Harvest for El Salvador Species List Created 12 Oct 16:49

Stage: completed
Fetched: 12 Oct 16:49
Validated: 12 Oct 16:49
Deltas Created 12 Oct 16:49
Units Normalized: 12 Oct 17:02
Ancestry Built: 12 Oct 16:52
Nodes Matched: 12 Oct 17:02
Names Parsed: 12 Oct 16:52
New Models Stored: 12 Oct 16:50
Indexed: 12 Oct 17:02
Completed: 12 Oct 17:05
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-12 16:49:41 -0400 by logger.rb/56815
[START] [2019-10-12 16:49:41] logged process
[START] [2019-10-12 16:49:41] create_harvest_instance
[STOP] [2019-10-12 16:49:42] create_harvest_instance
[START] [2019-10-12 16:49:42] fetch_files
[STOP] [2019-10-12 16:49:42] fetch_files
[START] [2019-10-12 16:49:42] validate_each_file
[STOP] [2019-10-12 16:49:43] validate_each_file
[START] [2019-10-12 16:49:43] convert_to_csv
[CMD] [2019-10-12 16:49:43] /usr/bin/sort /app/public/converted_csv/el_salvador_sp_l_refs_15651.csv > /app/public/converted_csv/el_salvador_sp_l_refs_15651.csv_sorted
[CMD] [2019-10-12 16:49:43] /usr/bin/sort /app/public/converted_csv/el_salvador_sp_l_nodes_15652.csv > /app/public/converted_csv/el_salvador_sp_l_nodes_15652.csv_sorted
[CMD] [2019-10-12 16:49:43] /usr/bin/sort /app/public/converted_csv/el_salvador_sp_l_occurrences_15653.csv > /app/public/converted_csv/el_salvador_sp_l_occurrences_15653.csv_sorted
[CMD] [2019-10-12 16:49:43] /usr/bin/sort /app/public/converted_csv/el_salvador_sp_l_measurements_15654.csv > /app/public/converted_csv/el_salvador_sp_l_measurements_15654.csv_sorted
[STOP] [2019-10-12 16:49:43] convert_to_csv
[START] [2019-10-12 16:49:43] calculate_delta
[CMD] [2019-10-12 16:49:43] echo "0a" > /app/public/diff/el_salvador_sp_l_refs_15651.diff
[CMD] [2019-10-12 16:49:43] tail -n +1 /app/public/converted_csv/el_salvador_sp_l_refs_15651.csv >> /app/public/diff/el_salvador_sp_l_refs_15651.diff
[CMD] [2019-10-12 16:49:44] echo "." >> /app/public/diff/el_salvador_sp_l_refs_15651.diff
[CMD] [2019-10-12 16:49:44] echo "0a" > /app/public/diff/el_salvador_sp_l_nodes_15652.diff
[CMD] [2019-10-12 16:49:44] tail -n +1 /app/public/converted_csv/el_salvador_sp_l_nodes_15652.csv >> /app/public/diff/el_salvador_sp_l_nodes_15652.diff
[CMD] [2019-10-12 16:49:44] echo "." >> /app/public/diff/el_salvador_sp_l_nodes_15652.diff
[CMD] [2019-10-12 16:49:44] echo "0a" > /app/public/diff/el_salvador_sp_l_occurrences_15653.diff
[CMD] [2019-10-12 16:49:44] tail -n +1 /app/public/converted_csv/el_salvador_sp_l_occurrences_15653.csv >> /app/public/diff/el_salvador_sp_l_occurrences_15653.diff
[CMD] [2019-10-12 16:49:44] echo "." >> /app/public/diff/el_salvador_sp_l_occurrences_15653.diff
[CMD] [2019-10-12 16:49:44] echo "0a" > /app/public/diff/el_salvador_sp_l_measurements_15654.diff
[CMD] [2019-10-12 16:49:44] tail -n +1 /app/public/converted_csv/el_salvador_sp_l_measurements_15654.csv >> /app/public/diff/el_salvador_sp_l_measurements_15654.diff
[CMD] [2019-10-12 16:49:44] echo "." >> /app/public/diff/el_salvador_sp_l_measurements_15654.diff
[STOP] [2019-10-12 16:49:44] calculate_delta
[START] [2019-10-12 16:49:44] parse_diff_and_store
[INFO] [2019-10-12 16:49:45] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 16:49:45] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 16:49:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 16:49:50] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 16:50:23] Storing 2 References
[INFO] [2019-10-12 16:50:23] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 16:50:23] Average Time: 0.0
[INFO] [2019-10-12 16:50:23] Total Time: 1s
[INFO] [2019-10-12 16:50:23] Storing 8908 ScientificNames
[INFO] [2019-10-12 16:50:23] Processing group of 8908 in 9 groups of 1000
[INFO] [2019-10-12 16:50:27] Average Time: 0.36
[INFO] [2019-10-12 16:50:27] Total Time: 4s
[INFO] [2019-10-12 16:50:27] last 3 / first 3: 0.82
[INFO] [2019-10-12 16:50:27] Std.Dev: 0.044721359549995794; Max: 0.47
[INFO] [2019-10-12 16:50:27] Storing 8908 Nodes
[INFO] [2019-10-12 16:50:27] Processing group of 8908 in 9 groups of 1000
[INFO] [2019-10-12 16:50:29] Average Time: 0.308
[INFO] [2019-10-12 16:50:29] Total Time: 3s
[INFO] [2019-10-12 16:50:29] last 3 / first 3: 0.98
[INFO] [2019-10-12 16:50:29] Std.Dev: 0.0; Max: 0.35
[INFO] [2019-10-12 16:50:29] Storing 5744 Occurrences
[INFO] [2019-10-12 16:50:29] Processing group of 5744 in 6 groups of 1000
[INFO] [2019-10-12 16:50:30] Average Time: 0.103
[INFO] [2019-10-12 16:50:30] Total Time: 1s
[INFO] [2019-10-12 16:50:30] Storing 11488 TraitsReferences
[INFO] [2019-10-12 16:50:30] Processing group of 11488 in 12 groups of 1000
[INFO] [2019-10-12 16:50:31] Average Time: 0.073
[INFO] [2019-10-12 16:50:31] Total Time: 1s
[INFO] [2019-10-12 16:50:31] last 3 / first 3: 0.59
[INFO] [2019-10-12 16:50:31] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-12 16:50:31] Storing 11488 Traits
[INFO] [2019-10-12 16:50:31] Processing group of 11488 in 12 groups of 1000
[INFO] [2019-10-12 16:50:35] Average Time: 0.338
[INFO] [2019-10-12 16:50:35] Total Time: 5s
[INFO] [2019-10-12 16:50:35] last 3 / first 3: 0.74
[INFO] [2019-10-12 16:50:35] Std.Dev: 0.10954451150103323; Max: 0.59
[INFO] [2019-10-12 16:50:35] Storing 11485 MetaTraits
[INFO] [2019-10-12 16:50:35] Processing group of 11485 in 12 groups of 1000
[INFO] [2019-10-12 16:50:37] Average Time: 0.121
[INFO] [2019-10-12 16:50:37] Total Time: 2s
[INFO] [2019-10-12 16:50:37] last 3 / first 3: 0.84
[INFO] [2019-10-12 16:50:37] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-12 16:50:37] parse_diff_and_store
[START] [2019-10-12 16:50:37] resolve_keys
[INFO] [2019-10-12 16:51:17] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 16:51:21] traits to occurrences...
[INFO] [2019-10-12 16:51:25] traits to nodes (through occurrences)...
[INFO] [2019-10-12 16:51:25] Traits to sex term...
[INFO] [2019-10-12 16:51:29] Traits to lifestage term...
[INFO] [2019-10-12 16:51:33] MetaTraits to traits...
[INFO] [2019-10-12 16:51:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 16:51:35] Assocs to occurrences...
[INFO] [2019-10-12 16:51:35] Assocs to nodes...
[INFO] [2019-10-12 16:51:35] Assoc to sex term...
[INFO] [2019-10-12 16:51:35] Assoc to lifestage term...
[STOP] [2019-10-12 16:51:35] resolve_keys
[START] [2019-10-12 16:51:35] hold_for_later_1
[STOP] [2019-10-12 16:51:35] hold_for_later_1
[START] [2019-10-12 16:51:35] hold_for_later_2
[STOP] [2019-10-12 16:51:35] hold_for_later_2
[START] [2019-10-12 16:51:35] resolve_missing_parents
[STOP] [2019-10-12 16:51:52] resolve_missing_parents
[START] [2019-10-12 16:51:52] rebuild_nodes
[START] [2019-10-12 16:51:52] Flattener#flatten
[START] [2019-10-12 16:51:52] Flattener#study_resource
[START] [2019-10-12 16:51:52] Flattener#build_ancestry
[STOP] [2019-10-12 16:51:52] Flattener#build_ancestry
[INFO] [2019-10-12 16:51:52] 8908 ancestry keys
[START] [2019-10-12 16:51:52] build_node_ancestors
[INFO] [2019-10-12 16:51:52] old ancestors deleted.
[STOP] [2019-10-12 16:51:56] build_node_ancestors
[START] [2019-10-12 16:52:00] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 16:52:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 16:52:01] Flattener#flatten
[STOP] [2019-10-12 16:52:01] rebuild_nodes
[START] [2019-10-12 16:52:01] resolve_missing_media_owners
[STOP] [2019-10-12 16:52:01] resolve_missing_media_owners
[START] [2019-10-12 16:52:01] sanitize_media_verbatims
[STOP] [2019-10-12 16:52:01] sanitize_media_verbatims
[START] [2019-10-12 16:52:01] queue_downloads
[STOP] [2019-10-12 16:52:01] queue_downloads
[START] [2019-10-12 16:52:01] parse_names
[WARN] [2019-10-12 16:52:01] I see 8908 names which still need to be parsed.
[STOP] [2019-10-12 16:52:09] parse_names
[START] [2019-10-12 16:52:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 16:52:09] denormalize_canonical_names_to_nodes
[START] [2019-10-12 16:52:09] match_nodes
[START] [2019-10-12 16:52:09] map_all_nodes_to_pages
[STOP] [2019-10-12 17:02:07] map_all_nodes_to_pages
[INFO] [2019-10-12 17:02:07] 455 Unmatched nodes (of 8908)! That's too many to output. First 10: Thryothorus modestus (#49531392); Thryothorus pleurostictus (#49531693); Thryothorus maculipectus (#49531801); Thryothorus rufalbus (#49532075); Thryothorus thoracicus (#49539192); Contopus borealis (#49534773); Pyrocephalus coronatus (#49535240); Basileuterus lachrymosa (#49531337); Oreothlypis peregrina (#49530651); Oreothlypis ruficapilla (#49532447)
[START] [2019-10-12 17:02:07] update_nodes
[STOP] [2019-10-12 17:02:10] update_nodes
[STOP] [2019-10-12 17:02:10] match_nodes
[START] [2019-10-12 17:02:10] reindex_search
[STOP] [2019-10-12 17:02:33] reindex_search
[START] [2019-10-12 17:02:33] normalize_units
[STOP] [2019-10-12 17:02:33] normalize_units
[START] [2019-10-12 17:02:33] calculate_statistics
[STOP] [2019-10-12 17:02:33] calculate_statistics
[START] [2019-10-12 17:02:33] complete_harvest_instance
[START] [2019-10-12 17:02:33] overall_tsv_creation
[INFO] [2019-10-12 17:02:33] Processing group of 8908 in 1 batches of 10000
[INFO] [2019-10-12 17:03:59] 5744 Traits (unfiltered)...
[INFO] [2019-10-12 17:04:13] 5744 Traits (filtered)...
[INFO] [2019-10-12 17:04:13] 0 Associations (filtered)...
[INFO] [2019-10-12 17:05:00] 28717 metadata added.
[INFO] [2019-10-12 17:05:00] 0 metadata added.
[INFO] [2019-10-12 17:05:00] Average Time: 119.9
[INFO] [2019-10-12 17:05:00] Total Time: 2m28s
[STOP] [2019-10-12 17:05:00] overall_tsv_creation
[INFO] [2019-10-12 17:05:00] Done. Check your files:
[INFO] [2019-10-12 17:05:01] (8908 lines) /app/public/data/el_salvador_sp_l/publish_nodes.tsv
[INFO] [2019-10-12 17:05:01] (48927 lines) /app/public/data/el_salvador_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-12 17:05:01] (8908 lines) /app/public/data/el_salvador_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-12 17:05:01] (5745 lines) /app/public/data/el_salvador_sp_l/publish_traits.tsv
[INFO] [2019-10-12 17:05:01] (28718 lines) /app/public/data/el_salvador_sp_l/publish_metadata.tsv
[STOP] [2019-10-12 17:05:01] complete_harvest_instance
[START] [2019-10-12 17:05:01] completed
[STOP] [2019-10-12 17:05:01] completed
[STOP] [2019-10-12 17:05:01] logged process, took 920.02
Latest Process

12 Oct 16:49 EXITED currently processing 0