Harvest for Baffin Bay Species List Created 22 Dec 19:25

Stage: completed
Fetched: 22 Dec 19:25
Validated: 22 Dec 19:25
Deltas Created 22 Dec 19:25
Units Normalized: 22 Dec 19:32
Ancestry Built: 22 Dec 19:26
Nodes Matched: 22 Dec 19:32
Names Parsed: 22 Dec 19:26
New Models Stored: 22 Dec 19:25
Indexed: 22 Dec 19:32
Completed: 22 Dec 19:34
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 19:25:33 -0500 by logger.rb/56815
[START] [2019-12-22 19:25:33] logged process
[START] [2019-12-22 19:25:33] create_harvest_instance
[STOP] [2019-12-22 19:25:34] create_harvest_instance
[START] [2019-12-22 19:25:34] fetch_files
[STOP] [2019-12-22 19:25:34] fetch_files
[START] [2019-12-22 19:25:34] validate_each_file
[STOP] [2019-12-22 19:25:35] validate_each_file
[START] [2019-12-22 19:25:35] convert_to_csv
[CMD] [2019-12-22 19:25:35] /usr/bin/sort /app/public/converted_csv/baffin_bay_sp_li_refs_19034.csv > /app/public/converted_csv/baffin_bay_sp_li_refs_19034.csv_sorted
[CMD] [2019-12-22 19:25:35] /usr/bin/sort /app/public/converted_csv/baffin_bay_sp_li_nodes_19035.csv > /app/public/converted_csv/baffin_bay_sp_li_nodes_19035.csv_sorted
[CMD] [2019-12-22 19:25:36] /usr/bin/sort /app/public/converted_csv/baffin_bay_sp_li_occurrences_19036.csv > /app/public/converted_csv/baffin_bay_sp_li_occurrences_19036.csv_sorted
[CMD] [2019-12-22 19:25:36] /usr/bin/sort /app/public/converted_csv/baffin_bay_sp_li_measurements_19037.csv > /app/public/converted_csv/baffin_bay_sp_li_measurements_19037.csv_sorted
[STOP] [2019-12-22 19:25:37] convert_to_csv
[START] [2019-12-22 19:25:37] calculate_delta
[CMD] [2019-12-22 19:25:37] echo "0a" > /app/public/diff/baffin_bay_sp_li_refs_19034.diff
[CMD] [2019-12-22 19:25:38] tail -n +1 /app/public/converted_csv/baffin_bay_sp_li_refs_19034.csv >> /app/public/diff/baffin_bay_sp_li_refs_19034.diff
[CMD] [2019-12-22 19:25:38] echo "." >> /app/public/diff/baffin_bay_sp_li_refs_19034.diff
[CMD] [2019-12-22 19:25:39] echo "0a" > /app/public/diff/baffin_bay_sp_li_nodes_19035.diff
[CMD] [2019-12-22 19:25:39] tail -n +1 /app/public/converted_csv/baffin_bay_sp_li_nodes_19035.csv >> /app/public/diff/baffin_bay_sp_li_nodes_19035.diff
[CMD] [2019-12-22 19:25:40] echo "." >> /app/public/diff/baffin_bay_sp_li_nodes_19035.diff
[CMD] [2019-12-22 19:25:41] echo "0a" > /app/public/diff/baffin_bay_sp_li_occurrences_19036.diff
[CMD] [2019-12-22 19:25:41] tail -n +1 /app/public/converted_csv/baffin_bay_sp_li_occurrences_19036.csv >> /app/public/diff/baffin_bay_sp_li_occurrences_19036.diff
[CMD] [2019-12-22 19:25:42] echo "." >> /app/public/diff/baffin_bay_sp_li_occurrences_19036.diff
[CMD] [2019-12-22 19:25:42] echo "0a" > /app/public/diff/baffin_bay_sp_li_measurements_19037.diff
[CMD] [2019-12-22 19:25:43] tail -n +1 /app/public/converted_csv/baffin_bay_sp_li_measurements_19037.csv >> /app/public/diff/baffin_bay_sp_li_measurements_19037.diff
[CMD] [2019-12-22 19:25:44] echo "." >> /app/public/diff/baffin_bay_sp_li_measurements_19037.diff
[STOP] [2019-12-22 19:25:44] calculate_delta
[START] [2019-12-22 19:25:44] parse_diff_and_store
[INFO] [2019-12-22 19:25:45] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 19:25:46] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 19:25:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 19:25:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 19:25:50] Storing 2 References
[INFO] [2019-12-22 19:25:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 19:25:50] Average Time: 0.0
[INFO] [2019-12-22 19:25:50] Total Time: 1s
[INFO] [2019-12-22 19:25:50] Storing 1421 ScientificNames
[INFO] [2019-12-22 19:25:50] Processing group of 1421 in 2 groups of 1000
[INFO] [2019-12-22 19:25:51] Average Time: 0.385
[INFO] [2019-12-22 19:25:51] Total Time: 1s
[INFO] [2019-12-22 19:25:51] Storing 1421 Nodes
[INFO] [2019-12-22 19:25:51] Processing group of 1421 in 2 groups of 1000
[INFO] [2019-12-22 19:25:52] Average Time: 0.26
[INFO] [2019-12-22 19:25:52] Total Time: 1s
[INFO] [2019-12-22 19:25:52] Storing 560 Occurrences
[INFO] [2019-12-22 19:25:52] Processing group of 560 in 1 groups of 1000
[INFO] [2019-12-22 19:25:52] Average Time: 0.19
[INFO] [2019-12-22 19:25:52] Total Time: 1s
[INFO] [2019-12-22 19:25:52] Storing 1120 TraitsReferences
[INFO] [2019-12-22 19:25:52] Processing group of 1120 in 2 groups of 1000
[INFO] [2019-12-22 19:25:52] Average Time: 0.07
[INFO] [2019-12-22 19:25:52] Total Time: 1s
[INFO] [2019-12-22 19:25:52] Storing 1120 Traits
[INFO] [2019-12-22 19:25:52] Processing group of 1120 in 2 groups of 1000
[INFO] [2019-12-22 19:25:52] Average Time: 0.235
[INFO] [2019-12-22 19:25:52] Total Time: 1s
[INFO] [2019-12-22 19:25:52] Storing 1120 MetaTraits
[INFO] [2019-12-22 19:25:52] Processing group of 1120 in 2 groups of 1000
[INFO] [2019-12-22 19:25:53] Average Time: 0.08
[INFO] [2019-12-22 19:25:53] Total Time: 1s
[STOP] [2019-12-22 19:25:53] parse_diff_and_store
[START] [2019-12-22 19:25:53] resolve_keys
[INFO] [2019-12-22 19:26:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 19:26:08] traits to occurrences...
[INFO] [2019-12-22 19:26:08] traits to nodes (through occurrences)...
[INFO] [2019-12-22 19:26:08] Traits to sex term...
[INFO] [2019-12-22 19:26:09] Traits to lifestage term...
[INFO] [2019-12-22 19:26:09] MetaTraits to traits...
[INFO] [2019-12-22 19:26:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 19:26:09] Assocs to occurrences...
[INFO] [2019-12-22 19:26:09] Assocs to nodes...
[INFO] [2019-12-22 19:26:09] Assoc to sex term...
[INFO] [2019-12-22 19:26:09] Assoc to lifestage term...
[STOP] [2019-12-22 19:26:09] resolve_keys
[START] [2019-12-22 19:26:09] hold_for_later_1
[STOP] [2019-12-22 19:26:09] hold_for_later_1
[START] [2019-12-22 19:26:09] hold_for_later_2
[STOP] [2019-12-22 19:26:09] hold_for_later_2
[START] [2019-12-22 19:26:09] resolve_missing_parents
[STOP] [2019-12-22 19:26:11] resolve_missing_parents
[START] [2019-12-22 19:26:11] rebuild_nodes
[START] [2019-12-22 19:26:11] Flattener#flatten
[START] [2019-12-22 19:26:11] Flattener#study_resource
[START] [2019-12-22 19:26:11] Flattener#build_ancestry
[STOP] [2019-12-22 19:26:11] Flattener#build_ancestry
[INFO] [2019-12-22 19:26:11] 1421 ancestry keys
[START] [2019-12-22 19:26:11] build_node_ancestors
[INFO] [2019-12-22 19:26:11] old ancestors deleted.
[STOP] [2019-12-22 19:26:11] build_node_ancestors
[START] [2019-12-22 19:26:12] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:26:12] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:26:12] Flattener#flatten
[STOP] [2019-12-22 19:26:12] rebuild_nodes
[START] [2019-12-22 19:26:12] resolve_missing_media_owners
[STOP] [2019-12-22 19:26:12] resolve_missing_media_owners
[START] [2019-12-22 19:26:12] sanitize_media_verbatims
[STOP] [2019-12-22 19:26:12] sanitize_media_verbatims
[START] [2019-12-22 19:26:12] queue_downloads
[STOP] [2019-12-22 19:26:12] queue_downloads
[START] [2019-12-22 19:26:12] parse_names
[WARN] [2019-12-22 19:26:12] I see 1421 names which still need to be parsed.
[STOP] [2019-12-22 19:26:14] parse_names
[START] [2019-12-22 19:26:14] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 19:26:14] denormalize_canonical_names_to_nodes
[START] [2019-12-22 19:26:14] match_nodes
[START] [2019-12-22 19:26:14] map_all_nodes_to_pages
[STOP] [2019-12-22 19:32:21] map_all_nodes_to_pages
[INFO] [2019-12-22 19:32:21] 89 Unmatched nodes (of 1421)! That's too many to output. First 10: Larus thayeri (#61698430); Chen (#61698520); Chen caerulescens (#61698519); Anas clypeata (#61699451); Scorpaeniformes (#61698658); Gasterosteiformes (#61699234); Enterogona (#61698797); Pleurogona (#61698822); Maxillopoda (#61698338); Poecilostomatoida (#61698396)
[START] [2019-12-22 19:32:21] update_nodes
[STOP] [2019-12-22 19:32:22] update_nodes
[STOP] [2019-12-22 19:32:22] match_nodes
[START] [2019-12-22 19:32:22] reindex_search
[STOP] [2019-12-22 19:32:26] reindex_search
[START] [2019-12-22 19:32:26] normalize_units
[STOP] [2019-12-22 19:32:26] normalize_units
[START] [2019-12-22 19:32:26] calculate_statistics
[STOP] [2019-12-22 19:32:26] calculate_statistics
[START] [2019-12-22 19:32:26] complete_harvest_instance
[START] [2019-12-22 19:32:26] overall_tsv_creation
[INFO] [2019-12-22 19:32:26] Processing group of 1421 in 1 batches of 10000
[INFO] [2019-12-22 19:33:17] 560 Traits (unfiltered)...
[INFO] [2019-12-22 19:33:30] 560 Traits (filtered)...
[INFO] [2019-12-22 19:33:30] 0 Associations (filtered)...
[INFO] [2019-12-22 19:34:08] 2800 metadata added.
[INFO] [2019-12-22 19:34:08] 0 metadata added.
[INFO] [2019-12-22 19:34:08] Average Time: 79.67
[INFO] [2019-12-22 19:34:08] Total Time: 1m43s
[STOP] [2019-12-22 19:34:08] overall_tsv_creation
[INFO] [2019-12-22 19:34:08] Done. Check your files:
[INFO] [2019-12-22 19:34:09] (1421 lines) /app/public/data/baffin_bay_sp_li/publish_nodes.tsv
[INFO] [2019-12-22 19:34:10] (6381 lines) /app/public/data/baffin_bay_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-22 19:34:11] (1421 lines) /app/public/data/baffin_bay_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-22 19:34:11] (561 lines) /app/public/data/baffin_bay_sp_li/publish_traits.tsv
[INFO] [2019-12-22 19:34:12] (2801 lines) /app/public/data/baffin_bay_sp_li/publish_metadata.tsv
[STOP] [2019-12-22 19:34:12] complete_harvest_instance
[START] [2019-12-22 19:34:12] completed
[STOP] [2019-12-22 19:34:12] completed
[STOP] [2019-12-22 19:34:12] logged process, took 518.42
Latest Process

22 Dec 19:25 EXITED currently processing 0