Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422021-03-01T21:07:39ZArvados
Redmine 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> GET-Evidence - Bug #466 (New): xmlrpc server is careless with huge temp fileshttps://dev.arvados.org/issues/4662011-02-11T17:42:02ZTom Cleggtom@curii.com
<p>For example, if processing aborts due to insufficient disk space while writing a huge temp file, the huge temp file (and perhaps other temp files) do not get deleted, and the disk stays full for no good reason.</p>
<p>Ideally, the processing code should use pipelines instead of temp files, or do "foreach record: foreach plugin: ..." instead of "foreach plugin: foreach record: ...".</p> longupload - Bug #451 (New): handle xmlhttprequest timeouts gracefullyhttps://dev.arvados.org/issues/4512011-01-13T19:04:50ZTom Cleggtom@curii.com
<p>Currently, browser may stall for a long time if a "send block to server" operation fails. Perhaps some browsers won't even call the onreadystatechange handler. The "send block" code should use a timer to detect this sort of thing and retry, like it does now after receiving a "fail" message from the server.</p> GET-Evidence - Feature #426 (In Progress): Use compute cloud for back-end processinghttps://dev.arvados.org/issues/4262010-11-28T20:28:11ZWard Vandewegeward@curii.com
We need to modify the background processing code so it can run on a "fresh" node:
<ul>
<li>Pre-process reference data (refFlat, hg18.2bit, hg19.2bit) and put it in warehouse storage</li>
<li>Make mr-get-evidence wrapper:
<ul>
<li>in step 0, scan the input, queue 1 jobstep per chromosome, and output the comments/metadata</li>
<li>fetch/extract the reference data (if not already extracted by previous jobstep)</li>
<li>grep for the desired chromosome, sort, do the rest of the processing</li>
</ul></li>
</ul>
<p>We should still support single-node installations. For this case we need a mechanism to prevent the server from overtaxing itself if many jobs are submitted at once (e.g., by default, max # concurrent jobs = # cpus).</p>
<ul>
<li>Possible solution: Try to flock() one of N lockfiles in /home/trait/lock/slot.X. If all are already locked, wait random# seconds and try again. When a flock succeeds, start the job (pass the lock to the job process, so the lock releases when the process quits).</li>
</ul>
<p>The xmlrpc server should be replaced with a job queue. The web gui should submit a job by inserting a row into a MySQL table.</p>
The background service (probably running on the same machine as the webgui) will check the queue every few seconds (and when triggered by webgui via named socket or something). For each job in the queue:
<ul>
<li>Just delete it if we've already started/queued a process for this dataset.</li>
<li>If cloud processing is available, submit a batch job and note job# J and queuetime</li>
<li>Start a local job if local processing slots are available <em>and</em>...
<ul>
<li>cloud processing is not available, <em>or</em></li>
<li>a batch job was submitted for this data set but failed, <em>or</em></li>
<li>a batch job was submitted for this data set >30 seconds ago <em>and</em> that job hasn't started yet (cloud is busy)</li>
</ul>
</li>
<li>If the batch job J for this data set has succeeded:
<ul>
<li>Make a symlink or something in {hash}-out/ so the web gui knows the results are available.</li>
<li>Delete the queue entry.</li>
<li>If there are some results in {hash}-out/ns.gff.gz etc. from previous analyses, delete them.</li>
<li>Get a local copy of the get-evidence.json file from the warehouse, but wait to get the other stuff from the warehouse until someone downloads them.</li>
</ul></li>
</ul>
Storage:
<ul>
<li>Copy the uploaded data to the cloud in the background service, while checking for new items in the queue. Make a symlink genotype.gff.archive -> warehouse:///{hash}/input.gff.gz</li>
<li>If user provides a warehouse:/// url instead of file:///, just make the genotype.gff.archive symlink instead of copying the file to local storage.</li>
</ul> GET-Evidence - Feature #483 (New): Handle/prevent edit conflicts more effectivelyhttps://dev.arvados.org/issues/4832010-05-07T18:52:35ZTom Cleggtom@curii.com
<ul>
<li>detect “version you’re editing already superseded” and ask user what to do</li>
<li>detect “someone else is editing this page/section” if logged in</li>
</ul> GET-Evidence - Feature #482 (New): add “affects self (hom or dominant)” checkbox (vs “affects off...https://dev.arvados.org/issues/4822010-05-07T18:51:38ZTom Cleggtom@curii.com
<p>add “affects self (hom or dominant)” checkbox (vs “affects offspring”) on result page</p> GET-Evidence - Feature #481 (New): Test Internet Explorer, possibly use Chrome Frame to make edit...https://dev.arvados.org/issues/4812010-05-07T18:50:36ZTom Cleggtom@curii.com
<p>Test Internet Explorer, possibly use Chrome Frame to make editing features work in IE</p> GET-Evidence - Bug #479 (New): NSF-Lys702Asn shows wrong hapmap frequencyhttps://dev.arvados.org/issues/4792010-05-07T18:48:33ZTom Cleggtom@curii.com
<p>NSF-Lys702Asn shows wrong hapmap frequency</p> GET-Evidence - Bug #478 (New): Keep "overall odds ratio" updated when editing individual sets of ...https://dev.arvados.org/issues/4782010-05-07T18:47:29ZTom Cleggtom@curii.com
<p>Keep "overall odds ratio" updated when editing individual sets of OR figures</p>