Ubuntu 22.04 current issues

[vjrj]

• [x] cas: Failed to update apt cache: E:The repository 'https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/4.4 Release' does not have a Release file.
• [x] postgresql/postgis packages missing as in #598
• [ ] postgres error in spatial:

  TASK [pg_instance : enable extensions for "geonetwork"] ************************
  Thursday 14 July 2022  22:46:55 +0200 (0:00:00.705)       0:01:36.990 ********* 
  An exception occurred during task execution. To see the full traceback, use -vvv. The error was: TypeError: '<' not supported between instances of 'str' and 'int'
  failed: [ala-install-test-3] (item=postgis) => {"ansible_loop_var": "item", "changed": false, "item": "postgis", "msg": "Database query failed: '<' not supported between instances of 'str' and 'int'"}

• [ ] Hadoop fails too

  TASK [pipelines : Create HDFS base directories] ********************************
  Thursday 14 July 2022  23:38:58 +0200 (0:00:01.139)       0:12:57.628 ********* 
  failed: [ala-install-test-2] (item=/dwca-exports) => {"ansible_loop_var": "item", "changed": true, "cmd": "/data/hadoop/bin/hdfs dfs -mkdir -p /dwca-exports", "delta": "0:00:06.445958", "end": "2022-07-14 21:39:05.304141", "item": "/dwca-exports", "msg": "non-zero return code", "rc": 1, "start": "2022-07-14 21:38:58.858183", "stderr": "22/07/14 21:39:04 WARN ipc.Client: Failed to connect to server: ala-install-test-1/10.10.10.151:9000: try once and fail.\njava.net.ConnectException: Connection refused\n\tat sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)\n\tat sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:716)\n\tat org.apache.hadoop.net.SocketIOWithTimeout.connect(SocketIOWithTimeout.java:206)\n\tat 

• [ ] species-lists: Unable to load class: com.mysql.cj.jdbc.Driver from ClassLoader:ParallelWebappClassLoader (...) Caused by: java.lang.ClassNotFoundException: com.mysql.cj.jdbc.Driver
• [ ] alerts: Caused by: java.sql.SQLException: Unknown system variable 'query_cache_size' and Loading classcom.mysql.jdbc.Driver'. This is deprecated. The new driver class is com.mysql.cj.jdbc.Driver'. The driver is automatically registered via the SPI and manual loading of the driver class is generally unnecessary.
• [x] mysql 8 login issues #604

[geonbAtBiodiv]

I tried to set up atlas node on 22.04 server here is my documentation

in spatial postgres seems to automatically install postgis 3.3 but ansible referes to the scripts of 3.2 but it seems the change to postgis scripts 3.3 doesn't satisfy the implementation!

failed: [spatial] (item=/usr/share/postgresql/14/contrib/postgis-3.2/postgis.sql) => {"ansible_loop_var": "item", "changed": true, "cmd": ["psql", "-d", "postgis_template", "-f", "/usr/share/postgresql/14/contrib/postgis-3.2/postgis.sql"], "delta": "0:00:00.033540", "end": "2023-01-11 09:24:54.753608", "item": "/usr/share/postgresql/14/contrib/postgis-3.2/postgis.sql", "msg": "non-zero return code", "rc": 1, "start": "2023-01-11 09:24:54.720068", "stderr": "psql: error: /usr/share/postgresql/14/contrib/postgis-3.2/postgis.sql: No such file or directory", "stderr_lines": ["psql: error: /usr/share/postgresql/14/contrib/postgis-3.2/postgis.sql: No such file or directory"], "stdout": "", "stdout_lines": []}

in userdetails

TASK [userdetails : create auth ip in db if does not exists] *********************************************************** failed: [spatial] (item=176.9.166.203) => {"ansible_loop_var": "item", "changed": true, "cmd": "mysql --host=localhost --port=3306 --user=cas --password=servus emmet -e \"set @ip='176.9.166.203'; set @description=''; source /data/userdetails/setup/auth-ip.sql;\"", "delta": "0:00:00.007799", "end": "2023-01-11 16:37:13.126725", "item": "176.9.166.203", "msg": "non-zero return code", "rc": 1, "start": "2023-01-11 16:37:13.118926", "stderr": "mysql: [Warning] Using a password on the command line interface can be insecure.\nERROR 1267 (HY000) at line 2 in file: '/data/userdetails/setup/auth-ip.sql': Illegal mix of collations (utf8mb4_unicode_ci,IMPLICIT) and (utf8mb4_0900_ai_ci,IMPLICIT) for operation '='", "stderr_lines": ["mysql: [Warning] Using a password on the command line interface can be insecure.", "ERROR 1267 (HY000) at line 2 in file: '/data/userdetails/setup/auth-ip.sql': Illegal mix of collations (utf8mb4_unicode_ci,IMPLICIT) and (utf8mb4_0900_ai_ci,IMPLICIT) for operation '='"], "stdout": "", "stdout_lines": []}

there was probaply missing some configuration fact

userDetails.url=https://auth.biodivdev.at/userdetails/ userdetails.baseUrl=https://auth.biodivdev.at/userdetails/

it started after adding this details

image-service starts but I couldn't test because in collections upload of testdata failed admin section can not be tested

It's difficult to know what causes the issues to the other services I'm still not familiar to all of the services dependencies.

our setup: server 1 -> java 8: records records-ws, solr, sds, Branding, biocache-cli, nameindexer, namematching,biocache-store, ecodata server 2 -> java 11: collections, species, species-ws, images, Lists, Regions, Logger, Auth, User Deatails, API-keys, CAS Management, Spatial, Spatial Webservice, Geoserver, Webapi, Dashboard, Alerts, Data-quality, Biocollect, PDFgen, Ecodata-reporting

[geonbAtBiodiv]

TASK [biocollect : copy all config.properties] ************************************************************************* fatal: [spatial]: FAILED! => {"changed": false, "msg": "AnsibleUndefinedVariable: 'bie_ws_base_url' is undefined"}

bie_ws_base_url has to be added to the inventories

[vjrj]

Thanks @geonbAtBiodiv. Meanwhile I'll add that new variable to our generated inventories.

[vjrj]

Done, @geonbAtBiodiv : https://github.com/living-atlases/generator-living-atlas/commit/5a8467b185ac34b6eab943d5afbdefa541430fca