Stage:
completed
Fetched:
13 Oct 01:26
Validated:
13 Oct 01:26
Deltas Created
13 Oct 01:26
Units Normalized:
13 Oct 01:33
Ancestry Built:
13 Oct 01:27
Nodes Matched:
13 Oct 01:33
Names Parsed:
13 Oct 01:27
New Models Stored:
13 Oct 01:26
Indexed:
13 Oct 01:33
Completed:
13 Oct 01:35
Time to Harvest:
less than a minute
Harvesting Log
(149 lines)
# Logfile created on 2019-10-13 01:26:01 -0400 by logger.rb/56815
[START] [2019-10-13 01:26:01] logged process
[START] [2019-10-13 01:26:01] create_harvest_instance
[STOP] [2019-10-13 01:26:02] create_harvest_instance
[START] [2019-10-13 01:26:02] fetch_files
[STOP] [2019-10-13 01:26:02] fetch_files
[START] [2019-10-13 01:26:02] validate_each_file
[STOP] [2019-10-13 01:26:03] validate_each_file
[START] [2019-10-13 01:26:03] convert_to_csv
[CMD] [2019-10-13 01:26:03] /usr/bin/sort /app/public/converted_csv/georgia_sp_list_refs_15827.csv > /app/public/converted_csv/georgia_sp_list_refs_15827.csv_sorted
[CMD] [2019-10-13 01:26:03] /usr/bin/sort /app/public/converted_csv/georgia_sp_list_nodes_15828.csv > /app/public/converted_csv/georgia_sp_list_nodes_15828.csv_sorted
[CMD] [2019-10-13 01:26:03] /usr/bin/sort /app/public/converted_csv/georgia_sp_list_occurrences_15829.csv > /app/public/converted_csv/georgia_sp_list_occurrences_15829.csv_sorted
[CMD] [2019-10-13 01:26:03] /usr/bin/sort /app/public/converted_csv/georgia_sp_list_measurements_15830.csv > /app/public/converted_csv/georgia_sp_list_measurements_15830.csv_sorted
[STOP] [2019-10-13 01:26:03] convert_to_csv
[START] [2019-10-13 01:26:03] calculate_delta
[CMD] [2019-10-13 01:26:03] echo "0a" > /app/public/diff/georgia_sp_list_refs_15827.diff
[CMD] [2019-10-13 01:26:03] tail -n +1 /app/public/converted_csv/georgia_sp_list_refs_15827.csv >> /app/public/diff/georgia_sp_list_refs_15827.diff
[CMD] [2019-10-13 01:26:03] echo "." >> /app/public/diff/georgia_sp_list_refs_15827.diff
[CMD] [2019-10-13 01:26:03] echo "0a" > /app/public/diff/georgia_sp_list_nodes_15828.diff
[CMD] [2019-10-13 01:26:03] tail -n +1 /app/public/converted_csv/georgia_sp_list_nodes_15828.csv >> /app/public/diff/georgia_sp_list_nodes_15828.diff
[CMD] [2019-10-13 01:26:03] echo "." >> /app/public/diff/georgia_sp_list_nodes_15828.diff
[CMD] [2019-10-13 01:26:04] echo "0a" > /app/public/diff/georgia_sp_list_occurrences_15829.diff
[CMD] [2019-10-13 01:26:04] tail -n +1 /app/public/converted_csv/georgia_sp_list_occurrences_15829.csv >> /app/public/diff/georgia_sp_list_occurrences_15829.diff
[CMD] [2019-10-13 01:26:04] echo "." >> /app/public/diff/georgia_sp_list_occurrences_15829.diff
[CMD] [2019-10-13 01:26:04] echo "0a" > /app/public/diff/georgia_sp_list_measurements_15830.diff
[CMD] [2019-10-13 01:26:04] tail -n +1 /app/public/converted_csv/georgia_sp_list_measurements_15830.csv >> /app/public/diff/georgia_sp_list_measurements_15830.diff
[CMD] [2019-10-13 01:26:04] echo "." >> /app/public/diff/georgia_sp_list_measurements_15830.diff
[STOP] [2019-10-13 01:26:04] calculate_delta
[START] [2019-10-13 01:26:04] parse_diff_and_store
[INFO] [2019-10-13 01:26:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 01:26:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 01:26:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 01:26:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 01:26:30] Storing 2 References
[INFO] [2019-10-13 01:26:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 01:26:30] Average Time: 0.0
[INFO] [2019-10-13 01:26:30] Total Time: 1s
[INFO] [2019-10-13 01:26:30] Storing 6166 ScientificNames
[INFO] [2019-10-13 01:26:30] Processing group of 6166 in 7 groups of 1000
[INFO] [2019-10-13 01:26:33] Average Time: 0.379
[INFO] [2019-10-13 01:26:33] Total Time: 3s
[INFO] [2019-10-13 01:26:33] last 3 / first 3: 0.56
[INFO] [2019-10-13 01:26:33] Std.Dev: 0.2073644135332772; Max: 0.76
[INFO] [2019-10-13 01:26:33] Storing 6166 Nodes
[INFO] [2019-10-13 01:26:33] Processing group of 6166 in 7 groups of 1000
[INFO] [2019-10-13 01:26:35] Average Time: 0.254
[INFO] [2019-10-13 01:26:35] Total Time: 2s
[INFO] [2019-10-13 01:26:35] last 3 / first 3: 0.71
[INFO] [2019-10-13 01:26:35] Std.Dev: 0.08944271909999159; Max: 0.29
[INFO] [2019-10-13 01:26:35] Storing 3374 Occurrences
[INFO] [2019-10-13 01:26:35] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-13 01:26:35] Average Time: 0.085
[INFO] [2019-10-13 01:26:35] Total Time: 1s
[INFO] [2019-10-13 01:26:35] Storing 7680 TraitsReferences
[INFO] [2019-10-13 01:26:35] Processing group of 7680 in 8 groups of 1000
[INFO] [2019-10-13 01:26:36] Average Time: 0.074
[INFO] [2019-10-13 01:26:36] Total Time: 1s
[INFO] [2019-10-13 01:26:36] last 3 / first 3: 0.74
[INFO] [2019-10-13 01:26:36] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-13 01:26:36] Storing 7679 Traits
[INFO] [2019-10-13 01:26:36] Processing group of 7679 in 8 groups of 1000
[INFO] [2019-10-13 01:26:39] Average Time: 0.335
[INFO] [2019-10-13 01:26:39] Total Time: 3s
[INFO] [2019-10-13 01:26:39] last 3 / first 3: 0.82
[INFO] [2019-10-13 01:26:39] Std.Dev: 0.07745966692414834; Max: 0.45
[INFO] [2019-10-13 01:26:39] Storing 7677 MetaTraits
[INFO] [2019-10-13 01:26:39] Processing group of 7677 in 8 groups of 1000
[INFO] [2019-10-13 01:26:40] Average Time: 0.138
[INFO] [2019-10-13 01:26:40] Total Time: 2s
[INFO] [2019-10-13 01:26:40] last 3 / first 3: 0.73
[INFO] [2019-10-13 01:26:40] Std.Dev: 0.03162277660168379; Max: 0.2
[STOP] [2019-10-13 01:26:40] parse_diff_and_store
[START] [2019-10-13 01:26:40] resolve_keys
[INFO] [2019-10-13 01:27:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 01:27:08] traits to occurrences...
[INFO] [2019-10-13 01:27:10] traits to nodes (through occurrences)...
[INFO] [2019-10-13 01:27:10] Traits to sex term...
[INFO] [2019-10-13 01:27:11] Traits to lifestage term...
[INFO] [2019-10-13 01:27:13] MetaTraits to traits...
[INFO] [2019-10-13 01:27:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 01:27:14] Assocs to occurrences...
[INFO] [2019-10-13 01:27:14] Assocs to nodes...
[INFO] [2019-10-13 01:27:14] Assoc to sex term...
[INFO] [2019-10-13 01:27:14] Assoc to lifestage term...
[STOP] [2019-10-13 01:27:14] resolve_keys
[START] [2019-10-13 01:27:15] hold_for_later_1
[STOP] [2019-10-13 01:27:15] hold_for_later_1
[START] [2019-10-13 01:27:15] hold_for_later_2
[STOP] [2019-10-13 01:27:15] hold_for_later_2
[START] [2019-10-13 01:27:15] resolve_missing_parents
[STOP] [2019-10-13 01:27:28] resolve_missing_parents
[START] [2019-10-13 01:27:28] rebuild_nodes
[START] [2019-10-13 01:27:28] Flattener#flatten
[START] [2019-10-13 01:27:28] Flattener#study_resource
[START] [2019-10-13 01:27:28] Flattener#build_ancestry
[STOP] [2019-10-13 01:27:29] Flattener#build_ancestry
[INFO] [2019-10-13 01:27:29] 6166 ancestry keys
[START] [2019-10-13 01:27:29] build_node_ancestors
[INFO] [2019-10-13 01:27:29] old ancestors deleted.
[STOP] [2019-10-13 01:27:30] build_node_ancestors
[START] [2019-10-13 01:27:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 01:27:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 01:27:32] Flattener#flatten
[STOP] [2019-10-13 01:27:32] rebuild_nodes
[START] [2019-10-13 01:27:32] resolve_missing_media_owners
[STOP] [2019-10-13 01:27:32] resolve_missing_media_owners
[START] [2019-10-13 01:27:33] sanitize_media_verbatims
[STOP] [2019-10-13 01:27:33] sanitize_media_verbatims
[START] [2019-10-13 01:27:33] queue_downloads
[STOP] [2019-10-13 01:27:33] queue_downloads
[START] [2019-10-13 01:27:33] parse_names
[WARN] [2019-10-13 01:27:33] I see 6166 names which still need to be parsed.
[STOP] [2019-10-13 01:27:38] parse_names
[START] [2019-10-13 01:27:38] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 01:27:38] denormalize_canonical_names_to_nodes
[START] [2019-10-13 01:27:38] match_nodes
[START] [2019-10-13 01:27:38] map_all_nodes_to_pages
[STOP] [2019-10-13 01:33:23] map_all_nodes_to_pages
[INFO] [2019-10-13 01:33:23] 524 Unmatched nodes (of 6166)! That's too many to output. First 10: Pelophylax esculenta (#49802166); Pelophylax esculentus (#49804463); Pelophylax temporaria (#49805180); Coluber robertmertensi (#49805462); Vipera raddei (#49806021); Carduelis chloris (#49800965); Carduelis cannabina (#49801049); Carduelis flavirostris (#49801479); Carduelis spinus (#49801557); Hirundo rupestris (#49801262)
[START] [2019-10-13 01:33:23] update_nodes
[STOP] [2019-10-13 01:33:25] update_nodes
[STOP] [2019-10-13 01:33:25] match_nodes
[START] [2019-10-13 01:33:25] reindex_search
[STOP] [2019-10-13 01:33:39] reindex_search
[START] [2019-10-13 01:33:39] normalize_units
[STOP] [2019-10-13 01:33:39] normalize_units
[START] [2019-10-13 01:33:39] calculate_statistics
[STOP] [2019-10-13 01:33:39] calculate_statistics
[START] [2019-10-13 01:33:39] complete_harvest_instance
[START] [2019-10-13 01:33:39] overall_tsv_creation
[INFO] [2019-10-13 01:33:39] Processing group of 6166 in 1 batches of 10000
[INFO] [2019-10-13 01:34:54] 3374 Traits (unfiltered)...
[INFO] [2019-10-13 01:35:09] 3374 Traits (filtered)...
[INFO] [2019-10-13 01:35:09] 0 Associations (filtered)...
[INFO] [2019-10-13 01:35:55] 16867 metadata added.
[INFO] [2019-10-13 01:35:55] 0 metadata added.
[INFO] [2019-10-13 01:35:55] Average Time: 110.24
[INFO] [2019-10-13 01:35:55] Total Time: 2m17s
[STOP] [2019-10-13 01:35:55] overall_tsv_creation
[INFO] [2019-10-13 01:35:55] Done. Check your files:
[INFO] [2019-10-13 01:35:55] (6166 lines) /app/public/data/georgia_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 01:35:56] (21331 lines) /app/public/data/georgia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 01:35:56] (6166 lines) /app/public/data/georgia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 01:35:56] (3375 lines) /app/public/data/georgia_sp_list/publish_traits.tsv
[INFO] [2019-10-13 01:35:56] (16868 lines) /app/public/data/georgia_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 01:35:56] complete_harvest_instance
[START] [2019-10-13 01:35:56] completed
[STOP] [2019-10-13 01:35:56] completed
[STOP] [2019-10-13 01:35:56] logged process, took 594.99
Latest Process