(-1, nil)
+ continue
+ }
if pqEvent.Channel != "logs" {
+ logger(nil).WithField("pqEvent", pqEvent).Error("unexpected notify from wrong channel")
continue
}
logID, err := strconv.ParseUint(pqEvent.Extra, 10, 64)
// quickly as possible because when one sink stops being ready, all
// other sinks block.
func (ps *pgEventSource) NewSink() eventSink {
- ps.setupOnce.Do(ps.setup)
sink := &pgEventSink{
channel: make(chan *event, 1),
source: ps,
}
ps.mtx.Lock()
+ if ps.sinks == nil {
+ ps.sinks = make(map[*pgEventSink]bool)
+ }
ps.sinks[sink] = true
ps.mtx.Unlock()
return sink
}
func (ps *pgEventSource) DB() *sql.DB {
- ps.setupOnce.Do(ps.setup)
return ps.db
}
return sink.channel
}
+// Stop sending events to the sink's channel.
func (sink *pgEventSink) Stop() {
go func() {
// Ensure this sink cannot fill up and block the
}
}()
sink.source.mtx.Lock()
- delete(sink.source.sinks, sink)
+ if _, ok := sink.source.sinks[sink]; ok {
+ delete(sink.source.sinks, sink)
+ close(sink.channel)
+ }
sink.source.mtx.Unlock()
- close(sink.channel)
}
newPermChecker: func() permChecker { return newPermChecker(cfg.Client) },
},
}
- // Bootstrap the eventSource by attaching a dummy subscriber
- // and hanging up.
- eventSource.NewSink().Stop()
+
+ go func() {
+ eventSource.Run()
+ log.Fatal("event source stopped")
+ }()
if _, err := daemon.SdNotify(false, "READY=1"); err != nil {
log.WithError(err).Warn("error notifying init daemon")
auto_setup_new_users_with_vm_uuid: $vm_uuid
auto_setup_new_users_with_repository: true
default_collection_replication: 1
+ docker_image_formats: ["v1"]
EOF
(cd config && /usr/local/lib/arvbox/application_yml_override.py)
fi
if ! test -s /var/lib/arvados/superuser_token ; then
- bundle exec ./script/create_superuser_token.rb > /var/lib/arvados/superuser_token
+ superuser_tok=$(bundle exec ./script/create_superuser_token.rb)
+ echo "$superuser_tok" > /var/lib/arvados/superuser_token
fi
rm -rf tmp
if ! grep "^arvbox:" /etc/passwd >/dev/null 2>/dev/null ; then
HOSTUID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f4)
HOSTGID=$(ls -nd /usr/src/arvados | sed 's/ */ /' | cut -d' ' -f5)
- FUSEGID=$(ls -nd /dev/fuse | sed 's/ */ /' | cut -d' ' -f5)
mkdir -p /var/lib/arvados/git /var/lib/gems \
/var/lib/passenger /var/lib/gopath /var/lib/pip
groupadd --gid $HOSTGID --non-unique arvbox
- groupadd --gid $FUSEGID --non-unique fuse
groupadd --gid $HOSTGID --non-unique git
useradd --home-dir /var/lib/arvados \
--uid $HOSTUID --gid $HOSTGID \
--non-unique \
- --groups docker,fuse \
+ --groups docker \
arvbox
useradd --home-dir /var/lib/arvados/git --uid $HOSTUID --gid $HOSTGID --non-unique git
- useradd --groups docker,fuse crunch
+ useradd --groups docker crunch
chown arvbox:arvbox -R /usr/local /var/lib/arvados /var/lib/gems \
/var/lib/passenger /var/lib/postgresql \
echo "arvbox ALL=(crunch) NOPASSWD: ALL" >> /etc/sudoers
fi
+
+if ! grep "^fuse:" /etc/group >/dev/null 2>/dev/null ; then
+ if test -c /dev/fuse ; then
+ FUSEGID=$(ls -nd /dev/fuse | sed 's/ */ /' | cut -d' ' -f5)
+ groupadd --gid $FUSEGID --non-unique fuse
+ adduser arvbox fuse
+ adduser crunch fuse
+ fi
+fi
projects / arvados.git / commitdiff