Harvest for Bulgaria Species List Created 11 Oct 23:14

Stage: completed
Fetched: 11 Oct 23:14
Validated: 11 Oct 23:14
Deltas Created 11 Oct 23:14
Units Normalized: 11 Oct 23:21
Ancestry Built: 11 Oct 23:16
Nodes Matched: 11 Oct 23:21
Names Parsed: 11 Oct 23:16
New Models Stored: 11 Oct 23:15
Indexed: 11 Oct 23:21
Completed: 11 Oct 23:24
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-11 23:14:35 -0400 by logger.rb/56815
[START] [2019-10-11 23:14:35] logged process
[START] [2019-10-11 23:14:35] create_harvest_instance
[STOP] [2019-10-11 23:14:35] create_harvest_instance
[START] [2019-10-11 23:14:35] fetch_files
[STOP] [2019-10-11 23:14:35] fetch_files
[START] [2019-10-11 23:14:35] validate_each_file
[STOP] [2019-10-11 23:14:37] validate_each_file
[START] [2019-10-11 23:14:37] convert_to_csv
[CMD] [2019-10-11 23:14:37] /usr/bin/sort /app/public/converted_csv/bulgaria_sp_list_refs_15331.csv > /app/public/converted_csv/bulgaria_sp_list_refs_15331.csv_sorted
[CMD] [2019-10-11 23:14:37] /usr/bin/sort /app/public/converted_csv/bulgaria_sp_list_nodes_15332.csv > /app/public/converted_csv/bulgaria_sp_list_nodes_15332.csv_sorted
[CMD] [2019-10-11 23:14:37] /usr/bin/sort /app/public/converted_csv/bulgaria_sp_list_occurrences_15333.csv > /app/public/converted_csv/bulgaria_sp_list_occurrences_15333.csv_sorted
[CMD] [2019-10-11 23:14:37] /usr/bin/sort /app/public/converted_csv/bulgaria_sp_list_measurements_15334.csv > /app/public/converted_csv/bulgaria_sp_list_measurements_15334.csv_sorted
[STOP] [2019-10-11 23:14:37] convert_to_csv
[START] [2019-10-11 23:14:37] calculate_delta
[CMD] [2019-10-11 23:14:37] echo "0a" > /app/public/diff/bulgaria_sp_list_refs_15331.diff
[CMD] [2019-10-11 23:14:37] tail -n +1 /app/public/converted_csv/bulgaria_sp_list_refs_15331.csv >> /app/public/diff/bulgaria_sp_list_refs_15331.diff
[CMD] [2019-10-11 23:14:37] echo "." >> /app/public/diff/bulgaria_sp_list_refs_15331.diff
[CMD] [2019-10-11 23:14:37] echo "0a" > /app/public/diff/bulgaria_sp_list_nodes_15332.diff
[CMD] [2019-10-11 23:14:38] tail -n +1 /app/public/converted_csv/bulgaria_sp_list_nodes_15332.csv >> /app/public/diff/bulgaria_sp_list_nodes_15332.diff
[CMD] [2019-10-11 23:14:38] echo "." >> /app/public/diff/bulgaria_sp_list_nodes_15332.diff
[CMD] [2019-10-11 23:14:38] echo "0a" > /app/public/diff/bulgaria_sp_list_occurrences_15333.diff
[CMD] [2019-10-11 23:14:38] tail -n +1 /app/public/converted_csv/bulgaria_sp_list_occurrences_15333.csv >> /app/public/diff/bulgaria_sp_list_occurrences_15333.diff
[CMD] [2019-10-11 23:14:38] echo "." >> /app/public/diff/bulgaria_sp_list_occurrences_15333.diff
[CMD] [2019-10-11 23:14:38] echo "0a" > /app/public/diff/bulgaria_sp_list_measurements_15334.diff
[CMD] [2019-10-11 23:14:38] tail -n +1 /app/public/converted_csv/bulgaria_sp_list_measurements_15334.csv >> /app/public/diff/bulgaria_sp_list_measurements_15334.diff
[CMD] [2019-10-11 23:14:38] echo "." >> /app/public/diff/bulgaria_sp_list_measurements_15334.diff
[STOP] [2019-10-11 23:14:38] calculate_delta
[START] [2019-10-11 23:14:38] parse_diff_and_store
[INFO] [2019-10-11 23:14:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 23:14:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 23:14:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 23:14:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 23:15:12] Storing 2 References
[INFO] [2019-10-11 23:15:12] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 23:15:12] Average Time: 0.0
[INFO] [2019-10-11 23:15:12] Total Time: 1s
[INFO] [2019-10-11 23:15:12] Storing 8107 ScientificNames
[INFO] [2019-10-11 23:15:12] Processing group of 8107 in 9 groups of 1000
[INFO] [2019-10-11 23:15:15] Average Time: 0.337
[INFO] [2019-10-11 23:15:15] Total Time: 4s
[INFO] [2019-10-11 23:15:15] last 3 / first 3: 0.65
[INFO] [2019-10-11 23:15:15] Std.Dev: 0.11401754250991379; Max: 0.46
[INFO] [2019-10-11 23:15:15] Storing 8107 Nodes
[INFO] [2019-10-11 23:15:15] Processing group of 8107 in 9 groups of 1000
[INFO] [2019-10-11 23:15:18] Average Time: 0.316
[INFO] [2019-10-11 23:15:18] Total Time: 3s
[INFO] [2019-10-11 23:15:18] last 3 / first 3: 1.03
[INFO] [2019-10-11 23:15:18] Std.Dev: 0.1224744871391589; Max: 0.46
[INFO] [2019-10-11 23:15:18] Storing 4820 Occurrences
[INFO] [2019-10-11 23:15:18] Processing group of 4820 in 5 groups of 1000
[INFO] [2019-10-11 23:15:19] Average Time: 0.106
[INFO] [2019-10-11 23:15:19] Total Time: 1s
[INFO] [2019-10-11 23:15:19] Storing 9984 TraitsReferences
[INFO] [2019-10-11 23:15:19] Processing group of 9984 in 10 groups of 1000
[INFO] [2019-10-11 23:15:19] Average Time: 0.076
[INFO] [2019-10-11 23:15:19] Total Time: 1s
[INFO] [2019-10-11 23:15:19] last 3 / first 3: 0.69
[INFO] [2019-10-11 23:15:19] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-11 23:15:19] Storing 9983 Traits
[INFO] [2019-10-11 23:15:19] Processing group of 9983 in 10 groups of 1000
[INFO] [2019-10-11 23:15:23] Average Time: 0.329
[INFO] [2019-10-11 23:15:23] Total Time: 4s
[INFO] [2019-10-11 23:15:23] last 3 / first 3: 0.85
[INFO] [2019-10-11 23:15:23] Std.Dev: 0.044721359549995794; Max: 0.45
[INFO] [2019-10-11 23:15:23] Storing 9979 MetaTraits
[INFO] [2019-10-11 23:15:23] Processing group of 9979 in 10 groups of 1000
[INFO] [2019-10-11 23:15:24] Average Time: 0.138
[INFO] [2019-10-11 23:15:24] Total Time: 2s
[INFO] [2019-10-11 23:15:24] last 3 / first 3: 0.93
[INFO] [2019-10-11 23:15:24] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-11 23:15:24] parse_diff_and_store
[START] [2019-10-11 23:15:24] resolve_keys
[INFO] [2019-10-11 23:15:57] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 23:16:00] traits to occurrences...
[INFO] [2019-10-11 23:16:04] traits to nodes (through occurrences)...
[INFO] [2019-10-11 23:16:04] Traits to sex term...
[INFO] [2019-10-11 23:16:07] Traits to lifestage term...
[INFO] [2019-10-11 23:16:11] MetaTraits to traits...
[INFO] [2019-10-11 23:16:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 23:16:13] Assocs to occurrences...
[INFO] [2019-10-11 23:16:13] Assocs to nodes...
[INFO] [2019-10-11 23:16:13] Assoc to sex term...
[INFO] [2019-10-11 23:16:13] Assoc to lifestage term...
[STOP] [2019-10-11 23:16:13] resolve_keys
[START] [2019-10-11 23:16:13] hold_for_later_1
[STOP] [2019-10-11 23:16:13] hold_for_later_1
[START] [2019-10-11 23:16:13] hold_for_later_2
[STOP] [2019-10-11 23:16:13] hold_for_later_2
[START] [2019-10-11 23:16:13] resolve_missing_parents
[STOP] [2019-10-11 23:16:29] resolve_missing_parents
[START] [2019-10-11 23:16:29] rebuild_nodes
[START] [2019-10-11 23:16:29] Flattener#flatten
[START] [2019-10-11 23:16:29] Flattener#study_resource
[START] [2019-10-11 23:16:29] Flattener#build_ancestry
[STOP] [2019-10-11 23:16:29] Flattener#build_ancestry
[INFO] [2019-10-11 23:16:29] 8107 ancestry keys
[START] [2019-10-11 23:16:29] build_node_ancestors
[INFO] [2019-10-11 23:16:29] old ancestors deleted.
[STOP] [2019-10-11 23:16:30] build_node_ancestors
[START] [2019-10-11 23:16:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:16:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:16:32] Flattener#flatten
[STOP] [2019-10-11 23:16:32] rebuild_nodes
[START] [2019-10-11 23:16:32] resolve_missing_media_owners
[STOP] [2019-10-11 23:16:32] resolve_missing_media_owners
[START] [2019-10-11 23:16:32] sanitize_media_verbatims
[STOP] [2019-10-11 23:16:32] sanitize_media_verbatims
[START] [2019-10-11 23:16:32] queue_downloads
[STOP] [2019-10-11 23:16:32] queue_downloads
[START] [2019-10-11 23:16:32] parse_names
[WARN] [2019-10-11 23:16:32] I see 8107 names which still need to be parsed.
[STOP] [2019-10-11 23:16:39] parse_names
[START] [2019-10-11 23:16:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 23:16:39] denormalize_canonical_names_to_nodes
[START] [2019-10-11 23:16:39] match_nodes
[START] [2019-10-11 23:16:39] map_all_nodes_to_pages
[STOP] [2019-10-11 23:21:18] map_all_nodes_to_pages
[INFO] [2019-10-11 23:21:18] 718 Unmatched nodes (of 8107)! That's too many to output. First 10: Aurinia uechtritzianum (#48977816); Sinapis arvense (#48979181); Pelophylax esculenta (#48976946); Hirundo rupestris (#48975296); Delichon urbica (#48973912); Carduelis cannabina (#48974106); Carduelis chloris (#48975043); Carduelis spinus (#48975387); Parus caeruleus (#48974160); Parus lugubris (#48974407)
[START] [2019-10-11 23:21:18] update_nodes
[STOP] [2019-10-11 23:21:21] update_nodes
[STOP] [2019-10-11 23:21:21] match_nodes
[START] [2019-10-11 23:21:21] reindex_search
[STOP] [2019-10-11 23:21:36] reindex_search
[START] [2019-10-11 23:21:36] normalize_units
[STOP] [2019-10-11 23:21:36] normalize_units
[START] [2019-10-11 23:21:36] calculate_statistics
[STOP] [2019-10-11 23:21:36] calculate_statistics
[START] [2019-10-11 23:21:36] complete_harvest_instance
[START] [2019-10-11 23:21:36] overall_tsv_creation
[INFO] [2019-10-11 23:21:36] Processing group of 8107 in 1 batches of 10000
[INFO] [2019-10-11 23:23:00] 4820 Traits (unfiltered)...
[INFO] [2019-10-11 23:23:14] 4820 Traits (filtered)...
[INFO] [2019-10-11 23:23:14] 0 Associations (filtered)...
[INFO] [2019-10-11 23:24:00] 24097 metadata added.
[INFO] [2019-10-11 23:24:00] 0 metadata added.
[INFO] [2019-10-11 23:24:00] Average Time: 115.39
[INFO] [2019-10-11 23:24:00] Total Time: 2m25s
[STOP] [2019-10-11 23:24:00] overall_tsv_creation
[INFO] [2019-10-11 23:24:00] Done. Check your files:
[INFO] [2019-10-11 23:24:00] (8107 lines) /app/public/data/bulgaria_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 23:24:01] (19297 lines) /app/public/data/bulgaria_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 23:24:01] (8107 lines) /app/public/data/bulgaria_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 23:24:01] (4821 lines) /app/public/data/bulgaria_sp_list/publish_traits.tsv
[INFO] [2019-10-11 23:24:01] (24098 lines) /app/public/data/bulgaria_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 23:24:01] complete_harvest_instance
[START] [2019-10-11 23:24:01] completed
[STOP] [2019-10-11 23:24:01] completed
[STOP] [2019-10-11 23:24:01] logged process, took 566.2
Latest Process

11 Oct 23:14 EXITED currently processing 0