Sync Maven data to graph #2048

msrb · 2018-01-25T08:56:13Z

Description

There were times when data ingestion pipeline was broken or certain parts of the pipeline were disabled. During such times, we analyzed plenty of packages and stored results in S3, but never ingested the data to graph database. With #1085 implemented, we want to sync all missing data from S3 to graph.

Acceptance criteria

all Maven data from production S3 buckets are available in graph

abs51295 · 2018-01-25T09:13:19Z

Fixed a typo @msrb :)

msrb · 2018-01-29T20:04:05Z

@sivaavkd description updated, is it better now?

tuxdna · 2018-01-30T04:52:19Z

Carrying forward from - #1085 (comment)

Some intermittent failures encountered in Graph layer. This seems to be happening very sparsely:


g.V().has('ecosystem','maven').has('name','org.apache.tomcat:tomcat-servlet-api').properties('tokens','libio_usedby').drop().iterate();pkg = g.V().has('ecosystem','maven').has('name', 'org.apache.tomcat:tomcat-servlet-api').tryNext().orElseGet{graph.addVertex('ecosystem', 'maven', 'name', 'org.apache.tomcat:tomcat-servlet-api', 'vertex_label', 'Package')};pkg.property('last_updated', 1517286212.43);pkg.property('tokens', 'org'); pkg.property('tokens', 'apache'); pkg.property('tokens', 'tomcat'); pkg.property('tokens', 'tomcat'); pkg.property('tokens', 'servlet'); pkg.property('tokens', 'api');pkg.property('latest_version', '9.0.0.M17');pkg.property('libio_latest_release', '1500854400.0');pkg.property('libio_usedby', 'keycloak/keycloak:1359');pkg.property('libio_usedby', 'SungardAS/enhanced-snapshots:35');pkg.property('libio_usedby', 'cf-unik/unik:1239');pkg.property('libio_usedby', 'entando/entando-components:15');pkg.property('libio_usedby', 'indeedeng/proctor:198');pkg.property('libio_usedby', 'magro/memcached-session-manager:552');pkg.property('libio_usedby', 'nysenate/OpenLegislation:163');pkg.property('libio_usedby', 'Red5/red5-server:1254');pkg.property('libio_usedby', 'aspose-words/Aspose.Words-for-Java:52');pkg.property('libio_usedby', 'google/identity-toolkit-java-client:32');pkg.property('libio_dependents_projects', '65');pkg.property('libio_dependents_repos', '2.05K');pkg.property('libio_total_releases', '124');pkg.property('libio_latest_version', '8.5.19');g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.19').property('gh_release_date', 1500854400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M25').property('gh_release_date',1500854400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M19').property('gh_release_date',1490572800.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.
5.16').property('gh_release_date',1498003200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.14').property('gh_release_date',1492041600.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.15').property('gh_release_date',1493942400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M21').property('gh_release_date',1493856000.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M20').property('gh_release_date',1491955200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M22').property('gh_release_date',1498003200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.13').property('gh_release_date',1490572800.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M1').properties('licenses','cve_ids','declared_licenses').drop().iterate();ver = g.V().has('pecosystem', 'maven').has('pname', 'org.apache.tomcat:tomcat-servlet-api').has('version', '9.0.0.M1').tryNext().orElseGet{graph.addVertex('pecosystem','maven', 'pname','org.apache.tomcat:tomcat-servlet-api', 'version', '9.0.0.M1', 'vertex_label', 'Version')};ver.property('last_updated',1517286212.43);ver.property('description','javax.servlet package');ver.property('cm_num_files',112);ver.property('cm_avg_cyclomatic_complexity', 1.23);ver.property('cm_loc',42622);ver.property('licenses', 'ASL 2.0'); ver.property('licenses', 'CDDL');ver.property('cve_ids', 'CVE-2017-6056:5.0'); ver.property('cve_ids', 'CVE-2016-8735:7.5'); ver.property('cve_ids', 'CVE-2016-6816:6.8'); ver.property('cve_ids', 'CVE-2016-6325:7.2'); ver.property('cve_ids', 'CVE-2016-5425:7.2'); ver.property('cve_ids', 'CVE-2016-3092:7.8'); ver.property('cve_ids', 'CVE-2016-0763:6.5'); ver.property('cve_ids', 'CVE-2016-0714:6.
5'); ver.property('cve_ids', 'CVE-2016-0706:4.0'); ver.property('cve_ids', 'CVE-2015-5351:6.8'); ver.property('cve_ids', 'CVE-2015-5346:6.8'); ver.property('cve_ids', 'CVE-2015-5345:5.0');ver.property('declared_licenses', 'Apache License'); ver.property('declared_licenses', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0');lic = g.V().has('lname', 'Apache License').tryNext().orElseGet{graph.addVertex('vertex_label', 'License', 'lname', 'Apache License', 'last_updated',1517286212.43)}; g.V(ver).out('has_declared_license').has('lname', 'Apache License').tryNext().orElseGet{ver.addEdge('has_declared_license', lic)};lic = g.V().has('lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0').tryNext().orElseGet{graph.addVertex('vertex_label', 'License', 'lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0', 'last_updated',1517286212.43)}; g.V(ver).out('has_declared_license').has('lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0').tryNext().orElseGet{ver.addEdge('has_declared_license', lic)};edge_c = g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M1').in('has_version').tryNext().orElseGet{pkg.addEdge('has_version', ver)};
ERROR:data_importer:The import failed: 'status'
ERROR:data_importer:Traceback for latest failure in import call: Traceback (most recent call last):
  File "/src/data_importer.py", line 101, in _import_keys_from_s3_http
    if resp['status']['code'] == 200:
KeyError: 'status'

g.V().has('ecosystem','maven').has('name','org.apache.tomcat:tomcat-servlet-api').properties('tokens','libio_usedby').drop().iterate();pkg = g.V().has('ecosystem','maven').has('name', 'org.apache.tomcat:tomcat-servlet-api').tryNext().orElseGet{graph.addVertex('ecosystem', 'maven', 'name', 'org.apache.tomcat:tomcat-servlet-api', 'vertex_label', 'Package')};pkg.property('last_updated', 1517286213.63);pkg.property('tokens', 'org'); pkg.property('tokens', 'apache'); pkg.property('tokens', 'tomcat'); pkg.property('tokens', 'tomcat'); pkg.property('tokens', 'servlet'); pkg.property('tokens', 'api');pkg.property('latest_version', '9.0.0.M17');pkg.property('libio_latest_release', '1500854400.0');pkg.property('libio_usedby', 'keycloak/keycloak:1359');pkg.property('libio_usedby', 'SungardAS/enhanced-snapshots:35');pkg.property('libio_usedby', 'cf-unik/unik:1239');pkg.property('libio_usedby', 'entando/entando-components:15');pkg.property('libio_usedby', 'indeedeng/proctor:198');pkg.property('libio_usedby', 'magro/memcached-session-manager:552');pkg.property('libio_usedby', 'nysenate/OpenLegislation:163');pkg.property('libio_usedby', 'Red5/red5-server:1254');pkg.property('libio_usedby', 'aspose-words/Aspose.Words-for-Java:52');pkg.property('libio_usedby', 'google/identity-toolkit-java-client:32');pkg.property('libio_dependents_projects', '65');pkg.property('libio_dependents_repos', '2.05K');pkg.property('libio_total_releases', '124');pkg.property('libio_latest_version', '8.5.19');g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.19').property('gh_release_date', 1500854400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M25').property('gh_release_date',1500854400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M19').property('gh_release_date',1490572800.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.
5.16').property('gh_release_date',1498003200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.14').property('gh_release_date',1492041600.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.15').property('gh_release_date',1493942400.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M21').property('gh_release_date',1493856000.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M20').property('gh_release_date',1491955200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M22').property('gh_release_date',1498003200.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.13').property('gh_release_date',1490572800.0);g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M11').properties('licenses','cve_ids','declared_licenses').drop().iterate();ver = g.V().has('pecosystem', 'maven').has('pname', 'org.apache.tomcat:tomcat-servlet-api').has('version', '9.0.0.M11').tryNext().orElseGet{graph.addVertex('pecosystem','maven', 'pname','org.apache.tomcat:tomcat-servlet-api', 'version', '9.0.0.M11', 'vertex_label', 'Version')};ver.property('last_updated',1517286213.63);ver.property('description','javax.servlet package');ver.property('cm_num_files',114);ver.property('cm_avg_cyclomatic_complexity', 1.23);ver.property('cm_loc',42800);ver.property('licenses', 'ASL 2.0'); ver.property('licenses', 'CDDL');ver.property('cve_ids', 'CVE-2017-6056:5.0'); ver.property('cve_ids', 'CVE-2016-8747:5.0'); ver.property('cve_ids', 'CVE-2016-8735:7.5'); ver.property('cve_ids', 'CVE-2016-6816:6.8'); ver.property('cve_ids', 'CVE-2016-6325:7.2'); ver.property('cve_ids', 'CVE-2016-5425:7.2');ver.property('declared_licenses', 'Apache License'); ver.property('declared_licenses'
, ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0');lic = g.V().has('lname', 'Apache License').tryNext().orElseGet{graph.addVertex('vertex_label', 'License', 'lname', 'Apache License', 'last_updated',1517286213.63)}; g.V(ver).out('has_declared_license').has('lname', 'Apache License').tryNext().orElseGet{ver.addEdge('has_declared_license', lic)};lic = g.V().has('lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0').tryNext().orElseGet{graph.addVertex('vertex_label', 'License', 'lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0', 'last_updated',1517286213.63)}; g.V(ver).out('has_declared_license').has('lname', ' Version 2.0 and
        Common Development And Distribution License (CDDL) Version 1.0').tryNext().orElseGet{ver.addEdge('has_declared_license', lic)};edge_c = g.V().has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','9.0.0.M11').in('has_version').tryNext().orElseGet{pkg.addEdge('has_version', ver)};
ERROR:data_importer:The import failed: HTTPConnectionPool(host='172.30.80.86', port=8182): Read timed out. (read timeout=30)
ERROR:data_importer:Traceback for latest failure in import call: Traceback (most recent call last):
  File "/src/data_importer.py", line 98, in _import_keys_from_s3_http
    data=json.dumps(payload), timeout=30)
  File "/usr/lib/python2.7/site-packages/requests/api.py", line 112, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/usr/lib/python2.7/site-packages/requests/api.py", line 58, in request
    return session.request(method=method, url=url, **kwargs)
  File "/usr/lib/python2.7/site-packages/requests/sessions.py", line 508, in request
    resp = self.send(prep, **send_kwargs)
  File "/usr/lib/python2.7/site-packages/requests/sessions.py", line 618, in send
    r = adapter.send(request, **kwargs)
  File "/usr/lib/python2.7/site-packages/requests/adapters.py", line 521, in send
    raise ReadTimeout(e, request=request)
ReadTimeout: HTTPConnectionPool(host='172.30.80.86', port=8182): Read timed out. (read timeout=30)

tuxdna · 2018-01-30T05:39:59Z

Figured out the cause of above error from gremlin server logs:

39989555 [gremlin-server-worker-1] WARN  org.apache.tinkerpop.gremlin.server.handler.HttpGremlinEndpointHandler  - Invalid request - responding with 500 Internal Server Error and startup failed:
Script3023.groovy: 1: expecting ''', found '\n' @ line 1, column 4116.
   d_licenses', ' Version 2.0 and
                                 ^

1 error

org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
Script3023.groovy: 1: expecting ''', found '\n' @ line 1, column 4116.
   d_licenses', ' Version 2.0 and
                                 ^

1 error

	at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:310)
	at org.codehaus.groovy.control.ErrorCollector.addFatalError(ErrorCollector.java:150)
	at org.codehaus.groovy.control.ErrorCollector.addError(ErrorCollector.java:120)
	at org.codehaus.groovy.control.ErrorCollector.addError(ErrorCollector.java:132)
	at org.codehaus.groovy.control.SourceUnit.addError(SourceUnit.java:360)
	at org.codehaus.groovy.antlr.AntlrParserPlugin.transformCSTIntoAST(AntlrParserPlugin.java:140)
	at org.codehaus.groovy.antlr.AntlrParserPlugin.parseCST(AntlrParserPlugin.java:111)
	at org.codehaus.groovy.control.SourceUnit.parse(SourceUnit.java:237)
	at org.codehaus.groovy.control.CompilationUnit$1.call(CompilationUnit.java:167)
	at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:931)
	at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:593)
	at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:569)
	at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:546)
	at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:298)
	at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:268)
	at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:254)
	at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:211)
	at org.apache.tinkerpop.gremlin.groovy.jsr223.GremlinGroovyScriptEngine.getScriptClass(GremlinGroovyScriptEngine.java:527)
	at org.apache.tinkerpop.gremlin.groovy.jsr223.GremlinGroovyScriptEngine.eval(GremlinGroovyScriptEngine.java:446)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:233)
	at org.apache.tinkerpop.gremlin.groovy.engine.ScriptEngines.eval(ScriptEngines.java:119)
	at org.apache.tinkerpop.gremlin.groovy.engine.GremlinExecutor.lambda$eval$2(GremlinExecutor.java:287)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Essentially the queries are not formed should factor in special characters like newlines correctly in existing code here:

https://github.com/fabric8-analytics/fabric8-analytics-data-model/blame/51ae4e1ecbd03e352a1a8e63a003bf2d7264a1a1/src/graph_populator.py#L112-L124

                drop_props.append('declared_licenses')


                prp_version += " ".join(["ver.property('declared_licenses', '{}');".format
                                         (dl) for dl in declared_licenses])
                # Create License Node and edge from EPV
                for lic in declared_licenses:
                    prp_version += "lic = g.V().has('lname', '{lic}').tryNext().orElseGet{{" \
                                   "graph.addVertex('vertex_label', 'License', 'lname', '{lic}', " \
                                   "'last_updated',{last_updated})}}; g.V(ver).out(" \
                                   "'has_declared_license').has('lname', '{lic}').tryNext()." \
                                   "orElseGet{{ver.addEdge('has_declared_license', lic)}};".format(
                                       lic=lic, last_updated=str(time.time())
                                   )

Happens for this package

has('pecosystem','maven').has('pname','org.apache.tomcat:tomcat-servlet-api').has('version','8.5.14')

tuxdna · 2018-01-30T05:58:24Z

metadata.json for the above EPV contains

"declared_license": "Apache License, Version 2.0 and\n        Common Development And Distribution License (CDDL) Version 1.0",

Notice the newline.

tuxdna · 2018-01-31T11:35:32Z

Fixed issue -

Fails to import packages where declared license is multiline fabric8-analytics/fabric8-analytics-data-model#71

Another issues encountered

No such bucket error encountered fabric8-analytics/fabric8-analytics-data-model#74

tuxdna · 2018-02-02T10:37:59Z

More issues encountered

tuxdna · 2018-02-12T11:49:40Z

Last time I checked the progress of Maven graph sync, it went till package named org.ops4j.pax.exam:pax-exam-spi which is ranked 104495 out of total 131460 Maven packages ( considering lexicographic order by name ). This is about 79% of all Maven packages which were synced.

msrb · 2018-02-12T13:55:12Z

@miteshvp can we query graph for exact numbers of Maven packages/components please?

tuxdna · 2018-02-13T15:55:51Z

In the first pass, less than 11402 packages remain from Maven graph sync. This is

100 * (1 - 11402 / 131460) = 91.32 %

There could be some packages skipped due to Gateway Timeouts. We can sync those once first pass is complete.

tuxdna · 2018-02-14T08:00:27Z

First pass is complete. Many of the Maven packages failed to sync in graph due to multiple reasons:

service unavailable
gateway timeout
bugs in data model importer

I have scheduled the sync of those (pending) packages again now.

msrb · 2018-02-14T08:12:47Z

Thanks Saleem 👍

I've created #2256 for improving test coverage in data-importer.

miteshvp · 2018-02-14T15:13:04Z

Late reply but here it is - there are total 137389 Maven packages in our graph

tuxdna · 2018-02-21T17:49:17Z

@miteshvp How did you figure this out ?

msrb · 2018-02-22T13:45:59Z

Maven is in graph, closing. Thanks @tuxdna 😉

msrb added type/task team/analytics team/analytics/core labels Jan 25, 2018

msrb added this to the Sprint 144 milestone Jan 25, 2018

tuxdna mentioned this issue Jan 30, 2018

Fails to import packages where declared license is multiline fabric8-analytics/fabric8-analytics-data-model#71

Closed

tuxdna self-assigned this Feb 5, 2018

krishnapaparaju mentioned this issue Feb 13, 2018

Sprint plan for Fabric8 Analytics: #145 #2216

Closed

48 tasks

msrb modified the milestones: Sprint 144, Sprint 145 Feb 14, 2018

msrb closed this as completed Feb 22, 2018

krishnapaparaju mentioned this issue Mar 5, 2018

Sprint plan for Fabric8 Analytics: #146 #2433

Closed

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Sync Maven data to graph #2048

Sync Maven data to graph #2048

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Sync Maven data to graph #2048

Sync Maven data to graph #2048

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