Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422024-03-27T15:52:03ZArvados
Redmine Arvados - Bug #21622 (New): Mail delivery failure should not cause API calls to failhttps://dev.arvados.org/issues/216222024-03-27T15:52:03ZPeter Amstutzpeter.amstutz@curii.comArvados - Bug #21618 (New): cloudtest should give up if test instance disappears from listing bef...https://dev.arvados.org/issues/216182024-03-25T16:52:07ZTom Cleggtom@curii.com
<p>Currently, if an instance/image has a problem that causes it to shutdown before responding to a boot probe, cloudtest keeps probing after it disappears, which is clearly futile.</p> Arvados - Bug #21617 (In Progress): Timeout error reading content from collection on a remote clu...https://dev.arvados.org/issues/216172024-03-25T14:43:50ZTom Cleggtom@curii.com
In a 3-way federation with login cluster z1111:
<ul>
<li>a collection stored on z1111 can be read from z2222 (e.g., workbench.z2222/collections/z1111-4zz18-...)</li>
<li>a collection stored on z2222 cannot be read from z1111 (timeout)</li>
<li>a collection stored on z2222 cannot be read from z3333 (timeout)</li>
</ul>
<p>It looks like the intermediate cluster's keepstore process cannot retrieve the list of keep services from the cluster where the data is stored ("failed to validate remote token") -- this auto-retries in the background for a while, then eventually blockReadRemote gives up.</p>
<p>Manual testing, with jutro/tordo/pirca playing the roles of z1111/z2222/z3333, indicates the same problem existed before and after <a class="issue tracker-2 status-2 priority-4 priority-default parent" title="Feature: Keepstore can stream GET and PUT requests using keep-gateway API (In Progress)" href="https://dev.arvados.org/issues/2960">#2960</a> was merged and deployed to tordo.</p> Arvados - Bug #21612 (New): a-c-r with --debug can try to log entire input/output objects, which ...https://dev.arvados.org/issues/216122024-03-20T20:22:22ZBrett Smithbrett.smith@curii.com
<p>User got this error while running aws-s3-bulk-download.cwl with >6K input URLs, using <code>a-c-r --submit --debug</code>.</p>
<p>I don't think it actually interfered with the workflow's run at all, but it clogs the logs and looks scary.</p>
<p>IMO a-c-r (along with the rest of our code) should not try to log data that can be arbitrarily large.</p>
<p>Three instances where this came up:</p>
<pre>
--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3.7/logging/__init__.py", line 1037, in emit
stream.write(msg + self.terminator)
BlockingIOError: [Errno 11] write could not complete without blocking
Call stack:
File "/usr/bin/arvados-cwl-runner", line 8, in <module>
sys.exit(main())
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/__init__.py", line 440, in main
input_required=not workflow_op)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/main.py", line 1302, in main
tool, initialized_job_order_object, runtimeContext, logger=_logger
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 874, in arv_executor
self.start_run(runnable, runtimeContext)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 248, in start_run
self.workflow_eval_lock, self.stop_polling)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/task_queue.py", line 85, in add
task()
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 202, in run
self.output_callback(cast(Optional[CWLObjectType], ev), "success")
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 321, in wrapped_callback
cb(obj, st)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow.py", line 429, in receive_output
output_callback(output, processStatus)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 564, in receive_output
_logger.debug("[%s] produced output %s", step.name, json_dumps(jobout, indent=4))
</pre>
<pre>--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3.7/logging/__init__.py", line 1037, in emit
stream.write(msg + self.terminator)
BlockingIOError: [Errno 11] write could not complete without blocking
Call stack:
File "/usr/bin/arvados-cwl-runner", line 8, in <module>
sys.exit(main())
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/__init__.py", line 440, in main
input_required=not workflow_op)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/main.py", line 1302, in main
tool, initialized_job_order_object, runtimeContext, logger=_logger
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 863, in arv_executor
for runnable in jobiter:
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow.py", line 175, in job
yield from job.job(builder.job, output_callbacks, runtimeContext)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 821, in job
for newjob in step.iterable:
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 751, in try_make_job
yield from jobs
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 77, in job
yield from self.step.job(joborder, output_callback, runtimeContext)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow.py", line 462, in job
runtimeContext,
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow.py", line 175, in job
yield from job.job(builder.job, output_callbacks, runtimeContext)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 821, in job
for newjob in step.iterable:
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 735, in try_make_job
json_dumps(inputobj, indent=4),
</pre>
<pre>--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3.7/logging/__init__.py", line 1037, in emit
stream.write(msg + self.terminator)
BlockingIOError: [Errno 11] write could not complete without blocking
Call stack:
File "/usr/bin/arvados-cwl-runner", line 8, in <module>
sys.exit(main())
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/__init__.py", line 440, in main
input_required=not workflow_op)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/main.py", line 1302, in main
tool, initialized_job_order_object, runtimeContext, logger=_logger
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 874, in arv_executor
self.start_run(runnable, runtimeContext)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 248, in start_run
self.workflow_eval_lock, self.stop_polling)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/task_queue.py", line 85, in add
task()
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/command_line_tool.py", line 202, in run
self.output_callback(cast(Optional[CWLObjectType], ev), "success")
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/arvados_cwl/executor.py", line 321, in wrapped_callback
cb(obj, st)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow.py", line 429, in receive_output
output_callback(output, processStatus)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 582, in receive_output
self.do_output_callback(final_output_callback)
File "/usr/share/python3/dist/python3-arvados-cwl-runner/lib/python3.7/site-packages/cwltool/workflow_job.py", line 541, in do_output_callback
_logger.debug("[%s] outputs %s", self.name, json_dumps(wo, indent=4))
</pre> Arvados - Bug #21607 (New): arv-mount memory usage grows over timehttps://dev.arvados.org/issues/216072024-03-19T13:15:14ZPeter Amstutzpeter.amstutz@curii.com
<p>arv-mount releases metadata (collection and project listings) for files and directories that haven't been used recently to prevent unlimited memory growth.</p>
<p>Ideally it should reach a ceiling and then level off as new stuff replaces the memory used by old stuff. However, in the current version, memory usage still creeps up.</p>
<p>arv-mount would benefit from additional debugging and memory profiling to determine if there are objects being held past their intended lifetime.</p> Arvados - Bug #21601 (In Progress): fpm virtualenv packages not using branch versions for depende...https://dev.arvados.org/issues/216012024-03-15T20:38:09ZPeter Amstutzpeter.amstutz@curii.com
<p><a class="external" href="https://dev.arvados.org/issues/19744#note-30">https://dev.arvados.org/issues/19744#note-30</a></p>
<p>The python3-arvados-cwl-runner_2.8.0~dev20240314145937-1_amd64.deb package has arvados-python-client 2.7.1 and crunchstat-summary 2.7.1, when it should have the dev versions from the same commit.</p>
<p>I went back and looked at earlier packages: python3-arvados-cwl-runner_2.7.1~rc3-1_amd64.deb has arvados-python-client 2.7.1rc3 (as expected) and python3-arvados-cwl-runner_2.7.0~dev20230908133938-1_amd64.deb has arvados-python-client 2.7.0.dev20230908133938 (also as expected).</p>
<p>My current theory is that this behavior got lost in the changes made in 20846-package-build-fixes, but I need to find out how it worked before.</p> Arvados - Bug #21598 (New): Local keepstore invoked by crunch-run should never do EmptyTrash workhttps://dev.arvados.org/issues/215982024-03-15T18:32:48ZTom Cleggtom@curii.com
<p>We don't want N compute nodes periodically checking expiry times on all of the trashed blocks on all backend volumes.</p> Arvados - Bug #21583 (In Progress): Running RailsAPI with Passenger implicity requires Ruby 3.3 v...https://dev.arvados.org/issues/215832024-03-13T11:03:08ZBrett Smithbrett.smith@curii.com
<p>Some useful background:</p>
<ul>
<li>base64 has been a default Gem for a while, but it will not be included in Ruby 3.4, and Ruby 3.3 warns you about this.</li>
<li>To make the warning go away, libraries have started declaring a dependency on the base64 gem. The library that's relevant to our story is <a href="https://github.com/lostisland/faraday/commit/ea30bd0b543882f1cf26e75ac4e46e0705fa7e68" class="external">faraday</a>, which is used by our ruby-google-api-client fork.</li>
<li>The current version of base64 is 0.2.0. This version is included in Ruby 3.3. Older versions of Ruby we support have 0.1.1.</li>
</ul>
<p>With this background, when we started using our ruby-google-api-client fork in RailsAPI in <a class="changeset" title="21384: Update arvados-google-api-client in RailsAPI There's no functional need for this. The mai..." href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/cbfdb1b66ab9c1b6e69d1c9cd589633386267177">cbfdb1b66ab9c1b6e69d1c9cd589633386267177</a>, <a class="source" href="https://dev.arvados.org/projects/arvados/repository/arvados/entry/services/api/Gemfile.lock">source:services/api/Gemfile.lock</a> gained a dependency on base64 0.2.0. This works fine in development, because Bundler can load this newer version before any code requires it.</p>
<p>However, Passenger loads the base64 Gem <em>before</em> it starts anything related to your application, including Bundler. Because of this, running RailsAPI behind Passenger with Ruby<3.3 now fails with this error in the Passenger log:</p>
<pre>[ E 2024-03-12 15:12:44.8347 907382/Tf age/Cor/App/Implementation.cpp:221 ]: Could not spawn process for application /var/www/arvados-api/current: The application encountered the following error: You have already activated base64 0.1.1, but your Gemfile requires base64 0.2.0. Since base64 is a default gem, you can either remove your dependency on it or try updating to a newer version of bundler that supports base64 as a default gem. (Gem::LoadError)
</pre>
<p>This is the root cause of <a class="issue tracker-1 status-1 priority-4 priority-default parent" title="Bug: test-provision-ubuntu2004 intermittently times out waiting for the controller to come up (New)" href="https://dev.arvados.org/issues/21524">#21524</a>. Note how test-provision-ubuntu2004 started failing immediately after <a class="changeset" title="21384: Update arvados-google-api-client in RailsAPI There's no functional need for this. The mai..." href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/cbfdb1b66ab9c1b6e69d1c9cd589633386267177">cbfdb1b66ab9c1b6e69d1c9cd589633386267177</a>:</p>
<p><img src="https://dev.arvados.org/attachments/download/3541/clipboard-202403130702-u2cmy.png" alt="" /></p>
<p>What can we do?</p>
<p>There is no single version of base64 that we can lock to that will keep everyone happy. The current lock breaks Ruby<3.3. If we change the lock to base64 0.1.1, we'll break Ruby>=3.3.</p>
<p>We cannot address the problem indirectly by tweaking our faraday dependency. We need version ~>2.8.0 to keep compatibility with the range of Ruby versions we're trying to support, and all those releases declare the base64 dependency.</p>
<p><a href="https://myrtana.sk/articles/my-passenger-was-really-old" class="external">This random blog post with cool styling</a> says you can upgrade Passenger, but note they upgrade Passenger to the version in bookworm, which is the version I'm testing and have reproduced this problem with:</p>
<pre>% apt list --installed '*passenger*'
libnginx-mod-http-passenger/bookworm,now 1:6.0.20-1~bookworm1 amd64 [installed]
passenger-dev/bookworm,now 1:6.0.20-1~bookworm1 amd64 [installed,automatic]
passenger-doc/bookworm,now 1:6.0.20-1~bookworm1 all [installed,automatic]
passenger/bookworm,now 1:6.0.20-1~bookworm1 amd64 [installed,automatic]
</pre>
<p>We could just revert <a class="changeset" title="21384: Update arvados-google-api-client in RailsAPI There's no functional need for this. The mai..." href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/cbfdb1b66ab9c1b6e69d1c9cd589633386267177">cbfdb1b66ab9c1b6e69d1c9cd589633386267177</a>. That has all the downsides implied by the commit message, but it would work.</p>
<p>We can just cheat and remove the lock by hand, but then we have to remember to keep doing that every time we update a RailsAPI gem for as long as we support Ruby<3.3. That sucks. We could write an extremely stupid test to help us remember this I guess.</p>
<p>🤷</p> Arvados - Bug #17434 (New): project not shown in hierarchy on the left of wb2https://dev.arvados.org/issues/174342021-03-01T21:07:39ZDaniel Kutyła
<p>Project that is being shared is not visible in the left tree menu</p> Arvados - Bug #17396 (New): Favorites copy dialog further issueshttps://dev.arvados.org/issues/173962021-02-16T22:31:18ZDaniel Kutyła
<p><a class="issue tracker-1 status-3 priority-4 priority-default closed parent" title="Bug: Favorites in copy dialog is different to favorite list (Resolved)" href="https://dev.arvados.org/issues/17306">#17306</a> solved main issues reported by our users but there are some stuff that came out while fixing those:</p>
<p>- We can not copy element which is located in a subdir without copying other elements as parent folder will not be selected and thus it will be removed <br />- For a large collections files copy operation might be very slow as we remove non selected elements in a post copy operation</p> Arvados - Bug #17300 (New): array of array of File causes 'NoneType' object has no attribute 'res...https://dev.arvados.org/issues/173002021-01-29T14:19:14ZStanislaw Adaszewski
<p>When running an ExpressionTool which has an output of the following type:</p>
<pre>
outputs:
subject_images:
type:
type: array # subjects
items:
type: array # timepoints
items: File
</pre>
<p>I receive the following error:</p>
<pre>
ERROR Unhandled error:
'NoneType' object has no attribute 'resolved'
Traceback (most recent call last):
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/main.py", line 833, in main
logger=_logger)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 767, in arv_executor
self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 467, in make_output_collection
adjustFileObjs(outputObj, rewrite)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/pathmapper.py", line 48, in adjustFileObjs
visit_class(rec, ("File",), op)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 221, in visit_class
visit_class(rec[d], cls, op)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 224, in visit_class
visit_class(d, cls, op)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 224, in visit_class
visit_class(d, cls, op)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 219, in visit_class
op(rec)
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 461, in rewrite
fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 332, in mapper
return MapperEnt(v.resolved, v.target + src[i:], v.type, v.staged)
AttributeError: 'NoneType' object has no attribute 'resolved'
</pre>
<p>If I replace type: File with type: string and store locations instead of File objects the request finishes successfully and returns the expected list of locations.</p> Arvados - Bug #16228 (New): NullPointerException while uploading file using Java SDKhttps://dev.arvados.org/issues/162282020-03-10T07:28:41ZKrzysztof Majewski
<p>When trying to upload a files using Java SDK I get the following error:</p>
<pre>
2020-03-10 08:07:23 ERROR - Cannot upload file to Keep server.
org.arvados.client.exception.ArvadosApiException: java.net.ConnectException: Failed to connect to keep1.ardev.roche.com/10.115.164.103:25107
at org.arvados.client.api.client.BaseApiClient.getResponseBody(BaseApiClient.java:76)
at org.arvados.client.api.client.BaseApiClient.newCall(BaseApiClient.java:49)
at org.arvados.client.api.client.KeepServerApiClient.upload(KeepServerApiClient.java:42)
at org.arvados.client.logic.keep.FileTransferHandler.put(FileTransferHandler.java:35)
at org.arvados.client.logic.keep.KeepClient.lambda$put$1(KeepClient.java:110)
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1590)
at java.util.concurrent.CompletableFuture$AsyncSupply.exec(CompletableFuture.java:1582)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
Caused by: java.net.ConnectException: Failed to connect to keep1.ardev.roche.com/10.115.164.103:25107
at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:270)
at okhttp3.internal.connection.RealConnection.connect(RealConnection.kt:176)
at okhttp3.internal.connection.ExchangeFinder.findConnection(ExchangeFinder.kt:236)
at okhttp3.internal.connection.ExchangeFinder.findHealthyConnection(ExchangeFinder.kt:109)
at okhttp3.internal.connection.ExchangeFinder.find(ExchangeFinder.kt:77)
at okhttp3.internal.connection.Transmitter.newExchange$okhttp(Transmitter.kt:162)
at okhttp3.internal.connection.ConnectInterceptor.intercept(ConnectInterceptor.kt:35)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:112)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:87)
at okhttp3.internal.cache.CacheInterceptor.intercept(CacheInterceptor.kt:82)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:112)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:87)
at okhttp3.internal.http.BridgeInterceptor.intercept(BridgeInterceptor.kt:84)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:112)
at okhttp3.internal.http.RetryAndFollowUpInterceptor.intercept(RetryAndFollowUpInterceptor.kt:71)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:112)
at okhttp3.internal.http.RealInterceptorChain.proceed(RealInterceptorChain.kt:87)
at okhttp3.RealCall.getResponseWithInterceptorChain(RealCall.kt:184)
at okhttp3.RealCall.execute(RealCall.kt:66)
at org.arvados.client.api.client.BaseApiClient.getResponseBody(BaseApiClient.java:63)
... 10 more
Caused by: java.net.ConnectException: Connection refused: connect
at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at okhttp3.internal.platform.Platform.connectSocket(Platform.kt:126)
at okhttp3.internal.connection.RealConnection.connectSocket(RealConnection.kt:268)
... 29 more
</pre>
<p>The keep1 server is taken from: <a class="external" href="https://api.ardev.roche.com/arvados/v1/keep_services/accessible">https://api.ardev.roche.com/arvados/v1/keep_services/accessible</a>. If I manipulate the response and remove it, leaving just keep2 everything works fine.</p>
<p>This is my code used for this example:</p>
<pre>
String serverUrl = "ardev.roche.com";
ExternalConfigProvider config = ExternalConfigProvider.builder()
.apiToken("api_token")
.apiHost(format("api.%s", serverUrl))
.apiPort(443)
.keepWebHost(format("collections.%s", serverUrl))
.keepWebPort(443)
.apiProtocol("https")
.apiHostInsecure(true)
.fileSplitSize(64)
.fileSplitDirectory(new File("C:\\file-split"))
.numberOfCopies(2)
.numberOfRetries(0)
.build();
List<File> files = asList(new File("C:\\samples\\sample.fcs"));
Collection collection = new CollectionsApiClient(config).get("collection_uuid");
new ArvadosFacade(config).uploadToExistingCollection(files, collection.getUuid());
</pre> Arvados - Bug #15183 (New): [Workbench2] No errors reported when file is missing a blockhttps://dev.arvados.org/issues/151832019-05-01T21:39:26ZTom Morristfmorris@veritasgenetics.com
<p>When looking at collection <a href="https://arvadosapi.com/su92l-4zz18-44qy35pg0lxshkf">su92l-4zz18-44qy35pg0lxshkf</a>/cwl.input.yml the file is cwl.output.json is listed as containing 361 bytes, but when downloaded from Workbench, it produces a zero byte file, but without giving any error or warning.</p>
<pre>
$ md5sum keep/by_id/su92l-4zz18-44qy35pg0lxshkf/*
a890894f5a748d2a93440fd046c73069 keep/by_id/su92l-4zz18-44qy35pg0lxshkf/cwl.input.yml
md5sum: keep/by_id/su92l-4zz18-44qy35pg0lxshkf/cwl.output.json: Input/output error
d41d8cd98f00b204e9800998ecf8427e keep/by_id/su92l-4zz18-44qy35pg0lxshkf/hu27FD1F_var-GS000034212-ASM.bed
b02868b9ac1264bd1f04b61d04518f57 keep/by_id/su92l-4zz18-44qy35pg0lxshkf/workflow.cwl
</pre> GET-Evidence - Bug #835 (New): Error when saving edits or submittinghttps://dev.arvados.org/issues/8352012-02-06T16:44:19ZMadeleine Ballmpball@gmail.com
<p>When saving or submitting we're seeing this error message now: "Save failed -- received bogus response from server."</p>
<p>Seems to date to changes made in commit <a class="changeset" title="if session is expired when "save draft" is clicked, pop-up a login window instead of falsely proc..." href="https://dev.arvados.org/projects/get-evidence/repository/8/revisions/5dc9adee7bd5cde0d1c9b16652cf0b5e8d6229d3">5dc9adee</a> ?</p>
<p>Sasha pointed out that the changes still get saved, but it's still a serious bug -- especially since we just sent the paper out for review and were planning to encourage people to edit...</p> GET-Evidence - Bug #468 (New): latest-flat incorrectly displays non single-base substitution vari...https://dev.arvados.org/issues/4682011-02-15T11:15:42ZMadeleine Ballmpball@gmail.com
<p>I haven't checked, but this problem likely extends to deletion & other new length changing or multiple-aa variants.</p>
<p>This bug blocks creating a flatfile version of gff_getevidence_map.py</p>
<p>For example, FIG4-K278Shift is showing up like this (2nd and 3rd columns are incorrect):<br />FIG4 278 278 pathogenic Moderate clinical importance, Uncertain pathogenic recessive 0 0 0 0 0 3 Y -- - Y 0 Y 3 - 2 - Y - - - - Y 4 Y 2N 1 0 This variant is predicted to cause a frameshift and may cause Charcot-Marie-Tooth Disease Type 4J in an autosomal recessive manner. Other variants in this gene which cause frameshift and premature termination have been implicated in causing this disease when compound heterozygous with another FIG4 variant.</p>
<p>While MYL2-A13T shows up like this:<br />MYL2 Ala13Thr A13T pathogenic Low clinical importance, Uncertain pathogenic dominant 1 1 1 6 6 3 Y 4Y 0 Y ! Y 4 Y 3 Y Y Y - - Y Y 1 - Familial Hypertrophic Cardiomyopathy 4596 1 455 3.054 4 N 0 0 This rare variant is implicated in causing late-onset familial hypertrophic cardiomyopathy. The variant has been found in five affected Caucasian individuals (in four families), but affected non-carriers and unaffected carriers have also been observed. No statistically significant enrichment of this variant in cases vs. controls has been shown.</p>