Harvest for Laos Species List Created 14 Oct 01:14

Stage: completed
Fetched: 14 Oct 01:14
Validated: 14 Oct 01:14
Deltas Created 14 Oct 01:14
Units Normalized: 14 Oct 01:22
Ancestry Built: 14 Oct 01:16
Nodes Matched: 14 Oct 01:22
Names Parsed: 14 Oct 01:16
New Models Stored: 14 Oct 01:15
Indexed: 14 Oct 01:22
Completed: 14 Oct 01:24
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-14 01:14:22 -0400 by logger.rb/56815
[START] [2019-10-14 01:14:22] logged process
[START] [2019-10-14 01:14:22] create_harvest_instance
[STOP] [2019-10-14 01:14:23] create_harvest_instance
[START] [2019-10-14 01:14:23] fetch_files
[STOP] [2019-10-14 01:14:23] fetch_files
[START] [2019-10-14 01:14:23] validate_each_file
[STOP] [2019-10-14 01:14:24] validate_each_file
[START] [2019-10-14 01:14:24] convert_to_csv
[CMD] [2019-10-14 01:14:24] /usr/bin/sort /app/public/converted_csv/laos_sp_list_refs_16355.csv > /app/public/converted_csv/laos_sp_list_refs_16355.csv_sorted
[CMD] [2019-10-14 01:14:24] /usr/bin/sort /app/public/converted_csv/laos_sp_list_nodes_16356.csv > /app/public/converted_csv/laos_sp_list_nodes_16356.csv_sorted
[CMD] [2019-10-14 01:14:24] /usr/bin/sort /app/public/converted_csv/laos_sp_list_occurrences_16357.csv > /app/public/converted_csv/laos_sp_list_occurrences_16357.csv_sorted
[CMD] [2019-10-14 01:14:24] /usr/bin/sort /app/public/converted_csv/laos_sp_list_measurements_16358.csv > /app/public/converted_csv/laos_sp_list_measurements_16358.csv_sorted
[STOP] [2019-10-14 01:14:24] convert_to_csv
[START] [2019-10-14 01:14:25] calculate_delta
[CMD] [2019-10-14 01:14:25] echo "0a" > /app/public/diff/laos_sp_list_refs_16355.diff
[CMD] [2019-10-14 01:14:25] tail -n +1 /app/public/converted_csv/laos_sp_list_refs_16355.csv >> /app/public/diff/laos_sp_list_refs_16355.diff
[CMD] [2019-10-14 01:14:25] echo "." >> /app/public/diff/laos_sp_list_refs_16355.diff
[CMD] [2019-10-14 01:14:25] echo "0a" > /app/public/diff/laos_sp_list_nodes_16356.diff
[CMD] [2019-10-14 01:14:25] tail -n +1 /app/public/converted_csv/laos_sp_list_nodes_16356.csv >> /app/public/diff/laos_sp_list_nodes_16356.diff
[CMD] [2019-10-14 01:14:25] echo "." >> /app/public/diff/laos_sp_list_nodes_16356.diff
[CMD] [2019-10-14 01:14:25] echo "0a" > /app/public/diff/laos_sp_list_occurrences_16357.diff
[CMD] [2019-10-14 01:14:25] tail -n +1 /app/public/converted_csv/laos_sp_list_occurrences_16357.csv >> /app/public/diff/laos_sp_list_occurrences_16357.diff
[CMD] [2019-10-14 01:14:25] echo "." >> /app/public/diff/laos_sp_list_occurrences_16357.diff
[CMD] [2019-10-14 01:14:26] echo "0a" > /app/public/diff/laos_sp_list_measurements_16358.diff
[CMD] [2019-10-14 01:14:26] tail -n +1 /app/public/converted_csv/laos_sp_list_measurements_16358.csv >> /app/public/diff/laos_sp_list_measurements_16358.diff
[CMD] [2019-10-14 01:14:26] echo "." >> /app/public/diff/laos_sp_list_measurements_16358.diff
[STOP] [2019-10-14 01:14:26] calculate_delta
[START] [2019-10-14 01:14:26] parse_diff_and_store
[INFO] [2019-10-14 01:14:26] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 01:14:26] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 01:14:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 01:14:30] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 01:14:54] Storing 2 References
[INFO] [2019-10-14 01:14:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 01:14:54] Average Time: 0.0
[INFO] [2019-10-14 01:14:54] Total Time: 1s
[INFO] [2019-10-14 01:14:54] Storing 6902 ScientificNames
[INFO] [2019-10-14 01:14:54] Processing group of 6902 in 7 groups of 1000
[INFO] [2019-10-14 01:14:57] Average Time: 0.363
[INFO] [2019-10-14 01:14:57] Total Time: 3s
[INFO] [2019-10-14 01:14:57] last 3 / first 3: 0.93
[INFO] [2019-10-14 01:14:57] Std.Dev: 0.03162277660168379; Max: 0.42
[INFO] [2019-10-14 01:14:57] Storing 6902 Nodes
[INFO] [2019-10-14 01:14:57] Processing group of 6902 in 7 groups of 1000
[INFO] [2019-10-14 01:14:59] Average Time: 0.319
[INFO] [2019-10-14 01:14:59] Total Time: 3s
[INFO] [2019-10-14 01:14:59] last 3 / first 3: 1.02
[INFO] [2019-10-14 01:14:59] Std.Dev: 0.05477225575051661; Max: 0.42
[INFO] [2019-10-14 01:14:59] Storing 3856 Occurrences
[INFO] [2019-10-14 01:14:59] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-14 01:15:00] Average Time: 0.098
[INFO] [2019-10-14 01:15:00] Total Time: 1s
[INFO] [2019-10-14 01:15:00] Storing 8590 TraitsReferences
[INFO] [2019-10-14 01:15:00] Processing group of 8590 in 9 groups of 1000
[INFO] [2019-10-14 01:15:00] Average Time: 0.072
[INFO] [2019-10-14 01:15:00] Total Time: 1s
[INFO] [2019-10-14 01:15:00] last 3 / first 3: 0.61
[INFO] [2019-10-14 01:15:00] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-14 01:15:00] Storing 8589 Traits
[INFO] [2019-10-14 01:15:00] Processing group of 8589 in 9 groups of 1000
[INFO] [2019-10-14 01:15:03] Average Time: 0.302
[INFO] [2019-10-14 01:15:03] Total Time: 3s
[INFO] [2019-10-14 01:15:03] last 3 / first 3: 0.86
[INFO] [2019-10-14 01:15:03] Std.Dev: 0.05477225575051661; Max: 0.37
[INFO] [2019-10-14 01:15:03] Storing 8584 MetaTraits
[INFO] [2019-10-14 01:15:03] Processing group of 8584 in 9 groups of 1000
[INFO] [2019-10-14 01:15:04] Average Time: 0.117
[INFO] [2019-10-14 01:15:04] Total Time: 2s
[INFO] [2019-10-14 01:15:04] last 3 / first 3: 0.77
[INFO] [2019-10-14 01:15:04] Std.Dev: 0.03162277660168379; Max: 0.16
[STOP] [2019-10-14 01:15:04] parse_diff_and_store
[START] [2019-10-14 01:15:04] resolve_keys
[INFO] [2019-10-14 01:15:33] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 01:15:36] traits to occurrences...
[INFO] [2019-10-14 01:15:38] traits to nodes (through occurrences)...
[INFO] [2019-10-14 01:15:38] Traits to sex term...
[INFO] [2019-10-14 01:15:39] Traits to lifestage term...
[INFO] [2019-10-14 01:15:41] MetaTraits to traits...
[INFO] [2019-10-14 01:15:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 01:15:43] Assocs to occurrences...
[INFO] [2019-10-14 01:15:43] Assocs to nodes...
[INFO] [2019-10-14 01:15:43] Assoc to sex term...
[INFO] [2019-10-14 01:15:43] Assoc to lifestage term...
[STOP] [2019-10-14 01:15:43] resolve_keys
[START] [2019-10-14 01:15:43] hold_for_later_1
[STOP] [2019-10-14 01:15:43] hold_for_later_1
[START] [2019-10-14 01:15:43] hold_for_later_2
[STOP] [2019-10-14 01:15:43] hold_for_later_2
[START] [2019-10-14 01:15:43] resolve_missing_parents
[STOP] [2019-10-14 01:15:57] resolve_missing_parents
[START] [2019-10-14 01:15:57] rebuild_nodes
[START] [2019-10-14 01:15:57] Flattener#flatten
[START] [2019-10-14 01:15:58] Flattener#study_resource
[START] [2019-10-14 01:15:58] Flattener#build_ancestry
[STOP] [2019-10-14 01:15:58] Flattener#build_ancestry
[INFO] [2019-10-14 01:15:58] 6902 ancestry keys
[START] [2019-10-14 01:15:58] build_node_ancestors
[INFO] [2019-10-14 01:15:58] old ancestors deleted.
[STOP] [2019-10-14 01:15:59] build_node_ancestors
[START] [2019-10-14 01:16:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:16:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:16:01] Flattener#flatten
[STOP] [2019-10-14 01:16:01] rebuild_nodes
[START] [2019-10-14 01:16:01] resolve_missing_media_owners
[STOP] [2019-10-14 01:16:01] resolve_missing_media_owners
[START] [2019-10-14 01:16:01] sanitize_media_verbatims
[STOP] [2019-10-14 01:16:01] sanitize_media_verbatims
[START] [2019-10-14 01:16:01] queue_downloads
[STOP] [2019-10-14 01:16:01] queue_downloads
[START] [2019-10-14 01:16:01] parse_names
[WARN] [2019-10-14 01:16:01] I see 6902 names which still need to be parsed.
[STOP] [2019-10-14 01:16:07] parse_names
[START] [2019-10-14 01:16:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 01:16:07] denormalize_canonical_names_to_nodes
[START] [2019-10-14 01:16:07] match_nodes
[START] [2019-10-14 01:16:07] map_all_nodes_to_pages
[STOP] [2019-10-14 01:22:13] map_all_nodes_to_pages
[INFO] [2019-10-14 01:22:13] 350 Unmatched nodes (of 6902)! That's too many to output. First 10: Rhacophorus maximus (#50521359); Seicercus (#50522364); Seicercus poliogenys (#50522363); Seicercus tephrocephalus (#50523245); Seicercus valentini (#50524046); Seicercus burkii (#50524165); Seicercus castaniceps (#50524634); Seicercus soror (#50525244); Seicercus affinis (#50525623); Phylloscopus davisoni (#50521766)
[START] [2019-10-14 01:22:13] update_nodes
[STOP] [2019-10-14 01:22:16] update_nodes
[STOP] [2019-10-14 01:22:16] match_nodes
[START] [2019-10-14 01:22:16] reindex_search
[STOP] [2019-10-14 01:22:31] reindex_search
[START] [2019-10-14 01:22:31] normalize_units
[STOP] [2019-10-14 01:22:31] normalize_units
[START] [2019-10-14 01:22:31] calculate_statistics
[STOP] [2019-10-14 01:22:31] calculate_statistics
[START] [2019-10-14 01:22:31] complete_harvest_instance
[START] [2019-10-14 01:22:31] overall_tsv_creation
[INFO] [2019-10-14 01:22:31] Processing group of 6902 in 1 batches of 10000
[INFO] [2019-10-14 01:23:47] 3856 Traits (unfiltered)...
[INFO] [2019-10-14 01:24:01] 3856 Traits (filtered)...
[INFO] [2019-10-14 01:24:01] 0 Associations (filtered)...
[INFO] [2019-10-14 01:24:46] 19276 metadata added.
[INFO] [2019-10-14 01:24:46] 0 metadata added.
[INFO] [2019-10-14 01:24:46] Average Time: 109.29
[INFO] [2019-10-14 01:24:46] Total Time: 2m16s
[STOP] [2019-10-14 01:24:46] overall_tsv_creation
[INFO] [2019-10-14 01:24:46] Done. Check your files:
[INFO] [2019-10-14 01:24:46] (6902 lines) /app/public/data/laos_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 01:24:47] (17134 lines) /app/public/data/laos_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 01:24:47] (6902 lines) /app/public/data/laos_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 01:24:47] (3857 lines) /app/public/data/laos_sp_list/publish_traits.tsv
[INFO] [2019-10-14 01:24:47] (19277 lines) /app/public/data/laos_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 01:24:47] complete_harvest_instance
[START] [2019-10-14 01:24:47] completed
[STOP] [2019-10-14 01:24:47] completed
[STOP] [2019-10-14 01:24:47] logged process, took 624.8

Latest Process