Harvest for Sea of Japan Species List Created 25 Dec 10:57

Harvesting Log

# Logfile created on 2019-12-25 10:57:47 -0500 by logger.rb/56815
[START] [2019-12-25 10:57:47] logged process
[START] [2019-12-25 10:57:47] create_harvest_instance
[STOP] [2019-12-25 10:57:47] create_harvest_instance
[START] [2019-12-25 10:57:47] fetch_files
[STOP] [2019-12-25 10:57:47] fetch_files
[START] [2019-12-25 10:57:47] validate_each_file
[STOP] [2019-12-25 10:57:48] validate_each_file
[START] [2019-12-25 10:57:48] convert_to_csv
[CMD] [2019-12-25 10:57:48] /usr/bin/sort /app/public/converted_csv/sea_japan_sp_lis_refs_19626.csv > /app/public/converted_csv/sea_japan_sp_lis_refs_19626.csv_sorted
[CMD] [2019-12-25 10:57:49] /usr/bin/sort /app/public/converted_csv/sea_japan_sp_lis_nodes_19627.csv > /app/public/converted_csv/sea_japan_sp_lis_nodes_19627.csv_sorted
[CMD] [2019-12-25 10:57:49] /usr/bin/sort /app/public/converted_csv/sea_japan_sp_lis_occurrences_19628.csv > /app/public/converted_csv/sea_japan_sp_lis_occurrences_19628.csv_sorted
[CMD] [2019-12-25 10:57:49] /usr/bin/sort /app/public/converted_csv/sea_japan_sp_lis_measurements_19629.csv > /app/public/converted_csv/sea_japan_sp_lis_measurements_19629.csv_sorted
[STOP] [2019-12-25 10:57:49] convert_to_csv
[START] [2019-12-25 10:57:49] calculate_delta
[CMD] [2019-12-25 10:57:49] echo "0a" > /app/public/diff/sea_japan_sp_lis_refs_19626.diff
[CMD] [2019-12-25 10:57:49] tail -n +1 /app/public/converted_csv/sea_japan_sp_lis_refs_19626.csv >> /app/public/diff/sea_japan_sp_lis_refs_19626.diff
[CMD] [2019-12-25 10:57:50] echo "." >> /app/public/diff/sea_japan_sp_lis_refs_19626.diff
[CMD] [2019-12-25 10:57:50] echo "0a" > /app/public/diff/sea_japan_sp_lis_nodes_19627.diff
[CMD] [2019-12-25 10:57:50] tail -n +1 /app/public/converted_csv/sea_japan_sp_lis_nodes_19627.csv >> /app/public/diff/sea_japan_sp_lis_nodes_19627.diff
[CMD] [2019-12-25 10:57:50] echo "." >> /app/public/diff/sea_japan_sp_lis_nodes_19627.diff
[CMD] [2019-12-25 10:57:50] echo "0a" > /app/public/diff/sea_japan_sp_lis_occurrences_19628.diff
[CMD] [2019-12-25 10:57:50] tail -n +1 /app/public/converted_csv/sea_japan_sp_lis_occurrences_19628.csv >> /app/public/diff/sea_japan_sp_lis_occurrences_19628.diff
[CMD] [2019-12-25 10:57:51] echo "." >> /app/public/diff/sea_japan_sp_lis_occurrences_19628.diff
[CMD] [2019-12-25 10:57:51] echo "0a" > /app/public/diff/sea_japan_sp_lis_measurements_19629.diff
[CMD] [2019-12-25 10:57:51] tail -n +1 /app/public/converted_csv/sea_japan_sp_lis_measurements_19629.csv >> /app/public/diff/sea_japan_sp_lis_measurements_19629.diff
[CMD] [2019-12-25 10:57:51] echo "." >> /app/public/diff/sea_japan_sp_lis_measurements_19629.diff
[STOP] [2019-12-25 10:57:51] calculate_delta
[START] [2019-12-25 10:57:51] parse_diff_and_store
[INFO] [2019-12-25 10:57:51] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 10:57:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 10:57:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 10:57:55] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 10:58:17] Storing 2 References
[INFO] [2019-12-25 10:58:17] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 10:58:17] Average Time: 0.0
[INFO] [2019-12-25 10:58:17] Total Time: 1s
[INFO] [2019-12-25 10:58:17] Storing 7400 ScientificNames
[INFO] [2019-12-25 10:58:17] Processing group of 7400 in 8 groups of 1000
[INFO] [2019-12-25 10:58:20] Average Time: 0.388
[INFO] [2019-12-25 10:58:20] Total Time: 4s
[INFO] [2019-12-25 10:58:20] last 3 / first 3: 0.76
[INFO] [2019-12-25 10:58:20] Std.Dev: 0.08944271909999159; Max: 0.46
[INFO] [2019-12-25 10:58:20] Storing 7400 Nodes
[INFO] [2019-12-25 10:58:20] Processing group of 7400 in 8 groups of 1000
[INFO] [2019-12-25 10:58:22] Average Time: 0.301
[INFO] [2019-12-25 10:58:22] Total Time: 3s
[INFO] [2019-12-25 10:58:22] last 3 / first 3: 0.72
[INFO] [2019-12-25 10:58:22] Std.Dev: 0.07745966692414834; Max: 0.38
[INFO] [2019-12-25 10:58:22] Storing 3775 Occurrences
[INFO] [2019-12-25 10:58:22] Processing group of 3775 in 4 groups of 1000
[INFO] [2019-12-25 10:58:23] Average Time: 0.12
[INFO] [2019-12-25 10:58:23] Total Time: 1s
[INFO] [2019-12-25 10:58:23] Storing 7550 TraitsReferences
[INFO] [2019-12-25 10:58:23] Processing group of 7550 in 8 groups of 1000
[INFO] [2019-12-25 10:58:23] Average Time: 0.083
[INFO] [2019-12-25 10:58:23] Total Time: 1s
[INFO] [2019-12-25 10:58:23] last 3 / first 3: 0.7
[INFO] [2019-12-25 10:58:23] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-12-25 10:58:23] Storing 7550 Traits
[INFO] [2019-12-25 10:58:23] Processing group of 7550 in 8 groups of 1000
[INFO] [2019-12-25 10:58:26] Average Time: 0.332
[INFO] [2019-12-25 10:58:26] Total Time: 3s
[INFO] [2019-12-25 10:58:26] last 3 / first 3: 0.76
[INFO] [2019-12-25 10:58:26] Std.Dev: 0.07071067811865475; Max: 0.44
[INFO] [2019-12-25 10:58:26] Storing 7540 MetaTraits
[INFO] [2019-12-25 10:58:26] Processing group of 7540 in 8 groups of 1000
[INFO] [2019-12-25 10:58:27] Average Time: 0.144
[INFO] [2019-12-25 10:58:27] Total Time: 2s
[INFO] [2019-12-25 10:58:27] last 3 / first 3: 0.71
[INFO] [2019-12-25 10:58:27] Std.Dev: 0.03162277660168379; Max: 0.17
[STOP] [2019-12-25 10:58:27] parse_diff_and_store
[START] [2019-12-25 10:58:27] resolve_keys
[INFO] [2019-12-25 10:58:58] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 10:59:01] traits to occurrences...
[INFO] [2019-12-25 10:59:04] traits to nodes (through occurrences)...
[INFO] [2019-12-25 10:59:05] Traits to sex term...
[INFO] [2019-12-25 10:59:07] Traits to lifestage term...
[INFO] [2019-12-25 10:59:11] MetaTraits to traits...
[INFO] [2019-12-25 10:59:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 10:59:12] Assocs to occurrences...
[INFO] [2019-12-25 10:59:12] Assocs to nodes...
[INFO] [2019-12-25 10:59:12] Assoc to sex term...
[INFO] [2019-12-25 10:59:12] Assoc to lifestage term...
[STOP] [2019-12-25 10:59:12] resolve_keys
[START] [2019-12-25 10:59:12] hold_for_later_1
[STOP] [2019-12-25 10:59:12] hold_for_later_1
[START] [2019-12-25 10:59:12] hold_for_later_2
[STOP] [2019-12-25 10:59:12] hold_for_later_2
[START] [2019-12-25 10:59:12] resolve_missing_parents
[STOP] [2019-12-25 10:59:26] resolve_missing_parents
[START] [2019-12-25 10:59:26] rebuild_nodes
[START] [2019-12-25 10:59:26] Flattener#flatten
[START] [2019-12-25 10:59:26] Flattener#study_resource
[START] [2019-12-25 10:59:26] Flattener#build_ancestry
[STOP] [2019-12-25 10:59:27] Flattener#build_ancestry
[INFO] [2019-12-25 10:59:27] 7400 ancestry keys
[START] [2019-12-25 10:59:27] build_node_ancestors
[INFO] [2019-12-25 10:59:27] old ancestors deleted.
[STOP] [2019-12-25 10:59:30] build_node_ancestors
[START] [2019-12-25 10:59:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:59:34] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:59:34] Flattener#flatten
[STOP] [2019-12-25 10:59:34] rebuild_nodes
[START] [2019-12-25 10:59:34] resolve_missing_media_owners
[STOP] [2019-12-25 10:59:34] resolve_missing_media_owners
[START] [2019-12-25 10:59:34] sanitize_media_verbatims
[STOP] [2019-12-25 10:59:34] sanitize_media_verbatims
[START] [2019-12-25 10:59:34] queue_downloads
[STOP] [2019-12-25 10:59:34] queue_downloads
[START] [2019-12-25 10:59:34] parse_names
[WARN] [2019-12-25 10:59:34] I see 7400 names which still need to be parsed.
[STOP] [2019-12-25 10:59:41] parse_names
[START] [2019-12-25 10:59:41] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 10:59:41] denormalize_canonical_names_to_nodes
[START] [2019-12-25 10:59:41] match_nodes
[START] [2019-12-25 10:59:41] map_all_nodes_to_pages
[STOP] [2019-12-25 11:59:56] map_all_nodes_to_pages
[INFO] [2019-12-25 11:59:56] 472 Unmatched nodes (of 7400)! That's too many to output. First 10: Globorotalia puncticulata (#62436651); Cassidulina norcrossi (#62432749); Cassidulina crassa (#62438550); Stainforthia complanata (#62432881); Bulimina rostrata (#62436403); Oridorsalis tener (#62432862); Bolivina pacifica (#62432949); Bolivina subspinescens (#62434752); Bolivina seminuda (#62438263); Nonion scapha (#62438922)
[START] [2019-12-25 11:59:56] update_nodes
[STOP] [2019-12-25 11:59:59] update_nodes
[STOP] [2019-12-25 11:59:59] match_nodes
[START] [2019-12-25 11:59:59] reindex_search
[STOP] [2019-12-25 12:00:31] reindex_search
[ERR] [2019-12-25 12:00:31] Faraday::ConnectionFailed
[ERR] [2019-12-25 12:00:31] Failed to open TCP connection to elasticsearch:9200 (Connection refused - connect(2) for "elasticsearch" port 9200)
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:615:in `reindex_search'
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2019-12-25 12:00:31] ../models/logged_process.rb:19:in `run_step'
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2019-12-25 12:00:31] ../models/resource.rb:139:in `lock'
[ERR] [2019-12-25 12:00:31] ../models/resource_harvester.rb:72:in `start'
[ERR] [2019-12-25 12:00:31] ../models/resource.rb:223:in `harvest'
[ERR] [2019-12-25 12:00:31] ../models/resource.rb:199:in `re_download_opendata_and_harvest'
[STOP] [2019-12-25 12:00:31] logged process, took 3764.44
[START] [2019-12-25 13:35:36] logged process
[INFO] [2019-12-25 13:35:36] Already completed stage create_harvest_instance, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage fetch_files, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage validate_each_file, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage convert_to_csv, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage calculate_delta, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage parse_diff_and_store, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage resolve_keys, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage hold_for_later_1, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage hold_for_later_2, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage resolve_missing_parents, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage rebuild_nodes, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage resolve_missing_media_owners, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage sanitize_media_verbatims, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage queue_downloads, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage parse_names, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage denormalize_canonical_names_to_nodes, skipping...
[INFO] [2019-12-25 13:35:36] Already completed stage match_nodes, skipping...
[START] [2019-12-25 13:35:36] reindex_search
[STOP] [2019-12-25 13:35:50] reindex_search
[START] [2019-12-25 13:35:50] normalize_units
[STOP] [2019-12-25 13:35:50] normalize_units
[START] [2019-12-25 13:35:50] calculate_statistics
[STOP] [2019-12-25 13:35:50] calculate_statistics
[START] [2019-12-25 13:35:50] complete_harvest_instance
[START] [2019-12-25 13:35:50] overall_tsv_creation
[INFO] [2019-12-25 13:35:50] Processing group of 7400 in 1 batches of 10000
[INFO] [2019-12-25 13:37:09] 3775 Traits (unfiltered)...
[INFO] [2019-12-25 13:37:21] 3775 Traits (filtered)...
[INFO] [2019-12-25 13:37:21] 0 Associations (filtered)...
[INFO] [2019-12-25 13:38:10] 18865 metadata added.
[INFO] [2019-12-25 13:38:10] 0 metadata added.
[INFO] [2019-12-25 13:38:10] Average Time: 110.82
[INFO] [2019-12-25 13:38:10] Total Time: 2m20s
[STOP] [2019-12-25 13:38:10] overall_tsv_creation
[INFO] [2019-12-25 13:38:10] Done. Check your files:
[INFO] [2019-12-25 13:38:10] (7400 lines) /app/public/data/sea_japan_sp_lis/publish_nodes.tsv
[INFO] [2019-12-25 13:38:11] (37002 lines) /app/public/data/sea_japan_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-25 13:38:12] (7400 lines) /app/public/data/sea_japan_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-25 13:38:12] (3776 lines) /app/public/data/sea_japan_sp_lis/publish_traits.tsv
[INFO] [2019-12-25 13:38:13] (18866 lines) /app/public/data/sea_japan_sp_lis/publish_metadata.tsv
[STOP] [2019-12-25 13:38:13] complete_harvest_instance
[START] [2019-12-25 13:38:13] completed
[STOP] [2019-12-25 13:38:13] completed
[STOP] [2019-12-25 13:38:13] logged process, took 156.69

Latest Process

25 Dec 13:35 EXITED currently processing 0