Harvest for Andaman Sea Species List Created 22 Dec 17:36

Stage: completed
Fetched: 22 Dec 17:36
Validated: 22 Dec 17:36
Deltas Created 22 Dec 17:36
Units Normalized: 22 Dec 17:56
Ancestry Built: 22 Dec 17:38
Nodes Matched: 22 Dec 17:56
Names Parsed: 22 Dec 17:38
New Models Stored: 22 Dec 17:37
Indexed: 22 Dec 17:56
Completed: 22 Dec 17:59
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 17:36:15 -0500 by logger.rb/56815
[START] [2019-12-22 17:36:15] logged process
[START] [2019-12-22 17:36:15] create_harvest_instance
[STOP] [2019-12-22 17:36:16] create_harvest_instance
[START] [2019-12-22 17:36:16] fetch_files
[STOP] [2019-12-22 17:36:16] fetch_files
[START] [2019-12-22 17:36:16] validate_each_file
[STOP] [2019-12-22 17:36:17] validate_each_file
[START] [2019-12-22 17:36:17] convert_to_csv
[CMD] [2019-12-22 17:36:17] /usr/bin/sort /app/public/converted_csv/andaman_sea_sp_l_refs_19002.csv > /app/public/converted_csv/andaman_sea_sp_l_refs_19002.csv_sorted
[CMD] [2019-12-22 17:36:17] /usr/bin/sort /app/public/converted_csv/andaman_sea_sp_l_nodes_19003.csv > /app/public/converted_csv/andaman_sea_sp_l_nodes_19003.csv_sorted
[CMD] [2019-12-22 17:36:18] /usr/bin/sort /app/public/converted_csv/andaman_sea_sp_l_occurrences_19004.csv > /app/public/converted_csv/andaman_sea_sp_l_occurrences_19004.csv_sorted
[CMD] [2019-12-22 17:36:19] /usr/bin/sort /app/public/converted_csv/andaman_sea_sp_l_measurements_19005.csv > /app/public/converted_csv/andaman_sea_sp_l_measurements_19005.csv_sorted
[STOP] [2019-12-22 17:36:19] convert_to_csv
[START] [2019-12-22 17:36:19] calculate_delta
[CMD] [2019-12-22 17:36:19] echo "0a" > /app/public/diff/andaman_sea_sp_l_refs_19002.diff
[CMD] [2019-12-22 17:36:20] tail -n +1 /app/public/converted_csv/andaman_sea_sp_l_refs_19002.csv >> /app/public/diff/andaman_sea_sp_l_refs_19002.diff
[CMD] [2019-12-22 17:36:21] echo "." >> /app/public/diff/andaman_sea_sp_l_refs_19002.diff
[CMD] [2019-12-22 17:36:21] echo "0a" > /app/public/diff/andaman_sea_sp_l_nodes_19003.diff
[CMD] [2019-12-22 17:36:22] tail -n +1 /app/public/converted_csv/andaman_sea_sp_l_nodes_19003.csv >> /app/public/diff/andaman_sea_sp_l_nodes_19003.diff
[CMD] [2019-12-22 17:36:23] echo "." >> /app/public/diff/andaman_sea_sp_l_nodes_19003.diff
[CMD] [2019-12-22 17:36:23] echo "0a" > /app/public/diff/andaman_sea_sp_l_occurrences_19004.diff
[CMD] [2019-12-22 17:36:24] tail -n +1 /app/public/converted_csv/andaman_sea_sp_l_occurrences_19004.csv >> /app/public/diff/andaman_sea_sp_l_occurrences_19004.diff
[CMD] [2019-12-22 17:36:25] echo "." >> /app/public/diff/andaman_sea_sp_l_occurrences_19004.diff
[CMD] [2019-12-22 17:36:26] echo "0a" > /app/public/diff/andaman_sea_sp_l_measurements_19005.diff
[CMD] [2019-12-22 17:36:26] tail -n +1 /app/public/converted_csv/andaman_sea_sp_l_measurements_19005.csv >> /app/public/diff/andaman_sea_sp_l_measurements_19005.diff
[CMD] [2019-12-22 17:36:27] echo "." >> /app/public/diff/andaman_sea_sp_l_measurements_19005.diff
[STOP] [2019-12-22 17:36:28] calculate_delta
[START] [2019-12-22 17:36:28] parse_diff_and_store
[INFO] [2019-12-22 17:36:28] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 17:36:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 17:36:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 17:36:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 17:37:00] Storing 2 References
[INFO] [2019-12-22 17:37:00] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 17:37:00] Average Time: 0.0
[INFO] [2019-12-22 17:37:00] Total Time: 1s
[INFO] [2019-12-22 17:37:00] Storing 7844 ScientificNames
[INFO] [2019-12-22 17:37:00] Processing group of 7844 in 8 groups of 1000
[INFO] [2019-12-22 17:37:03] Average Time: 0.447
[INFO] [2019-12-22 17:37:03] Total Time: 4s
[INFO] [2019-12-22 17:37:03] last 3 / first 3: 1.12
[INFO] [2019-12-22 17:37:03] Std.Dev: 0.11832159566199232; Max: 0.71
[INFO] [2019-12-22 17:37:03] Storing 7844 Nodes
[INFO] [2019-12-22 17:37:03] Processing group of 7844 in 8 groups of 1000
[INFO] [2019-12-22 17:37:06] Average Time: 0.328
[INFO] [2019-12-22 17:37:06] Total Time: 3s
[INFO] [2019-12-22 17:37:06] last 3 / first 3: 0.95
[INFO] [2019-12-22 17:37:06] Std.Dev: 0.03162277660168379; Max: 0.37
[INFO] [2019-12-22 17:37:06] Storing 4460 Occurrences
[INFO] [2019-12-22 17:37:06] Processing group of 4460 in 5 groups of 1000
[INFO] [2019-12-22 17:37:07] Average Time: 0.112
[INFO] [2019-12-22 17:37:07] Total Time: 1s
[INFO] [2019-12-22 17:37:07] Storing 8920 TraitsReferences
[INFO] [2019-12-22 17:37:07] Processing group of 8920 in 9 groups of 1000
[INFO] [2019-12-22 17:37:08] Average Time: 0.087
[INFO] [2019-12-22 17:37:08] Total Time: 1s
[INFO] [2019-12-22 17:37:08] last 3 / first 3: 0.74
[INFO] [2019-12-22 17:37:08] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-12-22 17:37:08] Storing 8920 Traits
[INFO] [2019-12-22 17:37:08] Processing group of 8920 in 9 groups of 1000
[INFO] [2019-12-22 17:37:11] Average Time: 0.372
[INFO] [2019-12-22 17:37:11] Total Time: 4s
[INFO] [2019-12-22 17:37:11] last 3 / first 3: 0.74
[INFO] [2019-12-22 17:37:11] Std.Dev: 0.07071067811865475; Max: 0.49
[INFO] [2019-12-22 17:37:11] Storing 8916 MetaTraits
[INFO] [2019-12-22 17:37:11] Processing group of 8916 in 9 groups of 1000
[INFO] [2019-12-22 17:37:12] Average Time: 0.163
[INFO] [2019-12-22 17:37:12] Total Time: 2s
[INFO] [2019-12-22 17:37:12] last 3 / first 3: 0.68
[INFO] [2019-12-22 17:37:12] Std.Dev: 0.07745966692414834; Max: 0.36
[STOP] [2019-12-22 17:37:12] parse_diff_and_store
[START] [2019-12-22 17:37:12] resolve_keys
[INFO] [2019-12-22 17:37:44] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 17:37:47] traits to occurrences...
[INFO] [2019-12-22 17:37:49] traits to nodes (through occurrences)...
[INFO] [2019-12-22 17:37:49] Traits to sex term...
[INFO] [2019-12-22 17:37:51] Traits to lifestage term...
[INFO] [2019-12-22 17:37:52] MetaTraits to traits...
[INFO] [2019-12-22 17:37:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 17:37:54] Assocs to occurrences...
[INFO] [2019-12-22 17:37:54] Assocs to nodes...
[INFO] [2019-12-22 17:37:54] Assoc to sex term...
[INFO] [2019-12-22 17:37:54] Assoc to lifestage term...
[STOP] [2019-12-22 17:37:54] resolve_keys
[START] [2019-12-22 17:37:54] hold_for_later_1
[STOP] [2019-12-22 17:37:54] hold_for_later_1
[START] [2019-12-22 17:37:54] hold_for_later_2
[STOP] [2019-12-22 17:37:54] hold_for_later_2
[START] [2019-12-22 17:37:54] resolve_missing_parents
[STOP] [2019-12-22 17:38:10] resolve_missing_parents
[START] [2019-12-22 17:38:10] rebuild_nodes
[START] [2019-12-22 17:38:10] Flattener#flatten
[START] [2019-12-22 17:38:10] Flattener#study_resource
[START] [2019-12-22 17:38:10] Flattener#build_ancestry
[STOP] [2019-12-22 17:38:10] Flattener#build_ancestry
[INFO] [2019-12-22 17:38:10] 7844 ancestry keys
[START] [2019-12-22 17:38:10] build_node_ancestors
[INFO] [2019-12-22 17:38:10] old ancestors deleted.
[STOP] [2019-12-22 17:38:14] build_node_ancestors
[START] [2019-12-22 17:38:17] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:38:18] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:38:18] Flattener#flatten
[STOP] [2019-12-22 17:38:18] rebuild_nodes
[START] [2019-12-22 17:38:18] resolve_missing_media_owners
[STOP] [2019-12-22 17:38:18] resolve_missing_media_owners
[START] [2019-12-22 17:38:18] sanitize_media_verbatims
[STOP] [2019-12-22 17:38:18] sanitize_media_verbatims
[START] [2019-12-22 17:38:18] queue_downloads
[STOP] [2019-12-22 17:38:18] queue_downloads
[START] [2019-12-22 17:38:18] parse_names
[WARN] [2019-12-22 17:38:18] I see 7844 names which still need to be parsed.
[STOP] [2019-12-22 17:38:25] parse_names
[START] [2019-12-22 17:38:25] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 17:38:25] denormalize_canonical_names_to_nodes
[START] [2019-12-22 17:38:25] match_nodes
[START] [2019-12-22 17:38:25] map_all_nodes_to_pages
[STOP] [2019-12-22 17:56:32] map_all_nodes_to_pages
[INFO] [2019-12-22 17:56:32] 324 Unmatched nodes (of 7844)! That's too many to output. First 10: Limicola (#61662225); Limicola falcinellus (#61662224); Philomachus (#61665696); Philomachus pugnax (#61665695); Sterna melanogaster (#61660623); Ceyx erithacus (#61667591); Egretta intermedia (#61660111); Megalaima (#61660534); Megalaima haemacephala (#61660533); Eudynamys scolopacea (#61661410)
[START] [2019-12-22 17:56:32] update_nodes
[STOP] [2019-12-22 17:56:35] update_nodes
[STOP] [2019-12-22 17:56:35] match_nodes
[START] [2019-12-22 17:56:35] reindex_search
[STOP] [2019-12-22 17:56:50] reindex_search
[START] [2019-12-22 17:56:50] normalize_units
[STOP] [2019-12-22 17:56:50] normalize_units
[START] [2019-12-22 17:56:50] calculate_statistics
[STOP] [2019-12-22 17:56:51] calculate_statistics
[START] [2019-12-22 17:56:51] complete_harvest_instance
[START] [2019-12-22 17:56:51] overall_tsv_creation
[INFO] [2019-12-22 17:56:51] Processing group of 7844 in 1 batches of 10000
[INFO] [2019-12-22 17:58:10] 4460 Traits (unfiltered)...
[INFO] [2019-12-22 17:58:23] 4460 Traits (filtered)...
[INFO] [2019-12-22 17:58:23] 0 Associations (filtered)...
[INFO] [2019-12-22 17:59:09] 22296 metadata added.
[INFO] [2019-12-22 17:59:09] 0 metadata added.
[INFO] [2019-12-22 17:59:09] Average Time: 110.07
[INFO] [2019-12-22 17:59:09] Total Time: 2m19s
[STOP] [2019-12-22 17:59:09] overall_tsv_creation
[INFO] [2019-12-22 17:59:09] Done. Check your files:
[INFO] [2019-12-22 17:59:09] (7844 lines) /app/public/data/andaman_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 17:59:10] (41234 lines) /app/public/data/andaman_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 17:59:11] (7844 lines) /app/public/data/andaman_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 17:59:11] (4461 lines) /app/public/data/andaman_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 17:59:12] (22297 lines) /app/public/data/andaman_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 17:59:12] complete_harvest_instance
[START] [2019-12-22 17:59:12] completed
[STOP] [2019-12-22 17:59:12] completed
[STOP] [2019-12-22 17:59:12] logged process, took 1376.9

Latest Process