Harvest for Burundi Species List Created 11 Oct 23:30

Stage: completed
Fetched: 11 Oct 23:30
Validated: 11 Oct 23:30
Deltas Created 11 Oct 23:30
Units Normalized: 11 Oct 23:37
Ancestry Built: 11 Oct 23:32
Nodes Matched: 11 Oct 23:36
Names Parsed: 11 Oct 23:32
New Models Stored: 11 Oct 23:31
Indexed: 11 Oct 23:37
Completed: 11 Oct 23:39
Time to Harvest: less than a minute

Harvesting Log

(145 lines)
# Logfile created on 2019-10-11 23:30:43 -0400 by logger.rb/56815
[START] [2019-10-11 23:30:43] logged process
[START] [2019-10-11 23:30:43] create_harvest_instance
[STOP] [2019-10-11 23:30:44] create_harvest_instance
[START] [2019-10-11 23:30:44] fetch_files
[STOP] [2019-10-11 23:30:44] fetch_files
[START] [2019-10-11 23:30:44] validate_each_file
[STOP] [2019-10-11 23:30:45] validate_each_file
[START] [2019-10-11 23:30:45] convert_to_csv
[CMD] [2019-10-11 23:30:45] /usr/bin/sort /app/public/converted_csv/burundi_sp_list_refs_15347.csv > /app/public/converted_csv/burundi_sp_list_refs_15347.csv_sorted
[CMD] [2019-10-11 23:30:45] /usr/bin/sort /app/public/converted_csv/burundi_sp_list_nodes_15348.csv > /app/public/converted_csv/burundi_sp_list_nodes_15348.csv_sorted
[CMD] [2019-10-11 23:30:45] /usr/bin/sort /app/public/converted_csv/burundi_sp_list_occurrences_15349.csv > /app/public/converted_csv/burundi_sp_list_occurrences_15349.csv_sorted
[CMD] [2019-10-11 23:30:45] /usr/bin/sort /app/public/converted_csv/burundi_sp_list_measurements_15350.csv > /app/public/converted_csv/burundi_sp_list_measurements_15350.csv_sorted
[STOP] [2019-10-11 23:30:45] convert_to_csv
[START] [2019-10-11 23:30:45] calculate_delta
[CMD] [2019-10-11 23:30:45] echo "0a" > /app/public/diff/burundi_sp_list_refs_15347.diff
[CMD] [2019-10-11 23:30:45] tail -n +1 /app/public/converted_csv/burundi_sp_list_refs_15347.csv >> /app/public/diff/burundi_sp_list_refs_15347.diff
[CMD] [2019-10-11 23:30:45] echo "." >> /app/public/diff/burundi_sp_list_refs_15347.diff
[CMD] [2019-10-11 23:30:45] echo "0a" > /app/public/diff/burundi_sp_list_nodes_15348.diff
[CMD] [2019-10-11 23:30:45] tail -n +1 /app/public/converted_csv/burundi_sp_list_nodes_15348.csv >> /app/public/diff/burundi_sp_list_nodes_15348.diff
[CMD] [2019-10-11 23:30:45] echo "." >> /app/public/diff/burundi_sp_list_nodes_15348.diff
[CMD] [2019-10-11 23:30:46] echo "0a" > /app/public/diff/burundi_sp_list_occurrences_15349.diff
[CMD] [2019-10-11 23:30:46] tail -n +1 /app/public/converted_csv/burundi_sp_list_occurrences_15349.csv >> /app/public/diff/burundi_sp_list_occurrences_15349.diff
[CMD] [2019-10-11 23:30:46] echo "." >> /app/public/diff/burundi_sp_list_occurrences_15349.diff
[CMD] [2019-10-11 23:30:46] echo "0a" > /app/public/diff/burundi_sp_list_measurements_15350.diff
[CMD] [2019-10-11 23:30:46] tail -n +1 /app/public/converted_csv/burundi_sp_list_measurements_15350.csv >> /app/public/diff/burundi_sp_list_measurements_15350.diff
[CMD] [2019-10-11 23:30:46] echo "." >> /app/public/diff/burundi_sp_list_measurements_15350.diff
[STOP] [2019-10-11 23:30:46] calculate_delta
[START] [2019-10-11 23:30:46] parse_diff_and_store
[INFO] [2019-10-11 23:30:46] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 23:30:46] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 23:30:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 23:30:49] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 23:31:11] Storing 2 References
[INFO] [2019-10-11 23:31:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 23:31:11] Average Time: 0.0
[INFO] [2019-10-11 23:31:11] Total Time: 1s
[INFO] [2019-10-11 23:31:11] Storing 5697 ScientificNames
[INFO] [2019-10-11 23:31:11] Processing group of 5697 in 6 groups of 1000
[INFO] [2019-10-11 23:31:14] Average Time: 0.365
[INFO] [2019-10-11 23:31:14] Total Time: 3s
[INFO] [2019-10-11 23:31:14] Storing 5697 Nodes
[INFO] [2019-10-11 23:31:14] Processing group of 5697 in 6 groups of 1000
[INFO] [2019-10-11 23:31:15] Average Time: 0.312
[INFO] [2019-10-11 23:31:15] Total Time: 2s
[INFO] [2019-10-11 23:31:15] Storing 3732 Occurrences
[INFO] [2019-10-11 23:31:15] Processing group of 3732 in 4 groups of 1000
[INFO] [2019-10-11 23:31:16] Average Time: 0.098
[INFO] [2019-10-11 23:31:16] Total Time: 1s
[INFO] [2019-10-11 23:31:16] Storing 7464 TraitsReferences
[INFO] [2019-10-11 23:31:16] Processing group of 7464 in 8 groups of 1000
[INFO] [2019-10-11 23:31:17] Average Time: 0.069
[INFO] [2019-10-11 23:31:17] Total Time: 1s
[INFO] [2019-10-11 23:31:17] last 3 / first 3: 0.56
[INFO] [2019-10-11 23:31:17] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-11 23:31:17] Storing 7464 Traits
[INFO] [2019-10-11 23:31:17] Processing group of 7464 in 8 groups of 1000
[INFO] [2019-10-11 23:31:19] Average Time: 0.323
[INFO] [2019-10-11 23:31:19] Total Time: 3s
[INFO] [2019-10-11 23:31:19] last 3 / first 3: 0.75
[INFO] [2019-10-11 23:31:19] Std.Dev: 0.07071067811865475; Max: 0.41
[INFO] [2019-10-11 23:31:19] Storing 7461 MetaTraits
[INFO] [2019-10-11 23:31:19] Processing group of 7461 in 8 groups of 1000
[INFO] [2019-10-11 23:31:21] Average Time: 0.174
[INFO] [2019-10-11 23:31:21] Total Time: 2s
[INFO] [2019-10-11 23:31:21] last 3 / first 3: 1.6
[INFO] [2019-10-11 23:31:21] Std.Dev: 0.14491376746189438; Max: 0.52
[STOP] [2019-10-11 23:31:21] parse_diff_and_store
[START] [2019-10-11 23:31:21] resolve_keys
[INFO] [2019-10-11 23:31:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 23:31:48] traits to occurrences...
[INFO] [2019-10-11 23:31:52] traits to nodes (through occurrences)...
[INFO] [2019-10-11 23:31:52] Traits to sex term...
[INFO] [2019-10-11 23:31:54] Traits to lifestage term...
[INFO] [2019-10-11 23:31:57] MetaTraits to traits...
[INFO] [2019-10-11 23:31:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 23:31:59] Assocs to occurrences...
[INFO] [2019-10-11 23:31:59] Assocs to nodes...
[INFO] [2019-10-11 23:31:59] Assoc to sex term...
[INFO] [2019-10-11 23:31:59] Assoc to lifestage term...
[STOP] [2019-10-11 23:31:59] resolve_keys
[START] [2019-10-11 23:31:59] hold_for_later_1
[STOP] [2019-10-11 23:31:59] hold_for_later_1
[START] [2019-10-11 23:31:59] hold_for_later_2
[STOP] [2019-10-11 23:31:59] hold_for_later_2
[START] [2019-10-11 23:31:59] resolve_missing_parents
[STOP] [2019-10-11 23:32:11] resolve_missing_parents
[START] [2019-10-11 23:32:11] rebuild_nodes
[START] [2019-10-11 23:32:11] Flattener#flatten
[START] [2019-10-11 23:32:11] Flattener#study_resource
[START] [2019-10-11 23:32:11] Flattener#build_ancestry
[STOP] [2019-10-11 23:32:11] Flattener#build_ancestry
[INFO] [2019-10-11 23:32:11] 5697 ancestry keys
[START] [2019-10-11 23:32:11] build_node_ancestors
[INFO] [2019-10-11 23:32:11] old ancestors deleted.
[STOP] [2019-10-11 23:32:14] build_node_ancestors
[START] [2019-10-11 23:32:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:32:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:32:17] Flattener#flatten
[STOP] [2019-10-11 23:32:17] rebuild_nodes
[START] [2019-10-11 23:32:17] resolve_missing_media_owners
[STOP] [2019-10-11 23:32:17] resolve_missing_media_owners
[START] [2019-10-11 23:32:17] sanitize_media_verbatims
[STOP] [2019-10-11 23:32:17] sanitize_media_verbatims
[START] [2019-10-11 23:32:17] queue_downloads
[STOP] [2019-10-11 23:32:17] queue_downloads
[START] [2019-10-11 23:32:17] parse_names
[WARN] [2019-10-11 23:32:17] I see 5697 names which still need to be parsed.
[STOP] [2019-10-11 23:32:22] parse_names
[START] [2019-10-11 23:32:22] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 23:32:22] denormalize_canonical_names_to_nodes
[START] [2019-10-11 23:32:22] match_nodes
[START] [2019-10-11 23:32:22] map_all_nodes_to_pages
[STOP] [2019-10-11 23:36:46] map_all_nodes_to_pages
[INFO] [2019-10-11 23:36:46] 216 Unmatched nodes (of 5697)! That's too many to output. First 10: Appias epaphia (#48987006); Charaxes phaeus (#48989460); Bactrocera curcubitae (#48987529); Richardidae (#48987530); Sarcophaga zumpti (#48989947); Sarcophaga bulamatadi (#48991740); Sarcophaga calicifera (#48991941); Sarcophaga chapini (#48992056); Sarcophaga furcoides (#48992275); Eudicella smithi (#48990210)
[START] [2019-10-11 23:36:46] update_nodes
[STOP] [2019-10-11 23:36:48] update_nodes
[STOP] [2019-10-11 23:36:48] match_nodes
[START] [2019-10-11 23:36:48] reindex_search
[STOP] [2019-10-11 23:37:00] reindex_search
[START] [2019-10-11 23:37:00] normalize_units
[STOP] [2019-10-11 23:37:00] normalize_units
[START] [2019-10-11 23:37:00] calculate_statistics
[STOP] [2019-10-11 23:37:00] calculate_statistics
[START] [2019-10-11 23:37:00] complete_harvest_instance
[START] [2019-10-11 23:37:00] overall_tsv_creation
[INFO] [2019-10-11 23:37:00] Processing group of 5697 in 1 batches of 10000
[INFO] [2019-10-11 23:38:11] 3732 Traits (unfiltered)...
[INFO] [2019-10-11 23:38:25] 3732 Traits (filtered)...
[INFO] [2019-10-11 23:38:25] 0 Associations (filtered)...
[INFO] [2019-10-11 23:39:10] 18657 metadata added.
[INFO] [2019-10-11 23:39:10] 0 metadata added.
[INFO] [2019-10-11 23:39:10] Average Time: 105.12
[INFO] [2019-10-11 23:39:10] Total Time: 2m11s
[STOP] [2019-10-11 23:39:10] overall_tsv_creation
[INFO] [2019-10-11 23:39:10] Done. Check your files:
[INFO] [2019-10-11 23:39:10] (5697 lines) /app/public/data/burundi_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 23:39:10] (31377 lines) /app/public/data/burundi_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 23:39:10] (5697 lines) /app/public/data/burundi_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 23:39:10] (3733 lines) /app/public/data/burundi_sp_list/publish_traits.tsv
[INFO] [2019-10-11 23:39:10] (18658 lines) /app/public/data/burundi_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 23:39:10] complete_harvest_instance
[START] [2019-10-11 23:39:10] completed
[STOP] [2019-10-11 23:39:10] completed
[STOP] [2019-10-11 23:39:10] logged process, took 507.19

Latest Process