Harvest for Haiti Species List Created 13 Oct 10:27

Stage: completed
Fetched: 13 Oct 10:27
Validated: 13 Oct 10:27
Deltas Created 13 Oct 10:27
Units Normalized: 13 Oct 10:35
Ancestry Built: 13 Oct 10:29
Nodes Matched: 13 Oct 10:35
Names Parsed: 13 Oct 10:29
New Models Stored: 13 Oct 10:28
Indexed: 13 Oct 10:35
Completed: 13 Oct 10:37
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-13 10:27:55 -0400 by logger.rb/56815
[START] [2019-10-13 10:27:55] logged process
[START] [2019-10-13 10:27:55] create_harvest_instance
[STOP] [2019-10-13 10:27:55] create_harvest_instance
[START] [2019-10-13 10:27:55] fetch_files
[STOP] [2019-10-13 10:27:55] fetch_files
[START] [2019-10-13 10:27:55] validate_each_file
[STOP] [2019-10-13 10:27:56] validate_each_file
[START] [2019-10-13 10:27:56] convert_to_csv
[CMD] [2019-10-13 10:27:56] /usr/bin/sort /app/public/converted_csv/haiti_sp_list_refs_16075.csv > /app/public/converted_csv/haiti_sp_list_refs_16075.csv_sorted
[CMD] [2019-10-13 10:27:56] /usr/bin/sort /app/public/converted_csv/haiti_sp_list_nodes_16076.csv > /app/public/converted_csv/haiti_sp_list_nodes_16076.csv_sorted
[CMD] [2019-10-13 10:27:56] /usr/bin/sort /app/public/converted_csv/haiti_sp_list_occurrences_16077.csv > /app/public/converted_csv/haiti_sp_list_occurrences_16077.csv_sorted
[CMD] [2019-10-13 10:27:57] /usr/bin/sort /app/public/converted_csv/haiti_sp_list_measurements_16078.csv > /app/public/converted_csv/haiti_sp_list_measurements_16078.csv_sorted
[STOP] [2019-10-13 10:27:57] convert_to_csv
[START] [2019-10-13 10:27:57] calculate_delta
[CMD] [2019-10-13 10:27:57] echo "0a" > /app/public/diff/haiti_sp_list_refs_16075.diff
[CMD] [2019-10-13 10:27:57] tail -n +1 /app/public/converted_csv/haiti_sp_list_refs_16075.csv >> /app/public/diff/haiti_sp_list_refs_16075.diff
[CMD] [2019-10-13 10:27:57] echo "." >> /app/public/diff/haiti_sp_list_refs_16075.diff
[CMD] [2019-10-13 10:27:57] echo "0a" > /app/public/diff/haiti_sp_list_nodes_16076.diff
[CMD] [2019-10-13 10:27:57] tail -n +1 /app/public/converted_csv/haiti_sp_list_nodes_16076.csv >> /app/public/diff/haiti_sp_list_nodes_16076.diff
[CMD] [2019-10-13 10:27:57] echo "." >> /app/public/diff/haiti_sp_list_nodes_16076.diff
[CMD] [2019-10-13 10:27:57] echo "0a" > /app/public/diff/haiti_sp_list_occurrences_16077.diff
[CMD] [2019-10-13 10:27:57] tail -n +1 /app/public/converted_csv/haiti_sp_list_occurrences_16077.csv >> /app/public/diff/haiti_sp_list_occurrences_16077.diff
[CMD] [2019-10-13 10:27:57] echo "." >> /app/public/diff/haiti_sp_list_occurrences_16077.diff
[CMD] [2019-10-13 10:27:57] echo "0a" > /app/public/diff/haiti_sp_list_measurements_16078.diff
[CMD] [2019-10-13 10:27:58] tail -n +1 /app/public/converted_csv/haiti_sp_list_measurements_16078.csv >> /app/public/diff/haiti_sp_list_measurements_16078.diff
[CMD] [2019-10-13 10:27:58] echo "." >> /app/public/diff/haiti_sp_list_measurements_16078.diff
[STOP] [2019-10-13 10:27:58] calculate_delta
[START] [2019-10-13 10:27:58] parse_diff_and_store
[INFO] [2019-10-13 10:27:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 10:27:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 10:28:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 10:28:01] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 10:28:20] Storing 2 References
[INFO] [2019-10-13 10:28:20] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 10:28:20] Average Time: 0.0
[INFO] [2019-10-13 10:28:20] Total Time: 1s
[INFO] [2019-10-13 10:28:20] Storing 5290 ScientificNames
[INFO] [2019-10-13 10:28:20] Processing group of 5290 in 6 groups of 1000
[INFO] [2019-10-13 10:28:22] Average Time: 0.315
[INFO] [2019-10-13 10:28:22] Total Time: 2s
[INFO] [2019-10-13 10:28:22] Storing 5290 Nodes
[INFO] [2019-10-13 10:28:22] Processing group of 5290 in 6 groups of 1000
[INFO] [2019-10-13 10:28:24] Average Time: 0.332
[INFO] [2019-10-13 10:28:24] Total Time: 3s
[INFO] [2019-10-13 10:28:24] Storing 2892 Occurrences
[INFO] [2019-10-13 10:28:24] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-13 10:28:24] Average Time: 0.1
[INFO] [2019-10-13 10:28:24] Total Time: 1s
[INFO] [2019-10-13 10:28:24] Storing 6108 TraitsReferences
[INFO] [2019-10-13 10:28:24] Processing group of 6108 in 7 groups of 1000
[INFO] [2019-10-13 10:28:25] Average Time: 0.064
[INFO] [2019-10-13 10:28:25] Total Time: 1s
[INFO] [2019-10-13 10:28:25] last 3 / first 3: 0.5
[INFO] [2019-10-13 10:28:25] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-13 10:28:25] Storing 6107 Traits
[INFO] [2019-10-13 10:28:25] Processing group of 6107 in 7 groups of 1000
[INFO] [2019-10-13 10:28:27] Average Time: 0.301
[INFO] [2019-10-13 10:28:27] Total Time: 3s
[INFO] [2019-10-13 10:28:27] last 3 / first 3: 0.62
[INFO] [2019-10-13 10:28:27] Std.Dev: 0.1341640786499874; Max: 0.47
[INFO] [2019-10-13 10:28:27] Storing 6105 MetaTraits
[INFO] [2019-10-13 10:28:27] Processing group of 6105 in 7 groups of 1000
[INFO] [2019-10-13 10:28:28] Average Time: 0.126
[INFO] [2019-10-13 10:28:28] Total Time: 1s
[INFO] [2019-10-13 10:28:28] last 3 / first 3: 0.79
[INFO] [2019-10-13 10:28:28] Std.Dev: 0.05477225575051661; Max: 0.19
[STOP] [2019-10-13 10:28:28] parse_diff_and_store
[START] [2019-10-13 10:28:28] resolve_keys
[INFO] [2019-10-13 10:28:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 10:28:55] traits to occurrences...
[INFO] [2019-10-13 10:28:56] traits to nodes (through occurrences)...
[INFO] [2019-10-13 10:28:56] Traits to sex term...
[INFO] [2019-10-13 10:28:57] Traits to lifestage term...
[INFO] [2019-10-13 10:28:58] MetaTraits to traits...
[INFO] [2019-10-13 10:28:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 10:29:00] Assocs to occurrences...
[INFO] [2019-10-13 10:29:00] Assocs to nodes...
[INFO] [2019-10-13 10:29:00] Assoc to sex term...
[INFO] [2019-10-13 10:29:00] Assoc to lifestage term...
[STOP] [2019-10-13 10:29:00] resolve_keys
[START] [2019-10-13 10:29:00] hold_for_later_1
[STOP] [2019-10-13 10:29:00] hold_for_later_1
[START] [2019-10-13 10:29:00] hold_for_later_2
[STOP] [2019-10-13 10:29:00] hold_for_later_2
[START] [2019-10-13 10:29:00] resolve_missing_parents
[STOP] [2019-10-13 10:29:12] resolve_missing_parents
[START] [2019-10-13 10:29:12] rebuild_nodes
[START] [2019-10-13 10:29:12] Flattener#flatten
[START] [2019-10-13 10:29:12] Flattener#study_resource
[START] [2019-10-13 10:29:12] Flattener#build_ancestry
[STOP] [2019-10-13 10:29:12] Flattener#build_ancestry
[INFO] [2019-10-13 10:29:12] 5290 ancestry keys
[START] [2019-10-13 10:29:12] build_node_ancestors
[INFO] [2019-10-13 10:29:12] old ancestors deleted.
[STOP] [2019-10-13 10:29:13] build_node_ancestors
[START] [2019-10-13 10:29:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:29:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:29:14] Flattener#flatten
[STOP] [2019-10-13 10:29:14] rebuild_nodes
[START] [2019-10-13 10:29:14] resolve_missing_media_owners
[STOP] [2019-10-13 10:29:14] resolve_missing_media_owners
[START] [2019-10-13 10:29:14] sanitize_media_verbatims
[STOP] [2019-10-13 10:29:14] sanitize_media_verbatims
[START] [2019-10-13 10:29:14] queue_downloads
[STOP] [2019-10-13 10:29:14] queue_downloads
[START] [2019-10-13 10:29:14] parse_names
[WARN] [2019-10-13 10:29:14] I see 5290 names which still need to be parsed.
[STOP] [2019-10-13 10:29:19] parse_names
[START] [2019-10-13 10:29:19] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 10:29:19] denormalize_canonical_names_to_nodes
[START] [2019-10-13 10:29:19] match_nodes
[START] [2019-10-13 10:29:19] map_all_nodes_to_pages
[STOP] [2019-10-13 10:35:01] map_all_nodes_to_pages
[INFO] [2019-10-13 10:35:01] 398 Unmatched nodes (of 5290)! That's too many to output. First 10: Anolis wetmorei (#50063369); Anolis chlorocyaneus (#50063630); Norops (#50066534); Ameiva chrysolaema (#50061902); Ameiva taeniura (#50061906); Antillophis (#50061917); Antillophis alleni (#50064339); Ialtris wnigrum (#50065309); Liophis (#50062980); Alsophis portoricensis (#50066929)
[START] [2019-10-13 10:35:01] update_nodes
[STOP] [2019-10-13 10:35:03] update_nodes
[STOP] [2019-10-13 10:35:03] match_nodes
[START] [2019-10-13 10:35:03] reindex_search
[STOP] [2019-10-13 10:35:20] reindex_search
[START] [2019-10-13 10:35:20] normalize_units
[STOP] [2019-10-13 10:35:20] normalize_units
[START] [2019-10-13 10:35:20] calculate_statistics
[STOP] [2019-10-13 10:35:20] calculate_statistics
[START] [2019-10-13 10:35:20] complete_harvest_instance
[START] [2019-10-13 10:35:20] overall_tsv_creation
[INFO] [2019-10-13 10:35:20] Processing group of 5290 in 1 batches of 10000
[INFO] [2019-10-13 10:36:28] 2892 Traits (unfiltered)...
[INFO] [2019-10-13 10:36:42] 2892 Traits (filtered)...
[INFO] [2019-10-13 10:36:42] 0 Associations (filtered)...
[INFO] [2019-10-13 10:37:26] 14457 metadata added.
[INFO] [2019-10-13 10:37:26] 0 metadata added.
[INFO] [2019-10-13 10:37:26] Average Time: 102.55
[INFO] [2019-10-13 10:37:26] Total Time: 2m7s
[STOP] [2019-10-13 10:37:26] overall_tsv_creation
[INFO] [2019-10-13 10:37:26] Done. Check your files:
[INFO] [2019-10-13 10:37:26] (5290 lines) /app/public/data/haiti_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 10:37:26] (11732 lines) /app/public/data/haiti_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 10:37:26] (5290 lines) /app/public/data/haiti_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 10:37:26] (2893 lines) /app/public/data/haiti_sp_list/publish_traits.tsv
[INFO] [2019-10-13 10:37:27] (14458 lines) /app/public/data/haiti_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 10:37:27] complete_harvest_instance
[START] [2019-10-13 10:37:27] completed
[STOP] [2019-10-13 10:37:27] completed
[STOP] [2019-10-13 10:37:27] logged process, took 571.9
Latest Process

13 Oct 10:27 EXITED currently processing 0