Harvest for Philippines Species List Created 15 Oct 11:03

Stage: completed
Fetched: 15 Oct 11:03
Validated: 15 Oct 11:03
Deltas Created 15 Oct 11:03
Units Normalized: 15 Oct 12:08
Ancestry Built: 15 Oct 11:11
Nodes Matched: 15 Oct 12:07
Names Parsed: 15 Oct 11:11
New Models Stored: 15 Oct 11:07
Indexed: 15 Oct 12:08
Completed: 15 Oct 12:19
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-15 11:03:06 -0400 by logger.rb/56815
[START] [2019-10-15 11:03:06] logged process
[START] [2019-10-15 11:03:06] create_harvest_instance
[STOP] [2019-10-15 11:03:07] create_harvest_instance
[START] [2019-10-15 11:03:07] fetch_files
[STOP] [2019-10-15 11:03:07] fetch_files
[START] [2019-10-15 11:03:07] validate_each_file
[STOP] [2019-10-15 11:03:11] validate_each_file
[START] [2019-10-15 11:03:11] convert_to_csv
[CMD] [2019-10-15 11:03:11] /usr/bin/sort /app/public/converted_csv/philippines_sp_l_refs_16917.csv > /app/public/converted_csv/philippines_sp_l_refs_16917.csv_sorted
[CMD] [2019-10-15 11:03:12] /usr/bin/sort /app/public/converted_csv/philippines_sp_l_nodes_16918.csv > /app/public/converted_csv/philippines_sp_l_nodes_16918.csv_sorted
[CMD] [2019-10-15 11:03:12] /usr/bin/sort /app/public/converted_csv/philippines_sp_l_occurrences_16919.csv > /app/public/converted_csv/philippines_sp_l_occurrences_16919.csv_sorted
[CMD] [2019-10-15 11:03:12] /usr/bin/sort /app/public/converted_csv/philippines_sp_l_measurements_16920.csv > /app/public/converted_csv/philippines_sp_l_measurements_16920.csv_sorted
[STOP] [2019-10-15 11:03:12] convert_to_csv
[START] [2019-10-15 11:03:12] calculate_delta
[CMD] [2019-10-15 11:03:12] echo "0a" > /app/public/diff/philippines_sp_l_refs_16917.diff
[CMD] [2019-10-15 11:03:13] tail -n +1 /app/public/converted_csv/philippines_sp_l_refs_16917.csv >> /app/public/diff/philippines_sp_l_refs_16917.diff
[CMD] [2019-10-15 11:03:13] echo "." >> /app/public/diff/philippines_sp_l_refs_16917.diff
[CMD] [2019-10-15 11:03:13] echo "0a" > /app/public/diff/philippines_sp_l_nodes_16918.diff
[CMD] [2019-10-15 11:03:14] tail -n +1 /app/public/converted_csv/philippines_sp_l_nodes_16918.csv >> /app/public/diff/philippines_sp_l_nodes_16918.diff
[CMD] [2019-10-15 11:03:14] echo "." >> /app/public/diff/philippines_sp_l_nodes_16918.diff
[CMD] [2019-10-15 11:03:14] echo "0a" > /app/public/diff/philippines_sp_l_occurrences_16919.diff
[CMD] [2019-10-15 11:03:14] tail -n +1 /app/public/converted_csv/philippines_sp_l_occurrences_16919.csv >> /app/public/diff/philippines_sp_l_occurrences_16919.diff
[CMD] [2019-10-15 11:03:15] echo "." >> /app/public/diff/philippines_sp_l_occurrences_16919.diff
[CMD] [2019-10-15 11:03:15] echo "0a" > /app/public/diff/philippines_sp_l_measurements_16920.diff
[CMD] [2019-10-15 11:03:15] tail -n +1 /app/public/converted_csv/philippines_sp_l_measurements_16920.csv >> /app/public/diff/philippines_sp_l_measurements_16920.diff
[CMD] [2019-10-15 11:03:16] echo "." >> /app/public/diff/philippines_sp_l_measurements_16920.diff
[STOP] [2019-10-15 11:03:16] calculate_delta
[START] [2019-10-15 11:03:16] parse_diff_and_store
[INFO] [2019-10-15 11:03:16] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 11:03:16] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-15 11:03:24] Filtered Scientific Name `Ranina  ranina` to `Ranina ranina`
[INFO] [2019-10-15 11:03:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 11:03:35] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 11:06:06] Storing 2 References
[INFO] [2019-10-15 11:06:06] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 11:06:06] Average Time: 0.0
[INFO] [2019-10-15 11:06:06] Total Time: 1s
[INFO] [2019-10-15 11:06:06] Storing 37456 ScientificNames
[INFO] [2019-10-15 11:06:06] Processing group of 37456 in 38 groups of 1000
[INFO] [2019-10-15 11:06:21] Average Time: 0.394
[INFO] [2019-10-15 11:06:21] Total Time: 16s
[INFO] [2019-10-15 11:06:21] last 3 / first 3: 0.74
[INFO] [2019-10-15 11:06:21] Std.Dev: 0.11401754250991379; Max: 0.8
[INFO] [2019-10-15 11:06:21] Storing 37456 Nodes
[INFO] [2019-10-15 11:06:21] Processing group of 37456 in 38 groups of 1000
[INFO] [2019-10-15 11:06:33] Average Time: 0.298
[INFO] [2019-10-15 11:06:33] Total Time: 12s
[INFO] [2019-10-15 11:06:33] last 3 / first 3: 0.96
[INFO] [2019-10-15 11:06:33] Std.Dev: 0.044721359549995794; Max: 0.39
[INFO] [2019-10-15 11:06:33] Storing 26144 Occurrences
[INFO] [2019-10-15 11:06:33] Processing group of 26144 in 27 groups of 1000
[INFO] [2019-10-15 11:06:36] Average Time: 0.108
[INFO] [2019-10-15 11:06:36] Total Time: 4s
[INFO] [2019-10-15 11:06:36] last 3 / first 3: 0.77
[INFO] [2019-10-15 11:06:36] Std.Dev: 0.03162277660168379; Max: 0.24
[INFO] [2019-10-15 11:06:36] Storing 52288 TraitsReferences
[INFO] [2019-10-15 11:06:36] Processing group of 52288 in 53 groups of 1000
[INFO] [2019-10-15 11:06:42] Average Time: 0.104
[INFO] [2019-10-15 11:06:42] Total Time: 6s
[INFO] [2019-10-15 11:06:42] last 3 / first 3: 0.38
[INFO] [2019-10-15 11:06:42] Std.Dev: 0.130384048104053; Max: 1.0
[INFO] [2019-10-15 11:06:42] Storing 52288 Traits
[INFO] [2019-10-15 11:06:42] Processing group of 52288 in 53 groups of 1000
[INFO] [2019-10-15 11:07:00] Average Time: 0.346
[INFO] [2019-10-15 11:07:00] Total Time: 19s
[INFO] [2019-10-15 11:07:00] last 3 / first 3: 1.79
[INFO] [2019-10-15 11:07:00] Std.Dev: 0.15165750888103102; Max: 1.26
[INFO] [2019-10-15 11:07:00] Storing 52245 MetaTraits
[INFO] [2019-10-15 11:07:00] Processing group of 52245 in 53 groups of 1000
[INFO] [2019-10-15 11:07:08] Average Time: 0.15
[INFO] [2019-10-15 11:07:08] Total Time: 9s
[INFO] [2019-10-15 11:07:08] last 3 / first 3: 0.84
[INFO] [2019-10-15 11:07:08] Std.Dev: 0.11832159566199232; Max: 0.9
[STOP] [2019-10-15 11:07:08] parse_diff_and_store
[START] [2019-10-15 11:07:08] resolve_keys
[INFO] [2019-10-15 11:08:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 11:08:55] traits to occurrences...
[INFO] [2019-10-15 11:09:02] traits to nodes (through occurrences)...
[INFO] [2019-10-15 11:09:02] Traits to sex term...
[INFO] [2019-10-15 11:09:09] Traits to lifestage term...
[INFO] [2019-10-15 11:09:15] MetaTraits to traits...
[INFO] [2019-10-15 11:09:18] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 11:09:26] Assocs to occurrences...
[INFO] [2019-10-15 11:09:26] Assocs to nodes...
[INFO] [2019-10-15 11:09:26] Assoc to sex term...
[INFO] [2019-10-15 11:09:26] Assoc to lifestage term...
[STOP] [2019-10-15 11:09:26] resolve_keys
[START] [2019-10-15 11:09:26] hold_for_later_1
[STOP] [2019-10-15 11:09:26] hold_for_later_1
[START] [2019-10-15 11:09:26] hold_for_later_2
[STOP] [2019-10-15 11:09:26] hold_for_later_2
[START] [2019-10-15 11:09:26] resolve_missing_parents
[STOP] [2019-10-15 11:10:25] resolve_missing_parents
[START] [2019-10-15 11:10:25] rebuild_nodes
[START] [2019-10-15 11:10:25] Flattener#flatten
[START] [2019-10-15 11:10:25] Flattener#study_resource
[START] [2019-10-15 11:10:25] Flattener#build_ancestry
[STOP] [2019-10-15 11:10:32] Flattener#build_ancestry
[INFO] [2019-10-15 11:10:32] 37456 ancestry keys
[START] [2019-10-15 11:10:32] build_node_ancestors
[INFO] [2019-10-15 11:10:32] old ancestors deleted.
[STOP] [2019-10-15 11:11:04] build_node_ancestors
[START] [2019-10-15 11:11:05] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 11:11:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 11:11:10] Flattener#flatten
[STOP] [2019-10-15 11:11:10] rebuild_nodes
[START] [2019-10-15 11:11:10] resolve_missing_media_owners
[STOP] [2019-10-15 11:11:10] resolve_missing_media_owners
[START] [2019-10-15 11:11:10] sanitize_media_verbatims
[STOP] [2019-10-15 11:11:10] sanitize_media_verbatims
[START] [2019-10-15 11:11:10] queue_downloads
[STOP] [2019-10-15 11:11:10] queue_downloads
[START] [2019-10-15 11:11:10] parse_names
[WARN] [2019-10-15 11:11:10] I see 37456 names which still need to be parsed.
[STOP] [2019-10-15 11:11:39] parse_names
[START] [2019-10-15 11:11:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 11:11:39] denormalize_canonical_names_to_nodes
[START] [2019-10-15 11:11:39] match_nodes
[START] [2019-10-15 11:11:39] map_all_nodes_to_pages
[STOP] [2019-10-15 12:07:02] map_all_nodes_to_pages
[INFO] [2019-10-15 12:07:02] 2814 Unmatched nodes (of 37456)! That's too many to output. First 10: Gekko gekko (#51615433); Parvoscincus curtirostris (#51593456); Parvoscincus knollmanae (#51605800); Sphenomorphus jagori (#51588657); Sphenomorphus decipiens (#51589138); Brachymeles dalawangdaliri (#51601109); Calamaria gervaisi (#51588937); Lycodon mccroryi (#51622393); Rhabdophis conspicillata (#51623560); Calliophis calligaster (#51595696)
[START] [2019-10-15 12:07:02] update_nodes
[STOP] [2019-10-15 12:07:15] update_nodes
[STOP] [2019-10-15 12:07:16] match_nodes
[START] [2019-10-15 12:07:16] reindex_search
[STOP] [2019-10-15 12:08:52] reindex_search
[START] [2019-10-15 12:08:52] normalize_units
[STOP] [2019-10-15 12:08:52] normalize_units
[START] [2019-10-15 12:08:52] calculate_statistics
[STOP] [2019-10-15 12:08:52] calculate_statistics
[START] [2019-10-15 12:08:52] complete_harvest_instance
[START] [2019-10-15 12:08:52] overall_tsv_creation
[INFO] [2019-10-15 12:08:52] Processing group of 37456 in 4 batches of 10000
[INFO] [2019-10-15 12:10:21] 5942 Traits (unfiltered)...
[INFO] [2019-10-15 12:10:35] 5942 Traits (filtered)...
[INFO] [2019-10-15 12:10:35] 0 Associations (filtered)...
[INFO] [2019-10-15 12:11:25] 29708 metadata added.
[INFO] [2019-10-15 12:11:25] 0 metadata added.
[INFO] [2019-10-15 12:13:01] 6875 Traits (unfiltered)...
[INFO] [2019-10-15 12:13:15] 6875 Traits (filtered)...
[INFO] [2019-10-15 12:13:15] 0 Associations (filtered)...
[INFO] [2019-10-15 12:14:09] 34368 metadata added.
[INFO] [2019-10-15 12:14:09] 0 metadata added.
[INFO] [2019-10-15 12:15:48] 7482 Traits (unfiltered)...
[INFO] [2019-10-15 12:16:02] 7482 Traits (filtered)...
[INFO] [2019-10-15 12:16:02] 0 Associations (filtered)...
[INFO] [2019-10-15 12:16:57] 37394 metadata added.
[INFO] [2019-10-15 12:16:57] 0 metadata added.
[INFO] [2019-10-15 12:18:19] 5845 Traits (unfiltered)...
[INFO] [2019-10-15 12:18:33] 5845 Traits (filtered)...
[INFO] [2019-10-15 12:18:33] 0 Associations (filtered)...
[INFO] [2019-10-15 12:19:22] 29207 metadata added.
[INFO] [2019-10-15 12:19:22] 0 metadata added.
[INFO] [2019-10-15 12:19:22] Average Time: 130.63
[INFO] [2019-10-15 12:19:22] Total Time: 10m31s
[STOP] [2019-10-15 12:19:22] overall_tsv_creation
[INFO] [2019-10-15 12:19:22] Done. Check your files:
[INFO] [2019-10-15 12:19:23] (37456 lines) /app/public/data/philippines_sp_l/publish_nodes.tsv
[INFO] [2019-10-15 12:19:23] (208003 lines) /app/public/data/philippines_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-15 12:19:23] (37456 lines) /app/public/data/philippines_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-15 12:19:24] (26145 lines) /app/public/data/philippines_sp_l/publish_traits.tsv
[INFO] [2019-10-15 12:19:24] (130678 lines) /app/public/data/philippines_sp_l/publish_metadata.tsv
[STOP] [2019-10-15 12:19:24] complete_harvest_instance
[START] [2019-10-15 12:19:24] completed
[STOP] [2019-10-15 12:19:24] completed
[STOP] [2019-10-15 12:19:24] logged process, took 4578.15

Latest Process