Add Genomics API counters for Dataflow UI display. by deflaux · Pull Request #41 · googlegenomics/dataflow-java

deflaux · 2015-03-11T20:58:43Z

Also:

Update option descriptions.
Bump genomics API version.
Ensure that we have one task per core.

coveralls · 2015-03-11T21:11:01Z

Coverage decreased (-1.06%) to 30.11% when pulling 78d61e6 on deflaux:master into af2db8d on googlegenomics:master.

coveralls · 2015-03-11T21:16:28Z

Coverage decreased (-1.06%) to 30.11% when pulling 78d61e6 on deflaux:master into af2db8d on googlegenomics:master.

pgrosu · 2015-03-11T21:23:57Z

Hi Nicole,

On line 122 in DataflowWorkarounds.java it is currently written as:

if(3 == machineNameParts.length) {

It would be preferred as follows, or maybe a variable that can be assigned:

if(machineNameParts.length == 3) {

~p

pgrosu · 2015-03-11T21:30:02Z

On line 125 of the same file, it is currently written as:

numWorkers *= numCores;

Could we expand it just for clarification purposes:

numWorkers = numWorkers * numCores;

~p

pgrosu · 2015-03-11T21:34:57Z

Looks nice, I'll try it once merged.

Thanks,
~p

Its now in the codelabs repository.

--machineType does not have a default of n1-standard-4 in all contexts.

Now that we are doing client-side filtering for strict shard boundaries, we need to ensure that we are requesting the field that the filter will check.

coveralls · 2015-03-13T03:59:05Z

Coverage increased (+0.36%) to 23.92% when pulling cb269a9 on deflaux:master into 70bc9f7 on googlegenomics:master.

pgrosu · 2015-03-13T08:08:30Z

Hi Nicole,

Unfortunately it throws an error, since I cannot give it a range on a specific chromosome :( It wants a string for the reference, and I only want to count the reads within a specific range. Is there a solution?

$ java -cp target/google-genomics-dataflow-v1beta2-0.5-SNAPSHOT.jar com.google.cloud.genomics.dataflow.pipelines.CountReads --readGroupSetId=CMvnhpKTFhDq9e2Yy9G-Bg --references=1:1000:10000 --genomicsSecretsFile=client_secrets.json --project=<redacted> --datasetId=10473108253681171589 --numWorkers=10 --output=counts.txt
Mar 13, 2015 3:57:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Mar 13, 2015 3:57:30 AM org.reflections.Reflections scan
INFO: Reflections took 144 ms to scan 10 urls, producing 1 keys and 77 values
...
INFO: Turning 1 options into 10 workers
Mar 13, 2015 3:57:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds getPCollection
INFO: Adding collection with 0 to 1
Mar 13, 2015 3:57:30 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Mar 13, 2015 3:57:30 AM com.google.cloud.genomics.dataflow.readers.ReadReader processApiCall
INFO: Starting Reads read loop
Exception in thread "main" java.lang.RuntimeException: com.google.cloud.genomics.utils.Paginator$SearchException: com.google.api.client.googleapis.json.GoogleJsonResponseException: 400 Bad Request
{
"code" : 400,
"errors" : [ {
"domain" : "global",
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]",
"reason" : "invalidArgument"
} ],
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]"
}
at com.google.cloud.dataflow.sdk.Pipeline.run(Pipeline.java:151)
at com.google.cloud.genomics.dataflow.pipelines.CountReads.main(CountReads.java:127)
Caused by: com.google.cloud.genomics.utils.Paginator$SearchException: com.google.api.client.googleapis.json.GoogleJsonResponseException: 400 Bad Request
{
"code" : 400,
"errors" : [ {
"domain" : "global",
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]",
"reason" : "invalidArgument"
} ],
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]"
}
at com.google.cloud.genomics.utils.Paginator$5$1$1.apply(Paginator.java:1051)
at com.google.cloud.genomics.utils.Paginator$5$1$1.apply(Paginator.java:1038)
at com.google.common.base.Present.transform(Present.java:71)
at com.google.cloud.genomics.utils.Paginator$5$1.computeNext(Paginator.java:1036)
at com.google.cloud.genomics.utils.Paginator$5$1.computeNext(Paginator.java:1034)
at com.google.common.collect.AbstractSequentialIterator.next(AbstractSequentialIterator.java:77)
at com.google.common.collect.Iterators.advance(Iterators.java:909)
at com.google.common.collect.Iterables$10.iterator(Iterables.java:865)
at com.google.common.collect.Iterables$8.iterator(Iterables.java:713)
at com.google.common.collect.Iterables$8.iterator(Iterables.java:713)
at com.google.common.collect.Iterables.iterators(Iterables.java:508)
at com.google.common.collect.Iterables.access$100(Iterables.java:60)
at com.google.common.collect.Iterables$2.iterator(Iterables.java:498)
at com.google.cloud.genomics.dataflow.readers.ReadReader.processApiCall(ReadReader.java:58)
at com.google.cloud.genomics.dataflow.readers.ReadReader.processApiCall(ReadReader.java:29)
at com.google.cloud.genomics.dataflow.readers.GenomicsApiReader.processElement(GenomicsApiReader.java:58)
Caused by: com.google.api.client.googleapis.json.GoogleJsonResponseException: 400 Bad Request
{
"code" : 400,
"errors" : [ {
"domain" : "global",
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]",
"reason" : "invalidArgument"
} ],
"message" : "The given readGroupSets are not aligned to any reference with referenceName \"1:1000:10000\". Wanted one of [\"1\" \"2\" \"3\" \"4\" \"5\" \"6\" \"7\" \"8\" \"9\" \"10\" \"11\" \"12\" \"13\" \"14\" \"15\" \"16\" \"17\" \"18\" \"19\" \"20\" \"21\" \"22\" \"X\" \"Y\" \"MT\" \"GL000207.1\" \"GL000226.1\" \"GL000229.1\" \"GL000231.1\" \"GL000210.1\" \"GL000239.1\" \"GL000235.1\" \"GL000201.1\" \"GL000247.1\" \"GL000245.1\" \"GL000197.1\" \"GL000203.1\" \"GL000246.1\" \"GL000249.1\" \"GL000196.1\" \"GL000248.1\" \"GL000244.1\" \"GL000238.1\" \"GL000202.1\" \"GL000234.1\" \"GL000232.1\" \"GL000206.1\" \"GL000240.1\" \"GL000236.1\" \"GL000241.1\" \"GL000243.1\" \"GL000242.1\" \"GL000230.1\" \"GL000237.1\" \"GL000233.1\" \"GL000204.1\" \"GL000198.1\" \"GL000208.1\" \"GL000191.1\" \"GL000227.1\" \"GL000228.1\" \"GL000214.1\" \"GL000221.1\" \"GL000209.1\" \"GL000218.1\" \"GL000220.1\" \"GL000213.1\" \"GL000211.1\" \"GL000199.1\" \"GL000217.1\" \"GL000216.1\" \"GL000215.1\" \"GL000205.1\" \"GL000219.1\" \"GL000224.1\" \"GL000223.1\" \"GL000195.1\" \"GL000212.1\" \"GL000222.1\" \"GL000200.1\" \"GL000193.1\" \"GL000194.1\" \"GL000225.1\" \"GL000192.1\" \"NC_007605\" \"hs37d5\" \"*\"]"
}
at com.google.api.client.googleapis.json.GoogleJsonResponseException.from(GoogleJsonResponseException.java:145)
at com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:113)
at com.google.api.client.googleapis.services.json.AbstractGoogleJsonClientRequest.newExceptionOnError(AbstractGoogleJsonClientRequest.java:40)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest$1.interceptResponse(AbstractGoogleClientRequest.java:312)
at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:1049)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:410)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:343)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.execute(AbstractGoogleClientRequest.java:460)
at com.google.cloud.genomics.utils.RetryPolicy.execute(RetryPolicy.java:102)
at com.google.cloud.genomics.utils.Paginator$5$1$1.apply(Paginator.java:1042)
at com.google.cloud.genomics.utils.Paginator$5$1$1.apply(Paginator.java:1038)
at com.google.common.base.Present.transform(Present.java:71)
at com.google.cloud.genomics.utils.Paginator$5$1.computeNext(Paginator.java:1036)
at com.google.cloud.genomics.utils.Paginator$5$1.computeNext(Paginator.java:1034)
at com.google.common.collect.AbstractSequentialIterator.next(AbstractSequentialIterator.java:77)
at com.google.common.collect.Iterators.advance(Iterators.java:909)
at com.google.common.collect.Iterables$10.iterator(Iterables.java:865)
at com.google.common.collect.Iterables$8.iterator(Iterables.java:713)
at com.google.common.collect.Iterables$8.iterator(Iterables.java:713)
at com.google.common.collect.Iterables.iterators(Iterables.java:508)
at com.google.common.collect.Iterables.access$100(Iterables.java:60)
at com.google.common.collect.Iterables$2.iterator(Iterables.java:498)
at com.google.cloud.genomics.dataflow.readers.ReadReader.processApiCall(ReadReader.java:58)
at com.google.cloud.genomics.dataflow.readers.ReadReader.processApiCall(ReadReader.java:29)
at com.google.cloud.genomics.dataflow.readers.GenomicsApiReader.processElement(GenomicsApiReader.java:58)
at com.google.cloud.dataflow.sdk.util.DoFnRunner.processElement(DoFnRunner.java:126)
at com.google.cloud.dataflow.sdk.transforms.ParDo.evaluateHelper(ParDo.java:1058)
at com.google.cloud.dataflow.sdk.transforms.ParDo.evaluateSingleHelper(ParDo.java:963)
at com.google.cloud.dataflow.sdk.transforms.ParDo.access$000(ParDo.java:441)
at com.google.cloud.dataflow.sdk.transforms.ParDo$1.evaluate(ParDo.java:951)
at com.google.cloud.dataflow.sdk.transforms.ParDo$1.evaluate(ParDo.java:946)
at com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner$Evaluator.visitTransform(DirectPipelineRunner.java:611)
at com.google.cloud.dataflow.sdk.runners.TransformTreeNode.visit(TransformTreeNode.java:200)
at com.google.cloud.dataflow.sdk.runners.TransformTreeNode.visit(TransformTreeNode.java:196)
at com.google.cloud.dataflow.sdk.runners.TransformHierarchy.visit(TransformHierarchy.java:109)
at com.google.cloud.dataflow.sdk.Pipeline.traverseTopologically(Pipeline.java:204)
at com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner$Evaluator.run(DirectPipelineRunner.java:584)
at com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner.run(DirectPipelineRunner.java:328)
at com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner.run(DirectPipelineRunner.java:70)
at com.google.cloud.dataflow.sdk.Pipeline.run(Pipeline.java:145)
at com.google.cloud.genomics.dataflow.pipelines.CountReads.main(CountReads.java:127)
$

Thanks,
Paul

iliat · 2015-03-13T15:42:25Z

@pgrosu The API flavor of this pipeline was written as a very simplistic variant with just taking the reference and not ranges. The main purpose of this was to try the BAM file reading, not so much the API access. I will add more sophistication to the API side handling to make it compatible with what BAM reading part accepts.

pgrosu · 2015-03-13T15:48:49Z

Aha, thanks Ilia - I'll wait :) It was this part of the script that caused me think otherwise initially:

if [ "$1"="bam" ];then
bam_argument="--BAMFilePath=$BAM_FILE_PATH"fiif [ "$2"="cloud" ];then
additional_arguments="--stagingLocation=${STAGING} --numWorkers=1 --runner=BlockingDataflowPipelineRunner"else
additional_arguments="--numWorkers=1"fi

Thanks,
Paul

Add Genomics API counters for Dataflow UI display.

pgrosu · 2015-03-13T20:24:44Z

Thanks Nicole :)

Add Genomics API counters for Dataflow UI display.

deflaux added 5 commits March 11, 2015 13:48

Update option descriptions.
9e36c59

Bump genomics API version.
f1454e5

Ensure that we have one task per core.
e6872f8

Add Genomics API counters.
1ad45fc

Fixed counter names to be a bit more consistent.
78d61e6

deflaux added 5 commits March 12, 2015 20:30

Nuke pipeline that has moved elsewhere.
e4d7383
Its now in the codelabs repository.

Bug fix for dataflow workaround.
8d9e801
--machineType does not have a default of n1-standard-4 in all contexts.

Add 'start' to partial request fields.
f860346
Now that we are doing client-side filtering for strict shard boundaries, we need to ensure that we are requesting the field that the filter will check.

Merge remote-tracking branch 'upstream/master'
158f006

Update changes from upstream/master.
cb269a9

deflaux added a commit that referenced this pull request Mar 13, 2015
Merge pull request#41from deflaux/master
efd9219
Add Genomics API counters for Dataflow UI display.

deflaux merged commit efd9219 into googlegenomics:masterMar 13, 2015

jiridanek pushed a commit to jiridanek/dataflow-java that referenced this pull request Jan 18, 2016
Merge pull requestgooglegenomics#41from deflaux/master
d6c0453
Add Genomics API counters for Dataflow UI display.

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Add Genomics API counters for Dataflow UI display. - #41

Add Genomics API counters for Dataflow UI display.#41
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