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metrics generation is not done automatically in the parsing step #23

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syphax-bouazzouni opened this issue Apr 8, 2022 · 2 comments
Open

metrics generation is not done automatically in the parsing step #23

syphax-bouazzouni opened this issue Apr 8, 2022 · 2 comments
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syphax-bouazzouni commented Apr 8, 2022 •
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The issue

We had a lot of ontologies parsed well and with METRICS status on; but the metrics were not generated.
And in the logs, we see the message generation of metrics file finished

And the ncbo script ncbo_ontology_diagnostics.sh detect them with a status METRICS_MISSING now shown in the ontologies admin panel

But just re-running the ontology process script fixes the issue

Where does the status METRICS_MISSING comes from

The script ncbo_ontology_diagnostics.sh behind the scene call another script called ncbo_ontology_inspector with the following parameters -p flat,hasOntologyLanguage,metrics,submissionStatus

The ncbo_ontology_inspector check for each ontology the properties specified in the p parameter. So if the metrics property of an ontology is null, it returns METRICS_MISSING

Why metrics is null even if we got the generation of metrics file finished in logs

Use case OEEV

Got parsed in 2022-02-24T16:35:11
Logs


I, [2022-02-24T16:17:06.225783 #7043]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/OEEV/submissions/6"]
I, [2022-02-24T16:17:06.294931 #7043]  INFO -- : ["Starting to process OEEV/submissions/6"]
I, [2022-02-24T16:17:06.425611 #7043]  INFO -- : ["deleting old owlapi.xrdf .."]
I, [2022-02-24T16:17:06.426023 #7043]  INFO -- : ["deleted"]
I, [2022-02-24T16:17:06.433409 #7043]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/bin/owlapi-wrapper.jar -m /srv/ontoportal/data/repository/OEEV/6/oeev.owl -o /srv/ontoportal/data/repository/OEEV/6 -r true]"]
I, [2022-02-24T16:17:07.655282 #7043]  INFO -- : ["2022-02-24T16:17:06 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ontoportal/data/repository/OEEV/6, masterFileName=/srv/ontoportal/data/repository/OEEV/6/oeev.owl, invocationId=0, parserLog=, userReasoner= true]\n\n2022-02-24T16:17:06 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Calculating metrics for /srv/ontoportal/data/repository/OEEV/6/oeev.owl\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Finished metrics calculation for /srv/ontoportal/data/repository/OEEV/6/oeev.owl in 1 milliseconds\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Generated metrics CSV file for /srv/ontoportal/data/repository/OEEV/6/oeev.owl\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Ontology document format: org.semanticweb.owlapi.formats.OWLXMLDocumentFormat\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isPrefixOWLOntologyFormat: true\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isOBO: false\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serializing ontology in RDF ...\n\n2022-02-24T16:17:07 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serialization done!\n\n2022-02-24T16:17:07 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: true\n\n2022-02-24T16:17:07 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf\n\n2022-02-24T16:17:07 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-02-24T16:17:07.655362 #7043]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
I, [2022-02-24T16:17:07.658173 #7043]  INFO -- : ["Output size 30090 in `/srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf`"]
I, [2022-02-24T16:17:08.321317 #7043]  INFO -- : ["Triples /srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf appended in <http://data.bioontology.org/ontologies/OEEV/submissions/6>"]
I, [2022-02-24T16:17:08.327554 #7043]  INFO -- : ["Extraction metadata from ontology http://www.phenome-fppn.fr/vocabulary/2018/oeev"]
I, [2022-02-24T16:17:12.324968 #7043]  INFO -- : ["Additional metadata extracted."]
I, [2022-02-24T16:17:12.335387 #7043]  INFO -- : ["Default metadata set."]
I, [2022-02-24T16:17:12.634404 #7043]  INFO -- : ["6: page 1 of 1 - 45 ontology terms retrieved in 0.137416505 sec."]
E, [2022-02-24T16:17:16.261802 #7043] ERROR -- : ["SystemExit: exit\nbin/ncbo_ontology_process:4:in `exit'\n\tbin/ncbo_ontology_process:4:in `block in <main>'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/protocol.rb:217:in `wait_readable'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/protocol.rb:217:in `rbuf_fill'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/protocol.rb:179:in `read_all'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:302:in `block in read_body_0'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:279:in `inflater'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:284:in `read_body_0'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:204:in `read_body'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:229:in `body'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http/response.rb:166:in `reading_body'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http.rb:1517:in `transport_request'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/net/http.rb:1479:in `request'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/gems/net-http-persistent-2.9.4/lib/net/http/persistent.rb:999:in `request'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client.rb:744:in `request'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client.rb:395:in `response'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client.rb:320:in `query'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client.rb:249:in `block in call_query_method'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client/query.rb:343:in `result'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/sparql-client-fb4a89b420f8/lib/sparql/client/query.rb:336:in `each_solution'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/queries.rb:613:in `model_load_sliced'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/sparql/queries.rb:279:in `model_load'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/base/where.rb:214:in `process_query_intl'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/base/where.rb:131:in `process_query'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/goo-89a8f665f706/lib/goo/base/where.rb:282:in `all'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/mappings/mappings.rb:366:in `migrate_rest_mappings'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1495:in `generate_missing_labels_post_page'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1403:in `call'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1403:in `block (2 levels) in loop_classes'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1301:in `block in process_callbacks'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1297:in `delete_if'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1297:in `process_callbacks'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1402:in `block in loop_classes'\n\t/usr/local/rbenv/versions/2.6.9/lib/ruby/2.6.0/benchmark.rb:308:in `realtime'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1328:in `loop_classes'\n\t/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/lib/ontologies_linked_data/models/ontology_submission.rb:1809:in `process_submission'\n\t/srv/ontoportal/ncbo_cron_deployments/releases/20220124143731/lib/ncbo_cron/ontology_submission_parser.rb:193:in `process_submission'\n\tbin/ncbo_ontology_process:98:in `block in <main>'\n\tbin/ncbo_ontology_process:81:in `each'\n\tbin/ncbo_ontology_process:81:in `<main>'"]
I, [2022-02-24T16:17:26.970895 #7155]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/OEEV/submissions/6"]
I, [2022-02-24T16:17:27.005253 #7155]  INFO -- : ["Starting to process OEEV/submissions/6"]
I, [2022-02-24T16:17:27.131296 #7155]  INFO -- : ["deleting old owlapi.xrdf .."]
I, [2022-02-24T16:17:27.131652 #7155]  INFO -- : ["deleted"]
I, [2022-02-24T16:17:27.139964 #7155]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/bin/owlapi-wrapper.jar -m /srv/ontoportal/data/repository/OEEV/6/oeev.owl -o /srv/ontoportal/data/repository/OEEV/6 -r true]"]
I, [2022-02-24T16:17:28.364450 #7155]  INFO -- : ["2022-02-24T16:17:27 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ontoportal/data/repository/OEEV/6, masterFileName=/srv/ontoportal/data/repository/OEEV/6/oeev.owl, invocationId=0, parserLog=, userReasoner= true]\n\n2022-02-24T16:17:27 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2022-02-24T16:17:27 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Calculating metrics for /srv/ontoportal/data/repository/OEEV/6/oeev.owl\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Finished metrics calculation for /srv/ontoportal/data/repository/OEEV/6/oeev.owl in 1 milliseconds\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Generated metrics CSV file for /srv/ontoportal/data/repository/OEEV/6/oeev.owl\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Ontology document format: org.semanticweb.owlapi.formats.OWLXMLDocumentFormat\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isPrefixOWLOntologyFormat: true\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isOBO: false\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serializing ontology in RDF ...\n\n2022-02-24T16:17:28 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serialization done!\n\n2022-02-24T16:17:28 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: true\n\n2022-02-24T16:17:28 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf\n\n2022-02-24T16:17:28 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2022-02-24T16:17:28.364598 #7155]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
I, [2022-02-24T16:17:28.373181 #7155]  INFO -- : ["Output size 30090 in `/srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf`"]
I, [2022-02-24T16:17:28.965128 #7155]  INFO -- : ["Triples /srv/ontoportal/data/repository/OEEV/6/owlapi.xrdf appended in <http://data.bioontology.org/ontologies/OEEV/submissions/6>"]
I, [2022-02-24T16:17:28.979750 #7155]  INFO -- : ["Extraction metadata from ontology http://www.phenome-fppn.fr/vocabulary/2018/oeev"]
I, [2022-02-24T16:17:32.366285 #7155]  INFO -- : ["Additional metadata extracted."]
I, [2022-02-24T16:17:32.378285 #7155]  INFO -- : ["Default metadata set."]
I, [2022-02-24T16:17:32.644617 #7155]  INFO -- : ["6: page 1 of 1 - 45 ontology terms retrieved in 0.121111206 sec."]
I, [2022-02-24T16:19:28.858759 #7155]  INFO -- : ["Asserting 45 labels in <http://data.bioontology.org/ontologies/OEEV/submissions/6>"]
I, [2022-02-24T16:19:28.940305 #7155]  INFO -- : ["Labels asserted in 0.08126492 sec."]
I, [2022-02-24T16:19:28.940496 #7155]  INFO -- : ["Asserting 90 mappings in <http://data.bioontology.org/ontologies/OEEV/submissions/6>"]
I, [2022-02-24T16:19:29.020518 #7155]  INFO -- : ["Mapping labels asserted in 0.079637817 sec."]
I, [2022-02-24T16:19:29.020690 #7155]  INFO -- : ["end generate_missing_labels traversed 46 classes"]
I, [2022-02-24T16:19:29.020771 #7155]  INFO -- : ["Saved generated labels in /srv/ontoportal/data/repository/OEEV/6/labels.ttl"]
I, [2022-02-24T16:19:29.021175 #7155]  INFO -- : ["Completed Missing Labels Generation: 6 in 116.57157068816014 sec. 45 classes."]
I, [2022-02-24T16:19:29.375763 #7155]  INFO -- : ["Indexing ontology terms: OEEV..."]
I, [2022-02-24T16:19:29.439829 #7155]  INFO -- : ["Removed ontology terms index (0.063872676s)"]
I, [2022-02-24T16:19:29.629845 #7155]  INFO -- : ["Thread 1: Page 1 of 1 - 45 ontology terms retrieved in 1.9327e-05 sec."]
I, [2022-02-24T16:19:29.644407 #7155]  INFO -- : ["Thread 1: Page 1 of 1 attributes mapped in 0.014462505 sec."]
I, [2022-02-24T16:19:30.116779 #7155]  INFO -- : ["Thread 1: Page 1 of 1 - 45 ontology terms indexed in 0.472210088 sec."]
I, [2022-02-24T16:19:30.266053 #7155]  INFO -- : ["Ontology terms index commit in 0.148451249 sec."]
I, [2022-02-24T16:19:30.266204 #7155]  INFO -- : ["Completed indexing ontology terms: OEEV in 1.0891494250390679 sec. 45 classes."]
I, [2022-02-24T16:19:30.338484 #7155]  INFO -- : ["Indexing ontology properties: OEEV..."]
I, [2022-02-24T16:19:30.380252 #7155]  INFO -- : ["Removed ontology properties index in 0.041561668 seconds."]
I, [2022-02-24T16:19:30.427735 #7155]  INFO -- : ["Indexing a total of 1 pages of 2500 properties each."]
I, [2022-02-24T16:19:30.459600 #7155]  INFO -- : ["Page 1 of ontology properties indexed in 0.031666826 seconds."]
I, [2022-02-24T16:19:30.552629 #7155]  INFO -- : ["Ontology properties index commit in 0.092831963 seconds."]
I, [2022-02-24T16:19:30.552757 #7155]  INFO -- : ["Completed indexing ontology properties of OEEV in 0.21435109502635896 sec. Total of 14 properties indexed."]
I, [2022-02-24T16:19:30.624929 #7155]  INFO -- : ["metrics_for_submission start"]
I, [2022-02-24T16:19:31.154058 #7155]  INFO -- : ["Metrics groupby_children retrieved 13 in 0.398787921 sec."]
I, [2022-02-24T16:19:31.154788 #7155]  INFO -- : ["Metrics count_classes retrieved 46 in 0.000582238 sec."]
I, [2022-02-24T16:19:31.207785 #7155]  INFO -- : ["Metrics count cls with def 7 in 0.052866934 sec."]
I, [2022-02-24T16:19:31.207875 #7155]  INFO -- : ["Class metrics finished in 0.582825413 sec."]
I, [2022-02-24T16:19:31.207938 #7155]  INFO -- : ["class_metrics finished"]
I, [2022-02-24T16:19:31.208555 #7155]  INFO -- : ["individuals finished"]
I, [2022-02-24T16:19:31.208827 #7155]  INFO -- : ["properties finished"]
I, [2022-02-24T16:19:31.209300 #7155]  INFO -- : ["generation of metrics file finished"]
I, [2022-02-24T16:19:31.515419 #7155]  INFO -- : ["Java call [java -DentityExpansionLimit=1500000 -Xmx5120M -jar /srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/bin/bubastis.jar -ontology1 /srv/ontoportal/data/repository/OEEV/3/oeev.owl -ontology2 /srv/ontoportal/data/repository/OEEV/6/oeev.owl -output /srv/ontoportal/data/repository/OEEV/6/bubastis_diff.xml -format xml]"]
I, [2022-02-24T16:19:32.757858 #7155]  INFO -- : ["Bubastis diff finished OK."]
I, [2022-02-24T16:19:32.757959 #7155]  INFO -- : ["SLF4J: Failed to load class \"org.slf4j.impl.StaticLoggerBinder\".\nSLF4J: Defaulting to no-operation (NOP) logger implementation\nSLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.\nWARNING: An illegal reflective access operation has occurred\nWARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/srv/ontoportal/ncbo_cron_deployments/shared/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-ac4a68542c33/bin/bubastis_1_3.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)\nWARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1\nWARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations\nWARNING: All illegal access operations will be denied in a future release\n"]
I, [2022-02-24T16:19:32.758038 #7155]  INFO -- : ["ontology 1 is a file /srv/ontoportal/data/repository/OEEV/3/oeev.owl\nontology 2 is a file /srv/ontoportal/data/repository/OEEV/6/oeev.owl\ntrying load now\nloading ontology 1 complete\nloading ontology 2 complete\n\n@Ontology Change Summary\n@First ontology IRI: Optional.of(http://www.phenome-fppn.fr/vocabulary/2018/oeev)\n@Second ontology IRI: Optional.of(http://www.phenome-fppn.fr/vocabulary/2018/oeev)\n@Number of classes changed: 0\n@Number of classes added: 0\n@Number of classes deleted: 0\n"]
I, [2022-02-24T16:19:32.758138 #7155]  INFO -- : ["Output size 313 in `/srv/ontoportal/data/repository/OEEV/6/bubastis_diff.xml`"]
I, [2022-02-24T16:19:32.817587 #7155]  INFO -- : ["Bubastis diff generated successfully for http://data.bioontology.org/ontologies/OEEV/submissions/6"]
I, [2022-02-24T16:19:32.897921 #7155]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/OEEV/submissions/6 completed successfully"]
D, [2022-02-24T16:19:32.929526 #7155] DEBUG -- : ["Archiving submissions previous to http://data.bioontology.org/ontologies/OEEV/submissions/6..."]
D, [2022-02-24T16:19:32.944529 #7155] DEBUG -- : ["Completed archiving submissions previous to http://data.bioontology.org/ontologies/OEEV/submissions/6"]
I, [2022-02-24T16:19:32.988106 #7155]  INFO -- : [["Caching classes of OEEV"]]
I, [2022-02-24T16:19:32.988188 #7155]  INFO -- : ["Caching classes of OEEV"]
I, [2022-02-24T16:19:33.592256 #7155]  INFO -- : [["Page 1 of 1 - 45 classes retrieved in 0.603826011 sec."]]
I, [2022-02-24T16:19:33.592295 #7155]  INFO -- : ["Page 1 of 1 - 45 classes retrieved in 0.603826011 sec."]
I, [2022-02-24T16:19:33.617958 #7155]  INFO -- : [["Page 1 of 1 cached in Annotator in 0.025543001 sec."]]
I, [2022-02-24T16:19:33.618002 #7155]  INFO -- : ["Page 1 of 1 cached in Annotator in 0.025543001 sec."]
I, [2022-02-24T16:19:33.686342 #7155]  INFO -- : [["Completed caching ontology: OEEV (http://data.bioontology.org/ontologies/OEEV/submissions/6) in 0.6301156310364604 sec. 45 classes."]]
I, [2022-02-24T16:19:33.686431 #7155]  INFO -- : ["Completed caching ontology: OEEV (http://data.bioontology.org/ontologies/OEEV/submissions/6) in 0.6301156310364604 sec. 45 classes."]
D, [2022-02-24T16:35:11.508395 #7155] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/OEEV/submissions/6 in 1065.28s"]
I, [2022-02-24T16:35:11.527520 #7155]  INFO -- : ["Running ontologies report for ontologies OEEV...\n"]
I, [2022-02-24T16:35:11.527684 #7155]  INFO -- : ["Processing report for OEEV - 1 of 1 ontologies."]
I, [2022-02-24T16:35:12.568365 #7155]  INFO -- : ["Finished report for OEEV in 1.0402776061091572 sec."]
I, [2022-02-24T16:35:12.581428 #7155]  INFO -- : ["Finished updating report for ontologies OEEV. Wrote report data to /srv/ontoportal/data/reports/ontologies_report.json.\n"]
@syphax-bouazzouni syphax-bouazzouni self-assigned this Apr 8, 2022
@syphax-bouazzouni syphax-bouazzouni mentioned this issue Jan 20, 2023
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syphax-bouazzouni commented Jan 20, 2023 •
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Try in Stageportal

After uploading OEEV in Stageportal, there is no issue with the metrics
image

Try to re-run the script of adding to OEEV to queue_submission in Agroportal

Same, the metrics came back

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@syphax-bouazzouni
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Need to check this, because it occurred on all portals depending on Agroportal

Ecoportal: lifewatch-eric/ecoportal_web_ui#33
Earthportal:

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@syphax-bouazzouni syphax-bouazzouni changed the title indexation is not done automatically in the parsing step metrics generation is not done automatically in the parsing step Apr 9, 2024
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