Harvest for Santi et al 2013 Created 15 Apr 10:44

Stage: completed
Fetched: 15 Apr 10:44
Validated: 15 Apr 10:44
Deltas Created 15 Apr 10:45
Units Normalized: 15 Apr 10:45
Ancestry Built: 15 Apr 10:45
Nodes Matched: 15 Apr 10:45
Names Parsed: 15 Apr 10:45
New Models Stored: 15 Apr 10:45
Indexed: 15 Apr 10:45
Completed: 15 Apr 10:47
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2020-04-15 10:44:47 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:44:47] ## HARVEST: type = -harvest
[START] [2020-04-15 10:44:51] logged process
[START] [2020-04-15 10:44:51] create_harvest_instance
[STOP] [2020-04-15 10:44:52] create_harvest_instance
[START] [2020-04-15 10:44:52] fetch_files
[STOP] [2020-04-15 10:44:52] fetch_files
[START] [2020-04-15 10:44:52] validate_each_file
[STOP] [2020-04-15 10:44:52] validate_each_file
[START] [2020-04-15 10:44:52] convert_to_csv
[CMD] [2020-04-15 10:44:52] /usr/bin/sort /app/public/converted_csv/santi_et_al_sant_refs_20807.csv > /app/public/converted_csv/santi_et_al_sant_refs_20807.csv_sorted
[CMD] [2020-04-15 10:44:53] /usr/bin/sort /app/public/converted_csv/santi_et_al_sant_nodes_20808.csv > /app/public/converted_csv/santi_et_al_sant_nodes_20808.csv_sorted
[CMD] [2020-04-15 10:44:55] /usr/bin/sort /app/public/converted_csv/santi_et_al_sant_occurrences_20809.csv > /app/public/converted_csv/santi_et_al_sant_occurrences_20809.csv_sorted
[CMD] [2020-04-15 10:44:56] /usr/bin/sort /app/public/converted_csv/santi_et_al_sant_measurements_20810.csv > /app/public/converted_csv/santi_et_al_sant_measurements_20810.csv_sorted
[STOP] [2020-04-15 10:44:57] convert_to_csv
[START] [2020-04-15 10:44:57] calculate_delta
[CMD] [2020-04-15 10:44:57] echo "0a" > /app/public/diff/santi_et_al_sant_refs_20807.diff
[CMD] [2020-04-15 10:44:58] tail -n +1 /app/public/converted_csv/santi_et_al_sant_refs_20807.csv >> /app/public/diff/santi_et_al_sant_refs_20807.diff
[CMD] [2020-04-15 10:45:00] echo "." >> /app/public/diff/santi_et_al_sant_refs_20807.diff
[CMD] [2020-04-15 10:45:01] echo "0a" > /app/public/diff/santi_et_al_sant_nodes_20808.diff
[CMD] [2020-04-15 10:45:02] tail -n +1 /app/public/converted_csv/santi_et_al_sant_nodes_20808.csv >> /app/public/diff/santi_et_al_sant_nodes_20808.diff
[CMD] [2020-04-15 10:45:04] echo "." >> /app/public/diff/santi_et_al_sant_nodes_20808.diff
[CMD] [2020-04-15 10:45:05] echo "0a" > /app/public/diff/santi_et_al_sant_occurrences_20809.diff
[CMD] [2020-04-15 10:45:06] tail -n +1 /app/public/converted_csv/santi_et_al_sant_occurrences_20809.csv >> /app/public/diff/santi_et_al_sant_occurrences_20809.diff
[CMD] [2020-04-15 10:45:08] echo "." >> /app/public/diff/santi_et_al_sant_occurrences_20809.diff
[CMD] [2020-04-15 10:45:09] echo "0a" > /app/public/diff/santi_et_al_sant_measurements_20810.diff
[CMD] [2020-04-15 10:45:10] tail -n +1 /app/public/converted_csv/santi_et_al_sant_measurements_20810.csv >> /app/public/diff/santi_et_al_sant_measurements_20810.diff
[CMD] [2020-04-15 10:45:11] echo "." >> /app/public/diff/santi_et_al_sant_measurements_20810.diff
[STOP] [2020-04-15 10:45:13] calculate_delta
[START] [2020-04-15 10:45:13] parse_diff_and_store
[INFO] [2020-04-15 10:45:14] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:45:15] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:45:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:45:18] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:45:18] Storing 16 References
[INFO] [2020-04-15 10:45:18] Processing group of 16 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.0
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 12 ScientificNames
[INFO] [2020-04-15 10:45:18] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.03
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 12 Nodes
[INFO] [2020-04-15 10:45:18] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.01
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 12 Occurrences
[INFO] [2020-04-15 10:45:18] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.01
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 38 TraitsReferences
[INFO] [2020-04-15 10:45:18] Processing group of 38 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.01
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 19 Traits
[INFO] [2020-04-15 10:45:18] Processing group of 19 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.01
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[INFO] [2020-04-15 10:45:18] Storing 33 MetaTraits
[INFO] [2020-04-15 10:45:18] Processing group of 33 in 1 groups of 1000
[INFO] [2020-04-15 10:45:18] Average Time: 0.01
[INFO] [2020-04-15 10:45:18] Total Time: 1s
[STOP] [2020-04-15 10:45:18] parse_diff_and_store
[START] [2020-04-15 10:45:18] resolve_keys
[INFO] [2020-04-15 10:45:23] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:45:23] traits to occurrences...
[INFO] [2020-04-15 10:45:23] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:45:23] Traits to sex term...
[INFO] [2020-04-15 10:45:23] Traits to lifestage term...
[INFO] [2020-04-15 10:45:23] MetaTraits to traits...
[INFO] [2020-04-15 10:45:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:45:23] Assocs to occurrences...
[INFO] [2020-04-15 10:45:23] Assocs to nodes...
[INFO] [2020-04-15 10:45:23] Assoc to sex term...
[INFO] [2020-04-15 10:45:23] Assoc to lifestage term...
[STOP] [2020-04-15 10:45:23] resolve_keys
[START] [2020-04-15 10:45:23] hold_for_later_1
[STOP] [2020-04-15 10:45:23] hold_for_later_1
[START] [2020-04-15 10:45:23] hold_for_later_2
[STOP] [2020-04-15 10:45:23] hold_for_later_2
[START] [2020-04-15 10:45:23] resolve_missing_parents
[STOP] [2020-04-15 10:45:23] resolve_missing_parents
[START] [2020-04-15 10:45:23] rebuild_nodes
[START] [2020-04-15 10:45:23] Flattener#flatten
[START] [2020-04-15 10:45:23] Flattener#study_resource
[START] [2020-04-15 10:45:23] Flattener#build_ancestry
[STOP] [2020-04-15 10:45:23] Flattener#build_ancestry
[INFO] [2020-04-15 10:45:23] 12 ancestry keys
[START] [2020-04-15 10:45:23] build_node_ancestors
[INFO] [2020-04-15 10:45:23] old ancestors deleted.
[STOP] [2020-04-15 10:45:23] build_node_ancestors
[WARN] [2020-04-15 10:45:23] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:45:23] Flattener#flatten
[STOP] [2020-04-15 10:45:23] rebuild_nodes
[START] [2020-04-15 10:45:23] resolve_missing_media_owners
[STOP] [2020-04-15 10:45:23] resolve_missing_media_owners
[START] [2020-04-15 10:45:23] sanitize_media_verbatims
[STOP] [2020-04-15 10:45:23] sanitize_media_verbatims
[START] [2020-04-15 10:45:23] queue_downloads
[STOP] [2020-04-15 10:45:23] queue_downloads
[START] [2020-04-15 10:45:23] parse_names
[WARN] [2020-04-15 10:45:23] I see 12 names which still need to be parsed.
[STOP] [2020-04-15 10:45:25] parse_names
[START] [2020-04-15 10:45:25] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:45:25] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:45:25] match_nodes
[START] [2020-04-15 10:45:25] map_all_nodes_to_pages
[STOP] [2020-04-15 10:45:25] map_all_nodes_to_pages
[INFO] [2020-04-15 10:45:25] ZERO unmatched nodes (of 12)! Nicely done.
[START] [2020-04-15 10:45:25] update_nodes
[STOP] [2020-04-15 10:45:25] update_nodes
[STOP] [2020-04-15 10:45:25] match_nodes
[START] [2020-04-15 10:45:25] reindex_search
[STOP] [2020-04-15 10:45:25] reindex_search
[START] [2020-04-15 10:45:25] normalize_units
[STOP] [2020-04-15 10:45:25] normalize_units
[START] [2020-04-15 10:45:25] calculate_statistics
[2020-04-15 10:45:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:45:25] calculate_statistics
[START] [2020-04-15 10:45:25] complete_harvest_instance
[START] [2020-04-15 10:45:25] overall_tsv_creation
[INFO] [2020-04-15 10:45:25] Processing group of 12 in 1 batches of 10000
[INFO] [2020-04-15 10:46:16] 12 Traits (unfiltered)...
[INFO] [2020-04-15 10:46:28] 12 Traits (filtered)...
[INFO] [2020-04-15 10:46:28] 0 Associations (filtered)...
[INFO] [2020-04-15 10:47:04] 77 metadata added.
[INFO] [2020-04-15 10:47:04] 0 metadata added.
[INFO] [2020-04-15 10:47:04] Average Time: 70.71
[INFO] [2020-04-15 10:47:04] Total Time: 1m40s
[STOP] [2020-04-15 10:47:04] overall_tsv_creation
[INFO] [2020-04-15 10:47:04] Done. Check your files:
[INFO] [2020-04-15 10:47:06] (12 lines) /app/public/data/santi_et_al_sant/publish_nodes.tsv
[INFO] [2020-04-15 10:47:07] (12 lines) /app/public/data/santi_et_al_sant/publish_scientific_names.tsv
[INFO] [2020-04-15 10:47:08] (13 lines) /app/public/data/santi_et_al_sant/publish_traits.tsv
[INFO] [2020-04-15 10:47:10] (78 lines) /app/public/data/santi_et_al_sant/publish_metadata.tsv
[STOP] [2020-04-15 10:47:10] complete_harvest_instance
[START] [2020-04-15 10:47:10] completed
[STOP] [2020-04-15 10:47:10] completed
[STOP] [2020-04-15 10:47:10] logged process, took 138.84
Latest Process

15 Apr 10:44 EXITED currently processing 0