Stage:
completed
Fetched:
01 Oct 16:58
Validated:
01 Oct 16:58
Deltas Created
01 Oct 16:58
Units Normalized:
01 Oct 17:09
Ancestry Built:
01 Oct 17:01
Nodes Matched:
01 Oct 17:09
Names Parsed:
01 Oct 17:01
New Models Stored:
01 Oct 16:59
Indexed:
01 Oct 17:09
Completed:
01 Oct 17:14
Time to Harvest:
less than a minute
Harvesting Log
(156 lines)
# Logfile created on 2019-10-01 16:58:03 -0400 by logger.rb/56815
[START] [2019-10-01 16:58:03] logged process
[START] [2019-10-01 16:58:03] create_harvest_instance
[STOP] [2019-10-01 16:58:03] create_harvest_instance
[START] [2019-10-01 16:58:03] fetch_files
[STOP] [2019-10-01 16:58:03] fetch_files
[START] [2019-10-01 16:58:03] validate_each_file
[STOP] [2019-10-01 16:58:05] validate_each_file
[START] [2019-10-01 16:58:05] convert_to_csv
[CMD] [2019-10-01 16:58:05] /usr/bin/sort /app/public/converted_csv/angola_sp_list_refs_14782.csv > /app/public/converted_csv/angola_sp_list_refs_14782.csv_sorted
[CMD] [2019-10-01 16:58:06] /usr/bin/sort /app/public/converted_csv/angola_sp_list_nodes_14783.csv > /app/public/converted_csv/angola_sp_list_nodes_14783.csv_sorted
[CMD] [2019-10-01 16:58:08] /usr/bin/sort /app/public/converted_csv/angola_sp_list_occurrences_14784.csv > /app/public/converted_csv/angola_sp_list_occurrences_14784.csv_sorted
[CMD] [2019-10-01 16:58:09] /usr/bin/sort /app/public/converted_csv/angola_sp_list_measurements_14785.csv > /app/public/converted_csv/angola_sp_list_measurements_14785.csv_sorted
[STOP] [2019-10-01 16:58:11] convert_to_csv
[START] [2019-10-01 16:58:11] calculate_delta
[CMD] [2019-10-01 16:58:11] echo "0a" > /app/public/diff/angola_sp_list_refs_14782.diff
[CMD] [2019-10-01 16:58:12] tail -n +1 /app/public/converted_csv/angola_sp_list_refs_14782.csv >> /app/public/diff/angola_sp_list_refs_14782.diff
[CMD] [2019-10-01 16:58:14] echo "." >> /app/public/diff/angola_sp_list_refs_14782.diff
[CMD] [2019-10-01 16:58:15] echo "0a" > /app/public/diff/angola_sp_list_nodes_14783.diff
[CMD] [2019-10-01 16:58:17] tail -n +1 /app/public/converted_csv/angola_sp_list_nodes_14783.csv >> /app/public/diff/angola_sp_list_nodes_14783.diff
[CMD] [2019-10-01 16:58:18] echo "." >> /app/public/diff/angola_sp_list_nodes_14783.diff
[CMD] [2019-10-01 16:58:20] echo "0a" > /app/public/diff/angola_sp_list_occurrences_14784.diff
[CMD] [2019-10-01 16:58:21] tail -n +1 /app/public/converted_csv/angola_sp_list_occurrences_14784.csv >> /app/public/diff/angola_sp_list_occurrences_14784.diff
[CMD] [2019-10-01 16:58:23] echo "." >> /app/public/diff/angola_sp_list_occurrences_14784.diff
[CMD] [2019-10-01 16:58:24] echo "0a" > /app/public/diff/angola_sp_list_measurements_14785.diff
[CMD] [2019-10-01 16:58:26] tail -n +1 /app/public/converted_csv/angola_sp_list_measurements_14785.csv >> /app/public/diff/angola_sp_list_measurements_14785.diff
[CMD] [2019-10-01 16:58:27] echo "." >> /app/public/diff/angola_sp_list_measurements_14785.diff
[STOP] [2019-10-01 16:58:29] calculate_delta
[START] [2019-10-01 16:58:29] parse_diff_and_store
[INFO] [2019-10-01 16:58:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-01 16:58:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-01 16:58:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-01 16:58:40] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-01 16:59:24] Storing 2 References
[INFO] [2019-10-01 16:59:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-01 16:59:24] Average Time: 0.0
[INFO] [2019-10-01 16:59:24] Total Time: 1s
[INFO] [2019-10-01 16:59:24] Storing 11636 ScientificNames
[INFO] [2019-10-01 16:59:24] Processing group of 11636 in 12 groups of 1000
[INFO] [2019-10-01 16:59:28] Average Time: 0.326
[INFO] [2019-10-01 16:59:28] Total Time: 4s
[INFO] [2019-10-01 16:59:28] last 3 / first 3: 0.76
[INFO] [2019-10-01 16:59:28] Std.Dev: 0.044721359549995794; Max: 0.38
[INFO] [2019-10-01 16:59:28] Storing 11636 Nodes
[INFO] [2019-10-01 16:59:28] Processing group of 11636 in 12 groups of 1000
[INFO] [2019-10-01 16:59:31] Average Time: 0.278
[INFO] [2019-10-01 16:59:31] Total Time: 4s
[INFO] [2019-10-01 16:59:31] last 3 / first 3: 0.87
[INFO] [2019-10-01 16:59:31] Std.Dev: 0.044721359549995794; Max: 0.35
[INFO] [2019-10-01 16:59:31] Storing 7712 Occurrences
[INFO] [2019-10-01 16:59:31] Processing group of 7712 in 8 groups of 1000
[INFO] [2019-10-01 16:59:32] Average Time: 0.094
[INFO] [2019-10-01 16:59:32] Total Time: 1s
[INFO] [2019-10-01 16:59:32] last 3 / first 3: 0.97
[INFO] [2019-10-01 16:59:32] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-01 16:59:32] Storing 15750 TraitsReferences
[INFO] [2019-10-01 16:59:32] Processing group of 15750 in 16 groups of 1000
[INFO] [2019-10-01 16:59:33] Average Time: 0.079
[INFO] [2019-10-01 16:59:33] Total Time: 2s
[INFO] [2019-10-01 16:59:33] last 3 / first 3: 0.5
[INFO] [2019-10-01 16:59:33] Std.Dev: 0.03162277660168379; Max: 0.22
[INFO] [2019-10-01 16:59:33] Storing 15749 Traits
[INFO] [2019-10-01 16:59:33] Processing group of 15749 in 16 groups of 1000
[INFO] [2019-10-01 16:59:39] Average Time: 0.353
[INFO] [2019-10-01 16:59:39] Total Time: 6s
[INFO] [2019-10-01 16:59:39] last 3 / first 3: 0.85
[INFO] [2019-10-01 16:59:39] Std.Dev: 0.14491376746189438; Max: 0.88
[INFO] [2019-10-01 16:59:39] Storing 15735 MetaTraits
[INFO] [2019-10-01 16:59:39] Processing group of 15735 in 16 groups of 1000
[INFO] [2019-10-01 16:59:41] Average Time: 0.141
[INFO] [2019-10-01 16:59:41] Total Time: 3s
[INFO] [2019-10-01 16:59:41] last 3 / first 3: 0.91
[INFO] [2019-10-01 16:59:41] Std.Dev: 0.0; Max: 0.18
[STOP] [2019-10-01 16:59:41] parse_diff_and_store
[START] [2019-10-01 16:59:41] resolve_keys
[INFO] [2019-10-01 17:00:28] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-01 17:00:32] traits to occurrences...
[INFO] [2019-10-01 17:00:37] traits to nodes (through occurrences)...
[INFO] [2019-10-01 17:00:37] Traits to sex term...
[INFO] [2019-10-01 17:00:42] Traits to lifestage term...
[INFO] [2019-10-01 17:00:46] MetaTraits to traits...
[INFO] [2019-10-01 17:00:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-01 17:00:49] Assocs to occurrences...
[INFO] [2019-10-01 17:00:49] Assocs to nodes...
[INFO] [2019-10-01 17:00:49] Assoc to sex term...
[INFO] [2019-10-01 17:00:49] Assoc to lifestage term...
[STOP] [2019-10-01 17:00:49] resolve_keys
[START] [2019-10-01 17:00:49] hold_for_later_1
[STOP] [2019-10-01 17:00:49] hold_for_later_1
[START] [2019-10-01 17:00:49] hold_for_later_2
[STOP] [2019-10-01 17:00:50] hold_for_later_2
[START] [2019-10-01 17:00:50] resolve_missing_parents
[STOP] [2019-10-01 17:01:15] resolve_missing_parents
[START] [2019-10-01 17:01:15] rebuild_nodes
[START] [2019-10-01 17:01:15] Flattener#flatten
[START] [2019-10-01 17:01:15] Flattener#study_resource
[START] [2019-10-01 17:01:15] Flattener#build_ancestry
[STOP] [2019-10-01 17:01:16] Flattener#build_ancestry
[INFO] [2019-10-01 17:01:16] 11636 ancestry keys
[START] [2019-10-01 17:01:16] build_node_ancestors
[INFO] [2019-10-01 17:01:16] old ancestors deleted.
[STOP] [2019-10-01 17:01:18] build_node_ancestors
[START] [2019-10-01 17:01:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 17:01:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 17:01:21] Flattener#flatten
[STOP] [2019-10-01 17:01:21] rebuild_nodes
[START] [2019-10-01 17:01:21] resolve_missing_media_owners
[STOP] [2019-10-01 17:01:21] resolve_missing_media_owners
[START] [2019-10-01 17:01:21] sanitize_media_verbatims
[STOP] [2019-10-01 17:01:21] sanitize_media_verbatims
[START] [2019-10-01 17:01:21] queue_downloads
[STOP] [2019-10-01 17:01:21] queue_downloads
[START] [2019-10-01 17:01:21] parse_names
[WARN] [2019-10-01 17:01:21] I see 11636 names which still need to be parsed.
[STOP] [2019-10-01 17:01:30] parse_names
[START] [2019-10-01 17:01:30] denormalize_canonical_names_to_nodes
[STOP] [2019-10-01 17:01:30] denormalize_canonical_names_to_nodes
[START] [2019-10-01 17:01:30] match_nodes
[START] [2019-10-01 17:01:30] map_all_nodes_to_pages
[STOP] [2019-10-01 17:09:19] map_all_nodes_to_pages
[INFO] [2019-10-01 17:09:19] 615 Unmatched nodes (of 11636)! That's too many to output. First 10: Meliponula lendliana (#47370245); Axestotrigona erythra (#47369758); Epiclopus lendliana (#47370238); Leptothorax ambigua (#47379510); Megachile caerulea (#47379386); Lipotriches junodiella (#47380764); Gerbilliscus valida (#47369599); Myomyscus angolae (#47369566); Steatomys leucorhynchus (#47373775); Dendromus typica (#47379440)
[START] [2019-10-01 17:09:19] update_nodes
[STOP] [2019-10-01 17:09:23] update_nodes
[STOP] [2019-10-01 17:09:23] match_nodes
[START] [2019-10-01 17:09:23] reindex_search
[STOP] [2019-10-01 17:09:48] reindex_search
[START] [2019-10-01 17:09:48] normalize_units
[STOP] [2019-10-01 17:09:48] normalize_units
[START] [2019-10-01 17:09:48] calculate_statistics
[STOP] [2019-10-01 17:09:48] calculate_statistics
[START] [2019-10-01 17:09:48] complete_harvest_instance
[START] [2019-10-01 17:09:48] overall_tsv_creation
[INFO] [2019-10-01 17:09:48] Processing group of 11636 in 2 batches of 10000
[INFO] [2019-10-01 17:11:15] 6594 Traits (unfiltered)...
[INFO] [2019-10-01 17:11:28] 6594 Traits (filtered)...
[INFO] [2019-10-01 17:11:28] 0 Associations (filtered)...
[INFO] [2019-10-01 17:12:16] 32960 metadata added.
[INFO] [2019-10-01 17:12:16] 0 metadata added.
[INFO] [2019-10-01 17:13:07] 1118 Traits (unfiltered)...
[INFO] [2019-10-01 17:13:19] 1118 Traits (filtered)...
[INFO] [2019-10-01 17:13:19] 0 Associations (filtered)...
[INFO] [2019-10-01 17:13:57] 5585 metadata added.
[INFO] [2019-10-01 17:13:57] 0 metadata added.
[INFO] [2019-10-01 17:13:57] Average Time: 99.795
[INFO] [2019-10-01 17:13:57] Total Time: 4m10s
[STOP] [2019-10-01 17:13:57] overall_tsv_creation
[INFO] [2019-10-01 17:13:57] Done. Check your files:
[INFO] [2019-10-01 17:13:59] (11636 lines) /app/public/data/angola_sp_list/publish_nodes.tsv
[INFO] [2019-10-01 17:14:00] (29523 lines) /app/public/data/angola_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-01 17:14:02] (11636 lines) /app/public/data/angola_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-01 17:14:03] (7713 lines) /app/public/data/angola_sp_list/publish_traits.tsv
[INFO] [2019-10-01 17:14:05] (38546 lines) /app/public/data/angola_sp_list/publish_metadata.tsv
[STOP] [2019-10-01 17:14:05] complete_harvest_instance
[START] [2019-10-01 17:14:05] completed
[STOP] [2019-10-01 17:14:05] completed
[STOP] [2019-10-01 17:14:05] logged process, took 962.22
Latest Process