Harvest for Federated States of Micronesia Species List Created 12 Oct 20:49

Stage: completed
Fetched: 12 Oct 20:49
Validated: 12 Oct 20:49
Deltas Created 12 Oct 20:49
Units Normalized: 12 Oct 20:57
Ancestry Built: 12 Oct 20:50
Nodes Matched: 12 Oct 20:57
Names Parsed: 12 Oct 20:50
New Models Stored: 12 Oct 20:49
Indexed: 12 Oct 20:57
Completed: 12 Oct 20:59
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-12 20:49:20 -0400 by logger.rb/56815
[START] [2019-10-12 20:49:20] logged process
[START] [2019-10-12 20:49:20] create_harvest_instance
[STOP] [2019-10-12 20:49:20] create_harvest_instance
[START] [2019-10-12 20:49:20] fetch_files
[STOP] [2019-10-12 20:49:20] fetch_files
[START] [2019-10-12 20:49:20] validate_each_file
[STOP] [2019-10-12 20:49:21] validate_each_file
[START] [2019-10-12 20:49:21] convert_to_csv
[CMD] [2019-10-12 20:49:21] /usr/bin/sort /app/public/converted_csv/fsmsl_refs_15747.csv > /app/public/converted_csv/fsmsl_refs_15747.csv_sorted
[CMD] [2019-10-12 20:49:21] /usr/bin/sort /app/public/converted_csv/fsmsl_nodes_15748.csv > /app/public/converted_csv/fsmsl_nodes_15748.csv_sorted
[CMD] [2019-10-12 20:49:21] /usr/bin/sort /app/public/converted_csv/fsmsl_occurrences_15749.csv > /app/public/converted_csv/fsmsl_occurrences_15749.csv_sorted
[CMD] [2019-10-12 20:49:21] /usr/bin/sort /app/public/converted_csv/fsmsl_measurements_15750.csv > /app/public/converted_csv/fsmsl_measurements_15750.csv_sorted
[STOP] [2019-10-12 20:49:21] convert_to_csv
[START] [2019-10-12 20:49:21] calculate_delta
[CMD] [2019-10-12 20:49:21] echo "0a" > /app/public/diff/fsmsl_refs_15747.diff
[CMD] [2019-10-12 20:49:21] tail -n +1 /app/public/converted_csv/fsmsl_refs_15747.csv >> /app/public/diff/fsmsl_refs_15747.diff
[CMD] [2019-10-12 20:49:21] echo "." >> /app/public/diff/fsmsl_refs_15747.diff
[CMD] [2019-10-12 20:49:21] echo "0a" > /app/public/diff/fsmsl_nodes_15748.diff
[CMD] [2019-10-12 20:49:21] tail -n +1 /app/public/converted_csv/fsmsl_nodes_15748.csv >> /app/public/diff/fsmsl_nodes_15748.diff
[CMD] [2019-10-12 20:49:22] echo "." >> /app/public/diff/fsmsl_nodes_15748.diff
[CMD] [2019-10-12 20:49:22] echo "0a" > /app/public/diff/fsmsl_occurrences_15749.diff
[CMD] [2019-10-12 20:49:22] tail -n +1 /app/public/converted_csv/fsmsl_occurrences_15749.csv >> /app/public/diff/fsmsl_occurrences_15749.diff
[CMD] [2019-10-12 20:49:22] echo "." >> /app/public/diff/fsmsl_occurrences_15749.diff
[CMD] [2019-10-12 20:49:22] echo "0a" > /app/public/diff/fsmsl_measurements_15750.diff
[CMD] [2019-10-12 20:49:22] tail -n +1 /app/public/converted_csv/fsmsl_measurements_15750.csv >> /app/public/diff/fsmsl_measurements_15750.diff
[CMD] [2019-10-12 20:49:22] echo "." >> /app/public/diff/fsmsl_measurements_15750.diff
[STOP] [2019-10-12 20:49:22] calculate_delta
[START] [2019-10-12 20:49:22] parse_diff_and_store
[INFO] [2019-10-12 20:49:22] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 20:49:22] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 20:49:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 20:49:25] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 20:49:44] Storing 2 References
[INFO] [2019-10-12 20:49:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 20:49:44] Average Time: 0.0
[INFO] [2019-10-12 20:49:44] Total Time: 1s
[INFO] [2019-10-12 20:49:44] Storing 5913 ScientificNames
[INFO] [2019-10-12 20:49:44] Processing group of 5913 in 6 groups of 1000
[INFO] [2019-10-12 20:49:47] Average Time: 0.387
[INFO] [2019-10-12 20:49:47] Total Time: 3s
[INFO] [2019-10-12 20:49:47] Storing 5913 Nodes
[INFO] [2019-10-12 20:49:47] Processing group of 5913 in 6 groups of 1000
[INFO] [2019-10-12 20:49:49] Average Time: 0.29
[INFO] [2019-10-12 20:49:49] Total Time: 2s
[INFO] [2019-10-12 20:49:49] Storing 2892 Occurrences
[INFO] [2019-10-12 20:49:49] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-12 20:49:49] Average Time: 0.107
[INFO] [2019-10-12 20:49:49] Total Time: 1s
[INFO] [2019-10-12 20:49:49] Storing 6710 TraitsReferences
[INFO] [2019-10-12 20:49:49] Processing group of 6710 in 7 groups of 1000
[INFO] [2019-10-12 20:49:50] Average Time: 0.08
[INFO] [2019-10-12 20:49:50] Total Time: 1s
[INFO] [2019-10-12 20:49:50] last 3 / first 3: 0.63
[INFO] [2019-10-12 20:49:50] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-12 20:49:50] Storing 6709 Traits
[INFO] [2019-10-12 20:49:50] Processing group of 6709 in 7 groups of 1000
[INFO] [2019-10-12 20:49:52] Average Time: 0.303
[INFO] [2019-10-12 20:49:52] Total Time: 3s
[INFO] [2019-10-12 20:49:52] last 3 / first 3: 0.82
[INFO] [2019-10-12 20:49:52] Std.Dev: 0.06324555320336758; Max: 0.44
[INFO] [2019-10-12 20:49:52] Storing 6706 MetaTraits
[INFO] [2019-10-12 20:49:52] Processing group of 6706 in 7 groups of 1000
[INFO] [2019-10-12 20:49:52] Average Time: 0.107
[INFO] [2019-10-12 20:49:52] Total Time: 1s
[INFO] [2019-10-12 20:49:52] last 3 / first 3: 0.83
[INFO] [2019-10-12 20:49:52] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-12 20:49:52] parse_diff_and_store
[START] [2019-10-12 20:49:52] resolve_keys
[INFO] [2019-10-12 20:50:18] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 20:50:20] traits to occurrences...
[INFO] [2019-10-12 20:50:21] traits to nodes (through occurrences)...
[INFO] [2019-10-12 20:50:21] Traits to sex term...
[INFO] [2019-10-12 20:50:22] Traits to lifestage term...
[INFO] [2019-10-12 20:50:24] MetaTraits to traits...
[INFO] [2019-10-12 20:50:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 20:50:25] Assocs to occurrences...
[INFO] [2019-10-12 20:50:25] Assocs to nodes...
[INFO] [2019-10-12 20:50:25] Assoc to sex term...
[INFO] [2019-10-12 20:50:25] Assoc to lifestage term...
[STOP] [2019-10-12 20:50:25] resolve_keys
[START] [2019-10-12 20:50:25] hold_for_later_1
[STOP] [2019-10-12 20:50:25] hold_for_later_1
[START] [2019-10-12 20:50:25] hold_for_later_2
[STOP] [2019-10-12 20:50:25] hold_for_later_2
[START] [2019-10-12 20:50:25] resolve_missing_parents
[STOP] [2019-10-12 20:50:38] resolve_missing_parents
[START] [2019-10-12 20:50:38] rebuild_nodes
[START] [2019-10-12 20:50:38] Flattener#flatten
[START] [2019-10-12 20:50:38] Flattener#study_resource
[START] [2019-10-12 20:50:38] Flattener#build_ancestry
[STOP] [2019-10-12 20:50:38] Flattener#build_ancestry
[INFO] [2019-10-12 20:50:38] 5913 ancestry keys
[START] [2019-10-12 20:50:38] build_node_ancestors
[INFO] [2019-10-12 20:50:38] old ancestors deleted.
[STOP] [2019-10-12 20:50:39] build_node_ancestors
[START] [2019-10-12 20:50:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:50:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:50:41] Flattener#flatten
[STOP] [2019-10-12 20:50:41] rebuild_nodes
[START] [2019-10-12 20:50:41] resolve_missing_media_owners
[STOP] [2019-10-12 20:50:41] resolve_missing_media_owners
[START] [2019-10-12 20:50:41] sanitize_media_verbatims
[STOP] [2019-10-12 20:50:41] sanitize_media_verbatims
[START] [2019-10-12 20:50:41] queue_downloads
[STOP] [2019-10-12 20:50:41] queue_downloads
[START] [2019-10-12 20:50:41] parse_names
[WARN] [2019-10-12 20:50:41] I see 5913 names which still need to be parsed.
[STOP] [2019-10-12 20:50:47] parse_names
[START] [2019-10-12 20:50:47] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 20:50:47] denormalize_canonical_names_to_nodes
[START] [2019-10-12 20:50:47] match_nodes
[START] [2019-10-12 20:50:47] map_all_nodes_to_pages
[STOP] [2019-10-12 20:57:15] map_all_nodes_to_pages
[INFO] [2019-10-12 20:57:15] 423 Unmatched nodes (of 5913)! That's too many to output. First 10: Melonis barleeanum (#49641407); Gavelinopsis lobatula (#49641267); Globorotalia theyeri (#49646256); Globorotalia merotumida (#49646508); Dentagloborotalia (#49647134); Dentagloborotalia anfracta (#49647133); Globoquadrina venezuelana (#49642751); Globorotaloides hexagona (#49643187); Hedbergella monmouthensis (#49641441); Hedbergella holmdelensis (#49641446)
[START] [2019-10-12 20:57:15] update_nodes
[STOP] [2019-10-12 20:57:17] update_nodes
[STOP] [2019-10-12 20:57:17] match_nodes
[START] [2019-10-12 20:57:17] reindex_search
[STOP] [2019-10-12 20:57:36] reindex_search
[START] [2019-10-12 20:57:36] normalize_units
[STOP] [2019-10-12 20:57:36] normalize_units
[START] [2019-10-12 20:57:36] calculate_statistics
[STOP] [2019-10-12 20:57:36] calculate_statistics
[START] [2019-10-12 20:57:36] complete_harvest_instance
[START] [2019-10-12 20:57:36] overall_tsv_creation
[INFO] [2019-10-12 20:57:36] Processing group of 5913 in 1 batches of 10000
[INFO] [2019-10-12 20:58:47] 2892 Traits (unfiltered)...
[INFO] [2019-10-12 20:59:01] 2892 Traits (filtered)...
[INFO] [2019-10-12 20:59:01] 0 Associations (filtered)...
[INFO] [2019-10-12 20:59:46] 14458 metadata added.
[INFO] [2019-10-12 20:59:46] 0 metadata added.
[INFO] [2019-10-12 20:59:46] Average Time: 104.8
[INFO] [2019-10-12 20:59:46] Total Time: 2m10s
[STOP] [2019-10-12 20:59:46] overall_tsv_creation
[INFO] [2019-10-12 20:59:46] Done. Check your files:
[INFO] [2019-10-12 20:59:46] (5913 lines) /app/public/data/fsmsl/publish_nodes.tsv
[INFO] [2019-10-12 20:59:46] (19245 lines) /app/public/data/fsmsl/publish_node_ancestors.tsv
[INFO] [2019-10-12 20:59:46] (5913 lines) /app/public/data/fsmsl/publish_scientific_names.tsv
[INFO] [2019-10-12 20:59:46] (2893 lines) /app/public/data/fsmsl/publish_traits.tsv
[INFO] [2019-10-12 20:59:46] (14459 lines) /app/public/data/fsmsl/publish_metadata.tsv
[STOP] [2019-10-12 20:59:46] complete_harvest_instance
[START] [2019-10-12 20:59:46] completed
[STOP] [2019-10-12 20:59:46] completed
[STOP] [2019-10-12 20:59:46] logged process, took 626.8
Latest Process

12 Oct 20:49 EXITED currently processing 0