Harvest for Puerto Rico Species List Created 15 Oct 13:30

Stage: completed
Fetched: 15 Oct 13:30
Validated: 15 Oct 13:31
Deltas Created 15 Oct 13:31
Units Normalized: 15 Oct 13:46
Ancestry Built: 15 Oct 13:33
Nodes Matched: 15 Oct 13:45
Names Parsed: 15 Oct 13:34
New Models Stored: 15 Oct 13:32
Indexed: 15 Oct 13:46
Completed: 15 Oct 13:50
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-15 13:30:58 -0400 by logger.rb/56815
[START] [2019-10-15 13:30:58] logged process
[START] [2019-10-15 13:30:58] create_harvest_instance
[STOP] [2019-10-15 13:30:59] create_harvest_instance
[START] [2019-10-15 13:30:59] fetch_files
[STOP] [2019-10-15 13:30:59] fetch_files
[START] [2019-10-15 13:30:59] validate_each_file
[STOP] [2019-10-15 13:31:01] validate_each_file
[START] [2019-10-15 13:31:01] convert_to_csv
[CMD] [2019-10-15 13:31:01] /usr/bin/sort /app/public/converted_csv/puerto_rico_sp_l_refs_16949.csv > /app/public/converted_csv/puerto_rico_sp_l_refs_16949.csv_sorted
[CMD] [2019-10-15 13:31:01] /usr/bin/sort /app/public/converted_csv/puerto_rico_sp_l_nodes_16950.csv > /app/public/converted_csv/puerto_rico_sp_l_nodes_16950.csv_sorted
[CMD] [2019-10-15 13:31:01] /usr/bin/sort /app/public/converted_csv/puerto_rico_sp_l_occurrences_16951.csv > /app/public/converted_csv/puerto_rico_sp_l_occurrences_16951.csv_sorted
[CMD] [2019-10-15 13:31:01] /usr/bin/sort /app/public/converted_csv/puerto_rico_sp_l_measurements_16952.csv > /app/public/converted_csv/puerto_rico_sp_l_measurements_16952.csv_sorted
[STOP] [2019-10-15 13:31:02] convert_to_csv
[START] [2019-10-15 13:31:02] calculate_delta
[CMD] [2019-10-15 13:31:02] echo "0a" > /app/public/diff/puerto_rico_sp_l_refs_16949.diff
[CMD] [2019-10-15 13:31:02] tail -n +1 /app/public/converted_csv/puerto_rico_sp_l_refs_16949.csv >> /app/public/diff/puerto_rico_sp_l_refs_16949.diff
[CMD] [2019-10-15 13:31:02] echo "." >> /app/public/diff/puerto_rico_sp_l_refs_16949.diff
[CMD] [2019-10-15 13:31:03] echo "0a" > /app/public/diff/puerto_rico_sp_l_nodes_16950.diff
[CMD] [2019-10-15 13:31:03] tail -n +1 /app/public/converted_csv/puerto_rico_sp_l_nodes_16950.csv >> /app/public/diff/puerto_rico_sp_l_nodes_16950.diff
[CMD] [2019-10-15 13:31:03] echo "." >> /app/public/diff/puerto_rico_sp_l_nodes_16950.diff
[CMD] [2019-10-15 13:31:03] echo "0a" > /app/public/diff/puerto_rico_sp_l_occurrences_16951.diff
[CMD] [2019-10-15 13:31:04] tail -n +1 /app/public/converted_csv/puerto_rico_sp_l_occurrences_16951.csv >> /app/public/diff/puerto_rico_sp_l_occurrences_16951.diff
[CMD] [2019-10-15 13:31:04] echo "." >> /app/public/diff/puerto_rico_sp_l_occurrences_16951.diff
[CMD] [2019-10-15 13:31:04] echo "0a" > /app/public/diff/puerto_rico_sp_l_measurements_16952.diff
[CMD] [2019-10-15 13:31:05] tail -n +1 /app/public/converted_csv/puerto_rico_sp_l_measurements_16952.csv >> /app/public/diff/puerto_rico_sp_l_measurements_16952.diff
[CMD] [2019-10-15 13:31:05] echo "." >> /app/public/diff/puerto_rico_sp_l_measurements_16952.diff
[STOP] [2019-10-15 13:31:05] calculate_delta
[START] [2019-10-15 13:31:05] parse_diff_and_store
[INFO] [2019-10-15 13:31:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 13:31:06] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 13:31:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 13:31:12] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 13:31:58] Storing 2 References
[INFO] [2019-10-15 13:31:58] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 13:31:58] Average Time: 0.0
[INFO] [2019-10-15 13:31:58] Total Time: 1s
[INFO] [2019-10-15 13:31:58] Storing 12766 ScientificNames
[INFO] [2019-10-15 13:31:58] Processing group of 12766 in 13 groups of 1000
[INFO] [2019-10-15 13:32:04] Average Time: 0.419
[INFO] [2019-10-15 13:32:04] Total Time: 6s
[INFO] [2019-10-15 13:32:04] last 3 / first 3: 0.54
[INFO] [2019-10-15 13:32:04] Std.Dev: 0.22135943621178655; Max: 1.14
[INFO] [2019-10-15 13:32:04] Storing 12766 Nodes
[INFO] [2019-10-15 13:32:04] Processing group of 12766 in 13 groups of 1000
[INFO] [2019-10-15 13:32:08] Average Time: 0.288
[INFO] [2019-10-15 13:32:08] Total Time: 4s
[INFO] [2019-10-15 13:32:08] last 3 / first 3: 0.94
[INFO] [2019-10-15 13:32:08] Std.Dev: 0.03162277660168379; Max: 0.35
[INFO] [2019-10-15 13:32:08] Storing 7230 Occurrences
[INFO] [2019-10-15 13:32:08] Processing group of 7230 in 8 groups of 1000
[INFO] [2019-10-15 13:32:08] Average Time: 0.09
[INFO] [2019-10-15 13:32:08] Total Time: 1s
[INFO] [2019-10-15 13:32:08] last 3 / first 3: 0.71
[INFO] [2019-10-15 13:32:08] Std.Dev: 0.03162277660168379; Max: 0.11
[INFO] [2019-10-15 13:32:08] Storing 15390 TraitsReferences
[INFO] [2019-10-15 13:32:08] Processing group of 15390 in 16 groups of 1000
[INFO] [2019-10-15 13:32:10] Average Time: 0.073
[INFO] [2019-10-15 13:32:10] Total Time: 2s
[INFO] [2019-10-15 13:32:10] last 3 / first 3: 0.61
[INFO] [2019-10-15 13:32:10] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-15 13:32:10] Storing 15389 Traits
[INFO] [2019-10-15 13:32:10] Processing group of 15389 in 16 groups of 1000
[INFO] [2019-10-15 13:32:14] Average Time: 0.291
[INFO] [2019-10-15 13:32:14] Total Time: 5s
[INFO] [2019-10-15 13:32:14] last 3 / first 3: 0.77
[INFO] [2019-10-15 13:32:14] Std.Dev: 0.05477225575051661; Max: 0.4
[INFO] [2019-10-15 13:32:14] Storing 15383 MetaTraits
[INFO] [2019-10-15 13:32:14] Processing group of 15383 in 16 groups of 1000
[INFO] [2019-10-15 13:32:16] Average Time: 0.109
[INFO] [2019-10-15 13:32:16] Total Time: 2s
[INFO] [2019-10-15 13:32:16] last 3 / first 3: 0.68
[INFO] [2019-10-15 13:32:16] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-15 13:32:16] parse_diff_and_store
[START] [2019-10-15 13:32:16] resolve_keys
[INFO] [2019-10-15 13:33:05] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 13:33:10] traits to occurrences...
[INFO] [2019-10-15 13:33:15] traits to nodes (through occurrences)...
[INFO] [2019-10-15 13:33:15] Traits to sex term...
[INFO] [2019-10-15 13:33:20] Traits to lifestage term...
[INFO] [2019-10-15 13:33:25] MetaTraits to traits...
[INFO] [2019-10-15 13:33:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 13:33:28] Assocs to occurrences...
[INFO] [2019-10-15 13:33:28] Assocs to nodes...
[INFO] [2019-10-15 13:33:28] Assoc to sex term...
[INFO] [2019-10-15 13:33:28] Assoc to lifestage term...
[STOP] [2019-10-15 13:33:28] resolve_keys
[START] [2019-10-15 13:33:28] hold_for_later_1
[STOP] [2019-10-15 13:33:28] hold_for_later_1
[START] [2019-10-15 13:33:28] hold_for_later_2
[STOP] [2019-10-15 13:33:28] hold_for_later_2
[START] [2019-10-15 13:33:28] resolve_missing_parents
[STOP] [2019-10-15 13:33:52] resolve_missing_parents
[START] [2019-10-15 13:33:52] rebuild_nodes
[START] [2019-10-15 13:33:52] Flattener#flatten
[START] [2019-10-15 13:33:52] Flattener#study_resource
[START] [2019-10-15 13:33:52] Flattener#build_ancestry
[STOP] [2019-10-15 13:33:54] Flattener#build_ancestry
[INFO] [2019-10-15 13:33:54] 12766 ancestry keys
[START] [2019-10-15 13:33:54] build_node_ancestors
[INFO] [2019-10-15 13:33:54] old ancestors deleted.
[STOP] [2019-10-15 13:33:56] build_node_ancestors
[START] [2019-10-15 13:33:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 13:33:59] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 13:33:59] Flattener#flatten
[STOP] [2019-10-15 13:33:59] rebuild_nodes
[START] [2019-10-15 13:33:59] resolve_missing_media_owners
[STOP] [2019-10-15 13:33:59] resolve_missing_media_owners
[START] [2019-10-15 13:33:59] sanitize_media_verbatims
[STOP] [2019-10-15 13:33:59] sanitize_media_verbatims
[START] [2019-10-15 13:33:59] queue_downloads
[STOP] [2019-10-15 13:33:59] queue_downloads
[START] [2019-10-15 13:33:59] parse_names
[WARN] [2019-10-15 13:33:59] I see 12766 names which still need to be parsed.
[STOP] [2019-10-15 13:34:09] parse_names
[START] [2019-10-15 13:34:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 13:34:09] denormalize_canonical_names_to_nodes
[START] [2019-10-15 13:34:09] match_nodes
[START] [2019-10-15 13:34:09] map_all_nodes_to_pages
[STOP] [2019-10-15 13:45:45] map_all_nodes_to_pages
[INFO] [2019-10-15 13:45:45] 813 Unmatched nodes (of 12766)! That's too many to output. First 10: Coerebidae (#51670403); Tiaris olivacea (#51676572); Seiurus aurocapillus (#51677156); Dendroica adelaidae (#51672073); Dendroica petechia (#51672265); Dendroica discolor (#51682010); Parula americana (#51676424); Oreothlypis peregrina (#51681433); Hirundo fulva (#51679557); Spermestes cucullatus (#51670639)
[START] [2019-10-15 13:45:45] update_nodes
[STOP] [2019-10-15 13:45:49] update_nodes
[STOP] [2019-10-15 13:45:49] match_nodes
[START] [2019-10-15 13:45:49] reindex_search
[STOP] [2019-10-15 13:46:21] reindex_search
[START] [2019-10-15 13:46:21] normalize_units
[STOP] [2019-10-15 13:46:21] normalize_units
[START] [2019-10-15 13:46:21] calculate_statistics
[STOP] [2019-10-15 13:46:21] calculate_statistics
[START] [2019-10-15 13:46:21] complete_harvest_instance
[START] [2019-10-15 13:46:21] overall_tsv_creation
[INFO] [2019-10-15 13:46:21] Processing group of 12766 in 2 batches of 10000
[INFO] [2019-10-15 13:47:50] 5759 Traits (unfiltered)...
[INFO] [2019-10-15 13:48:04] 5759 Traits (filtered)...
[INFO] [2019-10-15 13:48:04] 0 Associations (filtered)...
[INFO] [2019-10-15 13:48:53] 28790 metadata added.
[INFO] [2019-10-15 13:48:53] 0 metadata added.
[INFO] [2019-10-15 13:49:50] 1471 Traits (unfiltered)...
[INFO] [2019-10-15 13:50:04] 1471 Traits (filtered)...
[INFO] [2019-10-15 13:50:04] 0 Associations (filtered)...
[INFO] [2019-10-15 13:50:44] 7353 metadata added.
[INFO] [2019-10-15 13:50:44] 0 metadata added.
[INFO] [2019-10-15 13:50:44] Average Time: 107.14
[INFO] [2019-10-15 13:50:44] Total Time: 4m24s
[STOP] [2019-10-15 13:50:44] overall_tsv_creation
[INFO] [2019-10-15 13:50:44] Done. Check your files:
[INFO] [2019-10-15 13:50:44] (12766 lines) /app/public/data/puerto_rico_sp_l/publish_nodes.tsv
[INFO] [2019-10-15 13:50:45] (30874 lines) /app/public/data/puerto_rico_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-15 13:50:45] (12766 lines) /app/public/data/puerto_rico_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-15 13:50:45] (7231 lines) /app/public/data/puerto_rico_sp_l/publish_traits.tsv
[INFO] [2019-10-15 13:50:46] (36144 lines) /app/public/data/puerto_rico_sp_l/publish_metadata.tsv
[STOP] [2019-10-15 13:50:46] complete_harvest_instance
[START] [2019-10-15 13:50:46] completed
[STOP] [2019-10-15 13:50:46] completed
[STOP] [2019-10-15 13:50:46] logged process, took 1187.39
Latest Process

15 Oct 13:30 EXITED currently processing 0