Harvest for Myanmar Species List Created 14 Oct 10:50

Stage: completed
Fetched: 14 Oct 10:50
Validated: 14 Oct 10:50
Deltas Created 14 Oct 10:50
Units Normalized: 14 Oct 11:04
Ancestry Built: 14 Oct 10:53
Nodes Matched: 14 Oct 11:04
Names Parsed: 14 Oct 10:53
New Models Stored: 14 Oct 10:51
Indexed: 14 Oct 11:04
Completed: 14 Oct 11:08
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-14 10:50:42 -0400 by logger.rb/56815
[START] [2019-10-14 10:50:42] logged process
[START] [2019-10-14 10:50:42] create_harvest_instance
[STOP] [2019-10-14 10:50:42] create_harvest_instance
[START] [2019-10-14 10:50:42] fetch_files
[STOP] [2019-10-14 10:50:42] fetch_files
[START] [2019-10-14 10:50:42] validate_each_file
[STOP] [2019-10-14 10:50:44] validate_each_file
[START] [2019-10-14 10:50:44] convert_to_csv
[CMD] [2019-10-14 10:50:44] /usr/bin/sort /app/public/converted_csv/myanmar_sp_list_refs_16659.csv > /app/public/converted_csv/myanmar_sp_list_refs_16659.csv_sorted
[CMD] [2019-10-14 10:50:44] /usr/bin/sort /app/public/converted_csv/myanmar_sp_list_nodes_16660.csv > /app/public/converted_csv/myanmar_sp_list_nodes_16660.csv_sorted
[CMD] [2019-10-14 10:50:44] /usr/bin/sort /app/public/converted_csv/myanmar_sp_list_occurrences_16661.csv > /app/public/converted_csv/myanmar_sp_list_occurrences_16661.csv_sorted
[CMD] [2019-10-14 10:50:44] /usr/bin/sort /app/public/converted_csv/myanmar_sp_list_measurements_16662.csv > /app/public/converted_csv/myanmar_sp_list_measurements_16662.csv_sorted
[STOP] [2019-10-14 10:50:44] convert_to_csv
[START] [2019-10-14 10:50:44] calculate_delta
[CMD] [2019-10-14 10:50:44] echo "0a" > /app/public/diff/myanmar_sp_list_refs_16659.diff
[CMD] [2019-10-14 10:50:44] tail -n +1 /app/public/converted_csv/myanmar_sp_list_refs_16659.csv >> /app/public/diff/myanmar_sp_list_refs_16659.diff
[CMD] [2019-10-14 10:50:44] echo "." >> /app/public/diff/myanmar_sp_list_refs_16659.diff
[CMD] [2019-10-14 10:50:44] echo "0a" > /app/public/diff/myanmar_sp_list_nodes_16660.diff
[CMD] [2019-10-14 10:50:45] tail -n +1 /app/public/converted_csv/myanmar_sp_list_nodes_16660.csv >> /app/public/diff/myanmar_sp_list_nodes_16660.diff
[CMD] [2019-10-14 10:50:45] echo "." >> /app/public/diff/myanmar_sp_list_nodes_16660.diff
[CMD] [2019-10-14 10:50:45] echo "0a" > /app/public/diff/myanmar_sp_list_occurrences_16661.diff
[CMD] [2019-10-14 10:50:45] tail -n +1 /app/public/converted_csv/myanmar_sp_list_occurrences_16661.csv >> /app/public/diff/myanmar_sp_list_occurrences_16661.diff
[CMD] [2019-10-14 10:50:45] echo "." >> /app/public/diff/myanmar_sp_list_occurrences_16661.diff
[CMD] [2019-10-14 10:50:45] echo "0a" > /app/public/diff/myanmar_sp_list_measurements_16662.diff
[CMD] [2019-10-14 10:50:45] tail -n +1 /app/public/converted_csv/myanmar_sp_list_measurements_16662.csv >> /app/public/diff/myanmar_sp_list_measurements_16662.diff
[CMD] [2019-10-14 10:50:45] echo "." >> /app/public/diff/myanmar_sp_list_measurements_16662.diff
[STOP] [2019-10-14 10:50:45] calculate_delta
[START] [2019-10-14 10:50:45] parse_diff_and_store
[INFO] [2019-10-14 10:50:45] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 10:50:46] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 10:50:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 10:50:51] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 10:51:30] Storing 2 References
[INFO] [2019-10-14 10:51:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 10:51:30] Average Time: 0.0
[INFO] [2019-10-14 10:51:30] Total Time: 1s
[INFO] [2019-10-14 10:51:30] Storing 10692 ScientificNames
[INFO] [2019-10-14 10:51:30] Processing group of 10692 in 11 groups of 1000
[INFO] [2019-10-14 10:51:34] Average Time: 0.352
[INFO] [2019-10-14 10:51:34] Total Time: 4s
[INFO] [2019-10-14 10:51:34] last 3 / first 3: 0.87
[INFO] [2019-10-14 10:51:34] Std.Dev: 0.05477225575051661; Max: 0.47
[INFO] [2019-10-14 10:51:34] Storing 10692 Nodes
[INFO] [2019-10-14 10:51:34] Processing group of 10692 in 11 groups of 1000
[INFO] [2019-10-14 10:51:37] Average Time: 0.291
[INFO] [2019-10-14 10:51:37] Total Time: 4s
[INFO] [2019-10-14 10:51:37] last 3 / first 3: 0.97
[INFO] [2019-10-14 10:51:37] Std.Dev: 0.03162277660168379; Max: 0.38
[INFO] [2019-10-14 10:51:37] Storing 6266 Occurrences
[INFO] [2019-10-14 10:51:37] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-14 10:51:38] Average Time: 0.1
[INFO] [2019-10-14 10:51:38] Total Time: 1s
[INFO] [2019-10-14 10:51:38] last 3 / first 3: 0.71
[INFO] [2019-10-14 10:51:38] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-14 10:51:38] Storing 13230 TraitsReferences
[INFO] [2019-10-14 10:51:38] Processing group of 13230 in 14 groups of 1000
[INFO] [2019-10-14 10:51:39] Average Time: 0.074
[INFO] [2019-10-14 10:51:39] Total Time: 2s
[INFO] [2019-10-14 10:51:39] last 3 / first 3: 0.53
[INFO] [2019-10-14 10:51:39] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-14 10:51:39] Storing 13229 Traits
[INFO] [2019-10-14 10:51:39] Processing group of 13229 in 14 groups of 1000
[INFO] [2019-10-14 10:51:45] Average Time: 0.374
[INFO] [2019-10-14 10:51:45] Total Time: 6s
[INFO] [2019-10-14 10:51:45] last 3 / first 3: 1.34
[INFO] [2019-10-14 10:51:45] Std.Dev: 0.2683281572999748; Max: 1.05
[INFO] [2019-10-14 10:51:45] Storing 13201 MetaTraits
[INFO] [2019-10-14 10:51:45] Processing group of 13201 in 14 groups of 1000
[INFO] [2019-10-14 10:51:46] Average Time: 0.114
[INFO] [2019-10-14 10:51:46] Total Time: 2s
[INFO] [2019-10-14 10:51:46] last 3 / first 3: 0.63
[INFO] [2019-10-14 10:51:46] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-10-14 10:51:46] parse_diff_and_store
[START] [2019-10-14 10:51:46] resolve_keys
[INFO] [2019-10-14 10:52:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 10:52:32] traits to occurrences...
[INFO] [2019-10-14 10:52:37] traits to nodes (through occurrences)...
[INFO] [2019-10-14 10:52:37] Traits to sex term...
[INFO] [2019-10-14 10:52:41] Traits to lifestage term...
[INFO] [2019-10-14 10:52:46] MetaTraits to traits...
[INFO] [2019-10-14 10:52:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 10:52:49] Assocs to occurrences...
[INFO] [2019-10-14 10:52:49] Assocs to nodes...
[INFO] [2019-10-14 10:52:49] Assoc to sex term...
[INFO] [2019-10-14 10:52:49] Assoc to lifestage term...
[STOP] [2019-10-14 10:52:49] resolve_keys
[START] [2019-10-14 10:52:49] hold_for_later_1
[STOP] [2019-10-14 10:52:49] hold_for_later_1
[START] [2019-10-14 10:52:49] hold_for_later_2
[STOP] [2019-10-14 10:52:49] hold_for_later_2
[START] [2019-10-14 10:52:49] resolve_missing_parents
[STOP] [2019-10-14 10:53:10] resolve_missing_parents
[START] [2019-10-14 10:53:10] rebuild_nodes
[START] [2019-10-14 10:53:10] Flattener#flatten
[START] [2019-10-14 10:53:10] Flattener#study_resource
[START] [2019-10-14 10:53:10] Flattener#build_ancestry
[STOP] [2019-10-14 10:53:10] Flattener#build_ancestry
[INFO] [2019-10-14 10:53:10] 10692 ancestry keys
[START] [2019-10-14 10:53:10] build_node_ancestors
[INFO] [2019-10-14 10:53:10] old ancestors deleted.
[STOP] [2019-10-14 10:53:13] build_node_ancestors
[START] [2019-10-14 10:53:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 10:53:18] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 10:53:18] Flattener#flatten
[STOP] [2019-10-14 10:53:18] rebuild_nodes
[START] [2019-10-14 10:53:18] resolve_missing_media_owners
[STOP] [2019-10-14 10:53:18] resolve_missing_media_owners
[START] [2019-10-14 10:53:18] sanitize_media_verbatims
[STOP] [2019-10-14 10:53:18] sanitize_media_verbatims
[START] [2019-10-14 10:53:18] queue_downloads
[STOP] [2019-10-14 10:53:18] queue_downloads
[START] [2019-10-14 10:53:18] parse_names
[WARN] [2019-10-14 10:53:18] I see 10692 names which still need to be parsed.
[STOP] [2019-10-14 10:53:28] parse_names
[START] [2019-10-14 10:53:28] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 10:53:28] denormalize_canonical_names_to_nodes
[START] [2019-10-14 10:53:28] match_nodes
[START] [2019-10-14 10:53:28] map_all_nodes_to_pages
[STOP] [2019-10-14 11:04:12] map_all_nodes_to_pages
[INFO] [2019-10-14 11:04:12] 647 Unmatched nodes (of 10692)! That's too many to output. First 10: Limnonectes limborgii (#50846868); Hoplobatrachus tigerina (#50838472); Microhyla natatrix (#50846347); Gekko gekko (#50843446); Tropidophorus berdmorii (#50844024); Dendrelaphis gorei (#50839545); Ptyas nigromarginatus (#50844238); Elaphe leonardi (#50839029); Elaphe porphyraceus (#50839633); Dinodon septentrionalis (#50838859)
[START] [2019-10-14 11:04:12] update_nodes
[STOP] [2019-10-14 11:04:16] update_nodes
[STOP] [2019-10-14 11:04:16] match_nodes
[START] [2019-10-14 11:04:16] reindex_search
[STOP] [2019-10-14 11:04:47] reindex_search
[START] [2019-10-14 11:04:47] normalize_units
[STOP] [2019-10-14 11:04:47] normalize_units
[START] [2019-10-14 11:04:47] calculate_statistics
[STOP] [2019-10-14 11:04:47] calculate_statistics
[START] [2019-10-14 11:04:47] complete_harvest_instance
[START] [2019-10-14 11:04:47] overall_tsv_creation
[INFO] [2019-10-14 11:04:47] Processing group of 10692 in 2 batches of 10000
[INFO] [2019-10-14 11:06:16] 6110 Traits (unfiltered)...
[INFO] [2019-10-14 11:06:30] 6110 Traits (filtered)...
[INFO] [2019-10-14 11:06:30] 0 Associations (filtered)...
[INFO] [2019-10-14 11:07:20] 30527 metadata added.
[INFO] [2019-10-14 11:07:20] 0 metadata added.
[INFO] [2019-10-14 11:08:07] 156 Traits (unfiltered)...
[INFO] [2019-10-14 11:08:20] 156 Traits (filtered)...
[INFO] [2019-10-14 11:08:20] 0 Associations (filtered)...
[INFO] [2019-10-14 11:08:57] 776 metadata added.
[INFO] [2019-10-14 11:08:57] 0 metadata added.
[INFO] [2019-10-14 11:08:57] Average Time: 101.195
[INFO] [2019-10-14 11:08:57] Total Time: 4m11s
[STOP] [2019-10-14 11:08:57] overall_tsv_creation
[INFO] [2019-10-14 11:08:57] Done. Check your files:
[INFO] [2019-10-14 11:08:58] (10692 lines) /app/public/data/myanmar_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 11:08:58] (47168 lines) /app/public/data/myanmar_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 11:08:58] (10692 lines) /app/public/data/myanmar_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 11:08:58] (6267 lines) /app/public/data/myanmar_sp_list/publish_traits.tsv
[INFO] [2019-10-14 11:08:58] (31304 lines) /app/public/data/myanmar_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 11:08:58] complete_harvest_instance
[START] [2019-10-14 11:08:58] completed
[STOP] [2019-10-14 11:08:58] completed
[STOP] [2019-10-14 11:08:58] logged process, took 1096.26
Latest Process

14 Oct 10:50 EXITED currently processing 0