Stage:
completed
Fetched:
14 Jan 15:55
Validated:
14 Jan 15:55
Deltas Created
14 Jan 15:55
Units Normalized:
14 Jan 15:59
Ancestry Built:
14 Jan 15:55
Nodes Matched:
14 Jan 15:59
Names Parsed:
14 Jan 15:56
New Models Stored:
14 Jan 15:55
Indexed:
14 Jan 15:59
Completed:
14 Jan 16:01
Time to Harvest:
less than a minute
Harvesting Log
(128 lines)
# Logfile created on 2020-01-14 15:55:23 -0500 by logger.rb/56815
[START] [2020-01-14 15:55:23] logged process
[START] [2020-01-14 15:55:23] create_harvest_instance
[STOP] [2020-01-14 15:55:23] create_harvest_instance
[START] [2020-01-14 15:55:23] fetch_files
[STOP] [2020-01-14 15:55:23] fetch_files
[START] [2020-01-14 15:55:23] validate_each_file
[STOP] [2020-01-14 15:55:24] validate_each_file
[START] [2020-01-14 15:55:24] convert_to_csv
[CMD] [2020-01-14 15:55:24] /usr/bin/sort /app/public/converted_csv/sabath_et_al_sab_nodes_19911.csv > /app/public/converted_csv/sabath_et_al_sab_nodes_19911.csv_sorted
[CMD] [2020-01-14 15:55:24] /usr/bin/sort /app/public/converted_csv/sabath_et_al_sab_occurrences_19912.csv > /app/public/converted_csv/sabath_et_al_sab_occurrences_19912.csv_sorted
[CMD] [2020-01-14 15:55:24] /usr/bin/sort /app/public/converted_csv/sabath_et_al_sab_measurements_19913.csv > /app/public/converted_csv/sabath_et_al_sab_measurements_19913.csv_sorted
[STOP] [2020-01-14 15:55:24] convert_to_csv
[START] [2020-01-14 15:55:24] calculate_delta
[CMD] [2020-01-14 15:55:24] echo "0a" > /app/public/diff/sabath_et_al_sab_nodes_19911.diff
[CMD] [2020-01-14 15:55:24] tail -n +1 /app/public/converted_csv/sabath_et_al_sab_nodes_19911.csv >> /app/public/diff/sabath_et_al_sab_nodes_19911.diff
[CMD] [2020-01-14 15:55:24] echo "." >> /app/public/diff/sabath_et_al_sab_nodes_19911.diff
[CMD] [2020-01-14 15:55:25] echo "0a" > /app/public/diff/sabath_et_al_sab_occurrences_19912.diff
[CMD] [2020-01-14 15:55:25] tail -n +1 /app/public/converted_csv/sabath_et_al_sab_occurrences_19912.csv >> /app/public/diff/sabath_et_al_sab_occurrences_19912.diff
[CMD] [2020-01-14 15:55:25] echo "." >> /app/public/diff/sabath_et_al_sab_occurrences_19912.diff
[CMD] [2020-01-14 15:55:25] echo "0a" > /app/public/diff/sabath_et_al_sab_measurements_19913.diff
[CMD] [2020-01-14 15:55:25] tail -n +1 /app/public/converted_csv/sabath_et_al_sab_measurements_19913.csv >> /app/public/diff/sabath_et_al_sab_measurements_19913.diff
[CMD] [2020-01-14 15:55:25] echo "." >> /app/public/diff/sabath_et_al_sab_measurements_19913.diff
[STOP] [2020-01-14 15:55:26] calculate_delta
[START] [2020-01-14 15:55:26] parse_diff_and_store
[INFO] [2020-01-14 15:55:26] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-14 15:55:27] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-01-14 15:55:28] Loading measurements diff file into memory (true lines)...
[INFO] [2020-01-14 15:55:44] Storing 3720 ScientificNames
[INFO] [2020-01-14 15:55:44] Processing group of 3720 in 4 groups of 1000
[INFO] [2020-01-14 15:55:45] Average Time: 0.338
[INFO] [2020-01-14 15:55:45] Total Time: 2s
[INFO] [2020-01-14 15:55:45] Storing 3720 Nodes
[INFO] [2020-01-14 15:55:45] Processing group of 3720 in 4 groups of 1000
[INFO] [2020-01-14 15:55:46] Average Time: 0.265
[INFO] [2020-01-14 15:55:46] Total Time: 2s
[INFO] [2020-01-14 15:55:46] Storing 3713 Occurrences
[INFO] [2020-01-14 15:55:46] Processing group of 3713 in 4 groups of 1000
[INFO] [2020-01-14 15:55:47] Average Time: 0.093
[INFO] [2020-01-14 15:55:47] Total Time: 1s
[INFO] [2020-01-14 15:55:47] Storing 3713 Traits
[INFO] [2020-01-14 15:55:47] Processing group of 3713 in 4 groups of 1000
[INFO] [2020-01-14 15:55:48] Average Time: 0.275
[INFO] [2020-01-14 15:55:48] Total Time: 2s
[INFO] [2020-01-14 15:55:48] Storing 7632 MetaTraits
[INFO] [2020-01-14 15:55:48] Processing group of 7632 in 8 groups of 1000
[INFO] [2020-01-14 15:55:49] Average Time: 0.112
[INFO] [2020-01-14 15:55:49] Total Time: 1s
[INFO] [2020-01-14 15:55:49] last 3 / first 3: 0.84
[INFO] [2020-01-14 15:55:49] Std.Dev: 0.0; Max: 0.14
[STOP] [2020-01-14 15:55:49] parse_diff_and_store
[START] [2020-01-14 15:55:49] resolve_keys
[INFO] [2020-01-14 15:55:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-14 15:55:54] traits to occurrences...
[INFO] [2020-01-14 15:55:54] traits to nodes (through occurrences)...
[INFO] [2020-01-14 15:55:54] Traits to sex term...
[INFO] [2020-01-14 15:55:54] Traits to lifestage term...
[INFO] [2020-01-14 15:55:54] MetaTraits to traits...
[INFO] [2020-01-14 15:55:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-14 15:55:54] Assocs to occurrences...
[INFO] [2020-01-14 15:55:54] Assocs to nodes...
[INFO] [2020-01-14 15:55:54] Assoc to sex term...
[INFO] [2020-01-14 15:55:54] Assoc to lifestage term...
[STOP] [2020-01-14 15:55:54] resolve_keys
[START] [2020-01-14 15:55:54] hold_for_later_1
[STOP] [2020-01-14 15:55:54] hold_for_later_1
[START] [2020-01-14 15:55:54] hold_for_later_2
[STOP] [2020-01-14 15:55:54] hold_for_later_2
[START] [2020-01-14 15:55:54] resolve_missing_parents
[STOP] [2020-01-14 15:55:54] resolve_missing_parents
[START] [2020-01-14 15:55:54] rebuild_nodes
[START] [2020-01-14 15:55:54] Flattener#flatten
[START] [2020-01-14 15:55:54] Flattener#study_resource
[START] [2020-01-14 15:55:54] Flattener#build_ancestry
[STOP] [2020-01-14 15:55:54] Flattener#build_ancestry
[INFO] [2020-01-14 15:55:54] 3720 ancestry keys
[START] [2020-01-14 15:55:54] build_node_ancestors
[INFO] [2020-01-14 15:55:54] old ancestors deleted.
[STOP] [2020-01-14 15:55:56] build_node_ancestors
[START] [2020-01-14 15:55:58] Flattener#propagate_ancestor_ids
[STOP] [2020-01-14 15:55:59] Flattener#propagate_ancestor_ids
[STOP] [2020-01-14 15:55:59] Flattener#flatten
[STOP] [2020-01-14 15:55:59] rebuild_nodes
[START] [2020-01-14 15:55:59] resolve_missing_media_owners
[STOP] [2020-01-14 15:55:59] resolve_missing_media_owners
[START] [2020-01-14 15:55:59] sanitize_media_verbatims
[STOP] [2020-01-14 15:55:59] sanitize_media_verbatims
[START] [2020-01-14 15:55:59] queue_downloads
[STOP] [2020-01-14 15:55:59] queue_downloads
[START] [2020-01-14 15:55:59] parse_names
[WARN] [2020-01-14 15:55:59] I see 3720 names which still need to be parsed.
[STOP] [2020-01-14 15:56:02] parse_names
[START] [2020-01-14 15:56:02] denormalize_canonical_names_to_nodes
[STOP] [2020-01-14 15:56:02] denormalize_canonical_names_to_nodes
[START] [2020-01-14 15:56:03] match_nodes
[START] [2020-01-14 15:56:03] map_all_nodes_to_pages
[STOP] [2020-01-14 15:59:40] map_all_nodes_to_pages
[INFO] [2020-01-14 15:59:40] 41 Unmatched nodes (of 3720)! That's too many to output. First 10: Amaranthus aureus (#62795974); Amaranthus polygamus (#62796029); Begonia caroliniifolia (#62796419); Begonia guttata (#62796628); Begonia plebeja (#62796931); Begonia robinsonii (#62796995); Begonia tenuicaulis (#62797120); Begonia valida (#62797166); Boehmeria macrophylla (#62797220); Boehmeria spicata (#62797227)
[START] [2020-01-14 15:59:40] update_nodes
[STOP] [2020-01-14 15:59:41] update_nodes
[STOP] [2020-01-14 15:59:41] match_nodes
[START] [2020-01-14 15:59:41] reindex_search
[STOP] [2020-01-14 15:59:48] reindex_search
[START] [2020-01-14 15:59:48] normalize_units
[STOP] [2020-01-14 15:59:48] normalize_units
[START] [2020-01-14 15:59:48] calculate_statistics
[STOP] [2020-01-14 15:59:48] calculate_statistics
[START] [2020-01-14 15:59:48] complete_harvest_instance
[START] [2020-01-14 15:59:48] overall_tsv_creation
[INFO] [2020-01-14 15:59:48] Processing group of 3720 in 1 batches of 10000
[INFO] [2020-01-14 16:00:55] 3713 Traits (unfiltered)...
[INFO] [2020-01-14 16:01:09] 3713 Traits (filtered)...
[INFO] [2020-01-14 16:01:09] 0 Associations (filtered)...
[INFO] [2020-01-14 16:01:53] 7632 metadata added.
[INFO] [2020-01-14 16:01:53] 0 metadata added.
[INFO] [2020-01-14 16:01:53] Average Time: 94.45
[INFO] [2020-01-14 16:01:53] Total Time: 2m5s
[STOP] [2020-01-14 16:01:53] overall_tsv_creation
[INFO] [2020-01-14 16:01:53] Done. Check your files:
[INFO] [2020-01-14 16:01:53] (3720 lines) /app/public/data/sabath_et_al_sab/publish_nodes.tsv
[INFO] [2020-01-14 16:01:53] (26012 lines) /app/public/data/sabath_et_al_sab/publish_node_ancestors.tsv
[INFO] [2020-01-14 16:01:53] (3720 lines) /app/public/data/sabath_et_al_sab/publish_scientific_names.tsv
[INFO] [2020-01-14 16:01:54] (3714 lines) /app/public/data/sabath_et_al_sab/publish_traits.tsv
[INFO] [2020-01-14 16:01:54] (7633 lines) /app/public/data/sabath_et_al_sab/publish_metadata.tsv
[STOP] [2020-01-14 16:01:54] complete_harvest_instance
[START] [2020-01-14 16:01:54] completed
[STOP] [2020-01-14 16:01:54] completed
[STOP] [2020-01-14 16:01:54] logged process, took 391.18
Latest Process