Harvest for Gulf of Alaska Species List Created 23 Dec 03:35

Stage: completed
Fetched: 23 Dec 03:35
Validated: 23 Dec 03:35
Deltas Created 23 Dec 03:35
Units Normalized: 23 Dec 03:57
Ancestry Built: 23 Dec 03:36
Nodes Matched: 23 Dec 03:56
Names Parsed: 23 Dec 03:36
New Models Stored: 23 Dec 03:35
Indexed: 23 Dec 03:57
Completed: 23 Dec 03:59
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 03:35:21 -0500 by logger.rb/56815
[START] [2019-12-23 03:35:21] logged process
[START] [2019-12-23 03:35:21] create_harvest_instance
[STOP] [2019-12-23 03:35:22] create_harvest_instance
[START] [2019-12-23 03:35:22] fetch_files
[STOP] [2019-12-23 03:35:22] fetch_files
[START] [2019-12-23 03:35:22] validate_each_file
[STOP] [2019-12-23 03:35:23] validate_each_file
[START] [2019-12-23 03:35:23] convert_to_csv
[CMD] [2019-12-23 03:35:23] /usr/bin/sort /app/public/converted_csv/gulf_alaska_sp_l_refs_19266.csv > /app/public/converted_csv/gulf_alaska_sp_l_refs_19266.csv_sorted
[CMD] [2019-12-23 03:35:23] /usr/bin/sort /app/public/converted_csv/gulf_alaska_sp_l_nodes_19267.csv > /app/public/converted_csv/gulf_alaska_sp_l_nodes_19267.csv_sorted
[CMD] [2019-12-23 03:35:23] /usr/bin/sort /app/public/converted_csv/gulf_alaska_sp_l_occurrences_19268.csv > /app/public/converted_csv/gulf_alaska_sp_l_occurrences_19268.csv_sorted
[CMD] [2019-12-23 03:35:23] /usr/bin/sort /app/public/converted_csv/gulf_alaska_sp_l_measurements_19269.csv > /app/public/converted_csv/gulf_alaska_sp_l_measurements_19269.csv_sorted
[STOP] [2019-12-23 03:35:23] convert_to_csv
[START] [2019-12-23 03:35:23] calculate_delta
[CMD] [2019-12-23 03:35:23] echo "0a" > /app/public/diff/gulf_alaska_sp_l_refs_19266.diff
[CMD] [2019-12-23 03:35:23] tail -n +1 /app/public/converted_csv/gulf_alaska_sp_l_refs_19266.csv >> /app/public/diff/gulf_alaska_sp_l_refs_19266.diff
[CMD] [2019-12-23 03:35:23] echo "." >> /app/public/diff/gulf_alaska_sp_l_refs_19266.diff
[CMD] [2019-12-23 03:35:23] echo "0a" > /app/public/diff/gulf_alaska_sp_l_nodes_19267.diff
[CMD] [2019-12-23 03:35:23] tail -n +1 /app/public/converted_csv/gulf_alaska_sp_l_nodes_19267.csv >> /app/public/diff/gulf_alaska_sp_l_nodes_19267.diff
[CMD] [2019-12-23 03:35:23] echo "." >> /app/public/diff/gulf_alaska_sp_l_nodes_19267.diff
[CMD] [2019-12-23 03:35:23] echo "0a" > /app/public/diff/gulf_alaska_sp_l_occurrences_19268.diff
[CMD] [2019-12-23 03:35:23] tail -n +1 /app/public/converted_csv/gulf_alaska_sp_l_occurrences_19268.csv >> /app/public/diff/gulf_alaska_sp_l_occurrences_19268.diff
[CMD] [2019-12-23 03:35:23] echo "." >> /app/public/diff/gulf_alaska_sp_l_occurrences_19268.diff
[CMD] [2019-12-23 03:35:24] echo "0a" > /app/public/diff/gulf_alaska_sp_l_measurements_19269.diff
[CMD] [2019-12-23 03:35:24] tail -n +1 /app/public/converted_csv/gulf_alaska_sp_l_measurements_19269.csv >> /app/public/diff/gulf_alaska_sp_l_measurements_19269.diff
[CMD] [2019-12-23 03:35:24] echo "." >> /app/public/diff/gulf_alaska_sp_l_measurements_19269.diff
[STOP] [2019-12-23 03:35:24] calculate_delta
[START] [2019-12-23 03:35:24] parse_diff_and_store
[INFO] [2019-12-23 03:35:24] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 03:35:24] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 03:35:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 03:35:26] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 03:35:42] Storing 2 References
[INFO] [2019-12-23 03:35:42] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 03:35:42] Average Time: 0.0
[INFO] [2019-12-23 03:35:42] Total Time: 1s
[INFO] [2019-12-23 03:35:42] Storing 5722 ScientificNames
[INFO] [2019-12-23 03:35:42] Processing group of 5722 in 6 groups of 1000
[INFO] [2019-12-23 03:35:44] Average Time: 0.347
[INFO] [2019-12-23 03:35:44] Total Time: 3s
[INFO] [2019-12-23 03:35:44] Storing 5722 Nodes
[INFO] [2019-12-23 03:35:44] Processing group of 5722 in 6 groups of 1000
[INFO] [2019-12-23 03:35:46] Average Time: 0.345
[INFO] [2019-12-23 03:35:46] Total Time: 3s
[INFO] [2019-12-23 03:35:46] Storing 2934 Occurrences
[INFO] [2019-12-23 03:35:46] Processing group of 2934 in 3 groups of 1000
[INFO] [2019-12-23 03:35:46] Average Time: 0.123
[INFO] [2019-12-23 03:35:46] Total Time: 1s
[INFO] [2019-12-23 03:35:46] Storing 5868 TraitsReferences
[INFO] [2019-12-23 03:35:46] Processing group of 5868 in 6 groups of 1000
[INFO] [2019-12-23 03:35:47] Average Time: 0.085
[INFO] [2019-12-23 03:35:47] Total Time: 1s
[INFO] [2019-12-23 03:35:47] Storing 5868 Traits
[INFO] [2019-12-23 03:35:47] Processing group of 5868 in 6 groups of 1000
[INFO] [2019-12-23 03:35:49] Average Time: 0.337
[INFO] [2019-12-23 03:35:49] Total Time: 3s
[INFO] [2019-12-23 03:35:49] Storing 5847 MetaTraits
[INFO] [2019-12-23 03:35:49] Processing group of 5847 in 6 groups of 1000
[INFO] [2019-12-23 03:35:50] Average Time: 0.153
[INFO] [2019-12-23 03:35:50] Total Time: 1s
[STOP] [2019-12-23 03:35:50] parse_diff_and_store
[START] [2019-12-23 03:35:50] resolve_keys
[INFO] [2019-12-23 03:36:20] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 03:36:23] traits to occurrences...
[INFO] [2019-12-23 03:36:24] traits to nodes (through occurrences)...
[INFO] [2019-12-23 03:36:24] Traits to sex term...
[INFO] [2019-12-23 03:36:25] Traits to lifestage term...
[INFO] [2019-12-23 03:36:26] MetaTraits to traits...
[INFO] [2019-12-23 03:36:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 03:36:28] Assocs to occurrences...
[INFO] [2019-12-23 03:36:28] Assocs to nodes...
[INFO] [2019-12-23 03:36:28] Assoc to sex term...
[INFO] [2019-12-23 03:36:28] Assoc to lifestage term...
[STOP] [2019-12-23 03:36:28] resolve_keys
[START] [2019-12-23 03:36:28] hold_for_later_1
[STOP] [2019-12-23 03:36:28] hold_for_later_1
[START] [2019-12-23 03:36:28] hold_for_later_2
[STOP] [2019-12-23 03:36:28] hold_for_later_2
[START] [2019-12-23 03:36:28] resolve_missing_parents
[STOP] [2019-12-23 03:36:42] resolve_missing_parents
[START] [2019-12-23 03:36:42] rebuild_nodes
[START] [2019-12-23 03:36:42] Flattener#flatten
[START] [2019-12-23 03:36:42] Flattener#study_resource
[START] [2019-12-23 03:36:42] Flattener#build_ancestry
[STOP] [2019-12-23 03:36:43] Flattener#build_ancestry
[INFO] [2019-12-23 03:36:43] 5722 ancestry keys
[START] [2019-12-23 03:36:43] build_node_ancestors
[INFO] [2019-12-23 03:36:43] old ancestors deleted.
[STOP] [2019-12-23 03:36:45] build_node_ancestors
[START] [2019-12-23 03:36:47] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:36:48] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:36:48] Flattener#flatten
[STOP] [2019-12-23 03:36:48] rebuild_nodes
[START] [2019-12-23 03:36:48] resolve_missing_media_owners
[STOP] [2019-12-23 03:36:48] resolve_missing_media_owners
[START] [2019-12-23 03:36:48] sanitize_media_verbatims
[STOP] [2019-12-23 03:36:48] sanitize_media_verbatims
[START] [2019-12-23 03:36:48] queue_downloads
[STOP] [2019-12-23 03:36:48] queue_downloads
[START] [2019-12-23 03:36:48] parse_names
[WARN] [2019-12-23 03:36:48] I see 5722 names which still need to be parsed.
[STOP] [2019-12-23 03:36:53] parse_names
[START] [2019-12-23 03:36:53] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 03:36:53] denormalize_canonical_names_to_nodes
[START] [2019-12-23 03:36:53] match_nodes
[START] [2019-12-23 03:36:53] map_all_nodes_to_pages
[STOP] [2019-12-23 03:56:52] map_all_nodes_to_pages
[INFO] [2019-12-23 03:56:52] 303 Unmatched nodes (of 5722)! That's too many to output. First 10: Scorpaeniformes (#61898686); Ulcina (#61903484); Gasterosteiformes (#61899103); Scomberesocidae (#61900875); Anotopteridae (#61902938); Stephanoberyciformes (#61900953); Larus thayeri (#61899055); Limnodromus (#61898720); Aphriza (#61899652); Aphriza virgata (#61899651)
[START] [2019-12-23 03:56:52] update_nodes
[STOP] [2019-12-23 03:56:55] update_nodes
[STOP] [2019-12-23 03:56:55] match_nodes
[START] [2019-12-23 03:56:55] reindex_search
[STOP] [2019-12-23 03:57:12] reindex_search
[START] [2019-12-23 03:57:12] normalize_units
[STOP] [2019-12-23 03:57:12] normalize_units
[START] [2019-12-23 03:57:12] calculate_statistics
[STOP] [2019-12-23 03:57:13] calculate_statistics
[START] [2019-12-23 03:57:13] complete_harvest_instance
[START] [2019-12-23 03:57:13] overall_tsv_creation
[INFO] [2019-12-23 03:57:13] Processing group of 5722 in 1 batches of 10000
[INFO] [2019-12-23 03:58:26] 2934 Traits (unfiltered)...
[INFO] [2019-12-23 03:58:39] 2934 Traits (filtered)...
[INFO] [2019-12-23 03:58:39] 0 Associations (filtered)...
[INFO] [2019-12-23 03:59:23] 14649 metadata added.
[INFO] [2019-12-23 03:59:23] 0 metadata added.
[INFO] [2019-12-23 03:59:23] Average Time: 103.41
[INFO] [2019-12-23 03:59:23] Total Time: 2m11s
[STOP] [2019-12-23 03:59:23] overall_tsv_creation
[INFO] [2019-12-23 03:59:23] Done. Check your files:
[INFO] [2019-12-23 03:59:23] (5722 lines) /app/public/data/gulf_alaska_sp_l/publish_nodes.tsv
[INFO] [2019-12-23 03:59:23] (28862 lines) /app/public/data/gulf_alaska_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:59:23] (5722 lines) /app/public/data/gulf_alaska_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-23 03:59:23] (2935 lines) /app/public/data/gulf_alaska_sp_l/publish_traits.tsv
[INFO] [2019-12-23 03:59:23] (14650 lines) /app/public/data/gulf_alaska_sp_l/publish_metadata.tsv
[STOP] [2019-12-23 03:59:23] complete_harvest_instance
[START] [2019-12-23 03:59:23] completed
[STOP] [2019-12-23 03:59:23] completed
[STOP] [2019-12-23 03:59:23] logged process, took 1442.62
Latest Process

23 Dec 03:35 EXITED currently processing 0