Harvest for Flores Sea Species List Created 23 Dec 02:02

Stage: completed
Fetched: 23 Dec 02:02
Validated: 23 Dec 02:02
Deltas Created 23 Dec 02:02
Units Normalized: 23 Dec 02:17
Ancestry Built: 23 Dec 02:03
Nodes Matched: 23 Dec 02:17
Names Parsed: 23 Dec 02:03
New Models Stored: 23 Dec 02:02
Indexed: 23 Dec 02:17
Completed: 23 Dec 02:19
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 02:02:21 -0500 by logger.rb/56815
[START] [2019-12-23 02:02:21] logged process
[START] [2019-12-23 02:02:21] create_harvest_instance
[STOP] [2019-12-23 02:02:22] create_harvest_instance
[START] [2019-12-23 02:02:22] fetch_files
[STOP] [2019-12-23 02:02:22] fetch_files
[START] [2019-12-23 02:02:22] validate_each_file
[STOP] [2019-12-23 02:02:23] validate_each_file
[START] [2019-12-23 02:02:23] convert_to_csv
[CMD] [2019-12-23 02:02:23] /usr/bin/sort /app/public/converted_csv/flores_sea_sp_li_refs_19234.csv > /app/public/converted_csv/flores_sea_sp_li_refs_19234.csv_sorted
[CMD] [2019-12-23 02:02:23] /usr/bin/sort /app/public/converted_csv/flores_sea_sp_li_nodes_19235.csv > /app/public/converted_csv/flores_sea_sp_li_nodes_19235.csv_sorted
[CMD] [2019-12-23 02:02:23] /usr/bin/sort /app/public/converted_csv/flores_sea_sp_li_occurrences_19236.csv > /app/public/converted_csv/flores_sea_sp_li_occurrences_19236.csv_sorted
[CMD] [2019-12-23 02:02:23] /usr/bin/sort /app/public/converted_csv/flores_sea_sp_li_measurements_19237.csv > /app/public/converted_csv/flores_sea_sp_li_measurements_19237.csv_sorted
[STOP] [2019-12-23 02:02:23] convert_to_csv
[START] [2019-12-23 02:02:23] calculate_delta
[CMD] [2019-12-23 02:02:23] echo "0a" > /app/public/diff/flores_sea_sp_li_refs_19234.diff
[CMD] [2019-12-23 02:02:23] tail -n +1 /app/public/converted_csv/flores_sea_sp_li_refs_19234.csv >> /app/public/diff/flores_sea_sp_li_refs_19234.diff
[CMD] [2019-12-23 02:02:24] echo "." >> /app/public/diff/flores_sea_sp_li_refs_19234.diff
[CMD] [2019-12-23 02:02:24] echo "0a" > /app/public/diff/flores_sea_sp_li_nodes_19235.diff
[CMD] [2019-12-23 02:02:24] tail -n +1 /app/public/converted_csv/flores_sea_sp_li_nodes_19235.csv >> /app/public/diff/flores_sea_sp_li_nodes_19235.diff
[CMD] [2019-12-23 02:02:24] echo "." >> /app/public/diff/flores_sea_sp_li_nodes_19235.diff
[CMD] [2019-12-23 02:02:24] echo "0a" > /app/public/diff/flores_sea_sp_li_occurrences_19236.diff
[CMD] [2019-12-23 02:02:24] tail -n +1 /app/public/converted_csv/flores_sea_sp_li_occurrences_19236.csv >> /app/public/diff/flores_sea_sp_li_occurrences_19236.diff
[CMD] [2019-12-23 02:02:24] echo "." >> /app/public/diff/flores_sea_sp_li_occurrences_19236.diff
[CMD] [2019-12-23 02:02:24] echo "0a" > /app/public/diff/flores_sea_sp_li_measurements_19237.diff
[CMD] [2019-12-23 02:02:24] tail -n +1 /app/public/converted_csv/flores_sea_sp_li_measurements_19237.csv >> /app/public/diff/flores_sea_sp_li_measurements_19237.diff
[CMD] [2019-12-23 02:02:24] echo "." >> /app/public/diff/flores_sea_sp_li_measurements_19237.diff
[STOP] [2019-12-23 02:02:24] calculate_delta
[START] [2019-12-23 02:02:24] parse_diff_and_store
[INFO] [2019-12-23 02:02:24] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 02:02:24] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 02:02:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 02:02:26] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 02:02:36] Storing 2 References
[INFO] [2019-12-23 02:02:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 02:02:36] Average Time: 0.0
[INFO] [2019-12-23 02:02:36] Total Time: 1s
[INFO] [2019-12-23 02:02:36] Storing 3461 ScientificNames
[INFO] [2019-12-23 02:02:36] Processing group of 3461 in 4 groups of 1000
[INFO] [2019-12-23 02:02:38] Average Time: 0.355
[INFO] [2019-12-23 02:02:38] Total Time: 2s
[INFO] [2019-12-23 02:02:38] Storing 3461 Nodes
[INFO] [2019-12-23 02:02:38] Processing group of 3461 in 4 groups of 1000
[INFO] [2019-12-23 02:02:39] Average Time: 0.258
[INFO] [2019-12-23 02:02:39] Total Time: 2s
[INFO] [2019-12-23 02:02:39] Storing 1853 Occurrences
[INFO] [2019-12-23 02:02:39] Processing group of 1853 in 2 groups of 1000
[INFO] [2019-12-23 02:02:39] Average Time: 0.16
[INFO] [2019-12-23 02:02:39] Total Time: 1s
[INFO] [2019-12-23 02:02:39] Storing 3706 TraitsReferences
[INFO] [2019-12-23 02:02:39] Processing group of 3706 in 4 groups of 1000
[INFO] [2019-12-23 02:02:40] Average Time: 0.105
[INFO] [2019-12-23 02:02:40] Total Time: 1s
[INFO] [2019-12-23 02:02:40] Storing 3706 Traits
[INFO] [2019-12-23 02:02:40] Processing group of 3706 in 4 groups of 1000
[INFO] [2019-12-23 02:02:41] Average Time: 0.343
[INFO] [2019-12-23 02:02:41] Total Time: 2s
[INFO] [2019-12-23 02:02:41] Storing 3706 MetaTraits
[INFO] [2019-12-23 02:02:41] Processing group of 3706 in 4 groups of 1000
[INFO] [2019-12-23 02:02:42] Average Time: 0.128
[INFO] [2019-12-23 02:02:42] Total Time: 1s
[STOP] [2019-12-23 02:02:42] parse_diff_and_store
[START] [2019-12-23 02:02:42] resolve_keys
[INFO] [2019-12-23 02:02:58] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 02:03:00] traits to occurrences...
[INFO] [2019-12-23 02:03:00] traits to nodes (through occurrences)...
[INFO] [2019-12-23 02:03:01] Traits to sex term...
[INFO] [2019-12-23 02:03:01] Traits to lifestage term...
[INFO] [2019-12-23 02:03:02] MetaTraits to traits...
[INFO] [2019-12-23 02:03:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 02:03:03] Assocs to occurrences...
[INFO] [2019-12-23 02:03:03] Assocs to nodes...
[INFO] [2019-12-23 02:03:03] Assoc to sex term...
[INFO] [2019-12-23 02:03:03] Assoc to lifestage term...
[STOP] [2019-12-23 02:03:03] resolve_keys
[START] [2019-12-23 02:03:03] hold_for_later_1
[STOP] [2019-12-23 02:03:03] hold_for_later_1
[START] [2019-12-23 02:03:03] hold_for_later_2
[STOP] [2019-12-23 02:03:03] hold_for_later_2
[START] [2019-12-23 02:03:03] resolve_missing_parents
[STOP] [2019-12-23 02:03:09] resolve_missing_parents
[START] [2019-12-23 02:03:09] rebuild_nodes
[START] [2019-12-23 02:03:09] Flattener#flatten
[START] [2019-12-23 02:03:09] Flattener#study_resource
[START] [2019-12-23 02:03:09] Flattener#build_ancestry
[STOP] [2019-12-23 02:03:10] Flattener#build_ancestry
[INFO] [2019-12-23 02:03:10] 3461 ancestry keys
[START] [2019-12-23 02:03:10] build_node_ancestors
[INFO] [2019-12-23 02:03:10] old ancestors deleted.
[STOP] [2019-12-23 02:03:12] build_node_ancestors
[START] [2019-12-23 02:03:13] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 02:03:13] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 02:03:13] Flattener#flatten
[STOP] [2019-12-23 02:03:13] rebuild_nodes
[START] [2019-12-23 02:03:13] resolve_missing_media_owners
[STOP] [2019-12-23 02:03:13] resolve_missing_media_owners
[START] [2019-12-23 02:03:13] sanitize_media_verbatims
[STOP] [2019-12-23 02:03:13] sanitize_media_verbatims
[START] [2019-12-23 02:03:13] queue_downloads
[STOP] [2019-12-23 02:03:13] queue_downloads
[START] [2019-12-23 02:03:13] parse_names
[WARN] [2019-12-23 02:03:13] I see 3461 names which still need to be parsed.
[STOP] [2019-12-23 02:03:17] parse_names
[START] [2019-12-23 02:03:17] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 02:03:17] denormalize_canonical_names_to_nodes
[START] [2019-12-23 02:03:17] match_nodes
[START] [2019-12-23 02:03:17] map_all_nodes_to_pages
[STOP] [2019-12-23 02:17:45] map_all_nodes_to_pages
[INFO] [2019-12-23 02:17:45] 110 Unmatched nodes (of 3461)! That's too many to output. First 10: Acropora lutkeni (#61877160); Caulastrea (#61878168); Barabattoia (#61878541); Pectiniidae (#61876144); Acrhelia (#61876762); Paraclavarina (#61876342); Mussidae (#61876346); Symphyllia (#61876345); Trachyphylliidae (#61878494); Actinodendronidae (#61876712)
[START] [2019-12-23 02:17:45] update_nodes
[STOP] [2019-12-23 02:17:46] update_nodes
[STOP] [2019-12-23 02:17:46] match_nodes
[START] [2019-12-23 02:17:46] reindex_search
[STOP] [2019-12-23 02:17:55] reindex_search
[START] [2019-12-23 02:17:55] normalize_units
[STOP] [2019-12-23 02:17:55] normalize_units
[START] [2019-12-23 02:17:55] calculate_statistics
[STOP] [2019-12-23 02:17:56] calculate_statistics
[START] [2019-12-23 02:17:56] complete_harvest_instance
[START] [2019-12-23 02:17:56] overall_tsv_creation
[INFO] [2019-12-23 02:17:56] Processing group of 3461 in 1 batches of 10000
[INFO] [2019-12-23 02:18:57] 1853 Traits (unfiltered)...
[INFO] [2019-12-23 02:19:11] 1853 Traits (filtered)...
[INFO] [2019-12-23 02:19:11] 0 Associations (filtered)...
[INFO] [2019-12-23 02:19:52] 9265 metadata added.
[INFO] [2019-12-23 02:19:52] 0 metadata added.
[INFO] [2019-12-23 02:19:52] Average Time: 91.81
[INFO] [2019-12-23 02:19:52] Total Time: 1m57s
[STOP] [2019-12-23 02:19:52] overall_tsv_creation
[INFO] [2019-12-23 02:19:52] Done. Check your files:
[INFO] [2019-12-23 02:19:52] (3461 lines) /app/public/data/flores_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 02:19:52] (18009 lines) /app/public/data/flores_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 02:19:52] (3461 lines) /app/public/data/flores_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 02:19:52] (1854 lines) /app/public/data/flores_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-23 02:19:52] (9266 lines) /app/public/data/flores_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 02:19:53] complete_harvest_instance
[START] [2019-12-23 02:19:53] completed
[STOP] [2019-12-23 02:19:53] completed
[STOP] [2019-12-23 02:19:53] logged process, took 1051.66
Latest Process

23 Dec 02:02 EXITED currently processing 0