Stage:
completed
Fetched:
14 Oct 05:07
Validated:
14 Oct 05:07
Deltas Created
14 Oct 05:07
Units Normalized:
14 Oct 05:13
Ancestry Built:
14 Oct 05:08
Nodes Matched:
14 Oct 05:13
Names Parsed:
14 Oct 05:08
New Models Stored:
14 Oct 05:08
Indexed:
14 Oct 05:13
Completed:
14 Oct 05:15
Time to Harvest:
less than a minute
Harvesting Log
(139 lines)
# Logfile created on 2019-10-14 05:07:47 -0400 by logger.rb/56815
[START] [2019-10-14 05:07:47] logged process
[START] [2019-10-14 05:07:47] create_harvest_instance
[STOP] [2019-10-14 05:07:48] create_harvest_instance
[START] [2019-10-14 05:07:48] fetch_files
[STOP] [2019-10-14 05:07:48] fetch_files
[START] [2019-10-14 05:07:48] validate_each_file
[STOP] [2019-10-14 05:07:48] validate_each_file
[START] [2019-10-14 05:07:48] convert_to_csv
[CMD] [2019-10-14 05:07:48] /usr/bin/sort /app/public/converted_csv/marshall_islands_refs_16539.csv > /app/public/converted_csv/marshall_islands_refs_16539.csv_sorted
[CMD] [2019-10-14 05:07:48] /usr/bin/sort /app/public/converted_csv/marshall_islands_nodes_16540.csv > /app/public/converted_csv/marshall_islands_nodes_16540.csv_sorted
[CMD] [2019-10-14 05:07:48] /usr/bin/sort /app/public/converted_csv/marshall_islands_occurrences_16541.csv > /app/public/converted_csv/marshall_islands_occurrences_16541.csv_sorted
[CMD] [2019-10-14 05:07:48] /usr/bin/sort /app/public/converted_csv/marshall_islands_measurements_16542.csv > /app/public/converted_csv/marshall_islands_measurements_16542.csv_sorted
[STOP] [2019-10-14 05:07:49] convert_to_csv
[START] [2019-10-14 05:07:49] calculate_delta
[CMD] [2019-10-14 05:07:49] echo "0a" > /app/public/diff/marshall_islands_refs_16539.diff
[CMD] [2019-10-14 05:07:49] tail -n +1 /app/public/converted_csv/marshall_islands_refs_16539.csv >> /app/public/diff/marshall_islands_refs_16539.diff
[CMD] [2019-10-14 05:07:49] echo "." >> /app/public/diff/marshall_islands_refs_16539.diff
[CMD] [2019-10-14 05:07:49] echo "0a" > /app/public/diff/marshall_islands_nodes_16540.diff
[CMD] [2019-10-14 05:07:49] tail -n +1 /app/public/converted_csv/marshall_islands_nodes_16540.csv >> /app/public/diff/marshall_islands_nodes_16540.diff
[CMD] [2019-10-14 05:07:49] echo "." >> /app/public/diff/marshall_islands_nodes_16540.diff
[CMD] [2019-10-14 05:07:49] echo "0a" > /app/public/diff/marshall_islands_occurrences_16541.diff
[CMD] [2019-10-14 05:07:49] tail -n +1 /app/public/converted_csv/marshall_islands_occurrences_16541.csv >> /app/public/diff/marshall_islands_occurrences_16541.diff
[CMD] [2019-10-14 05:07:49] echo "." >> /app/public/diff/marshall_islands_occurrences_16541.diff
[CMD] [2019-10-14 05:07:49] echo "0a" > /app/public/diff/marshall_islands_measurements_16542.diff
[CMD] [2019-10-14 05:07:50] tail -n +1 /app/public/converted_csv/marshall_islands_measurements_16542.csv >> /app/public/diff/marshall_islands_measurements_16542.diff
[CMD] [2019-10-14 05:07:50] echo "." >> /app/public/diff/marshall_islands_measurements_16542.diff
[STOP] [2019-10-14 05:07:50] calculate_delta
[START] [2019-10-14 05:07:50] parse_diff_and_store
[INFO] [2019-10-14 05:07:50] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 05:07:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 05:07:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 05:07:52] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 05:08:09] Storing 2 References
[INFO] [2019-10-14 05:08:09] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 05:08:09] Average Time: 0.0
[INFO] [2019-10-14 05:08:09] Total Time: 1s
[INFO] [2019-10-14 05:08:09] Storing 4832 ScientificNames
[INFO] [2019-10-14 05:08:09] Processing group of 4832 in 5 groups of 1000
[INFO] [2019-10-14 05:08:11] Average Time: 0.374
[INFO] [2019-10-14 05:08:11] Total Time: 3s
[INFO] [2019-10-14 05:08:11] Storing 4832 Nodes
[INFO] [2019-10-14 05:08:11] Processing group of 4832 in 5 groups of 1000
[INFO] [2019-10-14 05:08:12] Average Time: 0.326
[INFO] [2019-10-14 05:08:12] Total Time: 2s
[INFO] [2019-10-14 05:08:12] Storing 2410 Occurrences
[INFO] [2019-10-14 05:08:12] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-14 05:08:13] Average Time: 0.087
[INFO] [2019-10-14 05:08:13] Total Time: 1s
[INFO] [2019-10-14 05:08:13] Storing 5590 TraitsReferences
[INFO] [2019-10-14 05:08:13] Processing group of 5590 in 6 groups of 1000
[INFO] [2019-10-14 05:08:13] Average Time: 0.08
[INFO] [2019-10-14 05:08:13] Total Time: 1s
[INFO] [2019-10-14 05:08:13] Storing 5589 Traits
[INFO] [2019-10-14 05:08:13] Processing group of 5589 in 6 groups of 1000
[INFO] [2019-10-14 05:08:15] Average Time: 0.297
[INFO] [2019-10-14 05:08:15] Total Time: 2s
[INFO] [2019-10-14 05:08:15] Storing 5586 MetaTraits
[INFO] [2019-10-14 05:08:15] Processing group of 5586 in 6 groups of 1000
[INFO] [2019-10-14 05:08:16] Average Time: 0.122
[INFO] [2019-10-14 05:08:16] Total Time: 1s
[STOP] [2019-10-14 05:08:16] parse_diff_and_store
[START] [2019-10-14 05:08:16] resolve_keys
[INFO] [2019-10-14 05:08:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 05:08:38] traits to occurrences...
[INFO] [2019-10-14 05:08:39] traits to nodes (through occurrences)...
[INFO] [2019-10-14 05:08:39] Traits to sex term...
[INFO] [2019-10-14 05:08:40] Traits to lifestage term...
[INFO] [2019-10-14 05:08:41] MetaTraits to traits...
[INFO] [2019-10-14 05:08:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 05:08:42] Assocs to occurrences...
[INFO] [2019-10-14 05:08:42] Assocs to nodes...
[INFO] [2019-10-14 05:08:42] Assoc to sex term...
[INFO] [2019-10-14 05:08:43] Assoc to lifestage term...
[STOP] [2019-10-14 05:08:43] resolve_keys
[START] [2019-10-14 05:08:43] hold_for_later_1
[STOP] [2019-10-14 05:08:43] hold_for_later_1
[START] [2019-10-14 05:08:43] hold_for_later_2
[STOP] [2019-10-14 05:08:43] hold_for_later_2
[START] [2019-10-14 05:08:43] resolve_missing_parents
[STOP] [2019-10-14 05:08:52] resolve_missing_parents
[START] [2019-10-14 05:08:52] rebuild_nodes
[START] [2019-10-14 05:08:52] Flattener#flatten
[START] [2019-10-14 05:08:52] Flattener#study_resource
[START] [2019-10-14 05:08:52] Flattener#build_ancestry
[STOP] [2019-10-14 05:08:52] Flattener#build_ancestry
[INFO] [2019-10-14 05:08:52] 4832 ancestry keys
[START] [2019-10-14 05:08:52] build_node_ancestors
[INFO] [2019-10-14 05:08:52] old ancestors deleted.
[STOP] [2019-10-14 05:08:53] build_node_ancestors
[START] [2019-10-14 05:08:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:08:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:08:55] Flattener#flatten
[STOP] [2019-10-14 05:08:55] rebuild_nodes
[START] [2019-10-14 05:08:55] resolve_missing_media_owners
[STOP] [2019-10-14 05:08:55] resolve_missing_media_owners
[START] [2019-10-14 05:08:55] sanitize_media_verbatims
[STOP] [2019-10-14 05:08:55] sanitize_media_verbatims
[START] [2019-10-14 05:08:55] queue_downloads
[STOP] [2019-10-14 05:08:55] queue_downloads
[START] [2019-10-14 05:08:55] parse_names
[WARN] [2019-10-14 05:08:55] I see 4832 names which still need to be parsed.
[STOP] [2019-10-14 05:08:59] parse_names
[START] [2019-10-14 05:08:59] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 05:08:59] denormalize_canonical_names_to_nodes
[START] [2019-10-14 05:08:59] match_nodes
[START] [2019-10-14 05:08:59] map_all_nodes_to_pages
[STOP] [2019-10-14 05:13:43] map_all_nodes_to_pages
[INFO] [2019-10-14 05:13:43] 384 Unmatched nodes (of 4832)! That's too many to output. First 10: Granuloreticulosea (#50657190); Foraminiferida (#50657189); Globoquadrina venezuelana (#50657206); Globoquadrina larmeui (#50657267); Globoquadrina tripartita (#50657317); Globoquadrina conglomerata (#50659600); Globorotalia merotumida (#50657324); Fohsella (#50657243); Fohsella peripheroronda (#50657242); Fohsella peripheroacuta (#50657263)
[START] [2019-10-14 05:13:43] update_nodes
[STOP] [2019-10-14 05:13:45] update_nodes
[STOP] [2019-10-14 05:13:45] match_nodes
[START] [2019-10-14 05:13:45] reindex_search
[STOP] [2019-10-14 05:13:55] reindex_search
[START] [2019-10-14 05:13:55] normalize_units
[STOP] [2019-10-14 05:13:55] normalize_units
[START] [2019-10-14 05:13:55] calculate_statistics
[STOP] [2019-10-14 05:13:55] calculate_statistics
[START] [2019-10-14 05:13:55] complete_harvest_instance
[START] [2019-10-14 05:13:55] overall_tsv_creation
[INFO] [2019-10-14 05:13:55] Processing group of 4832 in 1 batches of 10000
[INFO] [2019-10-14 05:15:00] 2410 Traits (unfiltered)...
[INFO] [2019-10-14 05:15:14] 2410 Traits (filtered)...
[INFO] [2019-10-14 05:15:14] 0 Associations (filtered)...
[INFO] [2019-10-14 05:15:56] 12047 metadata added.
[INFO] [2019-10-14 05:15:56] 0 metadata added.
[INFO] [2019-10-14 05:15:56] Average Time: 97.27
[INFO] [2019-10-14 05:15:56] Total Time: 2m1s
[STOP] [2019-10-14 05:15:56] overall_tsv_creation
[INFO] [2019-10-14 05:15:56] Done. Check your files:
[INFO] [2019-10-14 05:15:56] (4832 lines) /app/public/data/marshall_islands/publish_nodes.tsv
[INFO] [2019-10-14 05:15:56] (15649 lines) /app/public/data/marshall_islands/publish_node_ancestors.tsv
[INFO] [2019-10-14 05:15:56] (4832 lines) /app/public/data/marshall_islands/publish_scientific_names.tsv
[INFO] [2019-10-14 05:15:56] (2411 lines) /app/public/data/marshall_islands/publish_traits.tsv
[INFO] [2019-10-14 05:15:56] (12048 lines) /app/public/data/marshall_islands/publish_metadata.tsv
[STOP] [2019-10-14 05:15:57] complete_harvest_instance
[START] [2019-10-14 05:15:57] completed
[STOP] [2019-10-14 05:15:57] completed
[STOP] [2019-10-14 05:15:57] logged process, took 489.52
Latest Process