components_map { |cspec| cspec[:job][:log] rescue nil }
end
+ def job_ids
+ components_map { |cspec| cspec[:job][:uuid] rescue nil }
+ end
+
def stderr_log_object_uuids
result = job_uuids.values.compact
result << uuid
<div class="container-fluid">
<div class="row-fluid">
<%# column offset 0 %>
- <div class="col-md-3" style="word-break:break-all;">
+ <div class="col-md-2" style="word-break:break-all;">
<h4 class="panel-title">
<a data-toggle="collapse" href="#collapse<%= i %>">
<%= pj[:name] %> <span class="caret"></span>
</h4>
</div>
- <%# column offset 3 %>
+ <%# column offset 2 %>
<div class="col-md-2 pipeline-instance-spacing">
<%= pj[:progress_bar] %>
</div>
<% if current_job %>
+ <%# column offset 4 %>
+ <% if(pipeline_display rescue nil) %>
+ <% if current_job[:state].in? ["Complete", "Failed", "Cancelled"] %>
+ <div class="col-md-1">
+ <% if current_job[:log] %>
+ <% logCollection = Collection.find? current_job[:log] %>
+ <% if logCollection %>
+ <%= link_to "Log", job_path(current_job[:uuid], anchor: "Log") %>
+ <% else %>
+ Log unavailable
+ <% end %>
+ <% end %>
+ </div>
+ <% elsif current_job[:state] == "Running" %>
+ <div class="col-md-1">
+ <% job = Job.find? current_job[:uuid] %>
+ <% if job %>
+ <%= link_to "Log", job_path(current_job[:uuid], anchor: "Log") %>
+ <% else %>
+ Log unavailable
+ <% end %>
+ </div>
+ <% end %>
+ <% end %>
+
<%# column offset 5 %>
<% if current_job[:state] != "Queued" %>
<div class="col-md-3">
%>
<% pipeline_jobs.each_with_index do |pj, i| %>
- <%= render partial: 'running_component', locals: {pj: pj, i: i, expanded: false} %>
+ <%= render partial: 'running_component', locals: {pj: pj, i: i, expanded: false, pipeline_display: true} %>
<% end %>
<% log_ids = @object.job_log_ids
+ job_ids = @object.job_ids
still_logging, done_logging = log_ids.keys.partition { |k| log_ids[k].nil? }
%>
<tr>
<td><%= cname %></td>
<td><%= link_to("Log for #{cname}",
- {controller: "collections", action: "show", id: log_ids[cname]})
+ job_path(job_ids[cname], anchor: "Log"))
%></td>
</tr>
<% end %>
['pipeline_in_publicly_accessible_project_but_other_objects_elsewhere', true, 'admin'],
['completed_job_in_publicly_accessible_project', true],
+ ['running_job_in_publicly_accessible_project', true],
['job_in_publicly_accessible_project_but_other_objects_elsewhere', false],
].each do |fixture, objects_readable, user=nil|
test "access #{fixture} in public project with objects readable=#{objects_readable} with user #{user}" do
if pipeline_page
object = api_fixture('pipeline_instances')[fixture]
- page = "/pipeline_instances/#{object['uuid']}"
+ page_link = "/pipeline_instances/#{object['uuid']}"
expect_log_text = "Log for foo"
else # job
object = api_fixture('jobs')[fixture]
- page = "/jobs/#{object['uuid']}"
+ page_link = "/jobs/#{object['uuid']}"
expect_log_text = "stderr crunchstat"
end
if user
- visit page_with_token user, page
+ visit page_with_token user, page_link
else
- visit page
+ visit page_link
end
# click job link, if in pipeline page
assert_no_text 'Output data not available'
if pipeline_page
assert_text 'This pipeline was created from'
- assert_selector 'a', text: object['components']['foo']['job']['uuid']
+ job_id = object['components']['foo']['job']['uuid']
+ assert_selector 'a', text: job_id
+ assert_selector "a[href=\"/jobs/#{job_id}#Log\"]", text: 'Log'
+
# We'd like to test the Log tab on job pages too, but we can't right
# now because Poltergeist 1.x doesn't support JavaScript's
# Function.prototype.bind, which is used by job_log_graph.js.
- click_link "Log"
+ find(:xpath, "//a[@href='#Log']").click
assert_text expect_log_text
end
else
if pipeline_page
assert_no_text 'This pipeline was created from' # template is not readable
assert_no_selector 'a', text: object['components']['foo']['job']['uuid']
+ assert_text 'Log unavailable'
end
- click_link "Log"
+ find(:xpath, "//a[@href='#Log']").click
assert_text 'Output data not available'
assert_no_text expect_log_text
end
visit page_with_token("active", "/jobs/#{job['uuid']}")
assert page.has_text? job['script_version']
- click_link 'Log'
+ find(:xpath, "//a[@href='#Log']").click
wait_for_ajax
assert page.has_text? 'Started at'
assert page.has_text? 'Finished at'
visit page_with_token("active", "/jobs/#{job['uuid']}")
assert page.has_text? job['script_version']
- click_link 'Log'
+ find(:xpath, "//a[@href='#Log']").click
wait_for_ajax
assert page.has_text? 'Showing only 100 bytes of this log'
end
test "job logs linked for running pipeline" do
pi = api_fixture("pipeline_instances", "running_pipeline_with_complete_job")
visit(page_with_token("active", "/pipeline_instances/#{pi['uuid']}"))
- click_on "Log"
+ find(:xpath, "//a[@href='#Log']").click
within "#Log" do
assert_text "Log for previous"
log_link = find("a", text: "Log for previous")
assert_includes(log_link[:href],
- pi["components"]["previous"]["job"]["log"])
+ "/jobs/#{pi["components"]["previous"]["job"]["uuid"]}#Log")
assert_selector "#event_log_div"
end
end
test "job logs linked for complete pipeline" do
pi = api_fixture("pipeline_instances", "complete_pipeline_with_two_jobs")
visit(page_with_token("active", "/pipeline_instances/#{pi['uuid']}"))
- click_on "Log"
+ find(:xpath, "//a[@href='#Log']").click
within "#Log" do
assert_text "Log for previous"
pi["components"].each do |cname, cspec|
log_link = find("a", text: "Log for #{cname}")
- assert_includes(log_link[:href], cspec["job"]["log"])
+ assert_includes(log_link[:href], "/jobs/#{cspec["job"]["uuid"]}#Log")
end
assert_no_selector "#event_log_div"
end
test "job logs linked for failed pipeline" do
pi = api_fixture("pipeline_instances", "failed_pipeline_with_two_jobs")
visit(page_with_token("active", "/pipeline_instances/#{pi['uuid']}"))
- click_on "Log"
+ find(:xpath, "//a[@href='#Log']").click
within "#Log" do
assert_text "Log for previous"
pi["components"].each do |cname, cspec|
log_link = find("a", text: "Log for #{cname}")
- assert_includes(log_link[:href], cspec["job"]["log"])
+ assert_includes(log_link[:href], "/jobs/#{cspec["job"]["uuid"]}#Log")
end
assert_no_selector "#event_log_div"
end
end
module WaitForAjax
- Capybara.default_max_wait_time = 5
+ Capybara.default_max_wait_time = 10
def wait_for_ajax
Timeout.timeout(Capybara.default_max_wait_time) do
loop until finished_all_ajax_requests?
--- /dev/null
+#!/usr/bin/env python
+
+import arvados
+import arvados.crunch
+import hashlib
+import os
+
+out = arvados.crunch.TaskOutputDir()
+
+string = open(__file__).read()
+with open(os.path.join(out.path, 'example.out'), 'w') as f:
+ f.write(string)
+with open(os.path.join(out.path, 'example.out.SHA1'), 'w') as f:
+ f.write(hashlib.sha1(string).hexdigest() + "\n")
+
+arvados.current_task().set_output(out.manifest_text())
<notextile>
<pre><code>~$ <span class="userinput">cd tutorial</span>
-~$ <span class="userinput">git checkout -b tutorial_branch</span>
+~/tutorial$ <span class="userinput">git checkout -b tutorial_branch</span>
</code></pre>
</notextile>
-h2. Adding files or scripts to an Arvados repository
+h2. Adding scripts to an Arvados repository
-First, create a file named *tutorial.txt* in the local repository. Although this tutorial shows how to add a text file to Arvados, the same steps can be used to add any of your custom bash, R, or python scripts to an Arvados repository.
+Arvados crunch scripts need to be added in a *crunch_scripts* subdirectory in the repository. If this subdirectory does not exist, first create it in the local repository and change to that directory:
<notextile>
-<pre><code>~$ <span class="userinput">echo 'hello world' > tutorial.txt</span>
-</code></pre>
+<pre><code>~/tutorial$ <span class="userinput">mkdir crunch_scripts</span>
+~/tutorial$ <span class="userinput">cd crunch_scripts</span></code></pre>
</notextile>
-Next, add the new file to the git index.
+Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
-<notextile>
-<pre><code>~$ <span class="userinput">git add tutorial.txt</span>
-</code></pre>
-</notextile>
+notextile. <pre>~/tutorial/crunch_scripts$ <code class="userinput">nano hash.py</code></pre>
+
+Add the following code to compute the MD5 hash of each file in a collection
+
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
-Next, commit all the changes to the local repository, along with a commit message that describes what this script does.
+Make the file executable:
+
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
+
+Next, add the file to the git repository. This tells @git@ that the file should be included on the next commit.
+
+notextile. <pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git add hash.py</span></code></pre>
+
+Next, commit your changes. All staged changes are recorded into the local git repository:
<notextile>
-<pre><code>~$ <span class="userinput">git commit -a -m "Added tutorial.txt"</span>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git commit -m "my first script"</span>
</code></pre>
</notextile>
-Finally, push the changes in the local repository to the remote repository.
+Finally, upload your changes to the remote repository:
<notextile>
-<pre><code>~$ <span class="userinput">git push origin tutorial_branch</span>
+<pre><code>~/tutorial/crunch_scripts$ <span class="userinput">git push origin tutorial_branch</span>
</code></pre>
</notextile>
+
+Although this tutorial shows how to add a python script to Arvados, the same steps can be used to add any of your custom bash, R, or python scripts to an Arvados repository.
--- /dev/null
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
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s.email = 'gem-dev@curoverse.com'
#s.bindir = '.'
s.licenses = ['Apache License, Version 2.0']
- s.files = ["bin/arv","bin/arv-run-pipeline-instance","bin/arv-crunch-job","bin/arv-tag","bin/crunch-job"]
+ s.files = ["bin/arv", "bin/arv-run-pipeline-instance",
+ "bin/arv-crunch-job", "bin/arv-tag", "bin/crunch-job",
+ "LICENSE-2.0.txt"]
s.executables << "arv"
s.executables << "arv-run-pipeline-instance"
s.executables << "arv-crunch-job"
my $no_clear_tmp;
my $resume_stash;
my $docker_bin = "docker.io";
+my $docker_run_args = "";
GetOptions('force-unlock' => \$force_unlock,
'git-dir=s' => \$git_dir,
'job=s' => \$jobspec,
'no-clear-tmp' => \$no_clear_tmp,
'resume-stash=s' => \$resume_stash,
'docker-bin=s' => \$docker_bin,
+ 'docker-run-args=s' => \$docker_run_args,
);
if (defined $job_api_token) {
}
srun(["srun", "--nodelist=" . $node[0]],
["/bin/sh", "-ec",
- "a=`$docker_bin run $try_user_arg $docker_hash id --user` && " .
+ "a=`$docker_bin run $docker_run_args $try_user_arg $docker_hash id --user` && " .
" test \$a -ne 0"],
{fork => 1});
if ($? == 0) {
$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
$ENV{"TASK_WORK"} = $ENV{"CRUNCH_TMP"}."/task/$childslotname";
$ENV{"HOME"} = $ENV{"TASK_WORK"};
- $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
$ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
$ENV{"CRUNCH_NODE_SLOTS"} = $round_max_slots{$ENV{TASK_SLOT_NODE}};
$ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};
+ my $keep_mnt = $ENV{"TASK_WORK"}.".keep";
+
$ENV{"GZIP"} = "-n";
my @srunargs = (
}
my $command =
- "if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
- ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
- ."&& cd $ENV{CRUNCH_TMP} "
+ "if [ -e \Q$ENV{TASK_WORK}\E ]; then rm -rf \Q$ENV{TASK_WORK}\E; fi; "
+ ."mkdir -p \Q$ENV{CRUNCH_TMP}\E \Q$ENV{JOB_WORK}\E \Q$ENV{TASK_WORK}\E \Q$keep_mnt\E "
+ ."&& cd \Q$ENV{CRUNCH_TMP}\E "
# These environment variables get used explicitly later in
# $command. No tool is expected to read these values directly.
.q{&& MEM=$(awk '($1 == "MemTotal:"){print $2}' </proc/meminfo) }
.q{&& SWAP=$(awk '($1 == "SwapTotal:"){print $2}' </proc/meminfo) }
."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP ";
- $command .= "&& exec arv-mount --by-pdh --crunchstat-interval=10 --allow-other $arv_file_cache $ENV{TASK_KEEPMOUNT} --exec ";
+
+ $command .= "&& exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other $arv_file_cache \Q$keep_mnt\E --exec ";
+ $ENV{TASK_KEEPMOUNT} = "$keep_mnt/by_pdh";
+ $ENV{TASK_KEEPMOUNT_TMP} = "$keep_mnt/tmp";
+
if ($docker_hash)
{
my $containername = "$Jobstep->{arvados_task}->{uuid}-$Jobstep->{failures}";
my $cidfile = "$ENV{CRUNCH_TMP}/$containername.cid";
$command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$cidfile -poll=10000 ";
- $command .= "$docker_bin run --name=$containername --attach=stdout --attach=stderr --attach=stdin -i \Q$dockeruserarg\E --cidfile=$cidfile --sig-proxy ";
+ $command .= "$docker_bin run $docker_run_args --name=$containername --attach=stdout --attach=stderr --attach=stdin -i \Q$dockeruserarg\E --cidfile=$cidfile --sig-proxy ";
# We only set memory limits if Docker lets us limit both memory and swap.
# Memory limits alone have been supported longer, but subprocesses tend
# to get SIGKILL if they exceed that without any swap limit set.
$command .= "--volume=\Q$ENV{CRUNCH_SRC}:$ENV{CRUNCH_SRC}:ro\E ";
$command .= "--volume=\Q$ENV{CRUNCH_INSTALL}:$ENV{CRUNCH_INSTALL}:ro\E ";
- # Currently, we make arv-mount's mount point appear at /keep
- # inside the container (instead of using the same path as the
- # host like we do with CRUNCH_SRC and CRUNCH_INSTALL). However,
- # crunch scripts and utilities must not rely on this. They must
- # use $TASK_KEEPMOUNT.
+ # Currently, we make the "by_pdh" directory in arv-mount's mount
+ # point appear at /keep inside the container (instead of using
+ # the same path as the host like we do with CRUNCH_SRC and
+ # CRUNCH_INSTALL). However, crunch scripts and utilities must
+ # not rely on this. They must use $TASK_KEEPMOUNT.
$command .= "--volume=\Q$ENV{TASK_KEEPMOUNT}:/keep:ro\E ";
$ENV{TASK_KEEPMOUNT} = "/keep";
+ # Ditto TASK_KEEPMOUNT_TMP, as /keep_tmp.
+ $command .= "--volume=\Q$ENV{TASK_KEEPMOUNT_TMP}:/keep_tmp\E ";
+ $ENV{TASK_KEEPMOUNT_TMP} = "/keep_tmp";
+
# TASK_WORK is almost exactly like a docker data volume: it
# starts out empty, is writable, and persists until no
# containers use it any more. We don't use --volumes-from to
if (!defined $task_success) {
# task did not indicate one way or the other --> fail
Log($jobstepid, sprintf(
- "ERROR: Task process exited %d, but never updated its task record to indicate success and record its output.",
+ "ERROR: Task process exited %s, but never updated its task record to indicate success and record its output.",
exit_status_s($childstatus)));
$Jobstep->{'arvados_task'}->{success} = 0;
$Jobstep->{'arvados_task'}->save;
`./foo\040b\141r acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:b\141z\040w\141z` + "\n" +
"./foo acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:zero 0:3:foo\n" +
". acbd18db4cc2f85cedef654fccc4a4d8+3 0:0:foo/zero 0:3:foo/foo\n"
+
+// An MD5 collision.
+var (
+ MD5CollisionData = [][]byte{
+ []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9epO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\\\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef"),
+ []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9etO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\xdc\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef"),
+ }
+ MD5CollisionMD5 = "cee9a457e790cf20d4bdaa6d69f01e41"
+)
stream.offset += count
- stream.ManifestStream.Files = append(stream.ManifestStream.Files,
+ stream.ManifestStream.FileTokens = append(stream.ManifestStream.FileTokens,
fmt.Sprintf("%v:%v:%v", fileStart, count, fn))
return nil
buf.WriteString(" ")
buf.WriteString(b)
}
- for _, f := range v.Files {
+ for _, f := range v.FileTokens {
buf.WriteString(" ")
f = strings.Replace(f, " ", "\\040", -1)
f = strings.Replace(f, "\n", "", -1)
timer.Reset(interval)
if err := kc.DiscoverKeepServers(); err != nil {
- log.Println("Error retrieving services list: %v (retrying in %v)", err, errInterval)
+ log.Printf("WARNING: Error retrieving services list: %v (retrying in %v)", err, errInterval)
timer.Reset(errInterval)
continue
}
newRoots := []map[string]string{kc.LocalRoots(), kc.GatewayRoots()}
if !reflect.DeepEqual(previousRoots, newRoots) {
- log.Printf("Updated services list: locals %v gateways %v", newRoots[0], newRoots[1])
+ DebugPrintf("DEBUG: Updated services list: locals %v gateways %v", newRoots[0], newRoots[1])
previousRoots = newRoots
}
// replicasPerService is 1 for disks; unknown or unlimited otherwise
this.replicasPerService = 1
- this.Using_proxy = false
for _, service := range list.Items {
scheme := "http"
listed[url] = true
localRoots[service.Uuid] = url
- if service.SvcType == "proxy" {
- this.Using_proxy = true
- }
-
if service.ReadOnly == false {
writableLocalRoots[service.Uuid] = url
if service.SvcType != "disk" {
}
}
+ if service.SvcType != "disk" {
+ this.foundNonDiskSvc = true
+ }
+
// Gateway services are only used when specified by
// UUID, so there's nothing to gain by filtering them
// by service type. Including all accessible services
gatewayRoots[service.Uuid] = url
}
- if this.Using_proxy {
- this.setClientSettingsProxy()
+ if this.foundNonDiskSvc {
+ this.setClientSettingsNonDisk()
} else {
this.setClientSettingsDisk()
}
"git.curoverse.com/arvados.git/sdk/go/streamer"
"io"
"io/ioutil"
- "log"
"net/http"
"regexp"
"strconv"
type KeepClient struct {
Arvados *arvadosclient.ArvadosClient
Want_replicas int
- Using_proxy bool
localRoots *map[string]string
writableLocalRoots *map[string]string
gatewayRoots *map[string]string
// set to 1 if all writable services are of disk type, otherwise 0
replicasPerService int
+
+ // Any non-disk typed services found in the list of keepservers?
+ foundNonDiskSvc bool
}
// MakeKeepClient creates a new KeepClient by contacting the API server to discover Keep servers.
kc := &KeepClient{
Arvados: arv,
Want_replicas: defaultReplicationLevel,
- Using_proxy: false,
Client: &http.Client{Transport: &http.Transport{
TLSClientConfig: &tls.Config{InsecureSkipVerify: arv.ApiInsecure}}},
Retries: 2,
}
serversToTry = retryList
}
- log.Printf("DEBUG: %s %s failed: %v", method, locator, errs)
+ DebugPrintf("DEBUG: %s %s failed: %v", method, locator, errs)
var err error
if count404 == numServers {
"os"
"strings"
"testing"
+ "time"
)
// Gocheck boilerplate
status := <-upload_status
c.Check(status, DeepEquals, uploadStatus{nil, fmt.Sprintf("%s/%s", url, st.expectPath), 200, 1, ""})
})
-
- log.Printf("TestUploadToStubKeepServer done")
}
func (s *StandaloneSuite) TestUploadToStubKeepServerBufferReader(c *C) {
- log.Printf("TestUploadToStubKeepServerBufferReader")
-
st := StubPutHandler{
c,
"acbd18db4cc2f85cedef654fccc4a4d8",
status := <-upload_status
c.Check(status, DeepEquals, uploadStatus{nil, fmt.Sprintf("%s/%s", url, st.expectPath), 200, 1, ""})
})
-
- log.Printf("TestUploadToStubKeepServerBufferReader done")
}
type FailHandler struct {
}
func (s *StandaloneSuite) TestFailedUploadToStubKeepServer(c *C) {
- log.Printf("TestFailedUploadToStubKeepServer")
-
st := FailHandler{
make(chan string)}
c.Check(status.url, Equals, fmt.Sprintf("%s/%s", url, hash))
c.Check(status.statusCode, Equals, 500)
})
- log.Printf("TestFailedUploadToStubKeepServer done")
}
type KeepServer struct {
}
func (s *StandaloneSuite) TestPutB(c *C) {
- log.Printf("TestPutB")
-
hash := Md5String("foo")
st := StubPutHandler{
(s1 == shuff[1] && s2 == shuff[0]),
Equals,
true)
-
- log.Printf("TestPutB done")
}
func (s *StandaloneSuite) TestPutHR(c *C) {
- log.Printf("TestPutHR")
-
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
st := StubPutHandler{
kc.PutHR(hash, reader, 3)
shuff := NewRootSorter(kc.LocalRoots(), hash).GetSortedRoots()
- log.Print(shuff)
s1 := <-st.handled
s2 := <-st.handled
(s1 == shuff[1] && s2 == shuff[0]),
Equals,
true)
-
- log.Printf("TestPutHR done")
}
func (s *StandaloneSuite) TestPutWithFail(c *C) {
- log.Printf("TestPutWithFail")
-
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
st := StubPutHandler{
shuff := NewRootSorter(
kc.LocalRoots(), Md5String("foo")).GetSortedRoots()
+ c.Logf("%+v", shuff)
phash, replicas, err := kc.PutB([]byte("foo"))
}
func (s *StandaloneSuite) TestPutWithTooManyFail(c *C) {
- log.Printf("TestPutWithTooManyFail")
-
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
st := StubPutHandler{
c.Check(err, Equals, InsufficientReplicasError)
c.Check(replicas, Equals, 1)
c.Check(<-st.handled, Equals, ks1[0].url)
-
- log.Printf("TestPutWithTooManyFail done")
}
type StubGetHandler struct {
}
func (s *StandaloneSuite) TestGet(c *C) {
- log.Printf("TestGet")
-
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
st := StubGetHandler{
content, err2 := ioutil.ReadAll(r)
c.Check(err2, Equals, nil)
c.Check(content, DeepEquals, []byte("foo"))
-
- log.Printf("TestGet done")
}
func (s *StandaloneSuite) TestGet404(c *C) {
}
func (s *StandaloneSuite) TestPutProxy(c *C) {
- log.Printf("TestPutProxy")
-
st := StubProxyHandler{make(chan string, 1)}
arv, err := arvadosclient.MakeArvadosClient()
kc, _ := MakeKeepClient(&arv)
kc.Want_replicas = 2
- kc.Using_proxy = true
arv.ApiToken = "abc123"
localRoots := make(map[string]string)
writableLocalRoots := make(map[string]string)
c.Check(err, Equals, nil)
c.Check(replicas, Equals, 2)
-
- log.Printf("TestPutProxy done")
}
func (s *StandaloneSuite) TestPutProxyInsufficientReplicas(c *C) {
- log.Printf("TestPutProxy")
-
st := StubProxyHandler{make(chan string, 1)}
arv, err := arvadosclient.MakeArvadosClient()
kc, _ := MakeKeepClient(&arv)
kc.Want_replicas = 3
- kc.Using_proxy = true
arv.ApiToken = "abc123"
localRoots := make(map[string]string)
writableLocalRoots := make(map[string]string)
c.Check(err, Equals, InsufficientReplicasError)
c.Check(replicas, Equals, 2)
-
- log.Printf("TestPutProxy done")
}
func (s *StandaloneSuite) TestMakeLocator(c *C) {
c.Check(hash, Equals, "")
c.Check(replicas, Equals, 2)
}
+
+func (s *ServerRequiredSuite) TestMakeKeepClientWithNonDiskTypeService(c *C) {
+ arv, err := arvadosclient.MakeArvadosClient()
+ c.Assert(err, Equals, nil)
+
+ // Add an additional "testblobstore" keepservice
+ blobKeepService := make(arvadosclient.Dict)
+ err = arv.Create("keep_services",
+ arvadosclient.Dict{"keep_service": arvadosclient.Dict{
+ "service_host": "localhost",
+ "service_port": "21321",
+ "service_type": "testblobstore"}},
+ &blobKeepService)
+ c.Assert(err, Equals, nil)
+ defer func() { arv.Delete("keep_services", blobKeepService["uuid"].(string), nil, nil) }()
+
+ // Make a keepclient and ensure that the testblobstore is included
+ kc, err := MakeKeepClient(&arv)
+ c.Assert(err, Equals, nil)
+
+ // verify kc.LocalRoots
+ c.Check(len(kc.LocalRoots()), Equals, 3)
+ for _, root := range kc.LocalRoots() {
+ c.Check(root, Matches, "http://localhost:\\d+")
+ }
+ c.Assert(kc.LocalRoots()[blobKeepService["uuid"].(string)], Not(Equals), "")
+
+ // verify kc.GatewayRoots
+ c.Check(len(kc.GatewayRoots()), Equals, 3)
+ for _, root := range kc.GatewayRoots() {
+ c.Check(root, Matches, "http://localhost:\\d+")
+ }
+ c.Assert(kc.GatewayRoots()[blobKeepService["uuid"].(string)], Not(Equals), "")
+
+ // verify kc.WritableLocalRoots
+ c.Check(len(kc.WritableLocalRoots()), Equals, 3)
+ for _, root := range kc.WritableLocalRoots() {
+ c.Check(root, Matches, "http://localhost:\\d+")
+ }
+ c.Assert(kc.WritableLocalRoots()[blobKeepService["uuid"].(string)], Not(Equals), "")
+
+ c.Assert(kc.replicasPerService, Equals, 0)
+ c.Assert(kc.foundNonDiskSvc, Equals, true)
+ c.Assert(kc.Client.Timeout, Equals, 300*time.Second)
+}
"git.curoverse.com/arvados.git/sdk/go/streamer"
"io"
"io/ioutil"
- "log"
"math/rand"
"net"
"net/http"
return fmt.Sprintf("%x", md5.Sum([]byte(s)))
}
-// Set timeouts apply when connecting to keepproxy services (assumed to be over
-// the Internet).
-func (this *KeepClient) setClientSettingsProxy() {
+// Set timeouts applicable when connecting to non-disk services
+// (assumed to be over the Internet).
+func (this *KeepClient) setClientSettingsNonDisk() {
if this.Client.Timeout == 0 {
// Maximum time to wait for a complete response
this.Client.Timeout = 300 * time.Second
}
}
-// Set timeouts apply when connecting to keepstore services directly (assumed
-// to be on the local network).
+// Set timeouts applicable when connecting to keepstore services directly
+// (assumed to be on the local network).
func (this *KeepClient) setClientSettingsDisk() {
if this.Client.Timeout == 0 {
// Maximum time to wait for a complete response
var err error
var url = fmt.Sprintf("%s/%s", host, hash)
if req, err = http.NewRequest("PUT", url, nil); err != nil {
- log.Printf("[%08x] Error creating request PUT %v error: %v", requestID, url, err.Error())
+ DebugPrintf("DEBUG: [%08x] Error creating request PUT %v error: %v", requestID, url, err.Error())
upload_status <- uploadStatus{err, url, 0, 0, ""}
body.Close()
return
var resp *http.Response
if resp, err = this.Client.Do(req); err != nil {
- log.Printf("[%08x] Upload failed %v error: %v", requestID, url, err.Error())
+ DebugPrintf("DEBUG: [%08x] Upload failed %v error: %v", requestID, url, err.Error())
upload_status <- uploadStatus{err, url, 0, 0, ""}
return
}
respbody, err2 := ioutil.ReadAll(&io.LimitedReader{R: resp.Body, N: 4096})
response := strings.TrimSpace(string(respbody))
if err2 != nil && err2 != io.EOF {
- log.Printf("[%08x] Upload %v error: %v response: %v", requestID, url, err2.Error(), response)
+ DebugPrintf("DEBUG: [%08x] Upload %v error: %v response: %v", requestID, url, err2.Error(), response)
upload_status <- uploadStatus{err2, url, resp.StatusCode, rep, response}
} else if resp.StatusCode == http.StatusOK {
- log.Printf("[%08x] Upload %v success", requestID, url)
+ DebugPrintf("DEBUG: [%08x] Upload %v success", requestID, url)
upload_status <- uploadStatus{nil, url, resp.StatusCode, rep, response}
} else {
- log.Printf("[%08x] Upload %v error: %v response: %v", requestID, url, resp.StatusCode, response)
+ DebugPrintf("DEBUG: [%08x] Upload %v error: %v response: %v", requestID, url, resp.StatusCode, response)
upload_status <- uploadStatus{errors.New(resp.Status), url, resp.StatusCode, rep, response}
}
}
for active*replicasPerThread < remaining_replicas {
// Start some upload requests
if next_server < len(sv) {
- log.Printf("[%08x] Begin upload %s to %s", requestID, hash, sv[next_server])
+ DebugPrintf("DEBUG: [%08x] Begin upload %s to %s", requestID, hash, sv[next_server])
go this.uploadToKeepServer(sv[next_server], hash, tr.MakeStreamReader(), upload_status, expectedLength, requestID)
next_server += 1
active += 1
}
}
}
- log.Printf("[%08x] Replicas remaining to write: %v active uploads: %v",
+ DebugPrintf("DEBUG: [%08x] Replicas remaining to write: %v active uploads: %v",
requestID, remaining_replicas, active)
// Now wait for something to happen.
--- /dev/null
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+
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+
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+ "You" (or "Your") shall mean an individual or Legal Entity
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
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+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+ 8. Limitation of Liability. In no event and under no legal theory,
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+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
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+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+include LICENSE-2.0.txt
include README.rst
include examples/shellinabox
include lib/libpam_arvados.py
#!/usr/bin/env python
+import glob
import os
import sys
import setuptools.command.egg_info as egg_info_cmd
],
data_files=[
('lib/security', ['lib/libpam_arvados.py']),
- ('share/arvados-pam', ['examples/shellinabox']),
('share/pam-configs', ['pam-configs/arvados']),
+ ('share/doc/arvados-pam', ['LICENSE-2.0.txt', 'README.rst']),
+ ('share/doc/arvados-pam/examples', glob.glob('examples/*')),
],
install_requires=[
'arvados-python-client>=0.1.20150801000000',
--- /dev/null
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
+ publicly display, publicly perform, sublicense, and distribute the
+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+include LICENSE-2.0.txt
include README.rst
files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
if files:
- uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.num_retries, project=project)
+ uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.retries, project=project)
for i in xrange(1, len(slots)):
slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]]
--- /dev/null
+import json
+import os
+
+class TaskOutputDir(object):
+ """Keep-backed directory for staging outputs of Crunch tasks.
+
+ Example, in a crunch task whose output is a file called "out.txt"
+ containing "42":
+
+ import arvados
+ import arvados.crunch
+ import os
+
+ out = arvados.crunch.TaskOutputDir()
+ with open(os.path.join(out.path, 'out.txt'), 'w') as f:
+ f.write('42')
+ arvados.current_task().set_output(out.manifest_text())
+ """
+ def __init__(self):
+ self.path = os.environ['TASK_KEEPMOUNT_TMP']
+
+ def __str__(self):
+ return self.path
+
+ def manifest_text(self):
+ snapshot = os.path.join(self.path, '.arvados#collection')
+ return json.load(open(snapshot))['manifest_text']
'bin/arv-run',
'bin/arv-ws'
],
+ data_files=[
+ ('share/doc/arvados-python-client', ['LICENSE-2.0.txt', 'README.rst']),
+ ],
install_requires=[
'ciso8601',
'google-api-python-client',
--- /dev/null
+import arvados.crunch
+import os
+import shutil
+import tempfile
+import unittest
+
+class TaskOutputDirTest(unittest.TestCase):
+ def setUp(self):
+ self.tmp = tempfile.mkdtemp()
+ os.environ['TASK_KEEPMOUNT_TMP'] = self.tmp
+
+ def tearDown(self):
+ os.environ.pop('TASK_KEEPMOUNT_TMP')
+ shutil.rmtree(self.tmp)
+
+ def test_env_var(self):
+ out = arvados.crunch.TaskOutputDir()
+ self.assertEqual(out.path, self.tmp)
+
+ with open(os.path.join(self.tmp, '.arvados#collection'), 'w') as f:
+ f.write('{\n "manifest_text":"",\n "uuid":null\n}\n')
+ self.assertEqual(out.manifest_text(), '')
+
+ # Special file must be re-read on each call to manifest_text().
+ with open(os.path.join(self.tmp, '.arvados#collection'), 'w') as f:
+ f.write(r'{"manifest_text":". unparsed 0:3:foo\n","uuid":null}')
+ self.assertEqual(out.manifest_text(), ". unparsed 0:3:foo\n")
--- /dev/null
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
+ publicly display, publicly perform, sublicense, and distribute the
+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
s.email = 'gem-dev@curoverse.com'
s.licenses = ['Apache License, Version 2.0']
s.files = ["lib/arvados.rb", "lib/arvados/google_api_client.rb",
- "lib/arvados/collection.rb", "lib/arvados/keep.rb"]
+ "lib/arvados/collection.rb", "lib/arvados/keep.rb",
+ "README", "LICENSE-2.0.txt"]
s.required_ruby_version = '>= 2.1.0'
s.add_dependency('google-api-client', '~> 0.6.3', '>= 0.6.3')
s.add_dependency('activesupport', '>= 3.2.13')
if request.headers['X-External-Client'] == '1'
@objects = model_class.where('service_type=?', 'proxy')
else
- @objects = model_class.where('service_type=?', 'disk')
+ @objects = model_class.where(model_class.arel_table[:service_type].not_eq('proxy'))
end
render_list
end
end
@docker_bin = ENV['CRUNCH_JOB_DOCKER_BIN']
+ @docker_run_args = ENV['CRUNCH_JOB_DOCKER_RUN_ARGS']
@arvados_internal = Rails.configuration.git_internal_dir
if not File.exists? @arvados_internal
cmd_args += ['--docker-bin', @docker_bin]
end
+ if @docker_run_args
+ cmd_args += ['--docker-run-args', @docker_run_args]
+ end
+
if have_job_lock?(job)
cmd_args << "--force-unlock"
end
script_parameters:
input: fa7aeb5140e2848d39b416daeef4ffc5+45
input2: "stuff2"
- log: ~
+ log: zzzzz-4zz18-4en62shvi99lxd4
output: b519d9cb706a29fc7ea24dbea2f05851+93
job_in_publicly_accessible_project_but_other_objects_elsewhere:
class Arvados::V1::KeepServicesControllerTest < ActionController::TestCase
- test "search keep_services by service_port with < query" do
+ test "search by service_port with < query" do
authorize_with :active
get :index, {
filters: [['service_port', '<', 25107]]
assert_equal false, assigns(:objects).any?
end
- test "search keep_disks by service_port with >= query" do
+ test "search by service_port with >= query" do
authorize_with :active
get :index, {
filters: [['service_port', '>=', 25107]]
assert_equal true, assigns(:objects).any?
end
+ [:admin, :active, :inactive, :anonymous].each do |u|
+ test "accessible to #{u} user" do
+ authorize_with u
+ get :accessible
+ assert_response :success
+ assert_not_empty json_response['items']
+ json_response['items'].each do |ks|
+ assert_not_equal ks['service_type'], 'proxy'
+ end
+ end
+ end
+
end
var (
HeapProfileFilename string
- // globals for debugging
- totalManifestSize uint64
- maxManifestSize uint64
)
// Collection representation
CollectionUUIDToIndex map[string]int
CollectionIndexToUUID []string
BlockToCollectionIndices map[blockdigest.DigestWithSize][]int
- Err error
}
// GetCollectionsParams params
}
// GetCollectionsAndSummarize gets collections from api and summarizes
-func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections) {
- results, err := GetCollections(params)
+func GetCollectionsAndSummarize(params GetCollectionsParams) (results ReadCollections, err error) {
+ results, err = GetCollections(params)
if err != nil {
- results.Err = err
return
}
}
// Process collection and update our date filter.
- var latestModificationDate time.Time
- latestModificationDate, err = ProcessCollections(params.Logger,
+ latestModificationDate, maxManifestSize, totalManifestSize, err := ProcessCollections(params.Logger,
collections.Items,
defaultReplicationLevel,
results.UUIDToCollection)
if err != nil {
- return
+ return results, err
}
sdkParams["filters"].([][]string)[0][2] = latestModificationDate.Format(time.RFC3339)
func ProcessCollections(arvLogger *logger.Logger,
receivedCollections []SdkCollectionInfo,
defaultReplicationLevel int,
- UUIDToCollection map[string]Collection) (latestModificationDate time.Time, err error) {
+ UUIDToCollection map[string]Collection,
+) (
+ latestModificationDate time.Time,
+ maxManifestSize, totalManifestSize uint64,
+ err error,
+) {
for _, sdkCollection := range receivedCollections {
collection := Collection{UUID: StrCopy(sdkCollection.UUID),
OwnerUUID: StrCopy(sdkCollection.OwnerUUID),
BlockDigestToSize: make(map[blockdigest.BlockDigest]int)}
if sdkCollection.ModifiedAt.IsZero() {
- return latestModificationDate, fmt.Errorf(
+ err = fmt.Errorf(
"Arvados SDK collection returned with unexpected zero "+
"modification date. This probably means that either we failed to "+
"parse the modification date or the API server has changed how "+
"it returns modification dates: %+v",
collection)
+ return
}
if sdkCollection.ModifiedAt.After(latestModificationDate) {
}
// GetCollectionsAndSummarize
- results := GetCollectionsAndSummarize(GetCollectionsParams{arv, nil, 10})
+ _, err := GetCollectionsAndSummarize(GetCollectionsParams{arv, nil, 10})
if testData.expectedError == "" {
- c.Assert(results.Err, IsNil)
+ c.Assert(err, IsNil)
} else {
- c.Assert(results.Err, ErrorMatches, testData.expectedError)
+ c.Assert(err, ErrorMatches, testData.expectedError)
}
}
logEventTypePrefix string
logFrequencySeconds int
minutesBetweenRuns int
+ dryRun bool
)
func init() {
flag.IntVar(&minutesBetweenRuns,
"minutes-between-runs",
0,
- "How many minutes we wait betwen data manager runs. 0 means run once and exit.")
+ "How many minutes we wait between data manager runs. 0 means run once and exit.")
+ flag.BoolVar(&dryRun,
+ "dry-run",
+ false,
+ "Perform a dry run. Log how many blocks would be deleted/moved, but do not issue any changes to keepstore.")
}
func main() {
flag.Parse()
+
if minutesBetweenRuns == 0 {
arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
dataFetcher = BuildDataFetcher(arv)
}
- dataFetcher(arvLogger, &readCollections, &keepServerInfo)
-
- if readCollections.Err != nil {
- return readCollections.Err
+ err = dataFetcher(arvLogger, &readCollections, &keepServerInfo)
+ if err != nil {
+ return err
}
err = summary.MaybeWriteData(arvLogger, readCollections, keepServerInfo)
&keepServerInfo,
replicationSummary.KeepBlocksNotInCollections)
- err = summary.WritePullLists(arvLogger, pullLists)
+ err = summary.WritePullLists(arvLogger, pullLists, dryRun)
if err != nil {
return err
}
if trashErr != nil {
return err
}
- keep.SendTrashLists(kc, trashLists)
+ keep.SendTrashLists(arvLogger, kc, trashLists, dryRun)
return nil
}
// BuildDataFetcher returns a data fetcher that fetches data from remote servers.
func BuildDataFetcher(arv arvadosclient.ArvadosClient) summary.DataFetcher {
- return func(arvLogger *logger.Logger,
+ return func(
+ arvLogger *logger.Logger,
readCollections *collection.ReadCollections,
- keepServerInfo *keep.ReadServers) {
- collectionChannel := make(chan collection.ReadCollections)
-
+ keepServerInfo *keep.ReadServers,
+ ) error {
+ collDone := make(chan struct{})
+ var collErr error
go func() {
- collectionChannel <- collection.GetCollectionsAndSummarize(
+ *readCollections, collErr = collection.GetCollectionsAndSummarize(
collection.GetCollectionsParams{
Client: arv,
Logger: arvLogger,
BatchSize: 50})
+ collDone <- struct{}{}
}()
- var err error
- *keepServerInfo, err = keep.GetKeepServersAndSummarize(
+ var keepErr error
+ *keepServerInfo, keepErr = keep.GetKeepServersAndSummarize(
keep.GetKeepServersParams{
Client: arv,
Logger: arvLogger,
Limit: 1000})
- if err != nil {
- return
- }
+ <- collDone
- *readCollections = <-collectionChannel
+ // Return a nil error only if both parts succeeded.
+ if collErr != nil {
+ return collErr
+ }
+ return keepErr
}
}
keepClient = &keepclient.KeepClient{
Arvados: &arv,
Want_replicas: 2,
- Using_proxy: true,
Client: &http.Client{},
}
}
var locs []string
- for k, _ := range locators {
+ for k := range locators {
locs = append(locs, k)
}
// Also, create stray block and backdate it.
// After datamanager run: expect blocks from the collection, but not the stray block.
func TestManifestWithMultipleStreamsAndBlocks(t *testing.T) {
+ testManifestWithMultipleStreamsAndBlocks(t, 100, 10, "", false)
+}
+
+// Same test as TestManifestWithMultipleStreamsAndBlocks with an additional
+// keepstore of a service type other than "disk". Only the "disk" type services
+// will be indexed by datamanager and hence should work the same way.
+func TestManifestWithMultipleStreamsAndBlocks_WithOneUnsupportedKeepServer(t *testing.T) {
+ testManifestWithMultipleStreamsAndBlocks(t, 2, 2, "testblobstore", false)
+}
+
+// Test datamanager with dry-run. Expect no block to be deleted.
+func TestManifestWithMultipleStreamsAndBlocks_DryRun(t *testing.T) {
+ testManifestWithMultipleStreamsAndBlocks(t, 2, 2, "", true)
+}
+
+func testManifestWithMultipleStreamsAndBlocks(t *testing.T, numStreams, numBlocks int, createExtraKeepServerWithType string, isDryRun bool) {
defer TearDownDataManagerTest(t)
SetupDataManagerTest(t)
// create collection whose blocks will be backdated
- collectionWithOldBlocks, oldBlocks := createMultiStreamBlockCollection(t, "old block", 100, 10)
+ collectionWithOldBlocks, oldBlocks := createMultiStreamBlockCollection(t, "old block", numStreams, numBlocks)
if collectionWithOldBlocks == "" {
- t.Fatalf("Failed to create collection with 1000 blocks")
+ t.Fatalf("Failed to create collection with %d blocks", numStreams*numBlocks)
}
- if len(oldBlocks) != 1000 {
+ if len(oldBlocks) != numStreams*numBlocks {
t.Fatalf("Not all blocks are created: expected %v, found %v", 1000, len(oldBlocks))
}
// also backdate the stray old block
backdateBlocks(t, []string{strayOldBlock})
+ // If requested, create an extra keepserver with the given type
+ // This should be ignored during indexing and hence not change the datamanager outcome
+ var extraKeepServerUUID string
+ if createExtraKeepServerWithType != "" {
+ extraKeepServerUUID = addExtraKeepServer(t, createExtraKeepServerWithType)
+ defer deleteExtraKeepServer(extraKeepServerUUID)
+ }
+
// run datamanager
+ dryRun = isDryRun
dataManagerSingleRun(t)
- // verify that strayOldBlock is not to be found, but the collections blocks are still there
- verifyBlocks(t, []string{strayOldBlock}, oldBlocks, 2)
+ if dryRun {
+ // verify that all blocks, including strayOldBlock, are still to be found
+ verifyBlocks(t, nil, expected, 2)
+ } else {
+ // verify that strayOldBlock is not to be found, but the collections blocks are still there
+ verifyBlocks(t, []string{strayOldBlock}, oldBlocks, 2)
+ }
+}
+
+// Add one more keepstore with the given service type
+func addExtraKeepServer(t *testing.T, serviceType string) string {
+ defer switchToken(arvadostest.AdminToken)()
+
+ extraKeepService := make(arvadosclient.Dict)
+ err := arv.Create("keep_services",
+ arvadosclient.Dict{"keep_service": arvadosclient.Dict{
+ "service_host": "localhost",
+ "service_port": "21321",
+ "service_ssl_flag": false,
+ "service_type": serviceType}},
+ &extraKeepService)
+ if err != nil {
+ t.Fatal(err)
+ }
+
+ return extraKeepService["uuid"].(string)
+}
+
+func deleteExtraKeepServer(uuid string) {
+ defer switchToken(arvadostest.AdminToken)()
+ arv.Delete("keep_services", uuid, nil, nil)
}
"bufio"
"encoding/json"
"errors"
+ "flag"
"fmt"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
"git.curoverse.com/arvados.git/sdk/go/blockdigest"
KeepServers []ServerAddress `json:"items"`
}
+var serviceType string
+
+func init() {
+ flag.StringVar(&serviceType,
+ "service-type",
+ "disk",
+ "Operate only on keep_services with the specified service_type, ignoring all others.")
+}
+
// String
// TODO(misha): Change this to include the UUID as well.
func (s ServerAddress) String() string {
return
}
- // Currently, only "disk" types are supported. Stop if any other service types are found.
+ var keepServers []ServerAddress
for _, server := range sdkResponse.KeepServers {
- if server.ServiceType != "disk" {
- return results, fmt.Errorf("Unsupported service type %q found for: %v", server.ServiceType, server)
+ if server.ServiceType == serviceType {
+ keepServers = append(keepServers, server)
+ } else {
+ log.Printf("Skipping keep_service %q because its service_type %q does not match -service-type=%q", server, server.ServiceType, serviceType)
}
}
+ if len(keepServers) == 0 {
+ return results, fmt.Errorf("Found no keepservices with the service type %v", serviceType)
+ }
+
if params.Logger != nil {
params.Logger.Update(func(p map[string]interface{}, e map[string]interface{}) {
keepInfo := logger.GetOrCreateMap(p, "keep_info")
keepInfo["num_keep_servers_available"] = sdkResponse.ItemsAvailable
keepInfo["num_keep_servers_received"] = len(sdkResponse.KeepServers)
keepInfo["keep_servers"] = sdkResponse.KeepServers
+ keepInfo["indexable_keep_servers"] = keepServers
})
}
return results, fmt.Errorf("Did not receive all available keep servers: %+v", sdkResponse)
}
- results.KeepServerIndexToAddress = sdkResponse.KeepServers
+ results.KeepServerIndexToAddress = keepServers
results.KeepServerAddressToIndex = make(map[ServerAddress]int)
for i, address := range results.KeepServerIndexToAddress {
results.KeepServerAddressToIndex[address] = i
// Send off all the index requests concurrently
responseChan := make(chan ServerResponse)
- for _, keepServer := range sdkResponse.KeepServers {
+ for _, keepServer := range results.KeepServerIndexToAddress {
// The above keepsServer variable is reused for each iteration, so
// it would be shared across all goroutines. This would result in
// us querying one server n times instead of n different servers
results.BlockToServers = make(map[blockdigest.DigestWithSize][]BlockServerInfo)
// Read all the responses
- for i := range sdkResponse.KeepServers {
+ for i := range results.KeepServerIndexToAddress {
_ = i // Here to prevent go from complaining.
response := <-responseChan
type TrashList []TrashRequest
// SendTrashLists to trash queue
-func SendTrashLists(kc *keepclient.KeepClient, spl map[string]TrashList) (errs []error) {
+func SendTrashLists(arvLogger *logger.Logger, kc *keepclient.KeepClient, spl map[string]TrashList, dryRun bool) (errs []error) {
count := 0
barrier := make(chan error)
client := kc.Client
for url, v := range spl {
+ if arvLogger != nil {
+ // We need a local variable because Update doesn't call our mutator func until later,
+ // when our list variable might have been reused by the next loop iteration.
+ url := url
+ trashLen := len(v)
+ arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
+ trashListInfo := logger.GetOrCreateMap(p, "trash_list_len")
+ trashListInfo[url] = trashLen
+ })
+ }
+
+ if dryRun {
+ log.Printf("dry run, not sending trash list to service %s with %d blocks", url, len(v))
+ continue
+ }
+
count++
log.Printf("Sending trash list to %v", url)
barrier <- nil
}
})(url, v)
-
}
for i := 0; i < count; i++ {
map[string]string{"xxxx": server.URL},
map[string]string{})
- err := SendTrashLists(&kc, tl)
+ err := SendTrashLists(nil, &kc, tl, false)
c.Check(err, IsNil)
map[string]string{"xxxx": server.URL},
map[string]string{})
- err := SendTrashLists(&kc, tl)
+ err := SendTrashLists(nil, &kc, tl, false)
c.Check(err, NotNil)
c.Check(err[0], NotNil)
}
func (s *KeepSuite) TestGetKeepServers_UnsupportedServiceType(c *C) {
- testGetKeepServersFromAPI(c, APITestData{1, "notadisk", 200}, "Unsupported service type")
+ testGetKeepServersFromAPI(c, APITestData{1, "notadisk", 200}, "Found no keepservices with the service type disk")
}
func (s *KeepSuite) TestGetKeepServers_ReceivedTooFewServers(c *C) {
"git.curoverse.com/arvados.git/sdk/go/logger"
"git.curoverse.com/arvados.git/services/datamanager/collection"
"git.curoverse.com/arvados.git/services/datamanager/keep"
- "git.curoverse.com/arvados.git/services/datamanager/loggerutil"
"log"
"os"
)
// DataFetcher to fetch data from keep servers
type DataFetcher func(arvLogger *logger.Logger,
readCollections *collection.ReadCollections,
- keepServerInfo *keep.ReadServers)
+ keepServerInfo *keep.ReadServers) error
func init() {
flag.StringVar(&WriteDataTo,
// working with stale data.
func ReadData(arvLogger *logger.Logger,
readCollections *collection.ReadCollections,
- keepServerInfo *keep.ReadServers) {
+ keepServerInfo *keep.ReadServers) error {
if readDataFrom == "" {
- loggerutil.FatalWithMessage(arvLogger,
- "ReadData() called with empty filename.")
- } else {
- summaryFile, err := os.Open(readDataFrom)
- if err != nil {
- loggerutil.FatalWithMessage(arvLogger,
- fmt.Sprintf("Failed to open %s: %v", readDataFrom, err))
- }
- defer summaryFile.Close()
+ return fmt.Errorf("ReadData() called with empty filename.")
+ }
+ summaryFile, err := os.Open(readDataFrom)
+ if err != nil {
+ return err
+ }
+ defer summaryFile.Close()
- dec := gob.NewDecoder(summaryFile)
- data := serializedData{}
- err = dec.Decode(&data)
- if err != nil {
- loggerutil.FatalWithMessage(arvLogger,
- fmt.Sprintf("Failed to read summary data: %v", err))
- }
+ dec := gob.NewDecoder(summaryFile)
+ data := serializedData{}
+ err = dec.Decode(&data)
+ if err != nil {
+ return err
+ }
- // re-summarize data, so that we can update our summarizing
- // functions without needing to do all our network i/o
- data.ReadCollections.Summarize(arvLogger)
- data.KeepServerInfo.Summarize(arvLogger)
+ // re-summarize data, so that we can update our summarizing
+ // functions without needing to do all our network i/o
+ data.ReadCollections.Summarize(arvLogger)
+ data.KeepServerInfo.Summarize(arvLogger)
- *readCollections = data.ReadCollections
- *keepServerInfo = data.KeepServerInfo
- log.Printf("Read summary data from: %s", readDataFrom)
- }
+ *readCollections = data.ReadCollections
+ *keepServerInfo = data.KeepServerInfo
+ log.Printf("Read summary data from: %s", readDataFrom)
+ return nil
}
// This is just a hack for prototyping, it is not expected to be used
// in production.
func WritePullLists(arvLogger *logger.Logger,
- pullLists map[string]PullList) error {
+ pullLists map[string]PullList,
+ dryRun bool) error {
r := strings.NewReplacer(":", ".")
+
for host, list := range pullLists {
+ if arvLogger != nil {
+ // We need a local variable because Update doesn't call our mutator func until later,
+ // when our list variable might have been reused by the next loop iteration.
+ host := host
+ listLen := len(list)
+ arvLogger.Update(func(p map[string]interface{}, e map[string]interface{}) {
+ pullListInfo := logger.GetOrCreateMap(p, "pull_list_len")
+ pullListInfo[host] = listLen
+ })
+ }
+
+ if dryRun {
+ log.Print("dry run, not sending pull list to service %s with %d blocks", host, len(list))
+ continue
+ }
+
filename := fmt.Sprintf("pull_list.%s", r.Replace(RemoveProtocolPrefix(host)))
pullListFile, err := os.Create(filename)
if err != nil {
}
log.Printf("Wrote pull list to %s.", filename)
}
+
return nil
}
--- /dev/null
+include agpl-3.0.txt
--- /dev/null
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+ A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+ The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community. It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+ An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU Affero General Public License.
+
+ "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
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+"recipients" may be individuals or organizations.
+
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download_url="https://github.com/curoverse/arvados.git",
license="GNU Affero General Public License version 3.0",
packages=find_packages(),
+ data_files=[
+ ('share/doc/arvados-docker-cleaner', ['agpl-3.0.txt']),
+ ],
install_requires=[
'docker-py',
],
+include agpl-3.0.txt
include README.rst
--- /dev/null
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+ b) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by a
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+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
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+ more than your reasonable cost of physically performing this
+ conveying of source, or (2) access to copy the
+ Corresponding Source from a network server at no charge.
+
+ c) Convey individual copies of the object code with a copy of the
+ written offer to provide the Corresponding Source. This
+ alternative is allowed only occasionally and noncommercially, and
+ only if you received the object code with such an offer, in accord
+ with subsection 6b.
+
+ d) Convey the object code by offering access from a designated
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+ Corresponding Source in the same way through the same place at no
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+ Corresponding Source along with the object code. If the place to
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+
+ e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.
+
+ A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
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+ A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
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+specifically for use in, a User Product, and the conveying occurs as
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+unpacking, reading or copying.
+
+ 7. Additional Terms.
+
+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
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+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
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+ a) Disclaiming warranty or limiting liability differently from the
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+
+ All other non-permissive additional terms are considered "further
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+ If you add terms to a covered work in accord with this section, you
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+ Additional terms, permissive or non-permissive, may be stated in the
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+
+ 8. Termination.
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+ You may not propagate or modify a covered work except as expressly
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+
+ However, if you cease all violation of this License, then your
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+ Termination of your rights under this section does not terminate the
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+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
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+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
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+ An "entity transaction" is a transaction transferring control of an
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+any patent claim is infringed by making, using, selling, offering for
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+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
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+
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
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+
+ In the following three paragraphs, a "patent license" is any express
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+sue for patent infringement). To "grant" such a patent license to a
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+ If you convey a covered work, knowingly relying on a patent license,
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+available, or (2) arrange to deprive yourself of the benefit of the
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+consistent with the requirements of this License, to extend the patent
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+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
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+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
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+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
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+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
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+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
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+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
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+
+ If the Program specifies that a proxy can decide which future
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+
+ Later license versions may give you additional or different
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+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
import llfuse
import logging
import os
+import resource
import signal
import subprocess
import sys
if self.args.logfile:
self.args.logfile = os.path.realpath(self.args.logfile)
- # Daemonize as early as possible, so we don't accidentally close
- # file descriptors we're using.
- self.daemon_ctx = None
- if not (self.args.exec_args or self.args.foreground):
- os.chdir(self.args.mountpoint)
- self.daemon_ctx = daemon.DaemonContext(working_directory='.')
- self.daemon_ctx.open()
-
try:
self._setup_logging()
self._setup_api()
# Configure a log handler based on command-line switches.
if self.args.logfile:
log_handler = logging.FileHandler(self.args.logfile)
- elif self.daemon_ctx:
- log_handler = logging.NullHandler()
else:
log_handler = None
keep_params={
"block_cache": arvados.keep.KeepBlockCache(self.args.file_cache)
})
+ # Do a sanity check that we have a working arvados host + token.
+ self.api.users().current().execute()
def _setup_mount(self):
self.operations = Operations(
if self.args.collection is not None:
# Set up the request handler with the collection at the root
+ # First check that the collection is readable
+ self.api.collections().get(uuid=self.args.collection).execute()
self.args.mode = 'collection'
dir_class = CollectionDirectory
dir_args.append(self.args.collection)
try:
llfuse.init(self.operations, self.args.mountpoint, self._fuse_options())
+ if not (self.args.exec_args or self.args.foreground):
+ self.daemon_ctx = daemon.DaemonContext(working_directory=os.path.dirname(self.args.mountpoint),
+ files_preserve=range(3, resource.getrlimit(resource.RLIMIT_NOFILE)[1]))
+ self.daemon_ctx.open()
+
# Subscribe to change events from API server
self.operations.listen_for_events()
scripts=[
'bin/arv-mount'
],
+ data_files=[
+ ('share/doc/arvados_fuse', ['agpl-3.0.txt', 'README.rst']),
+ ],
install_requires=[
'arvados-python-client >= 0.1.20151118035730',
'llfuse>=0.40',
'--mount-tmp', name,
'--foreground', self.mntdir])
arvados_fuse.command.Mount(args)
+
+class MountErrorTest(unittest.TestCase):
+ def setUp(self):
+ self.mntdir = tempfile.mkdtemp()
+ run_test_server.run()
+ run_test_server.authorize_with("active")
+ self.logger = logging.getLogger("null")
+ self.logger.setLevel(logging.CRITICAL+1)
+
+ def tearDown(self):
+ if os.path.exists(self.mntdir):
+ # If the directory was not unmounted, this will raise an exception.
+ os.rmdir(self.mntdir)
+ run_test_server.reset()
+
+ def test_no_token(self):
+ del arvados.config._settings["ARVADOS_API_TOKEN"]
+ arvados.config._settings = {}
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_no_host(self):
+ del arvados.config._settings["ARVADOS_API_HOST"]
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_bogus_host(self):
+ arvados.config._settings["ARVADOS_API_HOST"] = "100::"
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_bogus_token(self):
+ arvados.config._settings["ARVADOS_API_TOKEN"] = "zzzzzzzzzzzzz"
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_bogus_mount_dir(self):
+ # All FUSE errors in llfuse.init() are raised as RuntimeError
+ # An easy error to trigger is to supply a nonexistent mount point,
+ # so test that one.
+ #
+ # Other possible errors that also raise RuntimeError (but are much
+ # harder to test automatically because they depend on operating
+ # system configuration):
+ #
+ # The user doesn't have permission to use FUSE
+ # The user specified --allow-other but user_allow_other is not set
+ # in /etc/fuse.conf
+ os.rmdir(self.mntdir)
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_unreadable_collection(self):
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([
+ "--collection", "zzzzz-4zz18-zzzzzzzzzzzzzzz", self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
+
+ def test_unreadable_project(self):
+ with self.assertRaises(SystemExit) as ex:
+ args = arvados_fuse.command.ArgumentParser().parse_args([
+ "--project", "zzzzz-j7d0g-zzzzzzzzzzzzzzz", self.mntdir])
+ arvados_fuse.command.Mount(args, logger=self.logger).run()
+ self.assertEqual(1, ex.exception.code)
}
kc.SetServiceRoots(sr, sr, sr)
kc.Arvados.External = true
- kc.Using_proxy = true
return kc
}
defer closeListener()
hash := fmt.Sprintf("%x", md5.Sum([]byte("foo")))
- for _, f := range []func()error {
+ for _, f := range []func() error{
func() error {
_, _, err := kc.Ask(hash)
return err
return compareReaderWithBuf(rdr, expect, loc[:32])
}
-// Put sotres a Keep block as a block blob in the container.
+// Put stores a Keep block as a block blob in the container.
func (v *AzureBlobVolume) Put(loc string, block []byte) error {
if v.readonly {
return MethodDisabledError
*AzureBlobVolume
azHandler *azStubHandler
azStub *httptest.Server
- t *testing.T
+ t TB
}
-func NewTestableAzureBlobVolume(t *testing.T, readonly bool, replication int) *TestableAzureBlobVolume {
+func NewTestableAzureBlobVolume(t TB, readonly bool, replication int) *TestableAzureBlobVolume {
azHandler := newAzStubHandler()
azStub := httptest.NewServer(azHandler)
}
azureWriteRaceInterval = time.Millisecond
azureWriteRacePollTime = time.Nanosecond
- DoGenericVolumeTests(t, func(t *testing.T) TestableVolume {
+ DoGenericVolumeTests(t, func(t TB) TestableVolume {
return NewTestableAzureBlobVolume(t, false, azureStorageReplication)
})
}
}
azureWriteRaceInterval = time.Millisecond
azureWriteRacePollTime = time.Nanosecond
- DoGenericVolumeTests(t, func(t *testing.T) TestableVolume {
+ DoGenericVolumeTests(t, func(t TB) TestableVolume {
return NewTestableAzureBlobVolume(t, true, azureStorageReplication)
})
}
import (
. "gopkg.in/check.v1"
- "testing"
"time"
)
-// Gocheck boilerplate
-func TestBufferPool(t *testing.T) {
- TestingT(t)
-}
-
var _ = Suite(&BufferPoolSuite{})
type BufferPoolSuite struct{}
import (
"bytes"
- "testing"
"testing/iotest"
check "gopkg.in/check.v1"
)
-// Gocheck boilerplate
-func Test(t *testing.T) {
- check.TestingT(t)
-}
-
var _ = check.Suite(&CollisionSuite{})
type CollisionSuite struct{}
--- /dev/null
+package main
+
+import (
+ "gopkg.in/check.v1"
+ "testing"
+)
+
+func TestGocheck(t *testing.T) {
+ check.TestingT(t)
+}
import (
"bytes"
- "testing"
)
// A TestableVolumeManagerFactory creates a volume manager with at least two TestableVolume instances.
// The factory function, and the TestableVolume instances it returns, can use "t" to write
// logs, fail the current test, etc.
-type TestableVolumeManagerFactory func(t *testing.T) (*RRVolumeManager, []TestableVolume)
+type TestableVolumeManagerFactory func(t TB) (*RRVolumeManager, []TestableVolume)
// DoHandlersWithGenericVolumeTests runs a set of handler tests with a
// Volume Manager comprised of TestableVolume instances.
// It calls factory to create a volume manager with TestableVolume
// instances for each test case, to avoid leaking state between tests.
-func DoHandlersWithGenericVolumeTests(t *testing.T, factory TestableVolumeManagerFactory) {
+func DoHandlersWithGenericVolumeTests(t TB, factory TestableVolumeManagerFactory) {
testGetBlock(t, factory, TestHash, TestBlock)
testGetBlock(t, factory, EmptyHash, EmptyBlock)
testPutRawBadDataGetBlock(t, factory, TestHash, TestBlock, []byte("baddata"))
}
// Setup RRVolumeManager with TestableVolumes
-func setupHandlersWithGenericVolumeTest(t *testing.T, factory TestableVolumeManagerFactory) []TestableVolume {
+func setupHandlersWithGenericVolumeTest(t TB, factory TestableVolumeManagerFactory) []TestableVolume {
vm, testableVolumes := factory(t)
KeepVM = vm
}
// Put a block using PutRaw in just one volume and Get it using GetBlock
-func testGetBlock(t *testing.T, factory TestableVolumeManagerFactory, testHash string, testBlock []byte) {
+func testGetBlock(t TB, factory TestableVolumeManagerFactory, testHash string, testBlock []byte) {
testableVolumes := setupHandlersWithGenericVolumeTest(t, factory)
// Put testBlock in one volume
}
// Put a bad block using PutRaw and get it.
-func testPutRawBadDataGetBlock(t *testing.T, factory TestableVolumeManagerFactory,
+func testPutRawBadDataGetBlock(t TB, factory TestableVolumeManagerFactory,
testHash string, testBlock []byte, badData []byte) {
testableVolumes := setupHandlersWithGenericVolumeTest(t, factory)
}
// Invoke PutBlock twice to ensure CompareAndTouch path is tested.
-func testPutBlock(t *testing.T, factory TestableVolumeManagerFactory, testHash string, testBlock []byte) {
+func testPutBlock(t TB, factory TestableVolumeManagerFactory, testHash string, testBlock []byte) {
setupHandlersWithGenericVolumeTest(t, factory)
// PutBlock
}
// Put a bad block using PutRaw, overwrite it using PutBlock and get it.
-func testPutBlockCorrupt(t *testing.T, factory TestableVolumeManagerFactory,
+func testPutBlockCorrupt(t TB, factory TestableVolumeManagerFactory,
testHash string, testBlock []byte, badData []byte) {
testableVolumes := setupHandlersWithGenericVolumeTest(t, factory)
keepClient := &keepclient.KeepClient{
Arvados: nil,
Want_replicas: 1,
- Using_proxy: true,
Client: &http.Client{},
}
"sort"
"strings"
"testing"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
)
var TestBlock = []byte("The quick brown fox jumps over the lazy dog.")
defer teardown()
// These blocks both hash to the MD5 digest cee9a457e790cf20d4bdaa6d69f01e41.
- var b1 = []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9epO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\\\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef")
- var b2 = []byte("\x0e0eaU\x9a\xa7\x87\xd0\x0b\xc6\xf7\x0b\xbd\xfe4\x04\xcf\x03e\x9etO\x854\xc0\x0f\xfbe\x9cL\x87@\xcc\x94/\xeb-\xa1\x15\xa3\xf4\x15\xdc\xbb\x86\x07Is\x86em}\x1f4\xa4 Y\xd7\x8fZ\x8d\xd1\xef")
- var locator = "cee9a457e790cf20d4bdaa6d69f01e41"
+ b1 := arvadostest.MD5CollisionData[0]
+ b2 := arvadostest.MD5CollisionData[1]
+ locator := arvadostest.MD5CollisionMD5
// Prepare two test Keep volumes.
KeepVM = MakeTestVolumeManager(2)
Length int
http.ResponseWriter
ResponseBody string
+ sentHdr time.Time
}
// WriteHeader writes header to ResponseWriter
func (loggingWriter *LoggingResponseWriter) WriteHeader(code int) {
+ if loggingWriter.sentHdr == zeroTime {
+ loggingWriter.sentHdr = time.Now()
+ }
loggingWriter.Status = code
loggingWriter.ResponseWriter.WriteHeader(code)
}
+var zeroTime time.Time
+
func (loggingWriter *LoggingResponseWriter) Write(data []byte) (int, error) {
+ if loggingWriter.Length == 0 && len(data) > 0 && loggingWriter.sentHdr == zeroTime {
+ loggingWriter.sentHdr = time.Now()
+ }
loggingWriter.Length += len(data)
if loggingWriter.Status >= 400 {
loggingWriter.ResponseBody += string(data)
func (loggingRouter *LoggingRESTRouter) ServeHTTP(resp http.ResponseWriter, req *http.Request) {
t0 := time.Now()
- loggingWriter := LoggingResponseWriter{http.StatusOK, 0, resp, ""}
+ loggingWriter := LoggingResponseWriter{http.StatusOK, 0, resp, "", zeroTime}
loggingRouter.router.ServeHTTP(&loggingWriter, req)
statusText := http.StatusText(loggingWriter.Status)
if loggingWriter.Status >= 400 {
statusText = strings.Replace(loggingWriter.ResponseBody, "\n", "", -1)
}
- log.Printf("[%s] %s %s %.6fs %d %d \"%s\"", req.RemoteAddr, req.Method, req.URL.Path[1:], time.Since(t0).Seconds(), loggingWriter.Status, loggingWriter.Length, statusText)
+ now := time.Now()
+ tTotal := now.Sub(t0)
+ tLatency := loggingWriter.sentHdr.Sub(t0)
+ tResponse := now.Sub(loggingWriter.sentHdr)
+ log.Printf("[%s] %s %s %.6fs %.6fs %.6fs %d %d \"%s\"", req.RemoteAddr, req.Method, req.URL.Path[1:], tTotal.Seconds(), tLatency.Seconds(), tResponse.Seconds(), loggingWriter.Status, loggingWriter.Length, statusText)
}
keepClient = &keepclient.KeepClient{
Arvados: &arv,
Want_replicas: 1,
- Using_proxy: true,
Client: &http.Client{},
}
. "gopkg.in/check.v1"
"io"
"net/http"
- "testing"
"time"
)
-type PullWorkerTestSuite struct{}
-
-// Gocheck boilerplate
-func TestPullWorker(t *testing.T) {
- TestingT(t)
-}
-
-// Gocheck boilerplate
var _ = Suite(&PullWorkerTestSuite{})
+type PullWorkerTestSuite struct{}
+
var testPullLists map[string]string
var readContent string
var readError error
--- /dev/null
+package main
+
+import (
+ "encoding/base64"
+ "encoding/hex"
+ "flag"
+ "fmt"
+ "io"
+ "log"
+ "net/http"
+ "os"
+ "regexp"
+ "time"
+
+ "github.com/AdRoll/goamz/aws"
+ "github.com/AdRoll/goamz/s3"
+)
+
+var (
+ ErrS3DeleteNotAvailable = fmt.Errorf("delete without -s3-unsafe-delete is not implemented")
+
+ s3AccessKeyFile string
+ s3SecretKeyFile string
+ s3RegionName string
+ s3Endpoint string
+ s3Replication int
+ s3UnsafeDelete bool
+
+ s3ACL = s3.Private
+)
+
+const (
+ maxClockSkew = 600 * time.Second
+ nearlyRFC1123 = "Mon, 2 Jan 2006 15:04:05 GMT"
+)
+
+type s3VolumeAdder struct {
+ *volumeSet
+}
+
+func (s *s3VolumeAdder) Set(bucketName string) error {
+ if bucketName == "" {
+ return fmt.Errorf("no container name given")
+ }
+ if s3AccessKeyFile == "" || s3SecretKeyFile == "" {
+ return fmt.Errorf("-s3-access-key-file and -s3-secret-key-file arguments must given before -s3-bucket-volume")
+ }
+ region, ok := aws.Regions[s3RegionName]
+ if s3Endpoint == "" {
+ if !ok {
+ return fmt.Errorf("unrecognized region %+q; try specifying -s3-endpoint instead", s3RegionName)
+ }
+ } else {
+ if ok {
+ return fmt.Errorf("refusing to use AWS region name %+q with endpoint %+q; "+
+ "specify empty endpoint (\"-s3-endpoint=\") or use a different region name", s3RegionName, s3Endpoint)
+ }
+ region = aws.Region{
+ Name: s3RegionName,
+ S3Endpoint: s3Endpoint,
+ }
+ }
+ var err error
+ var auth aws.Auth
+ auth.AccessKey, err = readKeyFromFile(s3AccessKeyFile)
+ if err != nil {
+ return err
+ }
+ auth.SecretKey, err = readKeyFromFile(s3SecretKeyFile)
+ if err != nil {
+ return err
+ }
+ if flagSerializeIO {
+ log.Print("Notice: -serialize is not supported by s3-bucket volumes.")
+ }
+ v := NewS3Volume(auth, region, bucketName, flagReadonly, s3Replication)
+ if err := v.Check(); err != nil {
+ return err
+ }
+ *s.volumeSet = append(*s.volumeSet, v)
+ return nil
+}
+
+func s3regions() (okList []string) {
+ for r, _ := range aws.Regions {
+ okList = append(okList, r)
+ }
+ return
+}
+
+func init() {
+ flag.Var(&s3VolumeAdder{&volumes},
+ "s3-bucket-volume",
+ "Use the given bucket as a storage volume. Can be given multiple times.")
+ flag.StringVar(
+ &s3RegionName,
+ "s3-region",
+ "",
+ fmt.Sprintf("AWS region used for subsequent -s3-bucket-volume arguments. Allowed values are %+q.", s3regions()))
+ flag.StringVar(
+ &s3Endpoint,
+ "s3-endpoint",
+ "",
+ "Endpoint URL used for subsequent -s3-bucket-volume arguments. If blank, use the AWS endpoint corresponding to the -s3-region argument. For Google Storage, use \"https://storage.googleapis.com\".")
+ flag.StringVar(
+ &s3AccessKeyFile,
+ "s3-access-key-file",
+ "",
+ "File containing the access key used for subsequent -s3-bucket-volume arguments.")
+ flag.StringVar(
+ &s3SecretKeyFile,
+ "s3-secret-key-file",
+ "",
+ "File containing the secret key used for subsequent -s3-bucket-volume arguments.")
+ flag.IntVar(
+ &s3Replication,
+ "s3-replication",
+ 2,
+ "Replication level reported to clients for subsequent -s3-bucket-volume arguments.")
+ flag.BoolVar(
+ &s3UnsafeDelete,
+ "s3-unsafe-delete",
+ false,
+ "EXPERIMENTAL. Enable deletion (garbage collection), even though there are known race conditions that can cause data loss.")
+}
+
+type S3Volume struct {
+ *s3.Bucket
+ readonly bool
+ replication int
+ indexPageSize int
+}
+
+// NewS3Volume returns a new S3Volume using the given auth, region,
+// and bucket name. The replication argument specifies the replication
+// level to report when writing data.
+func NewS3Volume(auth aws.Auth, region aws.Region, bucket string, readonly bool, replication int) *S3Volume {
+ return &S3Volume{
+ Bucket: &s3.Bucket{
+ S3: s3.New(auth, region),
+ Name: bucket,
+ },
+ readonly: readonly,
+ replication: replication,
+ indexPageSize: 1000,
+ }
+}
+
+func (v *S3Volume) Check() error {
+ return nil
+}
+
+func (v *S3Volume) Get(loc string) ([]byte, error) {
+ rdr, err := v.Bucket.GetReader(loc)
+ if err != nil {
+ return nil, v.translateError(err)
+ }
+ defer rdr.Close()
+ buf := bufs.Get(BlockSize)
+ n, err := io.ReadFull(rdr, buf)
+ switch err {
+ case nil, io.EOF, io.ErrUnexpectedEOF:
+ return buf[:n], nil
+ default:
+ bufs.Put(buf)
+ return nil, v.translateError(err)
+ }
+}
+
+func (v *S3Volume) Compare(loc string, expect []byte) error {
+ rdr, err := v.Bucket.GetReader(loc)
+ if err != nil {
+ return v.translateError(err)
+ }
+ defer rdr.Close()
+ return v.translateError(compareReaderWithBuf(rdr, expect, loc[:32]))
+}
+
+func (v *S3Volume) Put(loc string, block []byte) error {
+ if v.readonly {
+ return MethodDisabledError
+ }
+ var opts s3.Options
+ if len(block) > 0 {
+ md5, err := hex.DecodeString(loc)
+ if err != nil {
+ return err
+ }
+ opts.ContentMD5 = base64.StdEncoding.EncodeToString(md5)
+ }
+ return v.translateError(
+ v.Bucket.Put(
+ loc, block, "application/octet-stream", s3ACL, opts))
+}
+
+func (v *S3Volume) Touch(loc string) error {
+ if v.readonly {
+ return MethodDisabledError
+ }
+ result, err := v.Bucket.PutCopy(loc, s3ACL, s3.CopyOptions{
+ ContentType: "application/octet-stream",
+ MetadataDirective: "REPLACE",
+ }, v.Bucket.Name+"/"+loc)
+ if err != nil {
+ return v.translateError(err)
+ }
+ t, err := time.Parse(time.RFC3339, result.LastModified)
+ if err != nil {
+ return err
+ }
+ if time.Since(t) > maxClockSkew {
+ return fmt.Errorf("PutCopy returned old LastModified %s => %s (%s ago)", result.LastModified, t, time.Since(t))
+ }
+ return nil
+}
+
+func (v *S3Volume) Mtime(loc string) (time.Time, error) {
+ resp, err := v.Bucket.Head(loc, nil)
+ if err != nil {
+ return zeroTime, v.translateError(err)
+ }
+ hdr := resp.Header.Get("Last-Modified")
+ t, err := time.Parse(time.RFC1123, hdr)
+ if err != nil && hdr != "" {
+ // AWS example is "Sun, 1 Jan 2006 12:00:00 GMT",
+ // which isn't quite "Sun, 01 Jan 2006 12:00:00 GMT"
+ // as required by HTTP spec. If it's not a valid HTTP
+ // header value, it's probably AWS (or s3test) giving
+ // us a nearly-RFC1123 timestamp.
+ t, err = time.Parse(nearlyRFC1123, hdr)
+ }
+ return t, err
+}
+
+func (v *S3Volume) IndexTo(prefix string, writer io.Writer) error {
+ nextMarker := ""
+ for {
+ listResp, err := v.Bucket.List(prefix, "", nextMarker, v.indexPageSize)
+ if err != nil {
+ return err
+ }
+ for _, key := range listResp.Contents {
+ t, err := time.Parse(time.RFC3339, key.LastModified)
+ if err != nil {
+ return err
+ }
+ if !v.isKeepBlock(key.Key) {
+ continue
+ }
+ fmt.Fprintf(writer, "%s+%d %d\n", key.Key, key.Size, t.Unix())
+ }
+ if !listResp.IsTruncated {
+ break
+ }
+ nextMarker = listResp.NextMarker
+ }
+ return nil
+}
+
+func (v *S3Volume) Delete(loc string) error {
+ if v.readonly {
+ return MethodDisabledError
+ }
+ if t, err := v.Mtime(loc); err != nil {
+ return err
+ } else if time.Since(t) < blobSignatureTTL {
+ return nil
+ }
+ if !s3UnsafeDelete {
+ return ErrS3DeleteNotAvailable
+ }
+ return v.Bucket.Del(loc)
+}
+
+func (v *S3Volume) Status() *VolumeStatus {
+ return &VolumeStatus{
+ DeviceNum: 1,
+ BytesFree: BlockSize * 1000,
+ BytesUsed: 1,
+ }
+}
+
+func (v *S3Volume) String() string {
+ return fmt.Sprintf("s3-bucket:%+q", v.Bucket.Name)
+}
+
+func (v *S3Volume) Writable() bool {
+ return !v.readonly
+}
+func (v *S3Volume) Replication() int {
+ return v.replication
+}
+
+var s3KeepBlockRegexp = regexp.MustCompile(`^[0-9a-f]{32}$`)
+
+func (v *S3Volume) isKeepBlock(s string) bool {
+ return s3KeepBlockRegexp.MatchString(s)
+}
+
+func (v *S3Volume) translateError(err error) error {
+ switch err := err.(type) {
+ case *s3.Error:
+ if err.StatusCode == http.StatusNotFound && err.Code == "NoSuchKey" {
+ return os.ErrNotExist
+ }
+ // Other 404 errors like NoSuchVersion and
+ // NoSuchBucket are different problems which should
+ // get called out downstream, so we don't convert them
+ // to os.ErrNotExist.
+ }
+ return err
+}
--- /dev/null
+package main
+
+import (
+ "bytes"
+ "fmt"
+ "log"
+ "strings"
+ "time"
+
+ "github.com/AdRoll/goamz/aws"
+ "github.com/AdRoll/goamz/s3"
+ "github.com/AdRoll/goamz/s3/s3test"
+ check "gopkg.in/check.v1"
+)
+
+type TestableS3Volume struct {
+ *S3Volume
+ server *s3test.Server
+ c *check.C
+ serverClock *fakeClock
+}
+
+const (
+ TestBucketName = "testbucket"
+)
+
+type fakeClock struct {
+ now *time.Time
+}
+
+func (c *fakeClock) Now() time.Time {
+ if c.now == nil {
+ return time.Now()
+ }
+ return *c.now
+}
+
+func init() {
+ // Deleting isn't safe from races, but if it's turned on
+ // anyway we do expect it to pass the generic volume tests.
+ s3UnsafeDelete = true
+}
+
+func NewTestableS3Volume(c *check.C, readonly bool, replication int) *TestableS3Volume {
+ clock := &fakeClock{}
+ srv, err := s3test.NewServer(&s3test.Config{Clock: clock})
+ c.Assert(err, check.IsNil)
+ auth := aws.Auth{}
+ region := aws.Region{
+ Name: "test-region-1",
+ S3Endpoint: srv.URL(),
+ S3LocationConstraint: true,
+ }
+ bucket := &s3.Bucket{
+ S3: s3.New(auth, region),
+ Name: TestBucketName,
+ }
+ err = bucket.PutBucket(s3.ACL("private"))
+ c.Assert(err, check.IsNil)
+
+ return &TestableS3Volume{
+ S3Volume: NewS3Volume(auth, region, TestBucketName, readonly, replication),
+ server: srv,
+ serverClock: clock,
+ }
+}
+
+var _ = check.Suite(&StubbedS3Suite{})
+
+type StubbedS3Suite struct {
+ volumes []*TestableS3Volume
+}
+
+func (s *StubbedS3Suite) TestGeneric(c *check.C) {
+ DoGenericVolumeTests(c, func(t TB) TestableVolume {
+ return NewTestableS3Volume(c, false, 2)
+ })
+}
+
+func (s *StubbedS3Suite) TestGenericReadOnly(c *check.C) {
+ DoGenericVolumeTests(c, func(t TB) TestableVolume {
+ return NewTestableS3Volume(c, true, 2)
+ })
+}
+
+func (s *StubbedS3Suite) TestIndex(c *check.C) {
+ v := NewTestableS3Volume(c, false, 2)
+ v.indexPageSize = 3
+ for i := 0; i < 256; i++ {
+ v.PutRaw(fmt.Sprintf("%02x%030x", i, i), []byte{102, 111, 111})
+ }
+ for _, spec := range []struct {
+ prefix string
+ expectMatch int
+ }{
+ {"", 256},
+ {"c", 16},
+ {"bc", 1},
+ {"abc", 0},
+ } {
+ buf := new(bytes.Buffer)
+ err := v.IndexTo(spec.prefix, buf)
+ c.Check(err, check.IsNil)
+
+ idx := bytes.SplitAfter(buf.Bytes(), []byte{10})
+ c.Check(len(idx), check.Equals, spec.expectMatch+1)
+ c.Check(len(idx[len(idx)-1]), check.Equals, 0)
+ }
+}
+
+// PutRaw skips the ContentMD5 test
+func (v *TestableS3Volume) PutRaw(loc string, block []byte) {
+ err := v.Bucket.Put(loc, block, "application/octet-stream", s3ACL, s3.Options{})
+ if err != nil {
+ log.Printf("PutRaw: %+v", err)
+ }
+}
+
+// TouchWithDate turns back the clock while doing a Touch(). We assume
+// there are no other operations happening on the same s3test server
+// while we do this.
+func (v *TestableS3Volume) TouchWithDate(locator string, lastPut time.Time) {
+ v.serverClock.now = &lastPut
+ err := v.Touch(locator)
+ if err != nil && !strings.Contains(err.Error(), "PutCopy returned old LastModified") {
+ log.Printf("Touch: %+v", err)
+ }
+ v.serverClock.now = nil
+}
+
+func (v *TestableS3Volume) Teardown() {
+ v.server.Quit()
+}
"regexp"
"sort"
"strings"
- "testing"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
)
+type TB interface {
+ Error(args ...interface{})
+ Errorf(format string, args ...interface{})
+ Fail()
+ FailNow()
+ Failed() bool
+ Fatal(args ...interface{})
+ Fatalf(format string, args ...interface{})
+ Log(args ...interface{})
+ Logf(format string, args ...interface{})
+}
+
// A TestableVolumeFactory returns a new TestableVolume. The factory
// function, and the TestableVolume it returns, can use "t" to write
// logs, fail the current test, etc.
-type TestableVolumeFactory func(t *testing.T) TestableVolume
+type TestableVolumeFactory func(t TB) TestableVolume
// DoGenericVolumeTests runs a set of tests that every TestableVolume
// is expected to pass. It calls factory to create a new TestableVolume
// for each test case, to avoid leaking state between tests.
-func DoGenericVolumeTests(t *testing.T, factory TestableVolumeFactory) {
+func DoGenericVolumeTests(t TB, factory TestableVolumeFactory) {
testGet(t, factory)
testGetNoSuchBlock(t, factory)
testPutBlockWithSameContent(t, factory, TestHash, TestBlock)
testPutBlockWithSameContent(t, factory, EmptyHash, EmptyBlock)
- testPutBlockWithDifferentContent(t, factory, TestHash, TestBlock, TestBlock2)
- testPutBlockWithDifferentContent(t, factory, TestHash, EmptyBlock, TestBlock)
- testPutBlockWithDifferentContent(t, factory, TestHash, TestBlock, EmptyBlock)
- testPutBlockWithDifferentContent(t, factory, EmptyHash, EmptyBlock, TestBlock)
+ testPutBlockWithDifferentContent(t, factory, arvadostest.MD5CollisionMD5, arvadostest.MD5CollisionData[0], arvadostest.MD5CollisionData[1])
+ testPutBlockWithDifferentContent(t, factory, arvadostest.MD5CollisionMD5, EmptyBlock, arvadostest.MD5CollisionData[0])
+ testPutBlockWithDifferentContent(t, factory, arvadostest.MD5CollisionMD5, arvadostest.MD5CollisionData[0], EmptyBlock)
+ testPutBlockWithDifferentContent(t, factory, EmptyHash, EmptyBlock, arvadostest.MD5CollisionData[0])
testPutMultipleBlocks(t, factory)
testPutAndTouch(t, factory)
// Put a test block, get it and verify content
// Test should pass for both writable and read-only volumes
-func testGet(t *testing.T, factory TestableVolumeFactory) {
+func testGet(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Invoke get on a block that does not exist in volume; should result in error
// Test should pass for both writable and read-only volumes
-func testGetNoSuchBlock(t *testing.T, factory TestableVolumeFactory) {
+func testGetNoSuchBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Compare() should return os.ErrNotExist if the block does not exist.
// Otherwise, writing new data causes CompareAndTouch() to generate
// error logs even though everything is working fine.
-func testCompareNonexistent(t *testing.T, factory TestableVolumeFactory) {
+func testCompareNonexistent(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Put a test block and compare the locator with same content
// Test should pass for both writable and read-only volumes
-func testCompareSameContent(t *testing.T, factory TestableVolumeFactory, testHash string, testData []byte) {
+func testCompareSameContent(t TB, factory TestableVolumeFactory, testHash string, testData []byte) {
v := factory(t)
defer v.Teardown()
// testHash = md5(testDataA).
//
// Test should pass for both writable and read-only volumes
-func testCompareWithCollision(t *testing.T, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
+func testCompareWithCollision(t TB, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
v := factory(t)
defer v.Teardown()
// corrupted. Requires testHash = md5(testDataA) != md5(testDataB).
//
// Test should pass for both writable and read-only volumes
-func testCompareWithCorruptStoredData(t *testing.T, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
+func testCompareWithCorruptStoredData(t TB, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
v := factory(t)
defer v.Teardown()
// Put a block and put again with same content
// Test is intended for only writable volumes
-func testPutBlockWithSameContent(t *testing.T, factory TestableVolumeFactory, testHash string, testData []byte) {
+func testPutBlockWithSameContent(t TB, factory TestableVolumeFactory, testHash string, testData []byte) {
v := factory(t)
defer v.Teardown()
// Put a block and put again with different content
// Test is intended for only writable volumes
-func testPutBlockWithDifferentContent(t *testing.T, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
+func testPutBlockWithDifferentContent(t TB, factory TestableVolumeFactory, testHash string, testDataA, testDataB []byte) {
v := factory(t)
defer v.Teardown()
return
}
- err := v.Put(testHash, testDataA)
- if err != nil {
- t.Errorf("Got err putting block %q: %q, expected nil", testDataA, err)
- }
+ v.PutRaw(testHash, testDataA)
putErr := v.Put(testHash, testDataB)
buf, getErr := v.Get(testHash)
// Put and get multiple blocks
// Test is intended for only writable volumes
-func testPutMultipleBlocks(t *testing.T, factory TestableVolumeFactory) {
+func testPutMultipleBlocks(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Test that when applying PUT to a block that already exists,
// the block's modification time is updated.
// Test is intended for only writable volumes
-func testPutAndTouch(t *testing.T, factory TestableVolumeFactory) {
+func testPutAndTouch(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Touching a non-existing block should result in error.
// Test should pass for both writable and read-only volumes
-func testTouchNoSuchBlock(t *testing.T, factory TestableVolumeFactory) {
+func testTouchNoSuchBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Invoking Mtime on a non-existing block should result in error.
// Test should pass for both writable and read-only volumes
-func testMtimeNoSuchBlock(t *testing.T, factory TestableVolumeFactory) {
+func testMtimeNoSuchBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// * with a prefix
// * with no such prefix
// Test should pass for both writable and read-only volumes
-func testIndexTo(t *testing.T, factory TestableVolumeFactory) {
+func testIndexTo(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Calling Delete() for a block immediately after writing it (not old enough)
// should neither delete the data nor return an error.
// Test is intended for only writable volumes
-func testDeleteNewBlock(t *testing.T, factory TestableVolumeFactory) {
+func testDeleteNewBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
blobSignatureTTL = 300 * time.Second
// Calling Delete() for a block with a timestamp older than
// blobSignatureTTL seconds in the past should delete the data.
// Test is intended for only writable volumes
-func testDeleteOldBlock(t *testing.T, factory TestableVolumeFactory) {
+func testDeleteOldBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
blobSignatureTTL = 300 * time.Second
// Calling Delete() for a block that does not exist should result in error.
// Test should pass for both writable and read-only volumes
-func testDeleteNoSuchBlock(t *testing.T, factory TestableVolumeFactory) {
+func testDeleteNoSuchBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Invoke Status and verify that VolumeStatus is returned
// Test should pass for both writable and read-only volumes
-func testStatus(t *testing.T, factory TestableVolumeFactory) {
+func testStatus(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Invoke String for the volume; expect non-empty result
// Test should pass for both writable and read-only volumes
-func testString(t *testing.T, factory TestableVolumeFactory) {
+func testString(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Putting, updating, touching, and deleting blocks from a read-only volume result in error.
// Test is intended for only read-only volumes
-func testUpdateReadOnly(t *testing.T, factory TestableVolumeFactory) {
+func testUpdateReadOnly(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Launch concurrent Gets
// Test should pass for both writable and read-only volumes
-func testGetConcurrent(t *testing.T, factory TestableVolumeFactory) {
+func testGetConcurrent(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
// Launch concurrent Puts
// Test is intended for only writable volumes
-func testPutConcurrent(t *testing.T, factory TestableVolumeFactory) {
+func testPutConcurrent(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
}
// Write and read back a full size block
-func testPutFullBlock(t *testing.T, factory TestableVolumeFactory) {
+func testPutFullBlock(t TB, factory TestableVolumeFactory) {
v := factory(t)
defer v.Teardown()
type TestableUnixVolume struct {
UnixVolume
- t *testing.T
+ t TB
}
-func NewTestableUnixVolume(t *testing.T, serialize bool, readonly bool) *TestableUnixVolume {
+func NewTestableUnixVolume(t TB, serialize bool, readonly bool) *TestableUnixVolume {
d, err := ioutil.TempDir("", "volume_test")
if err != nil {
t.Fatal(err)
// serialize = false; readonly = false
func TestUnixVolumeWithGenericTests(t *testing.T) {
- DoGenericVolumeTests(t, func(t *testing.T) TestableVolume {
+ DoGenericVolumeTests(t, func(t TB) TestableVolume {
return NewTestableUnixVolume(t, false, false)
})
}
// serialize = false; readonly = true
func TestUnixVolumeWithGenericTestsReadOnly(t *testing.T) {
- DoGenericVolumeTests(t, func(t *testing.T) TestableVolume {
+ DoGenericVolumeTests(t, func(t TB) TestableVolume {
return NewTestableUnixVolume(t, false, true)
})
}
// serialize = true; readonly = false
func TestUnixVolumeWithGenericTestsSerialized(t *testing.T) {
- DoGenericVolumeTests(t, func(t *testing.T) TestableVolume {
+ DoGenericVolumeTests(t, func(t TB) TestableVolume {
return NewTestableUnixVolume(t, true, false)
})
}
// serialize = false; readonly = false
func TestUnixVolumeHandlersWithGenericVolumeTests(t *testing.T) {
- DoHandlersWithGenericVolumeTests(t, func(t *testing.T) (*RRVolumeManager, []TestableVolume) {
+ DoHandlersWithGenericVolumeTests(t, func(t TB) (*RRVolumeManager, []TestableVolume) {
vols := make([]Volume, 2)
testableUnixVols := make([]TestableVolume, 2)
--- /dev/null
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+above cannot be given local legal effect according to their terms,
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+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
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+to attach them to the start of each source file to most effectively
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+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
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+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
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+For more information on this, and how to apply and follow the GNU AGPL, see
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s.authors = ["Arvados Authors"]
s.email = 'gem-dev@curoverse.com'
s.licenses = ['GNU Affero General Public License, version 3.0']
- s.files = ["bin/arvados-login-sync"]
+ s.files = ["bin/arvados-login-sync", "agpl-3.0.txt"]
s.executables << "arvados-login-sync"
s.required_ruby_version = '>= 2.1.0'
s.add_runtime_dependency 'arvados', '~> 0.1', '>= 0.1.20150615153458'
+include agpl-3.0.txt
include README.rst
--- /dev/null
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+
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+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
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+
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+
+ How to Apply These Terms to Your New Programs
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+ If you develop a new program, and you want it to be of the greatest
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+ but WITHOUT ANY WARRANTY; without even the implied warranty of
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+
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+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
super(ComputeNodeDriver, self).__init__(
auth_kwargs, list_kwargs, create_kwargs,
driver_class)
+ self._sizes_by_name = {sz.name: sz for sz in self.sizes.itervalues()}
self._disktype_links = {dt.name: self._object_link(dt)
for dt in self.real.ex_list_disktypes()}
def list_nodes(self):
# The GCE libcloud driver only supports filtering node lists by zone.
# Do our own filtering based on tag list.
- return [node for node in
- super(ComputeNodeDriver, self).list_nodes()
- if self.node_tags.issubset(node.extra.get('tags', []))]
+ nodelist = [node for node in
+ super(ComputeNodeDriver, self).list_nodes()
+ if self.node_tags.issubset(node.extra.get('tags', []))]
+ # As of 0.18, the libcloud GCE driver sets node.size to the size's name.
+ # It's supposed to be the actual size object. Check that it's not,
+ # and monkeypatch the results when that's the case.
+ if nodelist and not hasattr(nodelist[0].size, 'id'):
+ for node in nodelist:
+ node.size = self._sizes_by_name[node.size]
+ return nodelist
@classmethod
def _find_metadata(cls, metadata_items, key):
import ConfigParser
import importlib
import logging
-import ssl
import sys
import arvados
import pykka
from apiclient import errors as apierror
-# IOError is the base class for socket.error and friends.
+# IOError is the base class for socket.error, ssl.SSLError, and friends.
# It seems like it hits the sweet spot for operations we want to retry:
# it's low-level, but unlikely to catch code bugs.
-NETWORK_ERRORS = (IOError, ssl.SSLError)
+NETWORK_ERRORS = (IOError,)
ARVADOS_ERRORS = NETWORK_ERRORS + (apierror.Error,)
actor_class = pykka.ThreadingActor
sec_words = sec_name.split(None, 2)
if sec_words[0] != 'Size':
continue
- size_kwargs[sec_words[1]] = self.get_section(sec_name, int)
+ size_spec = self.get_section(sec_name, int)
+ if 'price' in size_spec:
+ size_spec['price'] = float(size_spec['price'])
+ size_kwargs[sec_words[1]] = size_spec
# EC2 node sizes are identified by id. GCE sizes are identified by name.
matching_sizes = []
for size in all_sizes:
url="https://arvados.org",
license='GNU Affero General Public License, version 3.0',
packages=find_packages(),
+ scripts=['bin/arvados-node-manager'],
+ data_files=[
+ ('share/doc/arvados-node-manager', ['agpl-3.0.txt', 'README.rst']),
+ ],
install_requires=[
'apache-libcloud>=0.16',
'arvados-python-client>=0.1.20150206225333',
dependency_links = [
"https://github.com/curoverse/libcloud/archive/apache-libcloud-0.18.1.dev4.zip"
],
- scripts=['bin/arvados-node-manager'],
test_suite='tests',
tests_require=['pbr<1.7.0', 'mock>=1.0', "apache-libcloud==0.18.1.dev4"],
zip_safe=False,
self.assertEqual(
service_accounts,
self.driver_mock().create_node.call_args[1]['ex_service_accounts'])
+
+ def test_fix_string_size(self):
+ # As of 0.18, the libcloud GCE driver sets node.size to the size's name.
+ # It's supposed to be the actual size object. Make sure our driver
+ # patches that up in listings.
+ size = testutil.MockSize(2)
+ node = testutil.cloud_node_mock(size=size)
+ node.size = size.name
+ self.driver_mock().list_sizes.return_value = [size]
+ self.driver_mock().list_nodes.return_value = [node]
+ driver = self.new_driver()
+ nodelist = driver.list_nodes()
+ self.assertEqual(1, len(nodelist))
+ self.assertIs(node, nodelist[0])
+ self.assertIs(size, nodelist[0].size)
+
+ def test_skip_fix_when_size_not_string(self):
+ # Ensure we don't monkeypatch node sizes unless we need to.
+ size = testutil.MockSize(3)
+ node = testutil.cloud_node_mock(size=size)
+ self.driver_mock().list_nodes.return_value = [node]
+ driver = self.new_driver()
+ nodelist = driver.list_nodes()
+ self.assertEqual(1, len(nodelist))
+ self.assertIs(node, nodelist[0])
+ self.assertIs(size, nodelist[0].size)
+
+ def test_list_empty_nodes(self):
+ self.driver_mock().list_nodes.return_value = []
+ self.assertEqual([], self.new_driver().list_nodes())
[Size 1]
cores = 1
+price = 0.8
[Logging]
file = /dev/null
size, kwargs = sizes[0]
self.assertEqual('Small', size.name)
self.assertEqual(1, kwargs['cores'])
+ self.assertEqual(0.8, kwargs['price'])
def test_shutdown_windows(self):
config = self.load_config()
VaryThread = flag.Bool("vary-thread", false, "use -wthreads different data blocks")
Replicas = flag.Int("replicas", 1, "replication level for writing")
StatsInterval = flag.Duration("stats-interval", time.Second, "time interval between IO stats reports, or 0 to disable")
+ ServiceURL = flag.String("url", "", "specify scheme://host of a single keep service to exercise (instead of using all advertised services like normal clients)")
+ ServiceUUID = flag.String("uuid", "", "specify UUID of a single advertised keep service to exercise")
)
func main() {
kc.Want_replicas = *Replicas
kc.Client.Timeout = 10 * time.Minute
+ overrideServices(kc)
+
nextBuf := make(chan []byte, *WriteThreads)
nextLocator := make(chan string, *ReadThreads+*WriteThreads)
}
for {
if *VaryRequest {
+ buf = make([]byte, *BlockSize)
if _, err := io.ReadFull(rand.Reader, buf); err != nil {
log.Fatal(err)
}
bytesInChan <- uint64(n)
}
}
+
+func overrideServices(kc *keepclient.KeepClient) {
+ roots := make(map[string]string)
+ if *ServiceURL != "" {
+ roots["zzzzz-bi6l4-000000000000000"] = *ServiceURL
+ } else if *ServiceUUID != "" {
+ for uuid, url := range kc.GatewayRoots() {
+ if uuid == *ServiceUUID {
+ roots[uuid] = url
+ break
+ }
+ }
+ if len(roots) == 0 {
+ log.Fatalf("Service %q was not in list advertised by API %+q", *ServiceUUID, kc.GatewayRoots())
+ }
+ } else {
+ return
+ }
+ kc.SetServiceRoots(roots, roots, roots)
+}
projects / arvados.git / commitdiff