Harvest for Ukraine Species List Created 16 Oct 20:11

Stage: completed
Fetched: 16 Oct 20:11
Validated: 16 Oct 20:11
Deltas Created 16 Oct 20:11
Units Normalized: 16 Oct 20:20
Ancestry Built: 16 Oct 20:12
Nodes Matched: 16 Oct 20:20
Names Parsed: 16 Oct 20:13
New Models Stored: 16 Oct 20:11
Indexed: 16 Oct 20:20
Completed: 16 Oct 20:23
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-16 20:11:26 -0400 by logger.rb/56815
[START] [2019-10-16 20:11:26] logged process
[START] [2019-10-16 20:11:27] create_harvest_instance
[STOP] [2019-10-16 20:11:27] create_harvest_instance
[START] [2019-10-16 20:11:27] fetch_files
[STOP] [2019-10-16 20:11:27] fetch_files
[START] [2019-10-16 20:11:27] validate_each_file
[STOP] [2019-10-16 20:11:28] validate_each_file
[START] [2019-10-16 20:11:28] convert_to_csv
[CMD] [2019-10-16 20:11:28] /usr/bin/sort /app/public/converted_csv/ukraine_sp_list_refs_17609.csv > /app/public/converted_csv/ukraine_sp_list_refs_17609.csv_sorted
[CMD] [2019-10-16 20:11:28] /usr/bin/sort /app/public/converted_csv/ukraine_sp_list_nodes_17610.csv > /app/public/converted_csv/ukraine_sp_list_nodes_17610.csv_sorted
[CMD] [2019-10-16 20:11:28] /usr/bin/sort /app/public/converted_csv/ukraine_sp_list_occurrences_17611.csv > /app/public/converted_csv/ukraine_sp_list_occurrences_17611.csv_sorted
[CMD] [2019-10-16 20:11:28] /usr/bin/sort /app/public/converted_csv/ukraine_sp_list_measurements_17612.csv > /app/public/converted_csv/ukraine_sp_list_measurements_17612.csv_sorted
[STOP] [2019-10-16 20:11:28] convert_to_csv
[START] [2019-10-16 20:11:28] calculate_delta
[CMD] [2019-10-16 20:11:28] echo "0a" > /app/public/diff/ukraine_sp_list_refs_17609.diff
[CMD] [2019-10-16 20:11:29] tail -n +1 /app/public/converted_csv/ukraine_sp_list_refs_17609.csv >> /app/public/diff/ukraine_sp_list_refs_17609.diff
[CMD] [2019-10-16 20:11:29] echo "." >> /app/public/diff/ukraine_sp_list_refs_17609.diff
[CMD] [2019-10-16 20:11:29] echo "0a" > /app/public/diff/ukraine_sp_list_nodes_17610.diff
[CMD] [2019-10-16 20:11:29] tail -n +1 /app/public/converted_csv/ukraine_sp_list_nodes_17610.csv >> /app/public/diff/ukraine_sp_list_nodes_17610.diff
[CMD] [2019-10-16 20:11:29] echo "." >> /app/public/diff/ukraine_sp_list_nodes_17610.diff
[CMD] [2019-10-16 20:11:29] echo "0a" > /app/public/diff/ukraine_sp_list_occurrences_17611.diff
[CMD] [2019-10-16 20:11:29] tail -n +1 /app/public/converted_csv/ukraine_sp_list_occurrences_17611.csv >> /app/public/diff/ukraine_sp_list_occurrences_17611.diff
[CMD] [2019-10-16 20:11:29] echo "." >> /app/public/diff/ukraine_sp_list_occurrences_17611.diff
[CMD] [2019-10-16 20:11:29] echo "0a" > /app/public/diff/ukraine_sp_list_measurements_17612.diff
[CMD] [2019-10-16 20:11:29] tail -n +1 /app/public/converted_csv/ukraine_sp_list_measurements_17612.csv >> /app/public/diff/ukraine_sp_list_measurements_17612.diff
[CMD] [2019-10-16 20:11:29] echo "." >> /app/public/diff/ukraine_sp_list_measurements_17612.diff
[STOP] [2019-10-16 20:11:29] calculate_delta
[START] [2019-10-16 20:11:29] parse_diff_and_store
[INFO] [2019-10-16 20:11:29] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 20:11:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 20:11:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 20:11:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 20:11:51] Storing 2 References
[INFO] [2019-10-16 20:11:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 20:11:51] Average Time: 0.01
[INFO] [2019-10-16 20:11:51] Total Time: 1s
[INFO] [2019-10-16 20:11:51] Storing 6030 ScientificNames
[INFO] [2019-10-16 20:11:51] Processing group of 6030 in 7 groups of 1000
[INFO] [2019-10-16 20:11:53] Average Time: 0.316
[INFO] [2019-10-16 20:11:53] Total Time: 3s
[INFO] [2019-10-16 20:11:53] last 3 / first 3: 0.59
[INFO] [2019-10-16 20:11:53] Std.Dev: 0.14491376746189438; Max: 0.48
[INFO] [2019-10-16 20:11:53] Storing 6030 Nodes
[INFO] [2019-10-16 20:11:53] Processing group of 6030 in 7 groups of 1000
[INFO] [2019-10-16 20:11:55] Average Time: 0.264
[INFO] [2019-10-16 20:11:55] Total Time: 2s
[INFO] [2019-10-16 20:11:55] last 3 / first 3: 0.64
[INFO] [2019-10-16 20:11:55] Std.Dev: 0.11832159566199232; Max: 0.39
[INFO] [2019-10-16 20:11:55] Storing 3374 Occurrences
[INFO] [2019-10-16 20:11:55] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-16 20:11:56] Average Time: 0.085
[INFO] [2019-10-16 20:11:56] Total Time: 1s
[INFO] [2019-10-16 20:11:56] Storing 6980 TraitsReferences
[INFO] [2019-10-16 20:11:56] Processing group of 6980 in 7 groups of 1000
[INFO] [2019-10-16 20:11:56] Average Time: 0.079
[INFO] [2019-10-16 20:11:56] Total Time: 1s
[INFO] [2019-10-16 20:11:56] last 3 / first 3: 0.75
[INFO] [2019-10-16 20:11:56] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-16 20:11:56] Storing 6979 Traits
[INFO] [2019-10-16 20:11:56] Processing group of 6979 in 7 groups of 1000
[INFO] [2019-10-16 20:11:58] Average Time: 0.307
[INFO] [2019-10-16 20:11:58] Total Time: 3s
[INFO] [2019-10-16 20:11:58] last 3 / first 3: 0.76
[INFO] [2019-10-16 20:11:58] Std.Dev: 0.06324555320336758; Max: 0.4
[INFO] [2019-10-16 20:11:58] Storing 6970 MetaTraits
[INFO] [2019-10-16 20:11:58] Processing group of 6970 in 7 groups of 1000
[INFO] [2019-10-16 20:11:59] Average Time: 0.113
[INFO] [2019-10-16 20:11:59] Total Time: 1s
[INFO] [2019-10-16 20:11:59] last 3 / first 3: 0.86
[INFO] [2019-10-16 20:11:59] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-16 20:11:59] parse_diff_and_store
[START] [2019-10-16 20:11:59] resolve_keys
[INFO] [2019-10-16 20:12:26] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 20:12:29] traits to occurrences...
[INFO] [2019-10-16 20:12:32] traits to nodes (through occurrences)...
[INFO] [2019-10-16 20:12:32] Traits to sex term...
[INFO] [2019-10-16 20:12:35] Traits to lifestage term...
[INFO] [2019-10-16 20:12:38] MetaTraits to traits...
[INFO] [2019-10-16 20:12:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 20:12:39] Assocs to occurrences...
[INFO] [2019-10-16 20:12:39] Assocs to nodes...
[INFO] [2019-10-16 20:12:39] Assoc to sex term...
[INFO] [2019-10-16 20:12:39] Assoc to lifestage term...
[STOP] [2019-10-16 20:12:39] resolve_keys
[START] [2019-10-16 20:12:39] hold_for_later_1
[STOP] [2019-10-16 20:12:39] hold_for_later_1
[START] [2019-10-16 20:12:39] hold_for_later_2
[STOP] [2019-10-16 20:12:39] hold_for_later_2
[START] [2019-10-16 20:12:39] resolve_missing_parents
[STOP] [2019-10-16 20:12:51] resolve_missing_parents
[START] [2019-10-16 20:12:51] rebuild_nodes
[START] [2019-10-16 20:12:51] Flattener#flatten
[START] [2019-10-16 20:12:51] Flattener#study_resource
[START] [2019-10-16 20:12:51] Flattener#build_ancestry
[STOP] [2019-10-16 20:12:53] Flattener#build_ancestry
[INFO] [2019-10-16 20:12:53] 6030 ancestry keys
[START] [2019-10-16 20:12:53] build_node_ancestors
[INFO] [2019-10-16 20:12:53] old ancestors deleted.
[STOP] [2019-10-16 20:12:54] build_node_ancestors
[START] [2019-10-16 20:12:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 20:12:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 20:12:55] Flattener#flatten
[STOP] [2019-10-16 20:12:55] rebuild_nodes
[START] [2019-10-16 20:12:55] resolve_missing_media_owners
[STOP] [2019-10-16 20:12:55] resolve_missing_media_owners
[START] [2019-10-16 20:12:55] sanitize_media_verbatims
[STOP] [2019-10-16 20:12:55] sanitize_media_verbatims
[START] [2019-10-16 20:12:56] queue_downloads
[STOP] [2019-10-16 20:12:56] queue_downloads
[START] [2019-10-16 20:12:56] parse_names
[WARN] [2019-10-16 20:12:56] I see 6030 names which still need to be parsed.
[STOP] [2019-10-16 20:13:01] parse_names
[START] [2019-10-16 20:13:01] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 20:13:01] denormalize_canonical_names_to_nodes
[START] [2019-10-16 20:13:01] match_nodes
[START] [2019-10-16 20:13:01] map_all_nodes_to_pages
[STOP] [2019-10-16 20:20:39] map_all_nodes_to_pages
[INFO] [2019-10-16 20:20:39] 752 Unmatched nodes (of 6030)! That's too many to output. First 10: Parus caeruleus (#52554926); Parus ater (#52555906); Parus cristatus (#52557906); Corvus monedula (#52553853); Delichon urbica (#52554455); Carduelis spinus (#52553993); Carduelis cannabina (#52554132); Carduelis chloris (#52554887); Calandrella rufescens (#52554223); Phylloscopus sibillatrix (#52553444)
[START] [2019-10-16 20:20:39] update_nodes
[STOP] [2019-10-16 20:20:41] update_nodes
[STOP] [2019-10-16 20:20:41] match_nodes
[START] [2019-10-16 20:20:41] reindex_search
[STOP] [2019-10-16 20:20:59] reindex_search
[START] [2019-10-16 20:20:59] normalize_units
[STOP] [2019-10-16 20:20:59] normalize_units
[START] [2019-10-16 20:20:59] calculate_statistics
[STOP] [2019-10-16 20:20:59] calculate_statistics
[START] [2019-10-16 20:20:59] complete_harvest_instance
[START] [2019-10-16 20:20:59] overall_tsv_creation
[INFO] [2019-10-16 20:20:59] Processing group of 6030 in 1 batches of 10000
[INFO] [2019-10-16 20:22:09] 3374 Traits (unfiltered)...
[INFO] [2019-10-16 20:22:22] 3374 Traits (filtered)...
[INFO] [2019-10-16 20:22:22] 0 Associations (filtered)...
[INFO] [2019-10-16 20:23:06] 16862 metadata added.
[INFO] [2019-10-16 20:23:06] 0 metadata added.
[INFO] [2019-10-16 20:23:06] Average Time: 102.41
[INFO] [2019-10-16 20:23:06] Total Time: 2m8s
[STOP] [2019-10-16 20:23:06] overall_tsv_creation
[INFO] [2019-10-16 20:23:06] Done. Check your files:
[INFO] [2019-10-16 20:23:06] (6030 lines) /app/public/data/ukraine_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 20:23:06] (14005 lines) /app/public/data/ukraine_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 20:23:06] (6030 lines) /app/public/data/ukraine_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 20:23:06] (3375 lines) /app/public/data/ukraine_sp_list/publish_traits.tsv
[INFO] [2019-10-16 20:23:06] (16863 lines) /app/public/data/ukraine_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 20:23:07] complete_harvest_instance
[START] [2019-10-16 20:23:07] completed
[STOP] [2019-10-16 20:23:07] completed
[STOP] [2019-10-16 20:23:07] logged process, took 700.27
Latest Process

16 Oct 20:11 EXITED currently processing 0