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- 2 discussions
Hello,
Context:
We are currently developing an Early Alert system for invasive species
where all data transits through GBIF:
- one one side, we are helping multiple data providers to push their
observations to GBIF at a high frequency (probably daily)
- on the other side, we have a web application
<https://github.com/riparias/early-warning-webapp> that allows users to be
alerted of specific species in specific locations. To do so, that web
applicatio*n refreshes its internal database daily, by dropping and
recreating all occurrences based on an automated GBIF data download*. Data
in the gbifId field is used as a long-term occurrence identifier in this
web application.
It is crucial for our system that we can unambiguously distinguish new
occurrences from existing occurrences that were recently republished (and
maybe updated), and also detect occurrences that have been updated in the
source dataset.
Finally, the question:
in the GBIF infrastructure, when exactly is a new occurrence Gbif ID issued
(vs reused). Is it just a matter of following the publisher's occurrenceID,
or is the algorithm that chooses Gbif IDs more complex?
Or, more practically: what should I say to our data providers to guarantee
all new occurrences they publish get a new gbifId and existing occurrences
that get republished keep the same gbifId?
I'd be also interested to know if you think the concept of using GBIF ids
as stable identifiers in an external tool is fundamentally flawed (but I
hope not!)
Thanks a lot, don't hesitate to redirect me if this is not the right place
to ask this question.
Nicolas
My apologies if this quest
1
0
Dear all:
The last builds of ala-dev branch are falling because some docker
container name is in use:
{"message":"Conflict. The container name \"/ala-namematching-service-1\"
is already in use by container
I'm not sure if this is a temporarly issue that can be solved just
removing it manually or probably we have to fix it in the build
configuration.
Doing a fast search, here some flags to remove (or not) the containers:
https://stackoverflow.com/questions/48581627/fabrik8-delete-only-some-conta…
Also some discussion about the dynamic ports and this issue
https://github.com/fabric8io/docker-maven-plugin/issues/699#issuecomment-27…
Bests regards,
Vicente
-------- Mensaje reenviado --------
Asunto: Build failed in Jenkins: pipelines-la-dev #33
Fecha: Thu, 6 Aug 2020 16:12:47 +0000 (UTC)
De: builds <builds(a)gbif.org>
Para: djtfmartin(a)gmail.com, Doug.Palmer(a)csiro.au, noreply(a)github.com,
vjrj(a)ourproject.org
See
<https://builds.gbif.org/job/pipelines-la-dev/33/display/redirect?page=chang…>
Changes:
[vjrj] Added generated changelog with 'gbp dch' for automatic version
control
[vjrj] Readded debian specific ignores
[vjrj] Ignoring some debian lintian warns
[vjrj] Change obsolete bash completion directory
[vjrj] Using mvn for self build. Reusing M2_REPO to faster deb build
[vjrj] Ignoring debian generated file
------------------------------------------
[...truncated 2.18 MB...]
[WARNING] - com.sun.research.ws.wadl.Request
[WARNING] - com.sun.research.ws.wadl.package-info
[WARNING] - com.sun.research.ws.wadl.ResourceType
[WARNING] - com.sun.research.ws.wadl.Param
[WARNING] - com.sun.research.ws.wadl.Link
[WARNING] - com.sun.research.ws.wadl.Application
[WARNING] - com.sun.research.ws.wadl.ParamStyle
[WARNING] - com.sun.research.ws.wadl.Doc
[WARNING] - 8 more...
[WARNING] hadoop-common-2.6.0-cdh5.16.2.jar,
occurrence-persistence-0.124.jar define 2093 overlapping classes:
[WARNING] - org.apache.hadoop.io.compress.DecompressorStream
[WARNING] - org.apache.hadoop.metrics.spi.AbstractMetricsContext
[WARNING] -
org.apache.hadoop.crypto.key.kms.LoadBalancingKMSClientProvider$14
[WARNING] - org.apache.hadoop.record.XmlRecordInput$Value
[WARNING] - org.apache.hadoop.util.HeapSort
[WARNING] - org.apache.hadoop.metrics.ganglia.GangliaContext31
[WARNING] -
org.apache.hadoop.ha.protocolPB.HAServiceProtocolClientSideTranslatorPB$1
[WARNING] - org.apache.hadoop.util.ShutdownHookManager$2
[WARNING] - org.apache.hadoop.fs.crypto.CryptoFSDataInputStream
[WARNING] - org.apache.hadoop.io.compress.DirectDecompressionCodec
[WARNING] - 2083 more...
[WARNING] jsp-2.1-6.1.14.jar, jasper-compiler-5.5.23.jar,
jasper-runtime-5.5.23.jar define 1 overlapping classes: [WARNING] -
org.apache.jasper.compiler.Localizer
[WARNING] hsqldb-2.4.1.jar, hsqldb-1.8.0.10.jar define 176 overlapping
classes: [WARNING] - org.hsqldb.util.DatabaseManagerSwing$2
[WARNING] - org.hsqldb.SessionInterface
[WARNING] - org.hsqldb.util.DatabaseManagerSwing
[WARNING] - org.hsqldb.persist.LockFile$UnexpectedFileNotFoundException
[WARNING] - org.hsqldb.util.CommonSwing
[WARNING] - org.hsqldb.lib.IntKeyHashMap
[WARNING] - org.hsqldb.util.TableSorter$Arrow
[WARNING] - org.hsqldb.lib.IntValueHashMap
[WARNING] - org.hsqldb.util.DatabaseManagerSwing$5
[WARNING] - org.hsqldb.util.TableSorter$Directive
[WARNING] - 166 more...
[WARNING] jsp-2.1-6.1.14.jar, jasper-compiler-5.5.23.jar define 143
overlapping classes: [WARNING] - org.apache.jasper.compiler.Node$Nodes
[WARNING] - org.apache.jasper.compiler.tagplugin.TagPlugin
[WARNING] - org.apache.jasper.compiler.JspUtil
[WARNING] - org.apache.jasper.xmlparser.MyEntityResolver
[WARNING] - org.apache.jasper.compiler.Validator$TagExtraInfoVisitor
[WARNING] - org.apache.jasper.compiler.SmapStratum
[WARNING] - org.apache.jasper.compiler.SmapGenerator
[WARNING] - org.apache.jasper.compiler.tagplugin.TagPluginContext
[WARNING] - org.apache.jasper.compiler.JasperTagInfo
[WARNING] - org.apache.jasper.EmbeddedServletOptions
[WARNING] - 133 more...
[WARNING] slf4j-log4j12-1.7.5.jar, logback-classic-1.2.3.jar define 3
overlapping classes: [WARNING] - org.slf4j.impl.StaticMarkerBinder
[WARNING] - org.slf4j.impl.StaticLoggerBinder
[WARNING] - org.slf4j.impl.StaticMDCBinder
[WARNING] occurrence-persistence-0.124.jar,
hadoop-auth-2.6.0-cdh5.16.2.jar define 39 overlapping classes: [WARNING]
-
org.apache.hadoop.security.authentication.server.PseudoAuthenticationHandler
[WARNING] -
org.apache.hadoop.security.authentication.client.AuthenticatedURL
[WARNING] -
org.apache.hadoop.security.authentication.client.AuthenticatedURL$Token
[WARNING] - org.apache.hadoop.security.authentication.client.Authenticator
[WARNING] -
org.apache.hadoop.security.authentication.util.FileSignerSecretProvider
[WARNING] -
org.apache.hadoop.security.authentication.util.KerberosName$NoMatchingRule
[WARNING] -
org.apache.hadoop.security.authentication.util.KerberosName$Rule
[WARNING] -
org.apache.hadoop.security.authentication.server.AuthenticationHandler
[WARNING] -
org.apache.hadoop.security.authentication.util.RolloverSignerSecretProvider
[WARNING] -
org.apache.hadoop.security.authentication.util.KerberosName$BadFormatString
[WARNING] - 29 more...
[WARNING] hadoop-core-2.6.0-mr1-cdh5.16.2.jar,
hadoop-mapreduce-client-common-2.6.0-cdh5.16.2.jar define 4 overlapping
classes: [WARNING] - org.apache.hadoop.mapred.LocalJobRunner
[WARNING] - org.apache.hadoop.mapred.MRVersion
[WARNING] - org.apache.hadoop.mapred.LocalJobRunner$Job
[WARNING] - org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable
[WARNING] xml-apis-1.3.04.jar, batik-ext-1.7.jar define 8 overlapping
classes: [WARNING] - org.w3c.dom.events.MouseEvent
[WARNING] - org.w3c.dom.events.MutationEvent
[WARNING] - org.w3c.dom.events.Event
[WARNING] - org.w3c.dom.events.EventListener
[WARNING] - org.w3c.dom.events.DocumentEvent
[WARNING] - org.w3c.dom.events.EventException
[WARNING] - org.w3c.dom.events.EventTarget
[WARNING] - org.w3c.dom.events.UIEvent
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Attaching shaded artifact.
[INFO] [INFO] --- maven-jar-plugin:2.6:test-jar (attach-test-jar) @
pipelines ---
[INFO] Building jar:
<https://builds.gbif.org/job/pipelines-la-dev/ws/livingatlas/pipelines/targe…>
[INFO] [INFO] --- maven-site-plugin:3.4:attach-descriptor
(attach-descriptor) @ pipelines ---
[INFO] [INFO] --- download-maven-plugin:1.6.0:wget (install-shapefiles)
@ pipelines ---
[WARNING] No signatures were supplied, skipping file validation
[INFO] Got from cache:
/var/lib/jenkins/.m2/repository/.cache/download-maven-plugin/pipelines-shapefiles.zip_32b5126a782a32c28abe5075c9af9241
[INFO] [INFO] --- download-maven-plugin:1.6.0:wget (install-shapefiles2)
@ pipelines ---
[WARNING] No signatures were supplied, skipping file validation
[INFO] Got from cache:
/var/lib/jenkins/.m2/repository/.cache/download-maven-plugin/sds-layers.tgz_58a56e633cf360ff2cb519e104732e9d
[INFO] Expanding: /tmp/pipelines-shp/sds-layers.tgz into /tmp/pipelines-shp
[INFO] [INFO] --- docker-maven-plugin:0.33.0:start (start) @ pipelines ---
[INFO] DOCKER> [djtfmartin/biocache-pipelines-solr8:v3] "solr8": Start
container ac576b4993c9
[ERROR] DOCKER> Error occurred during container startup, shutting down...
[INFO] DOCKER> [djtfmartin/biocache-pipelines-solr8:v3] "solr8": Stop
and removed container ac576b4993c9 after 0 ms
[ERROR] DOCKER> I/O Error [Unable to create container for
[charvolant/ala-namematching-service:v20200214-5] :
{"message":"Conflict. The container name \"/ala-namematching-service-1\"
is already in use by container
\"4b7429e4ed5387f457ddc1a1d43f08e8fcdea3756c3861f6cc8c843627045920\".
You have to remove (or rename) that container to be able to reuse that
name."} (Conflict: 409)]
Started calculate disk usage of build
Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
Finished Calculation of disk usage of workspace in 0 seconds
[INFO] [INFO]
------------------------------------------------------------------------
[INFO] Skipping Pipelines :: Parent
[INFO] This project has been banned from the build due to previous failures.
[INFO]
------------------------------------------------------------------------
[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary for Pipelines :: Parent 2.5.5-SNAPSHOT:
[INFO] [INFO] Pipelines :: Parent ................................
SUCCESS [ 2.687 s]
[INFO] Pipelines :: Tools ................................. SUCCESS [
1.028 s]
[INFO] Pipelines :: Tools :: Maven plugin ................. SUCCESS [
5.797 s]
[INFO] Pipelines :: Tools :: Elasticsearch tools .......... SUCCESS
[01:07 min]
[INFO] Pipelines :: Pipelines ............................. SUCCESS [
0.958 s]
[INFO] Pipelines :: Pipelines :: Common ................... SUCCESS [
4.793 s]
[INFO] Pipelines :: Sdks .................................. SUCCESS [
0.987 s]
[INFO] Pipelines :: Sdks :: Models ........................ SUCCESS [
9.504 s]
[INFO] Pipelines :: Sdks :: Parsers ....................... SUCCESS [
27.005 s]
[INFO] Pipelines :: Sdks :: Keygen ........................ SUCCESS
[08:29 min]
[INFO] Pipelines :: Sdks :: Core .......................... SUCCESS [
55.367 s]
[INFO] Pipelines :: Tools :: Archives converters .......... SUCCESS
[01:34 min]
[INFO] Pipelines :: Pipelines :: Beam-common .............. SUCCESS [
21.964 s]
[INFO] Pipelines :: Pipelines :: Export Occurrence into Avro SUCCESS
[01:58 min]
[INFO] Pipelines :: Pipelines :: Ingest-fragmenter ........ SUCCESS
[03:07 min]
[INFO] Pipelines :: Pipelines :: Ingest-transforms ........ SUCCESS
[01:04 min]
[INFO] Pipelines :: Pipelines :: Ingest-GBIF .............. SUCCESS
[02:59 min]
[INFO] Pipelines :: Pipelines :: Ingest-GBIF Java version . SUCCESS
[02:21 min]
[INFO] Pipelines :: Pipelines :: Ingest-GBIF Standalone ... SUCCESS
[01:51 min]
[INFO] Pipelines :: Example ............................... SUCCESS [
0.975 s]
[INFO] Pipelines :: Examples :: Transform ................. SUCCESS [
45.347 s]
[INFO] Pipelines :: Examples :: Metrics ................... SUCCESS
[01:40 min]
[INFO] Pipelines :: CLI ................................... SUCCESS [
0.979 s]
[INFO] Pipelines :: CLI :: Crawler ........................ SUCCESS
[01:14 min]
[INFO] Pipelines :: CLI :: Crawler IT ..................... SUCCESS
[02:19 min]
[INFO] Living Atlas Pipelines Parent POM .................. SUCCESS [
1.264 s]
[INFO] Living Atlas Pipelines ............................. FAILURE
[02:15 min]
[INFO] Living Atlas Migration tools ....................... SKIPPED
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 35:57 min
[INFO] Finished at: 2020-08-06T16:12:38Z
[INFO]
------------------------------------------------------------------------
Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal
io.fabric8:docker-maven-plugin:0.33.0:start (start) on project
pipelines: I/O Error: Unable to create container for
[charvolant/ala-namematching-service:v20200214-5] :
{"message":"Conflict. The container name \"/ala-namematching-service-1\"
is already in use by container
\"4b7429e4ed5387f457ddc1a1d43f08e8fcdea3756c3861f6cc8c843627045920\".
You have to remove (or rename) that container to be able to reuse that
name."} (Conflict: 409) -> [Help 1]
[ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven
with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] [ERROR] For more information about the errors and possible
solutions, please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] [ERROR] After correcting the problems, you can resume the build
with the command
[ERROR] mvn <goals> -rf :pipelines
[JENKINS] Archiving
<https://builds.gbif.org/job/pipelines-la-dev/ws/pom.xml> to
org.gbif.pipelines/pipelines-parent/2.5.5-SNAPSHOT/pipelines-parent-2.5.5-SNAPSHOT.pom
[JENKINS] Archiving
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org.gbif.pipelines/examples/2.5.5-SNAPSHOT/examples-2.5.5-SNAPSHOT.pom
[JENKINS] Archiving
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[JENKINS] Archiving
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[JENKINS] Archiving
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[JENKINS] Archiving
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org.gbif.pipelines/examples-metrics/2.5.5-SNAPSHOT/examples-metrics-2.5.5-SNAPSHOT.jar
[JENKINS] Archiving
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org.gbif.pipelines/examples-metrics/2.5.5-SNAPSHOT/examples-metrics-2.5.5-SNAPSHOT-shaded.jar
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[JENKINS] Archiving
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[JENKINS] Archiving
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[JENKINS] Archiving
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[JENKINS] Archiving
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channel stopped
WARN: Unable to locate 'report-task.txt' in the workspace. Did the
SonarScanner succedeed?
[Set GitHub commit status (universal)] ERROR on repos
[GHRepository@13c81b9a[nodeId=MDEwOlJlcG9zaXRvcnkxMDQ4ODkxNjU=,description=Pipelines
for data processing (GBIF and
LivingAtlases),homepage=,name=pipelines,fork=false,archived=false,size=20981,milestones={},language=Java,commits={},source=<null>,parent=<null>,url=https://api.github.com/repos/gbif/pipelines,id=104889165,nodeId=<null>,createdAt=2017-09-26T13:36:09Z,updatedAt=2020-08-06T10:23:28Z]]
(sha:4a5eaa0) with context:pipelines-la-dev
Setting commit status on GitHub for
https://github.com/gbif/pipelines/commit/4a5eaa02f0781e9a796d7609d0e2e456c2…
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Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
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