Harvest for Sint Maarten Species List Created 15 Oct 18:52

Stage: completed
Fetched: 15 Oct 18:52
Validated: 15 Oct 18:52
Deltas Created 15 Oct 18:52
Units Normalized: 15 Oct 18:53
Ancestry Built: 15 Oct 18:52
Nodes Matched: 15 Oct 18:53
Names Parsed: 15 Oct 18:52
New Models Stored: 15 Oct 18:52
Indexed: 15 Oct 18:53
Completed: 15 Oct 18:54
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 18:52:01 -0400 by logger.rb/56815
[START] [2019-10-15 18:52:01] logged process
[START] [2019-10-15 18:52:01] create_harvest_instance
[STOP] [2019-10-15 18:52:01] create_harvest_instance
[START] [2019-10-15 18:52:01] fetch_files
[STOP] [2019-10-15 18:52:01] fetch_files
[START] [2019-10-15 18:52:01] validate_each_file
[STOP] [2019-10-15 18:52:01] validate_each_file
[START] [2019-10-15 18:52:01] convert_to_csv
[CMD] [2019-10-15 18:52:01] /usr/bin/sort /app/public/converted_csv/sint_maarten_sp__refs_17205.csv > /app/public/converted_csv/sint_maarten_sp__refs_17205.csv_sorted
[CMD] [2019-10-15 18:52:02] /usr/bin/sort /app/public/converted_csv/sint_maarten_sp__nodes_17206.csv > /app/public/converted_csv/sint_maarten_sp__nodes_17206.csv_sorted
[CMD] [2019-10-15 18:52:02] /usr/bin/sort /app/public/converted_csv/sint_maarten_sp__occurrences_17207.csv > /app/public/converted_csv/sint_maarten_sp__occurrences_17207.csv_sorted
[CMD] [2019-10-15 18:52:02] /usr/bin/sort /app/public/converted_csv/sint_maarten_sp__measurements_17208.csv > /app/public/converted_csv/sint_maarten_sp__measurements_17208.csv_sorted
[STOP] [2019-10-15 18:52:02] convert_to_csv
[START] [2019-10-15 18:52:02] calculate_delta
[CMD] [2019-10-15 18:52:02] echo "0a" > /app/public/diff/sint_maarten_sp__refs_17205.diff
[CMD] [2019-10-15 18:52:03] tail -n +1 /app/public/converted_csv/sint_maarten_sp__refs_17205.csv >> /app/public/diff/sint_maarten_sp__refs_17205.diff
[CMD] [2019-10-15 18:52:03] echo "." >> /app/public/diff/sint_maarten_sp__refs_17205.diff
[CMD] [2019-10-15 18:52:03] echo "0a" > /app/public/diff/sint_maarten_sp__nodes_17206.diff
[CMD] [2019-10-15 18:52:04] tail -n +1 /app/public/converted_csv/sint_maarten_sp__nodes_17206.csv >> /app/public/diff/sint_maarten_sp__nodes_17206.diff
[CMD] [2019-10-15 18:52:04] echo "." >> /app/public/diff/sint_maarten_sp__nodes_17206.diff
[CMD] [2019-10-15 18:52:04] echo "0a" > /app/public/diff/sint_maarten_sp__occurrences_17207.diff
[CMD] [2019-10-15 18:52:04] tail -n +1 /app/public/converted_csv/sint_maarten_sp__occurrences_17207.csv >> /app/public/diff/sint_maarten_sp__occurrences_17207.diff
[CMD] [2019-10-15 18:52:05] echo "." >> /app/public/diff/sint_maarten_sp__occurrences_17207.diff
[CMD] [2019-10-15 18:52:05] echo "0a" > /app/public/diff/sint_maarten_sp__measurements_17208.diff
[CMD] [2019-10-15 18:52:05] tail -n +1 /app/public/converted_csv/sint_maarten_sp__measurements_17208.csv >> /app/public/diff/sint_maarten_sp__measurements_17208.diff
[CMD] [2019-10-15 18:52:06] echo "." >> /app/public/diff/sint_maarten_sp__measurements_17208.diff
[STOP] [2019-10-15 18:52:06] calculate_delta
[START] [2019-10-15 18:52:06] parse_diff_and_store
[INFO] [2019-10-15 18:52:06] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 18:52:06] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 18:52:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 18:52:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 18:52:08] Storing 2 References
[INFO] [2019-10-15 18:52:08] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 18:52:08] Average Time: 0.0
[INFO] [2019-10-15 18:52:08] Total Time: 1s
[INFO] [2019-10-15 18:52:08] Storing 379 ScientificNames
[INFO] [2019-10-15 18:52:08] Processing group of 379 in 1 groups of 1000
[INFO] [2019-10-15 18:52:08] Average Time: 0.23
[INFO] [2019-10-15 18:52:08] Total Time: 1s
[INFO] [2019-10-15 18:52:08] Storing 379 Nodes
[INFO] [2019-10-15 18:52:08] Processing group of 379 in 1 groups of 1000
[INFO] [2019-10-15 18:52:08] Average Time: 0.14
[INFO] [2019-10-15 18:52:08] Total Time: 1s
[INFO] [2019-10-15 18:52:08] Storing 120 Occurrences
[INFO] [2019-10-15 18:52:08] Processing group of 120 in 1 groups of 1000
[INFO] [2019-10-15 18:52:08] Average Time: 0.03
[INFO] [2019-10-15 18:52:08] Total Time: 1s
[INFO] [2019-10-15 18:52:08] Storing 240 TraitsReferences
[INFO] [2019-10-15 18:52:08] Processing group of 240 in 1 groups of 1000
[INFO] [2019-10-15 18:52:08] Average Time: 0.09
[INFO] [2019-10-15 18:52:08] Total Time: 1s
[INFO] [2019-10-15 18:52:08] Storing 240 Traits
[INFO] [2019-10-15 18:52:08] Processing group of 240 in 1 groups of 1000
[INFO] [2019-10-15 18:52:09] Average Time: 0.14
[INFO] [2019-10-15 18:52:09] Total Time: 1s
[INFO] [2019-10-15 18:52:09] Storing 240 MetaTraits
[INFO] [2019-10-15 18:52:09] Processing group of 240 in 1 groups of 1000
[INFO] [2019-10-15 18:52:09] Average Time: 0.06
[INFO] [2019-10-15 18:52:09] Total Time: 1s
[STOP] [2019-10-15 18:52:09] parse_diff_and_store
[START] [2019-10-15 18:52:09] resolve_keys
[INFO] [2019-10-15 18:52:13] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 18:52:13] traits to occurrences...
[INFO] [2019-10-15 18:52:13] traits to nodes (through occurrences)...
[INFO] [2019-10-15 18:52:13] Traits to sex term...
[INFO] [2019-10-15 18:52:13] Traits to lifestage term...
[INFO] [2019-10-15 18:52:13] MetaTraits to traits...
[INFO] [2019-10-15 18:52:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 18:52:13] Assocs to occurrences...
[INFO] [2019-10-15 18:52:13] Assocs to nodes...
[INFO] [2019-10-15 18:52:13] Assoc to sex term...
[INFO] [2019-10-15 18:52:13] Assoc to lifestage term...
[STOP] [2019-10-15 18:52:13] resolve_keys
[START] [2019-10-15 18:52:13] hold_for_later_1
[STOP] [2019-10-15 18:52:13] hold_for_later_1
[START] [2019-10-15 18:52:13] hold_for_later_2
[STOP] [2019-10-15 18:52:13] hold_for_later_2
[START] [2019-10-15 18:52:13] resolve_missing_parents
[STOP] [2019-10-15 18:52:14] resolve_missing_parents
[START] [2019-10-15 18:52:14] rebuild_nodes
[START] [2019-10-15 18:52:14] Flattener#flatten
[START] [2019-10-15 18:52:14] Flattener#study_resource
[START] [2019-10-15 18:52:14] Flattener#build_ancestry
[STOP] [2019-10-15 18:52:14] Flattener#build_ancestry
[INFO] [2019-10-15 18:52:14] 379 ancestry keys
[START] [2019-10-15 18:52:14] build_node_ancestors
[INFO] [2019-10-15 18:52:14] old ancestors deleted.
[STOP] [2019-10-15 18:52:14] build_node_ancestors
[START] [2019-10-15 18:52:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 18:52:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 18:52:14] Flattener#flatten
[STOP] [2019-10-15 18:52:14] rebuild_nodes
[START] [2019-10-15 18:52:14] resolve_missing_media_owners
[STOP] [2019-10-15 18:52:14] resolve_missing_media_owners
[START] [2019-10-15 18:52:14] sanitize_media_verbatims
[STOP] [2019-10-15 18:52:14] sanitize_media_verbatims
[START] [2019-10-15 18:52:14] queue_downloads
[STOP] [2019-10-15 18:52:14] queue_downloads
[START] [2019-10-15 18:52:14] parse_names
[WARN] [2019-10-15 18:52:14] I see 379 names which still need to be parsed.
[STOP] [2019-10-15 18:52:15] parse_names
[START] [2019-10-15 18:52:15] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 18:52:15] denormalize_canonical_names_to_nodes
[START] [2019-10-15 18:52:15] match_nodes
[START] [2019-10-15 18:52:15] map_all_nodes_to_pages
[STOP] [2019-10-15 18:53:04] map_all_nodes_to_pages
[INFO] [2019-10-15 18:53:04] 15 Unmatched nodes (of 379)! That's too many to output. First 10: Strumigenys eggersi (#51817987); Coerebidae (#51817848); Fulica caribaea (#51818080); Thalaseus (#51817960); Thalaseus maximus (#51817959); Thalaseus sandvicensis (#51818194); Neotaenioglossa (#51818010); Cycloneritimorpha (#51818060); Archaeogastropoda (#51818198); Aiptasia pallida (#51818017)
[START] [2019-10-15 18:53:04] update_nodes
[STOP] [2019-10-15 18:53:04] update_nodes
[STOP] [2019-10-15 18:53:04] match_nodes
[START] [2019-10-15 18:53:04] reindex_search
[STOP] [2019-10-15 18:53:05] reindex_search
[START] [2019-10-15 18:53:05] normalize_units
[STOP] [2019-10-15 18:53:05] normalize_units
[START] [2019-10-15 18:53:05] calculate_statistics
[STOP] [2019-10-15 18:53:05] calculate_statistics
[START] [2019-10-15 18:53:05] complete_harvest_instance
[START] [2019-10-15 18:53:05] overall_tsv_creation
[INFO] [2019-10-15 18:53:05] Processing group of 379 in 1 batches of 10000
[INFO] [2019-10-15 18:53:50] 120 Traits (unfiltered)...
[INFO] [2019-10-15 18:54:04] 120 Traits (filtered)...
[INFO] [2019-10-15 18:54:04] 0 Associations (filtered)...
[INFO] [2019-10-15 18:54:41] 600 metadata added.
[INFO] [2019-10-15 18:54:41] 0 metadata added.
[INFO] [2019-10-15 18:54:41] Average Time: 75.0
[INFO] [2019-10-15 18:54:41] Total Time: 1m36s
[STOP] [2019-10-15 18:54:41] overall_tsv_creation
[INFO] [2019-10-15 18:54:41] Done. Check your files:
[INFO] [2019-10-15 18:54:41] (379 lines) /app/public/data/sint_maarten_sp_/publish_nodes.tsv
[INFO] [2019-10-15 18:54:41] (1677 lines) /app/public/data/sint_maarten_sp_/publish_node_ancestors.tsv
[INFO] [2019-10-15 18:54:42] (379 lines) /app/public/data/sint_maarten_sp_/publish_scientific_names.tsv
[INFO] [2019-10-15 18:54:42] (121 lines) /app/public/data/sint_maarten_sp_/publish_traits.tsv
[INFO] [2019-10-15 18:54:42] (601 lines) /app/public/data/sint_maarten_sp_/publish_metadata.tsv
[STOP] [2019-10-15 18:54:42] complete_harvest_instance
[START] [2019-10-15 18:54:42] completed
[STOP] [2019-10-15 18:54:42] completed
[STOP] [2019-10-15 18:54:42] logged process, took 161.42
Latest Process

15 Oct 18:52 EXITED currently processing 0