Harvest for Suzuki et al 2010 Created 03 Aug 16:01

Stage: completed
Fetched: 03 Aug 16:01
Validated: 03 Aug 16:01
Deltas Created 03 Aug 16:01
Units Normalized: 03 Aug 16:01
Ancestry Built: 03 Aug 16:01
Nodes Matched: 03 Aug 16:01
Names Parsed: 03 Aug 16:01
New Models Stored: 03 Aug 16:01
Indexed: 03 Aug 16:01
Completed: 03 Aug 16:03
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:01:21] Created harvest instance #4160
[STOP] [2022-08-03 16:01:21] create_harvest_instance
[START] [2022-08-03 16:01:21] fetch_files
[STOP] [2022-08-03 16:01:21] fetch_files
[START] [2022-08-03 16:01:21] validate_each_file
[INFO] [2022-08-03 16:01:21] Looping over 3 formats...
[INFO] [2022-08-03 16:01:21] ...nodes (/app/public/data/suzuki_et_al_suz/taxa.txt)
[INFO] [2022-08-03 16:01:21] Valid: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_nodes_29543.csv (1 lines)
[INFO] [2022-08-03 16:01:21] ...occurrences (/app/public/data/suzuki_et_al_suz/occurrences.txt)
[INFO] [2022-08-03 16:01:21] Valid: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_occurrences_29544.csv (1 lines)
[INFO] [2022-08-03 16:01:21] ...measurements (/app/public/data/suzuki_et_al_suz/measurementOrFact.txt)
[INFO] [2022-08-03 16:01:21] Valid: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_measurements_29545.csv (5 lines)
[STOP] [2022-08-03 16:01:21] validate_each_file
[START] [2022-08-03 16:01:21] convert_to_csv
[INFO] [2022-08-03 16:01:21] Looping over 3 formats...
[INFO] [2022-08-03 16:01:21] ...nodes (/app/public/data/suzuki_et_al_suz/taxa.txt)
[CMD] [2022-08-03 16:01:21] /usr/bin/sort /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_nodes_29543.csv > /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_nodes_29543.csv_sorted
[INFO] [2022-08-03 16:01:21] Converted: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_nodes_29543.csv (1 lines)
[INFO] [2022-08-03 16:01:21] ...occurrences (/app/public/data/suzuki_et_al_suz/occurrences.txt)
[CMD] [2022-08-03 16:01:21] /usr/bin/sort /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_occurrences_29544.csv > /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_occurrences_29544.csv_sorted
[INFO] [2022-08-03 16:01:21] Converted: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_occurrences_29544.csv (1 lines)
[INFO] [2022-08-03 16:01:21] ...measurements (/app/public/data/suzuki_et_al_suz/measurementOrFact.txt)
[CMD] [2022-08-03 16:01:21] /usr/bin/sort /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_measurements_29545.csv > /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_measurements_29545.csv_sorted
[INFO] [2022-08-03 16:01:21] Converted: /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_measurements_29545.csv (5 lines)
[STOP] [2022-08-03 16:01:21] convert_to_csv
[START] [2022-08-03 16:01:21] calculate_delta
[INFO] [2022-08-03 16:01:21] Looping over 3 formats...
[INFO] [2022-08-03 16:01:21] ...nodes (/app/public/data/suzuki_et_al_suz/taxa.txt)
[CMD] [2022-08-03 16:01:21] echo "0a" > /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_nodes_29543.diff
[CMD] [2022-08-03 16:01:21] tail -n +1 /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_nodes_29543.csv >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_nodes_29543.diff
[CMD] [2022-08-03 16:01:21] echo "." >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_nodes_29543.diff
[INFO] [2022-08-03 16:01:21] Created diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_nodes_29543.diff (3 lines)
[INFO] [2022-08-03 16:01:21] ...occurrences (/app/public/data/suzuki_et_al_suz/occurrences.txt)
[CMD] [2022-08-03 16:01:21] echo "0a" > /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_occurrences_29544.diff
[CMD] [2022-08-03 16:01:21] tail -n +1 /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_occurrences_29544.csv >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_occurrences_29544.diff
[CMD] [2022-08-03 16:01:21] echo "." >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_occurrences_29544.diff
[INFO] [2022-08-03 16:01:21] Created diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_occurrences_29544.diff (3 lines)
[INFO] [2022-08-03 16:01:21] ...measurements (/app/public/data/suzuki_et_al_suz/measurementOrFact.txt)
[CMD] [2022-08-03 16:01:21] echo "0a" > /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_measurements_29545.diff
[CMD] [2022-08-03 16:01:21] tail -n +1 /app/public/data/suzuki_et_al_suz/converted_csv/suzuki_et_al_suz_measurements_29545.csv >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_measurements_29545.diff
[CMD] [2022-08-03 16:01:21] echo "." >> /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_measurements_29545.diff
[INFO] [2022-08-03 16:01:21] Created diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_measurements_29545.diff (7 lines)
[STOP] [2022-08-03 16:01:21] calculate_delta
[START] [2022-08-03 16:01:21] parse_diff_and_store
[INFO] [2022-08-03 16:01:21] Handling diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_nodes_29543.diff (3 lines)
[INFO] [2022-08-03 16:01:21] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:01:21] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:01:21] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:01:21] Handling diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_occurrences_29544.diff (3 lines)
[INFO] [2022-08-03 16:01:21] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:01:21] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:01:21] Handling diff: /app/public/data/suzuki_et_al_suz/diff/suzuki_et_al_suz_measurements_29545.diff (7 lines)
[INFO] [2022-08-03 16:01:21] Loading measurements diff file into memory (7 lines)...
[INFO] [2022-08-03 16:01:21] Storing 5 Traits (8/5/7)
[INFO] [2022-08-03 16:01:21] Storing 3 MetaTraits (8/5/7)
[STOP] [2022-08-03 16:01:21] parse_diff_and_store
[START] [2022-08-03 16:01:21] resolve_keys
[2022-08-03 16:01:21] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:01:28] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:01:28] traits to occurrences...
[INFO] [2022-08-03 16:01:28] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:01:28] Traits to sex term...
[INFO] [2022-08-03 16:01:28] Traits to lifestage term...
[INFO] [2022-08-03 16:01:28] MetaTraits to traits...
[INFO] [2022-08-03 16:01:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:01:28] Assocs to occurrences...
[INFO] [2022-08-03 16:01:28] Assocs to nodes...
[INFO] [2022-08-03 16:01:28] Assoc to sex term...
[INFO] [2022-08-03 16:01:28] Assoc to lifestage term...
[INFO] [2022-08-03 16:01:28] MetaAssoc to assocs...
[STOP] [2022-08-03 16:01:28] resolve_keys
[START] [2022-08-03 16:01:28] hold_for_later_1
[STOP] [2022-08-03 16:01:28] hold_for_later_1
[START] [2022-08-03 16:01:28] hold_for_later_2
[STOP] [2022-08-03 16:01:28] hold_for_later_2
[START] [2022-08-03 16:01:28] resolve_missing_parents
[STOP] [2022-08-03 16:01:28] resolve_missing_parents
[START] [2022-08-03 16:01:28] rebuild_nodes
[START] [2022-08-03 16:01:28] Flattener#flatten
[START] [2022-08-03 16:01:28] Flattener#study_resource
[START] [2022-08-03 16:01:28] Flattener#build_ancestry
[STOP] [2022-08-03 16:01:28] Flattener#build_ancestry
[INFO] [2022-08-03 16:01:28] 1 ancestry keys
[START] [2022-08-03 16:01:28] build_node_ancestors
[INFO] [2022-08-03 16:01:28] old ancestors deleted.
[STOP] [2022-08-03 16:01:28] build_node_ancestors
[WARN] [2022-08-03 16:01:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:01:28] Flattener#flatten
[STOP] [2022-08-03 16:01:28] rebuild_nodes
[START] [2022-08-03 16:01:28] resolve_missing_media_owners
[STOP] [2022-08-03 16:01:28] resolve_missing_media_owners
[START] [2022-08-03 16:01:28] sanitize_media_verbatims
[STOP] [2022-08-03 16:01:28] sanitize_media_verbatims
[START] [2022-08-03 16:01:28] queue_downloads
[STOP] [2022-08-03 16:01:28] queue_downloads
[START] [2022-08-03 16:01:28] parse_names
[WARN] [2022-08-03 16:01:28] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:01:29] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:01:30] parse_names
[START] [2022-08-03 16:01:30] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:01:30] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:01:30] match_nodes
[START] [2022-08-03 16:01:30] map_all_nodes_to_pages
[STOP] [2022-08-03 16:01:30] map_all_nodes_to_pages
[INFO] [2022-08-03 16:01:30] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:01:30] update_nodes
[STOP] [2022-08-03 16:01:30] update_nodes
[STOP] [2022-08-03 16:01:30] match_nodes
[START] [2022-08-03 16:01:30] reindex_search
[STOP] [2022-08-03 16:01:30] reindex_search
[START] [2022-08-03 16:01:30] normalize_units
[STOP] [2022-08-03 16:01:30] normalize_units
[START] [2022-08-03 16:01:30] calculate_statistics
[2022-08-03 16:01:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:01:30] Duplicate page_id count: 0
[STOP] [2022-08-03 16:01:30] calculate_statistics
[START] [2022-08-03 16:01:30] complete_harvest_instance
[START] [2022-08-03 16:01:30] overall_tsv_creation
[INFO] [2022-08-03 16:01:30] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:01:30] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:02:11] 3 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:02:11] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:03:04] Mapped 3 traits (3 meta) for 1 nodes.
[INFO] [2022-08-03 16:03:04] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:03:04] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:03:04] Adding 3 traits...
[INFO] [2022-08-03 16:03:04] 2 metadata added.
[INFO] [2022-08-03 16:03:04] Adding 0 assocs...
[INFO] [2022-08-03 16:03:04] 0 metadata added.
[INFO] [2022-08-03 16:03:46] Processed 1/1 nodes
[INFO] [2022-08-03 16:03:46] Average Time: 110.72
[INFO] [2022-08-03 16:03:46] Total Time: 2m17s
[STOP] [2022-08-03 16:03:46] overall_tsv_creation
[INFO] [2022-08-03 16:03:46] Done. Check your files:
[INFO] [2022-08-03 16:03:46] (1 lines) /app/public/data/suzuki_et_al_suz/publish_nodes.tsv
[INFO] [2022-08-03 16:03:46] (1 lines) /app/public/data/suzuki_et_al_suz/publish_scientific_names.tsv
[INFO] [2022-08-03 16:03:46] (4 lines) /app/public/data/suzuki_et_al_suz/publish_traits.tsv
[INFO] [2022-08-03 16:03:46] (3 lines) /app/public/data/suzuki_et_al_suz/publish_metadata.tsv
[STOP] [2022-08-03 16:03:46] complete_harvest_instance
[START] [2022-08-03 16:03:46] completed
[STOP] [2022-08-03 16:03:46] completed
[STOP] [2022-08-03 16:03:46] logged process, took 145.54
Latest Process

03 Aug 15:59 EXITED currently processing 0