Harvest for Greece Species List Created 13 Oct 04:54

Harvesting Log

# Logfile created on 2019-10-13 04:54:51 -0400 by logger.rb/56815
[START] [2019-10-13 04:54:51] logged process
[START] [2019-10-13 04:54:51] create_harvest_instance
[STOP] [2019-10-13 04:54:51] create_harvest_instance
[START] [2019-10-13 04:54:51] fetch_files
[STOP] [2019-10-13 04:54:51] fetch_files
[START] [2019-10-13 04:54:51] validate_each_file
[STOP] [2019-10-13 04:54:54] validate_each_file
[START] [2019-10-13 04:54:54] convert_to_csv
[CMD] [2019-10-13 04:54:54] /usr/bin/sort /app/public/converted_csv/greece_sp_list_refs_15867.csv > /app/public/converted_csv/greece_sp_list_refs_15867.csv_sorted
[CMD] [2019-10-13 04:54:54] /usr/bin/sort /app/public/converted_csv/greece_sp_list_nodes_15868.csv > /app/public/converted_csv/greece_sp_list_nodes_15868.csv_sorted
[CMD] [2019-10-13 04:54:54] /usr/bin/sort /app/public/converted_csv/greece_sp_list_occurrences_15869.csv > /app/public/converted_csv/greece_sp_list_occurrences_15869.csv_sorted
[CMD] [2019-10-13 04:54:54] /usr/bin/sort /app/public/converted_csv/greece_sp_list_measurements_15870.csv > /app/public/converted_csv/greece_sp_list_measurements_15870.csv_sorted
[STOP] [2019-10-13 04:54:54] convert_to_csv
[START] [2019-10-13 04:54:54] calculate_delta
[CMD] [2019-10-13 04:54:54] echo "0a" > /app/public/diff/greece_sp_list_refs_15867.diff
[CMD] [2019-10-13 04:54:54] tail -n +1 /app/public/converted_csv/greece_sp_list_refs_15867.csv >> /app/public/diff/greece_sp_list_refs_15867.diff
[CMD] [2019-10-13 04:54:55] echo "." >> /app/public/diff/greece_sp_list_refs_15867.diff
[CMD] [2019-10-13 04:54:55] echo "0a" > /app/public/diff/greece_sp_list_nodes_15868.diff
[CMD] [2019-10-13 04:54:55] tail -n +1 /app/public/converted_csv/greece_sp_list_nodes_15868.csv >> /app/public/diff/greece_sp_list_nodes_15868.diff
[CMD] [2019-10-13 04:54:55] echo "." >> /app/public/diff/greece_sp_list_nodes_15868.diff
[CMD] [2019-10-13 04:54:55] echo "0a" > /app/public/diff/greece_sp_list_occurrences_15869.diff
[CMD] [2019-10-13 04:54:55] tail -n +1 /app/public/converted_csv/greece_sp_list_occurrences_15869.csv >> /app/public/diff/greece_sp_list_occurrences_15869.diff
[CMD] [2019-10-13 04:54:55] echo "." >> /app/public/diff/greece_sp_list_occurrences_15869.diff
[CMD] [2019-10-13 04:54:55] echo "0a" > /app/public/diff/greece_sp_list_measurements_15870.diff
[CMD] [2019-10-13 04:54:55] tail -n +1 /app/public/converted_csv/greece_sp_list_measurements_15870.csv >> /app/public/diff/greece_sp_list_measurements_15870.diff
[CMD] [2019-10-13 04:54:55] echo "." >> /app/public/diff/greece_sp_list_measurements_15870.diff
[STOP] [2019-10-13 04:54:56] calculate_delta
[START] [2019-10-13 04:54:56] parse_diff_and_store
[INFO] [2019-10-13 04:54:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 04:54:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 04:55:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 04:55:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 04:56:39] Storing 2 References
[INFO] [2019-10-13 04:56:39] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 04:56:39] Average Time: 0.0
[INFO] [2019-10-13 04:56:39] Total Time: 1s
[INFO] [2019-10-13 04:56:39] Storing 23029 ScientificNames
[INFO] [2019-10-13 04:56:39] Processing group of 23029 in 24 groups of 1000
[INFO] [2019-10-13 04:56:47] Average Time: 0.345
[INFO] [2019-10-13 04:56:47] Total Time: 9s
[INFO] [2019-10-13 04:56:47] last 3 / first 3: 0.57
[INFO] [2019-10-13 04:56:47] Std.Dev: 0.08366600265340755; Max: 0.5
[INFO] [2019-10-13 04:56:47] Storing 23029 Nodes
[INFO] [2019-10-13 04:56:47] Processing group of 23029 in 24 groups of 1000
[INFO] [2019-10-13 04:56:56] Average Time: 0.374
[INFO] [2019-10-13 04:56:56] Total Time: 10s
[INFO] [2019-10-13 04:56:56] last 3 / first 3: 0.75
[INFO] [2019-10-13 04:56:56] Std.Dev: 0.25495097567963926; Max: 1.31
[INFO] [2019-10-13 04:56:56] Storing 14942 Occurrences
[INFO] [2019-10-13 04:56:56] Processing group of 14942 in 15 groups of 1000
[INFO] [2019-10-13 04:56:58] Average Time: 0.103
[INFO] [2019-10-13 04:56:58] Total Time: 2s
[INFO] [2019-10-13 04:56:58] last 3 / first 3: 0.83
[INFO] [2019-10-13 04:56:58] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-13 04:56:58] Storing 30820 TraitsReferences
[INFO] [2019-10-13 04:56:58] Processing group of 30820 in 31 groups of 1000
[INFO] [2019-10-13 04:57:00] Average Time: 0.073
[INFO] [2019-10-13 04:57:00] Total Time: 3s
[INFO] [2019-10-13 04:57:00] last 3 / first 3: 0.5
[INFO] [2019-10-13 04:57:00] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-13 04:57:00] Storing 30819 Traits
[INFO] [2019-10-13 04:57:00] Processing group of 30819 in 31 groups of 1000
[INFO] [2019-10-13 04:57:11] Average Time: 0.347
[INFO] [2019-10-13 04:57:11] Total Time: 11s
[INFO] [2019-10-13 04:57:11] last 3 / first 3: 1.9
[INFO] [2019-10-13 04:57:11] Std.Dev: 0.15491933384829668; Max: 1.14
[INFO] [2019-10-13 04:57:11] Storing 30799 MetaTraits
[INFO] [2019-10-13 04:57:11] Processing group of 30799 in 31 groups of 1000
[INFO] [2019-10-13 04:57:15] Average Time: 0.127
[INFO] [2019-10-13 04:57:15] Total Time: 5s
[INFO] [2019-10-13 04:57:15] last 3 / first 3: 0.83
[INFO] [2019-10-13 04:57:15] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-10-13 04:57:15] parse_diff_and_store
[START] [2019-10-13 04:57:15] resolve_keys
[INFO] [2019-10-13 04:58:30] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 04:58:36] traits to occurrences...
[INFO] [2019-10-13 04:58:40] traits to nodes (through occurrences)...
[INFO] [2019-10-13 04:58:41] Traits to sex term...
[INFO] [2019-10-13 04:58:45] Traits to lifestage term...
[INFO] [2019-10-13 04:58:51] MetaTraits to traits...
[INFO] [2019-10-13 04:58:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 04:58:57] Assocs to occurrences...
[INFO] [2019-10-13 04:58:57] Assocs to nodes...
[INFO] [2019-10-13 04:58:57] Assoc to sex term...
[INFO] [2019-10-13 04:58:57] Assoc to lifestage term...
[STOP] [2019-10-13 04:58:57] resolve_keys
[START] [2019-10-13 04:58:57] hold_for_later_1
[STOP] [2019-10-13 04:58:57] hold_for_later_1
[START] [2019-10-13 04:58:57] hold_for_later_2
[STOP] [2019-10-13 04:58:57] hold_for_later_2
[START] [2019-10-13 04:58:57] resolve_missing_parents
[STOP] [2019-10-13 04:59:37] resolve_missing_parents
[START] [2019-10-13 04:59:37] rebuild_nodes
[START] [2019-10-13 04:59:37] Flattener#flatten
[START] [2019-10-13 04:59:37] Flattener#study_resource
[START] [2019-10-13 04:59:37] Flattener#build_ancestry
[STOP] [2019-10-13 04:59:40] Flattener#build_ancestry
[INFO] [2019-10-13 04:59:40] 23029 ancestry keys
[START] [2019-10-13 04:59:40] build_node_ancestors
[INFO] [2019-10-13 04:59:40] old ancestors deleted.
[STOP] [2019-10-13 04:59:45] build_node_ancestors
[START] [2019-10-13 04:59:51] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:59:53] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:59:53] Flattener#flatten
[STOP] [2019-10-13 04:59:53] rebuild_nodes
[START] [2019-10-13 04:59:53] resolve_missing_media_owners
[STOP] [2019-10-13 04:59:53] resolve_missing_media_owners
[START] [2019-10-13 04:59:53] sanitize_media_verbatims
[STOP] [2019-10-13 04:59:53] sanitize_media_verbatims
[START] [2019-10-13 04:59:53] queue_downloads
[STOP] [2019-10-13 04:59:53] queue_downloads
[START] [2019-10-13 04:59:53] parse_names
[WARN] [2019-10-13 04:59:53] I see 23029 names which still need to be parsed.
[STOP] [2019-10-13 05:00:11] parse_names
[START] [2019-10-13 05:00:11] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 05:00:11] denormalize_canonical_names_to_nodes
[START] [2019-10-13 05:00:11] match_nodes
[START] [2019-10-13 05:00:11] map_all_nodes_to_pages
[STOP] [2019-10-13 05:21:56] map_all_nodes_to_pages
[INFO] [2019-10-13 05:21:56] 2320 Unmatched nodes (of 23029)! That's too many to output. First 10: Corvus monedula (#49905196); Hirundo rupestris (#49907394); Delichon urbica (#49906086); Calandrella rufescens (#49917799); Carduelis cannabina (#49905501); Carduelis chloris (#49905903); Carduelis spinus (#49910774); Parus caeruleus (#49906353); Parus lugubris (#49910295); Parus ater (#49913958)
[START] [2019-10-13 05:21:56] update_nodes
[STOP] [2019-10-13 05:22:04] update_nodes
[STOP] [2019-10-13 05:22:04] match_nodes
[START] [2019-10-13 05:22:04] reindex_search
[STOP] [2019-10-13 05:23:04] reindex_search
[START] [2019-10-13 05:23:04] normalize_units
[STOP] [2019-10-13 05:23:04] normalize_units
[START] [2019-10-13 05:23:04] calculate_statistics
[STOP] [2019-10-13 05:23:04] calculate_statistics
[START] [2019-10-13 05:23:04] complete_harvest_instance
[START] [2019-10-13 05:23:04] overall_tsv_creation
[INFO] [2019-10-13 05:23:04] Processing group of 23029 in 3 batches of 10000
[INFO] [2019-10-13 05:24:35] 6293 Traits (unfiltered)...
[INFO] [2019-10-13 05:24:49] 6293 Traits (filtered)...
[INFO] [2019-10-13 05:24:49] 0 Associations (filtered)...
[INFO] [2019-10-13 05:25:38] 31461 metadata added.
[INFO] [2019-10-13 05:25:38] 0 metadata added.
[INFO] [2019-10-13 05:27:11] 6927 Traits (unfiltered)...
[INFO] [2019-10-13 05:27:25] 6927 Traits (filtered)...
[INFO] [2019-10-13 05:27:25] 0 Associations (filtered)...
[INFO] [2019-10-13 05:28:18] 34628 metadata added.
[INFO] [2019-10-13 05:28:18] 0 metadata added.
[INFO] [2019-10-13 05:29:19] 1722 Traits (unfiltered)...
[INFO] [2019-10-13 05:29:32] 1722 Traits (filtered)...
[INFO] [2019-10-13 05:29:32] 0 Associations (filtered)...
[INFO] [2019-10-13 05:30:12] 8602 metadata added.
[INFO] [2019-10-13 05:30:12] 0 metadata added.
[INFO] [2019-10-13 05:30:12] Average Time: 117.88
[INFO] [2019-10-13 05:30:12] Total Time: 7m9s
[STOP] [2019-10-13 05:30:12] overall_tsv_creation
[INFO] [2019-10-13 05:30:12] Done. Check your files:
[INFO] [2019-10-13 05:30:13] (23029 lines) /app/public/data/greece_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 05:30:13] (72606 lines) /app/public/data/greece_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 05:30:13] (23029 lines) /app/public/data/greece_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 05:30:13] (14943 lines) /app/public/data/greece_sp_list/publish_traits.tsv
[INFO] [2019-10-13 05:30:13] (74692 lines) /app/public/data/greece_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 05:30:13] complete_harvest_instance
[START] [2019-10-13 05:30:13] completed
[STOP] [2019-10-13 05:30:13] completed
[STOP] [2019-10-13 05:30:13] logged process, took 2122.56

Latest Process

13 Oct 04:54 EXITED currently processing 0