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341 Commits

Author SHA1 Message Date
Lampros Smyrnaios c858c02111 - Fix not using the "export HADOOP_USER_NAME" statement in "createPDFsAggregated.sh", which caused permission-issues when creating tables with Impala. 
- Remove unused "--user" parameter in "impala-shell" calls.
- Code polishing.
 2024-06-26 10:11:21 +02:00
Lampros Smyrnaios 3c9b8de892 Miscellaneous updates to the copying operation to Impala Cluster: 
- Fix not breaking out of the VIEWS-infinite-loop when the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" is set to "false".
- Exit the script when no HDFS-active-node was found, independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR".
- Fix view_name-recognition in a log-message, by using the more advanced "Perl-Compatible Regular Expressions" in "grep".
- Add error-handling for "compute stats" errors.
 2024-06-18 15:59:34 +02:00
Antonis Lempesis c67ef157d3 filtering out deletedbyinference and invinsible results from accessroute 2024-06-18 15:59:00 +02:00
Lampros Smyrnaios c23f3031ed Miscellaneous updates to the copying operation to Impala Cluster: 
- Show some counts and the elapsed time for various sub-tasks.
- Code polishing.
 2024-06-18 15:58:46 +02:00
Lampros Smyrnaios e3f28338c1 Miscellaneous updates to the copying operation to Impala Cluster: 
- Assign the WRITE and EXECUTE permissions to the DBs' HDFS-directories, in order to be able to create tables on top of them, in the Impala Cluster.
- Make sure the "copydb" function returns early, when it encounters a fatal error, while respecting the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config.
 2024-05-28 17:51:45 +03:00
Antonis Lempesis 15b54a345a added fos lvl4 2024-05-24 13:21:28 +03:00
Lampros Smyrnaios b48ed6e617 Change configuration in the copy-operation to Impala Cluster: 
Set the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" parameter to "false".
 2024-05-23 16:58:12 +03:00
Lampros Smyrnaios 68322843e2 Small updates to the copy-operation to Impala Cluster: 
- Add a configuration-"switch" to control whether the script exits upon an error or not.
- Allow the script to exit when a table could not be created.
- Show the elapsed time for processing each database.
 2024-05-23 15:07:49 +03:00
Lampros Smyrnaios c7b32bbacc Update CopyDataToImpalaCluster: 
Update the code of acquiring the entities from Ocean cluster, through hive, in order to optimize the process and account for additional reserved keywords in Impala.

Co-authored-by: Antonis Lempesis <antleb@di.uoa.gr>
 2024-05-23 13:00:19 +03:00
Antonis Lempesis 0cada3cc8f every step is run in the analytics queue. Hardcoded for now, will make a parameter later 2024-05-08 13:42:53 +03:00
Antonis Lempesis 90a4fb3547 fixed typos 2024-05-08 13:17:58 +03:00
Lampros Smyrnaios 49af2e5740 Miscellaneous updates to the copying operation to Impala Cluster: 
- Update the algorithm for creating views that depend on other views; overcome some bash-instabilities.
- Upon any error, fail the whole process, not just the current DB-creation, as those errors usually indicate a bug in the initial DB-creation, that should be fixed immediately.
- Enhance parallel-copy of large files by "hadoop distcp" command.
- Reduce the "invalidate metadata" commands to just the current DB's tables, in order to eliminate the general overhead on Impala.
- Show the number of tables and views in the logs.
- Fix some log-messages.
 2024-04-23 17:15:04 +03:00
Antonis Lempesis b52a5a753b Merge remote-tracking branch 'upstream/beta' into beta 2024-04-19 15:28:28 +03:00
Antonis Lempesis c3fe9662b2 all indicator tables are now stored as parquet 2024-04-19 12:45:36 +03:00
Claudio Atzori 57c678d904 integrating changes from PR#424 2024-04-18 11:38:35 +02:00
Claudio Atzori 5ab8cd1794 Various fixes for the stats DB update workflow, step16-createIndicatorsTables.sql 2024-04-18 11:28:18 +02:00
Antonis Lempesis 0c71c58df6 fixed the definition of gold_oa 2024-04-18 12:01:27 +03:00
Antonis Lempesis 43d05dbebb fixed the definition of result_country 2024-04-18 11:53:50 +03:00
Antonis Lempesis e728a0897c fixed the definition of indi_pub_bronze_oa 2024-04-18 11:07:55 +03:00
Antonis Lempesis 308ae580a9 slight optimization in indi_pub_gold_oa definition 2024-04-18 10:57:52 +03:00
Antonis Lempesis 27d22bd8f9 slight optimization in indi_pub_gold_oa definition 2024-04-17 23:59:52 +03:00
Antonis Lempesis 1f5aba12fa slight optimization in indi_pub_gold_oa definition 2024-04-17 23:54:23 +03:00
Lampros Smyrnaios d7da4f814b Minor updates to the copying operation to Impala Cluster: 
- Improve logging.
- Code optimization/polishing.
 2024-04-12 18:12:06 +03:00
Lampros Smyrnaios 14719dcd62 Miscellaneous updates to the copying operation to Impala Cluster: 
- Update the algorithm for creating views that depend on other views.
- Add check for successful execution of the "hadoop distcp" command.
- Add a check for successful copy operation of all entities.
- Upon facing an error in a DB, exit the method, instead of the whole script.
- Improve logging.
- Code polishing.
 2024-04-12 15:36:13 +03:00
Lampros Smyrnaios abf0b69f29 Upgrade the copying operation to Impala Cluster: 
- Use only hive commands in the Ocean Cluster, as the "impala-shell" will be removed from there to free-up resources.
- Hugely improve the performance in every aspect of the copying process: a) speedup file-transferring and DB-deletion, b) eliminate permissions-assignment, "load" operations and "use $db" queries, c) retry only the "create view" statements and only as long as they depend on other non-created views, instead of trying to recreate all tables and views 5 consecutive times.
- Add error-checks for the creation of tables and views.
 2024-04-11 17:12:12 +03:00
Lampros Smyrnaios b7c8acc563 - Update the code which acquires the "IMPALA_HDFS_NODE", to test the "tmp"-dir, instead of the base-dir and introduce retries, to overcome potential file-system failures. This change was suggested by "Sebastian Tymkow" and "Grzegorz Bakalarski". 
- Fix typos.
 2024-04-03 13:15:37 +03:00
Antonis Lempesis df6e3bda04 added new orgs in monitor 2024-04-01 22:45:29 +03:00
Antonis Lempesis 573b081f1d added new orgs in monitor 2024-04-01 22:24:46 +03:00
Antonis Lempesis 0bf2a7a359 fixed the result_country definition 2024-04-01 15:23:22 +03:00
Antonis Lempesis 9ff44eed96 fixed typo in indicator query 
added more institutions
 2024-03-27 14:39:01 +02:00
Antonis Lempesis 1fee4124e0 added missing EOS 2024-03-27 12:58:25 +02:00
Lampros Smyrnaios 036ba03fcd Generate tables with parquet-files, instead of csv, in "dhp-stats-update/.../contexts.sh" script. 2024-03-26 13:29:04 +02:00
Lampros Smyrnaios 92cc27e7eb Use the ACTIVE HDFS NODE for Impala cluster, in "copyDataToImpalaCluster.sh" script. 2024-03-26 12:34:11 +02:00
Antonis Lempesis 4c40c96e30 code cleanup 2024-03-22 10:16:49 +02:00
Antonis Lempesis 459167ac2f Merge branch 'beta' of https://code-repo.d4science.org/antonis.lempesis/dnet-hadoop into beta 2024-03-21 12:44:58 +02:00
Antonis Lempesis 07f634a46d code cleanup 2024-03-21 12:44:30 +02:00
Antonis Lempesis 9521625a07 code cleanup 2024-03-21 11:45:08 +02:00
Antonis Lempesis f74c7e8689 selecting distinct peer_reviewed 2024-03-12 02:13:04 +02:00
Antonis Lempesis 5ae4b4286c Merge branch 'beta' of https://code-repo.d3science.org/antonis.lempesis/dnet-hadoop into beta 2024-03-07 12:15:19 +02:00
Antonis Lempesis 316d585c8a using distinct apcs per publication to avoid huge sums 2024-03-07 02:07:59 +02:00
Antonis Lempesis dd4c27f4f3 added 2 new institutions in monitor 2024-02-08 12:57:57 +02:00
Antonis Lempesis a512ead447 changed orcid ids to all capital 2024-01-30 16:54:47 +02:00
Antonis Lempesis bb10a22290 merged changes from dnet-hadoop 2024-01-29 21:51:47 +02:00
Giambattista Bloisi 078df0b4d1 Use SparkSQL in place of Hive for executing step16-createIndicatorsTables.sql of stats update wf 2024-01-26 21:56:55 +01:00
Antonis Lempesis c548796463 Changed step16-createIndicatorsTables to use a spark oozie action instead of hive 2024-01-26 02:04:48 +02:00
Antonis Lempesis a7115cfa9e max mem of joins (hive.mapjoin.followby.gby.localtask.max.memory.usage) now 80%, up from 55%. 2024-01-25 15:13:16 +01:00
Antonis Lempesis fd43b0e84a max mem of joins (hive.mapjoin.followby.gby.localtask.max.memory.usage) now 80%, up from 55%. 2024-01-25 15:06:34 +01:00
Antonis Lempesis e024718f73 creating result_instances even when no pids exist for the instance 2024-01-10 22:25:50 +01:00
dimitrispie b920307bdd Changes to indicators 2024-01-09 00:47:09 +02:00
Antonis Lempesis 2e4cab026c fixed the result_country definition 2024-01-08 16:01:26 +02:00