Merge branch '1602-sbgn-compartment-ref' into 'devel_16.0.x'

set compartmentRef when exporting to SBGN

See merge request !1397
41 jobs for devel_16.0.x in 61 minutes and 30 seconds (queued for 7 seconds)
Status Name Job ID Coverage
  Test
failed test:backend:annotation:jdk-11 #320890

01:00:01

failed test:backend:annotation:jdk-11-hsql #320893

01:00:00

failed test:backend:annotation:jdk-8 #320887

01:00:01

passed test:backend:CellDesigner_plugin:jdk-8 #320894

00:01:44

85.1653%
passed test:backend:commons:jdk-11 #320884

00:02:13

84.146%
passed test:backend:commons:jdk-8 #320877

00:01:36

84.146%
passed test:backend:converter_CellDesigner:jdk-11 #320908

00:01:29

95.6634%
passed test:backend:converter_CellDesigner:jdk-8 #320905

00:01:20

95.6327%
passed test:backend:converter_graphics:jdk-11 #320914

00:01:22

73.8091%
passed test:backend:converter_graphics:jdk-8 #320912

00:01:35

73.815%
passed test:backend:converter:jdk-11 #320900

00:00:57

67.5814%
passed test:backend:converter:jdk-8 #320897

00:01:05

67.5522%
passed test:backend:converter_SBGNML:jdk-11 #320921

00:04:13

89.16%
passed test:backend:converter_SBGNML:jdk-11-hsql #320924

00:04:15

89.16%
passed test:backend:converter_SBGNML:jdk-8 #320917

00:01:44

89.1612%
passed test:backend:converter_SBML:jdk-11 #320931

00:03:02

90.9033%
passed test:backend:converter_SBML:jdk-8 #320927

00:02:44

90.9022%
passed test:backend:model_command:jdk-11 #320941

00:00:51

76.7991%
passed test:backend:model_command:jdk-8 #320938

00:01:13

76.8095%
passed test:backend:model:jdk-11 #320937

00:01:21

86.0226%
passed test:backend:model:jdk-8 #320934

00:00:55

86.0238%
passed test:backend:pathvisio:jdk-11 #320947

00:01:40

85.4038%
passed test:backend:pathvisio:jdk-8 #320944

00:01:21

85.4059%
passed test:backend:persist:hsql #320957

00:01:03

70.5309%
passed test:backend:persist:jdk-11 #320954

00:02:15

70.5309%
passed test:backend:persist:jdk-8 #320950

00:01:43

70.3829%
passed test:backend:rest:hsql #320967

00:05:08

40.4627%
passed test:backend:rest:jdk-11 #320963

00:07:28

40.4627%
passed test:backend:rest:jdk-8 #320960

00:05:20

40.4535%
failed test:backend:service:hsql #320973

00:04:14

failed test:backend:service:jdk-11 #320971

00:04:36

failed test:backend:service:jdk-8 #320969

00:05:40

passed test:backend:web:hsql #320979

00:12:45

47.5196%
passed test:backend:web:jdk-11 #320977

00:08:35

47.5196%
passed test:backend:web:jdk-8 #320975

00:13:31

47.5196%
passed test:dependency_conflict #320980

00:05:20

passed test:frontend #320875

00:01:55

84.63%
passed test:mvn_changelog_version_check #320983

00:00:17

passed test_postgres_10_compatibility #320986

00:01:19

passed test_postgres_11_compatibility #320987

00:01:15

passed test_postgres_9_3_compatibility #320985

00:01:30

 
Name Stage Failure
failed
test:backend:annotation:jdk-11 Test The script exceeded the maximum execution time set for the job
	at lcsb.mapviewer.annotation.cache.CachableInterface.getWebPageContent(CachableInterface.java:227)
at lcsb.mapviewer.annotation.cache.CachableInterface.getWebPageContent(CachableInterface.java:200)
at lcsb.mapviewer.annotation.services.annotators.CazyAnnotator.uniprotToCazy(CazyAnnotator.java:186)
... 65 more
Caused by: java.util.concurrent.TimeoutException
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:204)
at lcsb.mapviewer.annotation.cache.WebPageDownloader.getFromNetwork(WebPageDownloader.java:154)
... 68 more
ERROR: Job failed: execution took longer than 1h0m0s seconds

failed
test:backend:service:jdk-8 Test
[ERROR] -> [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/MojoFailureException
Cleaning up project directory and file based variables
ERROR: Job failed: exit code 1

failed
test:backend:annotation:jdk-8 Test The script exceeded the maximum execution time set for the job
	at lcsb.mapviewer.annotation.cache.CachableInterface.getWebPageContent(CachableInterface.java:200)
at lcsb.mapviewer.annotation.services.annotators.CazyAnnotator.uniprotToCazy(CazyAnnotator.java:186)
... 65 more
Caused by: java.util.concurrent.TimeoutException
at java.util.concurrent.FutureTask.get(FutureTask.java:205)
at lcsb.mapviewer.annotation.cache.WebPageDownloader.getFromNetwork(WebPageDownloader.java:154)
... 68 more
2021-12-07 05:02:55,222 ERROR [pool-701-thread-1] (WebPageDownloader.java:131) - Problem with fetching url (3 tries): http://www.cazy.org/search?page=recherche&recherche=Q00012&tag=10
ERROR: Job failed: execution took longer than 1h0m0s seconds

failed
test:backend:service:hsql Test
[ERROR] -> [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/MojoFailureException
Cleaning up project directory and file based variables
ERROR: Job failed: exit code 1

failed
test:backend:service:jdk-11 Test
[ERROR] -> [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/MojoFailureException
Cleaning up project directory and file based variables
ERROR: Job failed: exit code 1

failed
test:backend:annotation:jdk-11-hsql Test The script exceeded the maximum execution time set for the job
	at lcsb.mapviewer.annotation.cache.CachableInterface.getWebPageContent(CachableInterface.java:200)
at lcsb.mapviewer.annotation.services.annotators.CazyAnnotator.uniprotToCazy(CazyAnnotator.java:186)
... 46 more
Caused by: java.util.concurrent.TimeoutException
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:204)
at lcsb.mapviewer.annotation.cache.WebPageDownloader.getFromNetwork(WebPageDownloader.java:154)
... 49 more
2021-12-07 05:05:05,153 ERROR [pool-222-thread-1] (WebPageDownloader.java:131) - Problem with fetching url (3 tries): http://www.cazy.org/search?page=recherche&recherche=A8MCI6&tag=10
ERROR: Job failed: execution took longer than 1h0m0s seconds