Harvest for Rio de la Plata Species List Created 25 Dec 10:25

Stage: completed
Fetched: 25 Dec 10:25
Validated: 25 Dec 10:25
Deltas Created 25 Dec 10:25
Units Normalized: 25 Dec 10:31
Ancestry Built: 25 Dec 10:26
Nodes Matched: 25 Dec 10:31
Names Parsed: 25 Dec 10:26
New Models Stored: 25 Dec 10:26
Indexed: 25 Dec 10:31
Completed: 25 Dec 10:32
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 10:25:54 -0500 by logger.rb/56815
[START] [2019-12-25 10:25:54] logged process
[START] [2019-12-25 10:25:54] create_harvest_instance
[STOP] [2019-12-25 10:25:55] create_harvest_instance
[START] [2019-12-25 10:25:55] fetch_files
[STOP] [2019-12-25 10:25:55] fetch_files
[START] [2019-12-25 10:25:55] validate_each_file
[STOP] [2019-12-25 10:25:55] validate_each_file
[START] [2019-12-25 10:25:55] convert_to_csv
[CMD] [2019-12-25 10:25:55] /usr/bin/sort /app/public/converted_csv/rdlpsl_refs_19602.csv > /app/public/converted_csv/rdlpsl_refs_19602.csv_sorted
[CMD] [2019-12-25 10:25:55] /usr/bin/sort /app/public/converted_csv/rdlpsl_nodes_19603.csv > /app/public/converted_csv/rdlpsl_nodes_19603.csv_sorted
[CMD] [2019-12-25 10:25:55] /usr/bin/sort /app/public/converted_csv/rdlpsl_occurrences_19604.csv > /app/public/converted_csv/rdlpsl_occurrences_19604.csv_sorted
[CMD] [2019-12-25 10:25:55] /usr/bin/sort /app/public/converted_csv/rdlpsl_measurements_19605.csv > /app/public/converted_csv/rdlpsl_measurements_19605.csv_sorted
[STOP] [2019-12-25 10:25:55] convert_to_csv
[START] [2019-12-25 10:25:55] calculate_delta
[CMD] [2019-12-25 10:25:55] echo "0a" > /app/public/diff/rdlpsl_refs_19602.diff
[CMD] [2019-12-25 10:25:56] tail -n +1 /app/public/converted_csv/rdlpsl_refs_19602.csv >> /app/public/diff/rdlpsl_refs_19602.diff
[CMD] [2019-12-25 10:25:56] echo "." >> /app/public/diff/rdlpsl_refs_19602.diff
[CMD] [2019-12-25 10:25:56] echo "0a" > /app/public/diff/rdlpsl_nodes_19603.diff
[CMD] [2019-12-25 10:25:56] tail -n +1 /app/public/converted_csv/rdlpsl_nodes_19603.csv >> /app/public/diff/rdlpsl_nodes_19603.diff
[CMD] [2019-12-25 10:25:56] echo "." >> /app/public/diff/rdlpsl_nodes_19603.diff
[CMD] [2019-12-25 10:25:56] echo "0a" > /app/public/diff/rdlpsl_occurrences_19604.diff
[CMD] [2019-12-25 10:25:57] tail -n +1 /app/public/converted_csv/rdlpsl_occurrences_19604.csv >> /app/public/diff/rdlpsl_occurrences_19604.diff
[CMD] [2019-12-25 10:25:57] echo "." >> /app/public/diff/rdlpsl_occurrences_19604.diff
[CMD] [2019-12-25 10:25:57] echo "0a" > /app/public/diff/rdlpsl_measurements_19605.diff
[CMD] [2019-12-25 10:25:57] tail -n +1 /app/public/converted_csv/rdlpsl_measurements_19605.csv >> /app/public/diff/rdlpsl_measurements_19605.diff
[CMD] [2019-12-25 10:25:57] echo "." >> /app/public/diff/rdlpsl_measurements_19605.diff
[STOP] [2019-12-25 10:25:57] calculate_delta
[START] [2019-12-25 10:25:57] parse_diff_and_store
[INFO] [2019-12-25 10:25:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 10:25:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 10:25:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 10:25:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 10:26:00] Storing 2 References
[INFO] [2019-12-25 10:26:00] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 10:26:00] Average Time: 0.0
[INFO] [2019-12-25 10:26:00] Total Time: 1s
[INFO] [2019-12-25 10:26:00] Storing 765 ScientificNames
[INFO] [2019-12-25 10:26:00] Processing group of 765 in 1 groups of 1000
[INFO] [2019-12-25 10:26:00] Average Time: 0.4
[INFO] [2019-12-25 10:26:00] Total Time: 1s
[INFO] [2019-12-25 10:26:00] Storing 765 Nodes
[INFO] [2019-12-25 10:26:00] Processing group of 765 in 1 groups of 1000
[INFO] [2019-12-25 10:26:01] Average Time: 0.28
[INFO] [2019-12-25 10:26:01] Total Time: 1s
[INFO] [2019-12-25 10:26:01] Storing 275 Occurrences
[INFO] [2019-12-25 10:26:01] Processing group of 275 in 1 groups of 1000
[INFO] [2019-12-25 10:26:01] Average Time: 0.05
[INFO] [2019-12-25 10:26:01] Total Time: 1s
[INFO] [2019-12-25 10:26:01] Storing 550 TraitsReferences
[INFO] [2019-12-25 10:26:01] Processing group of 550 in 1 groups of 1000
[INFO] [2019-12-25 10:26:01] Average Time: 0.12
[INFO] [2019-12-25 10:26:01] Total Time: 1s
[INFO] [2019-12-25 10:26:01] Storing 550 Traits
[INFO] [2019-12-25 10:26:01] Processing group of 550 in 1 groups of 1000
[INFO] [2019-12-25 10:26:01] Average Time: 0.33
[INFO] [2019-12-25 10:26:01] Total Time: 1s
[INFO] [2019-12-25 10:26:01] Storing 550 MetaTraits
[INFO] [2019-12-25 10:26:01] Processing group of 550 in 1 groups of 1000
[INFO] [2019-12-25 10:26:01] Average Time: 0.11
[INFO] [2019-12-25 10:26:01] Total Time: 1s
[STOP] [2019-12-25 10:26:01] parse_diff_and_store
[START] [2019-12-25 10:26:01] resolve_keys
[INFO] [2019-12-25 10:26:07] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 10:26:07] traits to occurrences...
[INFO] [2019-12-25 10:26:08] traits to nodes (through occurrences)...
[INFO] [2019-12-25 10:26:08] Traits to sex term...
[INFO] [2019-12-25 10:26:08] Traits to lifestage term...
[INFO] [2019-12-25 10:26:08] MetaTraits to traits...
[INFO] [2019-12-25 10:26:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 10:26:08] Assocs to occurrences...
[INFO] [2019-12-25 10:26:08] Assocs to nodes...
[INFO] [2019-12-25 10:26:09] Assoc to sex term...
[INFO] [2019-12-25 10:26:09] Assoc to lifestage term...
[STOP] [2019-12-25 10:26:09] resolve_keys
[START] [2019-12-25 10:26:09] hold_for_later_1
[STOP] [2019-12-25 10:26:09] hold_for_later_1
[START] [2019-12-25 10:26:09] hold_for_later_2
[STOP] [2019-12-25 10:26:09] hold_for_later_2
[START] [2019-12-25 10:26:09] resolve_missing_parents
[STOP] [2019-12-25 10:26:09] resolve_missing_parents
[START] [2019-12-25 10:26:09] rebuild_nodes
[START] [2019-12-25 10:26:09] Flattener#flatten
[START] [2019-12-25 10:26:09] Flattener#study_resource
[START] [2019-12-25 10:26:09] Flattener#build_ancestry
[STOP] [2019-12-25 10:26:09] Flattener#build_ancestry
[INFO] [2019-12-25 10:26:09] 765 ancestry keys
[START] [2019-12-25 10:26:09] build_node_ancestors
[INFO] [2019-12-25 10:26:09] old ancestors deleted.
[STOP] [2019-12-25 10:26:09] build_node_ancestors
[START] [2019-12-25 10:26:10] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:26:10] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:26:10] Flattener#flatten
[STOP] [2019-12-25 10:26:10] rebuild_nodes
[START] [2019-12-25 10:26:10] resolve_missing_media_owners
[STOP] [2019-12-25 10:26:10] resolve_missing_media_owners
[START] [2019-12-25 10:26:10] sanitize_media_verbatims
[STOP] [2019-12-25 10:26:10] sanitize_media_verbatims
[START] [2019-12-25 10:26:10] queue_downloads
[STOP] [2019-12-25 10:26:10] queue_downloads
[START] [2019-12-25 10:26:10] parse_names
[WARN] [2019-12-25 10:26:10] I see 765 names which still need to be parsed.
[STOP] [2019-12-25 10:26:11] parse_names
[START] [2019-12-25 10:26:11] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 10:26:11] denormalize_canonical_names_to_nodes
[START] [2019-12-25 10:26:11] match_nodes
[START] [2019-12-25 10:26:11] map_all_nodes_to_pages
[STOP] [2019-12-25 10:31:14] map_all_nodes_to_pages
[INFO] [2019-12-25 10:31:14] 38 Unmatched nodes (of 765)! That's too many to output. First 10: Thalasseus maxima (#62429261); Anas versicolor (#62428576); Anas platalea (#62428634); Anas sibilatrix (#62428660); Anas cyanoptera (#62428674); Myoida (#62428684); Erodonidae (#62428683); Veneroida (#62428706); Dallocardia muricatum (#62429127); Petricolidae (#62429135)
[START] [2019-12-25 10:31:14] update_nodes
[STOP] [2019-12-25 10:31:14] update_nodes
[STOP] [2019-12-25 10:31:14] match_nodes
[START] [2019-12-25 10:31:14] reindex_search
[STOP] [2019-12-25 10:31:17] reindex_search
[START] [2019-12-25 10:31:17] normalize_units
[STOP] [2019-12-25 10:31:17] normalize_units
[START] [2019-12-25 10:31:17] calculate_statistics
[STOP] [2019-12-25 10:31:17] calculate_statistics
[START] [2019-12-25 10:31:17] complete_harvest_instance
[START] [2019-12-25 10:31:17] overall_tsv_creation
[INFO] [2019-12-25 10:31:17] Processing group of 765 in 1 batches of 10000
[INFO] [2019-12-25 10:32:05] 275 Traits (unfiltered)...
[INFO] [2019-12-25 10:32:18] 275 Traits (filtered)...
[INFO] [2019-12-25 10:32:18] 0 Associations (filtered)...
[INFO] [2019-12-25 10:32:56] 1375 metadata added.
[INFO] [2019-12-25 10:32:56] 0 metadata added.
[INFO] [2019-12-25 10:32:56] Average Time: 76.17
[INFO] [2019-12-25 10:32:56] Total Time: 1m39s
[STOP] [2019-12-25 10:32:56] overall_tsv_creation
[INFO] [2019-12-25 10:32:56] Done. Check your files:
[INFO] [2019-12-25 10:32:56] (765 lines) /app/public/data/rdlpsl/publish_nodes.tsv
[INFO] [2019-12-25 10:32:56] (3544 lines) /app/public/data/rdlpsl/publish_node_ancestors.tsv
[INFO] [2019-12-25 10:32:56] (765 lines) /app/public/data/rdlpsl/publish_scientific_names.tsv
[INFO] [2019-12-25 10:32:56] (276 lines) /app/public/data/rdlpsl/publish_traits.tsv
[INFO] [2019-12-25 10:32:57] (1376 lines) /app/public/data/rdlpsl/publish_metadata.tsv
[STOP] [2019-12-25 10:32:57] complete_harvest_instance
[START] [2019-12-25 10:32:57] completed
[STOP] [2019-12-25 10:32:57] completed
[STOP] [2019-12-25 10:32:57] logged process, took 422.55
Latest Process

25 Dec 10:25 EXITED currently processing 0