Harvest for Singapore Strait Species List Created 25 Dec 13:47

Stage: completed
Fetched: 25 Dec 13:47
Validated: 25 Dec 13:47
Deltas Created 25 Dec 13:47
Units Normalized: 25 Dec 13:58
Ancestry Built: 25 Dec 13:48
Nodes Matched: 25 Dec 13:58
Names Parsed: 25 Dec 13:48
New Models Stored: 25 Dec 13:48
Indexed: 25 Dec 13:58
Completed: 25 Dec 14:00
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 13:47:37 -0500 by logger.rb/56815
[START] [2019-12-25 13:47:37] logged process
[START] [2019-12-25 13:47:37] create_harvest_instance
[STOP] [2019-12-25 13:47:37] create_harvest_instance
[START] [2019-12-25 13:47:37] fetch_files
[STOP] [2019-12-25 13:47:37] fetch_files
[START] [2019-12-25 13:47:37] validate_each_file
[STOP] [2019-12-25 13:47:38] validate_each_file
[START] [2019-12-25 13:47:38] convert_to_csv
[CMD] [2019-12-25 13:47:38] /usr/bin/sort /app/public/converted_csv/singapore_strait_refs_19658.csv > /app/public/converted_csv/singapore_strait_refs_19658.csv_sorted
[CMD] [2019-12-25 13:47:38] /usr/bin/sort /app/public/converted_csv/singapore_strait_nodes_19659.csv > /app/public/converted_csv/singapore_strait_nodes_19659.csv_sorted
[CMD] [2019-12-25 13:47:39] /usr/bin/sort /app/public/converted_csv/singapore_strait_occurrences_19660.csv > /app/public/converted_csv/singapore_strait_occurrences_19660.csv_sorted
[CMD] [2019-12-25 13:47:40] /usr/bin/sort /app/public/converted_csv/singapore_strait_measurements_19661.csv > /app/public/converted_csv/singapore_strait_measurements_19661.csv_sorted
[STOP] [2019-12-25 13:47:41] convert_to_csv
[START] [2019-12-25 13:47:41] calculate_delta
[CMD] [2019-12-25 13:47:41] echo "0a" > /app/public/diff/singapore_strait_refs_19658.diff
[CMD] [2019-12-25 13:47:41] tail -n +1 /app/public/converted_csv/singapore_strait_refs_19658.csv >> /app/public/diff/singapore_strait_refs_19658.diff
[CMD] [2019-12-25 13:47:42] echo "." >> /app/public/diff/singapore_strait_refs_19658.diff
[CMD] [2019-12-25 13:47:43] echo "0a" > /app/public/diff/singapore_strait_nodes_19659.diff
[CMD] [2019-12-25 13:47:43] tail -n +1 /app/public/converted_csv/singapore_strait_nodes_19659.csv >> /app/public/diff/singapore_strait_nodes_19659.diff
[CMD] [2019-12-25 13:47:44] echo "." >> /app/public/diff/singapore_strait_nodes_19659.diff
[CMD] [2019-12-25 13:47:45] echo "0a" > /app/public/diff/singapore_strait_occurrences_19660.diff
[CMD] [2019-12-25 13:47:45] tail -n +1 /app/public/converted_csv/singapore_strait_occurrences_19660.csv >> /app/public/diff/singapore_strait_occurrences_19660.diff
[CMD] [2019-12-25 13:47:46] echo "." >> /app/public/diff/singapore_strait_occurrences_19660.diff
[CMD] [2019-12-25 13:47:47] echo "0a" > /app/public/diff/singapore_strait_measurements_19661.diff
[CMD] [2019-12-25 13:47:47] tail -n +1 /app/public/converted_csv/singapore_strait_measurements_19661.csv >> /app/public/diff/singapore_strait_measurements_19661.diff
[CMD] [2019-12-25 13:47:48] echo "." >> /app/public/diff/singapore_strait_measurements_19661.diff
[STOP] [2019-12-25 13:47:49] calculate_delta
[START] [2019-12-25 13:47:49] parse_diff_and_store
[INFO] [2019-12-25 13:47:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 13:47:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 13:47:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 13:47:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 13:48:06] Storing 2 References
[INFO] [2019-12-25 13:48:06] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 13:48:06] Average Time: 0.0
[INFO] [2019-12-25 13:48:06] Total Time: 1s
[INFO] [2019-12-25 13:48:06] Storing 4159 ScientificNames
[INFO] [2019-12-25 13:48:06] Processing group of 4159 in 5 groups of 1000
[INFO] [2019-12-25 13:48:07] Average Time: 0.346
[INFO] [2019-12-25 13:48:07] Total Time: 2s
[INFO] [2019-12-25 13:48:07] Storing 4159 Nodes
[INFO] [2019-12-25 13:48:07] Processing group of 4159 in 5 groups of 1000
[INFO] [2019-12-25 13:48:09] Average Time: 0.286
[INFO] [2019-12-25 13:48:09] Total Time: 2s
[INFO] [2019-12-25 13:48:09] Storing 2093 Occurrences
[INFO] [2019-12-25 13:48:09] Processing group of 2093 in 3 groups of 1000
[INFO] [2019-12-25 13:48:09] Average Time: 0.103
[INFO] [2019-12-25 13:48:09] Total Time: 1s
[INFO] [2019-12-25 13:48:09] Storing 4186 TraitsReferences
[INFO] [2019-12-25 13:48:09] Processing group of 4186 in 5 groups of 1000
[INFO] [2019-12-25 13:48:10] Average Time: 0.13
[INFO] [2019-12-25 13:48:10] Total Time: 1s
[INFO] [2019-12-25 13:48:10] Storing 4186 Traits
[INFO] [2019-12-25 13:48:10] Processing group of 4186 in 5 groups of 1000
[INFO] [2019-12-25 13:48:12] Average Time: 0.32
[INFO] [2019-12-25 13:48:12] Total Time: 2s
[INFO] [2019-12-25 13:48:12] Storing 4185 MetaTraits
[INFO] [2019-12-25 13:48:12] Processing group of 4185 in 5 groups of 1000
[INFO] [2019-12-25 13:48:12] Average Time: 0.136
[INFO] [2019-12-25 13:48:12] Total Time: 1s
[STOP] [2019-12-25 13:48:12] parse_diff_and_store
[START] [2019-12-25 13:48:12] resolve_keys
[INFO] [2019-12-25 13:48:32] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 13:48:33] traits to occurrences...
[INFO] [2019-12-25 13:48:36] traits to nodes (through occurrences)...
[INFO] [2019-12-25 13:48:36] Traits to sex term...
[INFO] [2019-12-25 13:48:38] Traits to lifestage term...
[INFO] [2019-12-25 13:48:39] MetaTraits to traits...
[INFO] [2019-12-25 13:48:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 13:48:40] Assocs to occurrences...
[INFO] [2019-12-25 13:48:40] Assocs to nodes...
[INFO] [2019-12-25 13:48:40] Assoc to sex term...
[INFO] [2019-12-25 13:48:40] Assoc to lifestage term...
[STOP] [2019-12-25 13:48:40] resolve_keys
[START] [2019-12-25 13:48:40] hold_for_later_1
[STOP] [2019-12-25 13:48:40] hold_for_later_1
[START] [2019-12-25 13:48:40] hold_for_later_2
[STOP] [2019-12-25 13:48:40] hold_for_later_2
[START] [2019-12-25 13:48:40] resolve_missing_parents
[STOP] [2019-12-25 13:48:48] resolve_missing_parents
[START] [2019-12-25 13:48:48] rebuild_nodes
[START] [2019-12-25 13:48:48] Flattener#flatten
[START] [2019-12-25 13:48:48] Flattener#study_resource
[START] [2019-12-25 13:48:48] Flattener#build_ancestry
[STOP] [2019-12-25 13:48:48] Flattener#build_ancestry
[INFO] [2019-12-25 13:48:48] 4159 ancestry keys
[START] [2019-12-25 13:48:48] build_node_ancestors
[INFO] [2019-12-25 13:48:48] old ancestors deleted.
[STOP] [2019-12-25 13:48:50] build_node_ancestors
[START] [2019-12-25 13:48:52] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:48:52] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:48:52] Flattener#flatten
[STOP] [2019-12-25 13:48:52] rebuild_nodes
[START] [2019-12-25 13:48:52] resolve_missing_media_owners
[STOP] [2019-12-25 13:48:52] resolve_missing_media_owners
[START] [2019-12-25 13:48:52] sanitize_media_verbatims
[STOP] [2019-12-25 13:48:52] sanitize_media_verbatims
[START] [2019-12-25 13:48:52] queue_downloads
[STOP] [2019-12-25 13:48:52] queue_downloads
[START] [2019-12-25 13:48:52] parse_names
[WARN] [2019-12-25 13:48:52] I see 4159 names which still need to be parsed.
[STOP] [2019-12-25 13:48:57] parse_names
[START] [2019-12-25 13:48:57] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 13:48:57] denormalize_canonical_names_to_nodes
[START] [2019-12-25 13:48:57] match_nodes
[START] [2019-12-25 13:48:57] map_all_nodes_to_pages
[STOP] [2019-12-25 13:58:37] map_all_nodes_to_pages
[INFO] [2019-12-25 13:58:37] 207 Unmatched nodes (of 4159)! That's too many to output. First 10: Egretta intermedia (#62446305); Limicola (#62446770); Limicola falcinellus (#62446769); Limnodromus (#62447829); Philomachus (#62449381); Philomachus pugnax (#62449380); Ceyx erithacus (#62446585); Megalaima (#62446314); Megalaima haemacephala (#62446313); Eudynamys scolopacea (#62446648)
[START] [2019-12-25 13:58:37] update_nodes
[STOP] [2019-12-25 13:58:39] update_nodes
[STOP] [2019-12-25 13:58:39] match_nodes
[START] [2019-12-25 13:58:39] reindex_search
[STOP] [2019-12-25 13:58:47] reindex_search
[START] [2019-12-25 13:58:47] normalize_units
[STOP] [2019-12-25 13:58:47] normalize_units
[START] [2019-12-25 13:58:47] calculate_statistics
[STOP] [2019-12-25 13:58:47] calculate_statistics
[START] [2019-12-25 13:58:47] complete_harvest_instance
[START] [2019-12-25 13:58:47] overall_tsv_creation
[INFO] [2019-12-25 13:58:47] Processing group of 4159 in 1 batches of 10000
[INFO] [2019-12-25 13:59:53] 2093 Traits (unfiltered)...
[INFO] [2019-12-25 14:00:07] 2093 Traits (filtered)...
[INFO] [2019-12-25 14:00:07] 0 Associations (filtered)...
[INFO] [2019-12-25 14:00:48] 10464 metadata added.
[INFO] [2019-12-25 14:00:48] 0 metadata added.
[INFO] [2019-12-25 14:00:48] Average Time: 95.03
[INFO] [2019-12-25 14:00:48] Total Time: 2m2s
[STOP] [2019-12-25 14:00:48] overall_tsv_creation
[INFO] [2019-12-25 14:00:48] Done. Check your files:
[INFO] [2019-12-25 14:00:49] (4159 lines) /app/public/data/singapore_strait/publish_nodes.tsv
[INFO] [2019-12-25 14:00:50] (21186 lines) /app/public/data/singapore_strait/publish_node_ancestors.tsv
[INFO] [2019-12-25 14:00:51] (4159 lines) /app/public/data/singapore_strait/publish_scientific_names.tsv
[INFO] [2019-12-25 14:00:51] (2094 lines) /app/public/data/singapore_strait/publish_traits.tsv
[INFO] [2019-12-25 14:00:52] (10465 lines) /app/public/data/singapore_strait/publish_metadata.tsv
[STOP] [2019-12-25 14:00:52] complete_harvest_instance
[START] [2019-12-25 14:00:52] completed
[STOP] [2019-12-25 14:00:52] completed
[STOP] [2019-12-25 14:00:52] logged process, took 795.48
Latest Process

25 Dec 13:47 EXITED currently processing 0