Harvest for Stal 2009 Created 15 Apr 10:18

Stage: completed
Fetched: 15 Apr 10:18
Validated: 15 Apr 10:18
Deltas Created 15 Apr 10:18
Units Normalized: 15 Apr 10:18
Ancestry Built: 15 Apr 10:18
Nodes Matched: 15 Apr 10:18
Names Parsed: 15 Apr 10:18
New Models Stored: 15 Apr 10:18
Indexed: 15 Apr 10:18
Completed: 15 Apr 10:20
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2020-04-15 10:17:58 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-15 10:17:58] ## HARVEST: type = -harvest
[START] [2020-04-15 10:18:02] logged process
[START] [2020-04-15 10:18:02] create_harvest_instance
[STOP] [2020-04-15 10:18:03] create_harvest_instance
[START] [2020-04-15 10:18:03] fetch_files
[STOP] [2020-04-15 10:18:03] fetch_files
[START] [2020-04-15 10:18:03] validate_each_file
[STOP] [2020-04-15 10:18:04] validate_each_file
[START] [2020-04-15 10:18:04] convert_to_csv
[CMD] [2020-04-15 10:18:04] /usr/bin/sort /app/public/converted_csv/stal_stal_2009_refs_20783.csv > /app/public/converted_csv/stal_stal_2009_refs_20783.csv_sorted
[CMD] [2020-04-15 10:18:05] /usr/bin/sort /app/public/converted_csv/stal_stal_2009_nodes_20784.csv > /app/public/converted_csv/stal_stal_2009_nodes_20784.csv_sorted
[CMD] [2020-04-15 10:18:06] /usr/bin/sort /app/public/converted_csv/stal_stal_2009_occurrences_20785.csv > /app/public/converted_csv/stal_stal_2009_occurrences_20785.csv_sorted
[CMD] [2020-04-15 10:18:07] /usr/bin/sort /app/public/converted_csv/stal_stal_2009_measurements_20786.csv > /app/public/converted_csv/stal_stal_2009_measurements_20786.csv_sorted
[STOP] [2020-04-15 10:18:09] convert_to_csv
[START] [2020-04-15 10:18:09] calculate_delta
[CMD] [2020-04-15 10:18:09] echo "0a" > /app/public/diff/stal_stal_2009_refs_20783.diff
[CMD] [2020-04-15 10:18:10] tail -n +1 /app/public/converted_csv/stal_stal_2009_refs_20783.csv >> /app/public/diff/stal_stal_2009_refs_20783.diff
[CMD] [2020-04-15 10:18:11] echo "." >> /app/public/diff/stal_stal_2009_refs_20783.diff
[CMD] [2020-04-15 10:18:13] echo "0a" > /app/public/diff/stal_stal_2009_nodes_20784.diff
[CMD] [2020-04-15 10:18:14] tail -n +1 /app/public/converted_csv/stal_stal_2009_nodes_20784.csv >> /app/public/diff/stal_stal_2009_nodes_20784.diff
[CMD] [2020-04-15 10:18:15] echo "." >> /app/public/diff/stal_stal_2009_nodes_20784.diff
[CMD] [2020-04-15 10:18:16] echo "0a" > /app/public/diff/stal_stal_2009_occurrences_20785.diff
[CMD] [2020-04-15 10:18:18] tail -n +1 /app/public/converted_csv/stal_stal_2009_occurrences_20785.csv >> /app/public/diff/stal_stal_2009_occurrences_20785.diff
[CMD] [2020-04-15 10:18:19] echo "." >> /app/public/diff/stal_stal_2009_occurrences_20785.diff
[CMD] [2020-04-15 10:18:20] echo "0a" > /app/public/diff/stal_stal_2009_measurements_20786.diff
[CMD] [2020-04-15 10:18:22] tail -n +1 /app/public/converted_csv/stal_stal_2009_measurements_20786.csv >> /app/public/diff/stal_stal_2009_measurements_20786.diff
[CMD] [2020-04-15 10:18:23] echo "." >> /app/public/diff/stal_stal_2009_measurements_20786.diff
[STOP] [2020-04-15 10:18:24] calculate_delta
[START] [2020-04-15 10:18:24] parse_diff_and_store
[INFO] [2020-04-15 10:18:25] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-15 10:18:27] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-15 10:18:28] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-15 10:18:29] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-15 10:18:29] Storing 5 References
[INFO] [2020-04-15 10:18:29] Processing group of 5 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 5 ScientificNames
[INFO] [2020-04-15 10:18:29] Processing group of 5 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 5 Nodes
[INFO] [2020-04-15 10:18:29] Processing group of 5 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 5 Occurrences
[INFO] [2020-04-15 10:18:29] Processing group of 5 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.01
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 5 TraitsReferences
[INFO] [2020-04-15 10:18:29] Processing group of 5 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 10 Traits
[INFO] [2020-04-15 10:18:29] Processing group of 10 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[INFO] [2020-04-15 10:18:29] Storing 13 MetaTraits
[INFO] [2020-04-15 10:18:29] Processing group of 13 in 1 groups of 1000
[INFO] [2020-04-15 10:18:29] Average Time: 0.0
[INFO] [2020-04-15 10:18:29] Total Time: 1s
[STOP] [2020-04-15 10:18:29] parse_diff_and_store
[START] [2020-04-15 10:18:29] resolve_keys
[INFO] [2020-04-15 10:18:35] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-15 10:18:35] traits to occurrences...
[INFO] [2020-04-15 10:18:35] traits to nodes (through occurrences)...
[INFO] [2020-04-15 10:18:35] Traits to sex term...
[INFO] [2020-04-15 10:18:35] Traits to lifestage term...
[INFO] [2020-04-15 10:18:35] MetaTraits to traits...
[INFO] [2020-04-15 10:18:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-15 10:18:35] Assocs to occurrences...
[INFO] [2020-04-15 10:18:35] Assocs to nodes...
[INFO] [2020-04-15 10:18:35] Assoc to sex term...
[INFO] [2020-04-15 10:18:35] Assoc to lifestage term...
[STOP] [2020-04-15 10:18:35] resolve_keys
[START] [2020-04-15 10:18:35] hold_for_later_1
[STOP] [2020-04-15 10:18:35] hold_for_later_1
[START] [2020-04-15 10:18:35] hold_for_later_2
[STOP] [2020-04-15 10:18:35] hold_for_later_2
[START] [2020-04-15 10:18:35] resolve_missing_parents
[STOP] [2020-04-15 10:18:35] resolve_missing_parents
[START] [2020-04-15 10:18:35] rebuild_nodes
[START] [2020-04-15 10:18:35] Flattener#flatten
[START] [2020-04-15 10:18:35] Flattener#study_resource
[START] [2020-04-15 10:18:35] Flattener#build_ancestry
[STOP] [2020-04-15 10:18:35] Flattener#build_ancestry
[INFO] [2020-04-15 10:18:35] 5 ancestry keys
[START] [2020-04-15 10:18:35] build_node_ancestors
[INFO] [2020-04-15 10:18:35] old ancestors deleted.
[STOP] [2020-04-15 10:18:35] build_node_ancestors
[WARN] [2020-04-15 10:18:35] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-15 10:18:35] Flattener#flatten
[STOP] [2020-04-15 10:18:35] rebuild_nodes
[START] [2020-04-15 10:18:35] resolve_missing_media_owners
[STOP] [2020-04-15 10:18:35] resolve_missing_media_owners
[START] [2020-04-15 10:18:35] sanitize_media_verbatims
[STOP] [2020-04-15 10:18:35] sanitize_media_verbatims
[START] [2020-04-15 10:18:35] queue_downloads
[STOP] [2020-04-15 10:18:35] queue_downloads
[START] [2020-04-15 10:18:35] parse_names
[WARN] [2020-04-15 10:18:35] I see 5 names which still need to be parsed.
[STOP] [2020-04-15 10:18:36] parse_names
[START] [2020-04-15 10:18:36] denormalize_canonical_names_to_nodes
[STOP] [2020-04-15 10:18:36] denormalize_canonical_names_to_nodes
[START] [2020-04-15 10:18:36] match_nodes
[START] [2020-04-15 10:18:36] map_all_nodes_to_pages
[STOP] [2020-04-15 10:18:36] map_all_nodes_to_pages
[INFO] [2020-04-15 10:18:36] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2020-04-15 10:18:36] update_nodes
[STOP] [2020-04-15 10:18:36] update_nodes
[STOP] [2020-04-15 10:18:36] match_nodes
[START] [2020-04-15 10:18:36] reindex_search
[STOP] [2020-04-15 10:18:36] reindex_search
[START] [2020-04-15 10:18:36] normalize_units
[STOP] [2020-04-15 10:18:36] normalize_units
[START] [2020-04-15 10:18:36] calculate_statistics
[2020-04-15 10:18:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-15 10:18:36] calculate_statistics
[START] [2020-04-15 10:18:36] complete_harvest_instance
[START] [2020-04-15 10:18:36] overall_tsv_creation
[INFO] [2020-04-15 10:18:36] Processing group of 5 in 1 batches of 10000
[INFO] [2020-04-15 10:19:27] 5 Traits (unfiltered)...
[INFO] [2020-04-15 10:19:39] 5 Traits (filtered)...
[INFO] [2020-04-15 10:19:39] 0 Associations (filtered)...
[INFO] [2020-04-15 10:20:16] 23 metadata added.
[INFO] [2020-04-15 10:20:16] 0 metadata added.
[INFO] [2020-04-15 10:20:16] Average Time: 70.7
[INFO] [2020-04-15 10:20:16] Total Time: 1m40s
[STOP] [2020-04-15 10:20:16] overall_tsv_creation
[INFO] [2020-04-15 10:20:16] Done. Check your files:
[INFO] [2020-04-15 10:20:17] (5 lines) /app/public/data/stal_stal_2009/publish_nodes.tsv
[INFO] [2020-04-15 10:20:18] (5 lines) /app/public/data/stal_stal_2009/publish_scientific_names.tsv
[INFO] [2020-04-15 10:20:19] (6 lines) /app/public/data/stal_stal_2009/publish_traits.tsv
[INFO] [2020-04-15 10:20:21] (24 lines) /app/public/data/stal_stal_2009/publish_metadata.tsv
[STOP] [2020-04-15 10:20:21] complete_harvest_instance
[START] [2020-04-15 10:20:21] completed
[STOP] [2020-04-15 10:20:21] completed
[STOP] [2020-04-15 10:20:21] logged process, took 138.39
Latest Process

15 Apr 10:18 EXITED currently processing 0