Harvest for Guatemala Species List Created 26 Aug 13:35

Stage: completed
Fetched: 26 Aug 13:35
Validated: 26 Aug 13:35
Deltas Created 26 Aug 13:36
Units Normalized: 26 Aug 13:50
Ancestry Built: 26 Aug 13:40
Nodes Matched: 26 Aug 13:50
Names Parsed: 26 Aug 13:40
New Models Stored: 26 Aug 13:38
Indexed: 26 Aug 13:50
Completed: 26 Aug 13:56
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-08-26 13:35:42 -0400 by logger.rb/56815
[START] [2019-08-26 13:35:42] logged process
[START] [2019-08-26 13:35:42] create_harvest_instance
[STOP] [2019-08-26 13:35:43] create_harvest_instance
[START] [2019-08-26 13:35:43] fetch_files
[STOP] [2019-08-26 13:35:43] fetch_files
[START] [2019-08-26 13:35:43] validate_each_file
[STOP] [2019-08-26 13:35:45] validate_each_file
[START] [2019-08-26 13:35:45] convert_to_csv
[CMD] [2019-08-26 13:35:45] /usr/bin/sort /app/public/converted_csv/guatemala_sp_lis_refs_14489.csv > /app/public/converted_csv/guatemala_sp_lis_refs_14489.csv_sorted
[CMD] [2019-08-26 13:35:47] /usr/bin/sort /app/public/converted_csv/guatemala_sp_lis_nodes_14490.csv > /app/public/converted_csv/guatemala_sp_lis_nodes_14490.csv_sorted
[CMD] [2019-08-26 13:35:48] /usr/bin/sort /app/public/converted_csv/guatemala_sp_lis_occurrences_14491.csv > /app/public/converted_csv/guatemala_sp_lis_occurrences_14491.csv_sorted
[CMD] [2019-08-26 13:35:49] /usr/bin/sort /app/public/converted_csv/guatemala_sp_lis_measurements_14492.csv > /app/public/converted_csv/guatemala_sp_lis_measurements_14492.csv_sorted
[STOP] [2019-08-26 13:35:51] convert_to_csv
[START] [2019-08-26 13:35:51] calculate_delta
[CMD] [2019-08-26 13:35:51] echo "0a" > /app/public/diff/guatemala_sp_lis_refs_14489.diff
[CMD] [2019-08-26 13:35:52] tail -n +1 /app/public/converted_csv/guatemala_sp_lis_refs_14489.csv >> /app/public/diff/guatemala_sp_lis_refs_14489.diff
[CMD] [2019-08-26 13:35:53] echo "." >> /app/public/diff/guatemala_sp_lis_refs_14489.diff
[CMD] [2019-08-26 13:35:55] echo "0a" > /app/public/diff/guatemala_sp_lis_nodes_14490.diff
[CMD] [2019-08-26 13:35:56] tail -n +1 /app/public/converted_csv/guatemala_sp_lis_nodes_14490.csv >> /app/public/diff/guatemala_sp_lis_nodes_14490.diff
[CMD] [2019-08-26 13:35:57] echo "." >> /app/public/diff/guatemala_sp_lis_nodes_14490.diff
[CMD] [2019-08-26 13:35:59] echo "0a" > /app/public/diff/guatemala_sp_lis_occurrences_14491.diff
[CMD] [2019-08-26 13:36:00] tail -n +1 /app/public/converted_csv/guatemala_sp_lis_occurrences_14491.csv >> /app/public/diff/guatemala_sp_lis_occurrences_14491.diff
[CMD] [2019-08-26 13:36:01] echo "." >> /app/public/diff/guatemala_sp_lis_occurrences_14491.diff
[CMD] [2019-08-26 13:36:02] echo "0a" > /app/public/diff/guatemala_sp_lis_measurements_14492.diff
[CMD] [2019-08-26 13:36:04] tail -n +1 /app/public/converted_csv/guatemala_sp_lis_measurements_14492.csv >> /app/public/diff/guatemala_sp_lis_measurements_14492.diff
[CMD] [2019-08-26 13:36:05] echo "." >> /app/public/diff/guatemala_sp_lis_measurements_14492.diff
[STOP] [2019-08-26 13:36:06] calculate_delta
[START] [2019-08-26 13:36:06] parse_diff_and_store
[INFO] [2019-08-26 13:36:08] Loading refs diff file into memory (true lines)...
[INFO] [2019-08-26 13:36:09] Loading nodes diff file into memory (true lines)...
[INFO] [2019-08-26 13:36:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-08-26 13:36:21] Loading measurements diff file into memory (true lines)...
[INFO] [2019-08-26 13:37:37] Storing 2 References
[INFO] [2019-08-26 13:37:37] Processing group of 2 in 1 groups of 1000
[INFO] [2019-08-26 13:37:37] Average Time: 0.01
[INFO] [2019-08-26 13:37:37] Total Time: 1s
[INFO] [2019-08-26 13:37:37] Storing 18096 ScientificNames
[INFO] [2019-08-26 13:37:37] Processing group of 18096 in 19 groups of 1000
[INFO] [2019-08-26 13:37:44] Average Time: 0.383
[INFO] [2019-08-26 13:37:44] Total Time: 8s
[INFO] [2019-08-26 13:37:44] last 3 / first 3: 0.44
[INFO] [2019-08-26 13:37:44] Std.Dev: 0.130384048104053; Max: 0.67
[INFO] [2019-08-26 13:37:44] Storing 18096 Nodes
[INFO] [2019-08-26 13:37:44] Processing group of 18096 in 19 groups of 1000
[INFO] [2019-08-26 13:37:50] Average Time: 0.291
[INFO] [2019-08-26 13:37:50] Total Time: 6s
[INFO] [2019-08-26 13:37:50] last 3 / first 3: 0.73
[INFO] [2019-08-26 13:37:50] Std.Dev: 0.06324555320336758; Max: 0.34
[INFO] [2019-08-26 13:37:50] Storing 13013 Occurrences
[INFO] [2019-08-26 13:37:50] Processing group of 13013 in 14 groups of 1000
[INFO] [2019-08-26 13:37:51] Average Time: 0.101
[INFO] [2019-08-26 13:37:51] Total Time: 2s
[INFO] [2019-08-26 13:37:51] last 3 / first 3: 0.67
[INFO] [2019-08-26 13:37:51] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-08-26 13:37:51] Storing 26254 TraitsReferences
[INFO] [2019-08-26 13:37:51] Processing group of 26254 in 27 groups of 1000
[INFO] [2019-08-26 13:37:54] Average Time: 0.076
[INFO] [2019-08-26 13:37:54] Total Time: 3s
[INFO] [2019-08-26 13:37:54] last 3 / first 3: 0.5
[INFO] [2019-08-26 13:37:54] Std.Dev: 0.03162277660168379; Max: 0.18
[INFO] [2019-08-26 13:37:54] Storing 26253 Traits
[INFO] [2019-08-26 13:37:54] Processing group of 26253 in 27 groups of 1000
[INFO] [2019-08-26 13:38:03] Average Time: 0.334
[INFO] [2019-08-26 13:38:03] Total Time: 10s
[INFO] [2019-08-26 13:38:03] last 3 / first 3: 0.36
[INFO] [2019-08-26 13:38:03] Std.Dev: 0.11832159566199232; Max: 0.74
[INFO] [2019-08-26 13:38:03] Storing 26238 MetaTraits
[INFO] [2019-08-26 13:38:03] Processing group of 26238 in 27 groups of 1000
[INFO] [2019-08-26 13:38:06] Average Time: 0.127
[INFO] [2019-08-26 13:38:06] Total Time: 4s
[INFO] [2019-08-26 13:38:06] last 3 / first 3: 0.57
[INFO] [2019-08-26 13:38:06] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-08-26 13:38:06] parse_diff_and_store
[START] [2019-08-26 13:38:06] resolve_keys
[INFO] [2019-08-26 13:39:17] Occurrences to nodes (through scientific_names)...
[INFO] [2019-08-26 13:39:23] traits to occurrences...
[INFO] [2019-08-26 13:39:27] traits to nodes (through occurrences)...
[INFO] [2019-08-26 13:39:28] Traits to sex term...
[INFO] [2019-08-26 13:39:31] Traits to lifestage term...
[INFO] [2019-08-26 13:39:36] MetaTraits to traits...
[INFO] [2019-08-26 13:39:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-08-26 13:39:41] Assocs to occurrences...
[INFO] [2019-08-26 13:39:41] Assocs to nodes...
[INFO] [2019-08-26 13:39:41] Assoc to sex term...
[INFO] [2019-08-26 13:39:41] Assoc to lifestage term...
[STOP] [2019-08-26 13:39:41] resolve_keys
[START] [2019-08-26 13:39:41] hold_for_later_1
[STOP] [2019-08-26 13:39:41] hold_for_later_1
[START] [2019-08-26 13:39:41] hold_for_later_2
[STOP] [2019-08-26 13:39:41] hold_for_later_2
[START] [2019-08-26 13:39:41] resolve_missing_parents
[STOP] [2019-08-26 13:40:19] resolve_missing_parents
[START] [2019-08-26 13:40:19] rebuild_nodes
[START] [2019-08-26 13:40:19] Flattener#flatten
[START] [2019-08-26 13:40:19] Flattener#study_resource
[START] [2019-08-26 13:40:19] Flattener#build_ancestry
[STOP] [2019-08-26 13:40:20] Flattener#build_ancestry
[INFO] [2019-08-26 13:40:20] 18096 ancestry keys
[START] [2019-08-26 13:40:20] build_node_ancestors
[INFO] [2019-08-26 13:40:20] old ancestors deleted.
[STOP] [2019-08-26 13:40:24] build_node_ancestors
[START] [2019-08-26 13:40:27] Flattener#propagate_ancestor_ids
[STOP] [2019-08-26 13:40:29] Flattener#propagate_ancestor_ids
[STOP] [2019-08-26 13:40:29] Flattener#flatten
[STOP] [2019-08-26 13:40:29] rebuild_nodes
[START] [2019-08-26 13:40:29] resolve_missing_media_owners
[STOP] [2019-08-26 13:40:29] resolve_missing_media_owners
[START] [2019-08-26 13:40:29] sanitize_media_verbatims
[STOP] [2019-08-26 13:40:29] sanitize_media_verbatims
[START] [2019-08-26 13:40:29] queue_downloads
[STOP] [2019-08-26 13:40:29] queue_downloads
[START] [2019-08-26 13:40:29] parse_names
[WARN] [2019-08-26 13:40:29] I see 18096 names which still need to be parsed.
[STOP] [2019-08-26 13:40:43] parse_names
[START] [2019-08-26 13:40:43] denormalize_canonical_names_to_nodes
[STOP] [2019-08-26 13:40:43] denormalize_canonical_names_to_nodes
[START] [2019-08-26 13:40:43] match_nodes
[START] [2019-08-26 13:40:43] map_all_nodes_to_pages
[STOP] [2019-08-26 13:50:20] map_all_nodes_to_pages
[INFO] [2019-08-26 13:50:20] 1114 Unmatched nodes (of 18096)! That's too many to output. First 10: Molothrus oryzivora (#46000946); Attila flammulatus (#45998973); Pyrocephalus coronatus (#45996071); Thryothorus maculipectus (#45993396); Thryothorus modestus (#45996634); Thryothorus pleurostictus (#46002432); Sporophila funerea (#45992276); Geothlypis formosus (#45995969); Seiurus noveboracensis (#45996495); Seiurus aurocapillus (#45998344)
[START] [2019-08-26 13:50:20] update_nodes
[STOP] [2019-08-26 13:50:26] update_nodes
[STOP] [2019-08-26 13:50:26] match_nodes
[START] [2019-08-26 13:50:26] reindex_search
[STOP] [2019-08-26 13:50:59] reindex_search
[START] [2019-08-26 13:50:59] normalize_units
[STOP] [2019-08-26 13:50:59] normalize_units
[START] [2019-08-26 13:50:59] calculate_statistics
[STOP] [2019-08-26 13:50:59] calculate_statistics
[START] [2019-08-26 13:51:00] complete_harvest_instance
[START] [2019-08-26 13:51:00] overall_tsv_creation
[INFO] [2019-08-26 13:51:00] Processing group of 18096 in 2 batches of 10000
[INFO] [2019-08-26 13:52:28] 6599 Traits (unfiltered)...
[INFO] [2019-08-26 13:52:41] 6599 Traits (filtered)...
[INFO] [2019-08-26 13:52:41] 0 Associations (filtered)...
[INFO] [2019-08-26 13:53:30] 32989 metadata added.
[INFO] [2019-08-26 13:53:30] 0 metadata added.
[INFO] [2019-08-26 13:54:52] 6414 Traits (unfiltered)...
[INFO] [2019-08-26 13:55:05] 6414 Traits (filtered)...
[INFO] [2019-08-26 13:55:05] 0 Associations (filtered)...
[INFO] [2019-08-26 13:55:55] 32060 metadata added.
[INFO] [2019-08-26 13:55:55] 0 metadata added.
[INFO] [2019-08-26 13:55:55] Average Time: 120.865
[INFO] [2019-08-26 13:55:55] Total Time: 4m56s
[STOP] [2019-08-26 13:55:55] overall_tsv_creation
[INFO] [2019-08-26 13:55:55] Done. Check your files:
[INFO] [2019-08-26 13:55:56] (18096 lines) /app/public/data/guatemala_sp_lis/publish_nodes.tsv
[INFO] [2019-08-26 13:55:57] (47533 lines) /app/public/data/guatemala_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-08-26 13:55:59] (18096 lines) /app/public/data/guatemala_sp_lis/publish_scientific_names.tsv
[INFO] [2019-08-26 13:56:00] (13014 lines) /app/public/data/guatemala_sp_lis/publish_traits.tsv
[INFO] [2019-08-26 13:56:01] (65050 lines) /app/public/data/guatemala_sp_lis/publish_metadata.tsv
[STOP] [2019-08-26 13:56:01] complete_harvest_instance
[START] [2019-08-26 13:56:01] completed
[STOP] [2019-08-26 13:56:01] completed
[STOP] [2019-08-26 13:56:01] logged process, took 1219.45

Latest Process