Harvest for Palestine Species List Created 15 Oct 06:20

Stage: completed
Fetched: 15 Oct 06:20
Validated: 15 Oct 06:20
Deltas Created 15 Oct 06:20
Units Normalized: 15 Oct 06:25
Ancestry Built: 15 Oct 06:21
Nodes Matched: 15 Oct 06:25
Names Parsed: 15 Oct 06:21
New Models Stored: 15 Oct 06:20
Indexed: 15 Oct 06:25
Completed: 15 Oct 06:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 06:20:28 -0400 by logger.rb/56815
[START] [2019-10-15 06:20:28] logged process
[START] [2019-10-15 06:20:28] create_harvest_instance
[STOP] [2019-10-15 06:20:28] create_harvest_instance
[START] [2019-10-15 06:20:28] fetch_files
[STOP] [2019-10-15 06:20:28] fetch_files
[START] [2019-10-15 06:20:28] validate_each_file
[STOP] [2019-10-15 06:20:29] validate_each_file
[START] [2019-10-15 06:20:29] convert_to_csv
[CMD] [2019-10-15 06:20:29] /usr/bin/sort /app/public/converted_csv/palestine_sp_lis_refs_16861.csv > /app/public/converted_csv/palestine_sp_lis_refs_16861.csv_sorted
[CMD] [2019-10-15 06:20:29] /usr/bin/sort /app/public/converted_csv/palestine_sp_lis_nodes_16862.csv > /app/public/converted_csv/palestine_sp_lis_nodes_16862.csv_sorted
[CMD] [2019-10-15 06:20:30] /usr/bin/sort /app/public/converted_csv/palestine_sp_lis_occurrences_16863.csv > /app/public/converted_csv/palestine_sp_lis_occurrences_16863.csv_sorted
[CMD] [2019-10-15 06:20:30] /usr/bin/sort /app/public/converted_csv/palestine_sp_lis_measurements_16864.csv > /app/public/converted_csv/palestine_sp_lis_measurements_16864.csv_sorted
[STOP] [2019-10-15 06:20:30] convert_to_csv
[START] [2019-10-15 06:20:30] calculate_delta
[CMD] [2019-10-15 06:20:30] echo "0a" > /app/public/diff/palestine_sp_lis_refs_16861.diff
[CMD] [2019-10-15 06:20:30] tail -n +1 /app/public/converted_csv/palestine_sp_lis_refs_16861.csv >> /app/public/diff/palestine_sp_lis_refs_16861.diff
[CMD] [2019-10-15 06:20:31] echo "." >> /app/public/diff/palestine_sp_lis_refs_16861.diff
[CMD] [2019-10-15 06:20:31] echo "0a" > /app/public/diff/palestine_sp_lis_nodes_16862.diff
[CMD] [2019-10-15 06:20:31] tail -n +1 /app/public/converted_csv/palestine_sp_lis_nodes_16862.csv >> /app/public/diff/palestine_sp_lis_nodes_16862.diff
[CMD] [2019-10-15 06:20:32] echo "." >> /app/public/diff/palestine_sp_lis_nodes_16862.diff
[CMD] [2019-10-15 06:20:32] echo "0a" > /app/public/diff/palestine_sp_lis_occurrences_16863.diff
[CMD] [2019-10-15 06:20:32] tail -n +1 /app/public/converted_csv/palestine_sp_lis_occurrences_16863.csv >> /app/public/diff/palestine_sp_lis_occurrences_16863.diff
[CMD] [2019-10-15 06:20:32] echo "." >> /app/public/diff/palestine_sp_lis_occurrences_16863.diff
[CMD] [2019-10-15 06:20:33] echo "0a" > /app/public/diff/palestine_sp_lis_measurements_16864.diff
[CMD] [2019-10-15 06:20:33] tail -n +1 /app/public/converted_csv/palestine_sp_lis_measurements_16864.csv >> /app/public/diff/palestine_sp_lis_measurements_16864.diff
[CMD] [2019-10-15 06:20:33] echo "." >> /app/public/diff/palestine_sp_lis_measurements_16864.diff
[STOP] [2019-10-15 06:20:34] calculate_delta
[START] [2019-10-15 06:20:34] parse_diff_and_store
[INFO] [2019-10-15 06:20:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 06:20:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 06:20:36] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 06:20:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 06:20:52] Storing 2 References
[INFO] [2019-10-15 06:20:52] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 06:20:52] Average Time: 0.0
[INFO] [2019-10-15 06:20:52] Total Time: 1s
[INFO] [2019-10-15 06:20:52] Storing 4244 ScientificNames
[INFO] [2019-10-15 06:20:52] Processing group of 4244 in 5 groups of 1000
[INFO] [2019-10-15 06:20:54] Average Time: 0.334
[INFO] [2019-10-15 06:20:54] Total Time: 2s
[INFO] [2019-10-15 06:20:54] Storing 4244 Nodes
[INFO] [2019-10-15 06:20:54] Processing group of 4244 in 5 groups of 1000
[INFO] [2019-10-15 06:20:55] Average Time: 0.25
[INFO] [2019-10-15 06:20:55] Total Time: 2s
[INFO] [2019-10-15 06:20:55] Storing 2410 Occurrences
[INFO] [2019-10-15 06:20:55] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-15 06:20:56] Average Time: 0.083
[INFO] [2019-10-15 06:20:56] Total Time: 1s
[INFO] [2019-10-15 06:20:56] Storing 5480 TraitsReferences
[INFO] [2019-10-15 06:20:56] Processing group of 5480 in 6 groups of 1000
[INFO] [2019-10-15 06:20:56] Average Time: 0.083
[INFO] [2019-10-15 06:20:56] Total Time: 1s
[INFO] [2019-10-15 06:20:56] Storing 5479 Traits
[INFO] [2019-10-15 06:20:56] Processing group of 5479 in 6 groups of 1000
[INFO] [2019-10-15 06:20:58] Average Time: 0.303
[INFO] [2019-10-15 06:20:58] Total Time: 2s
[INFO] [2019-10-15 06:20:58] Storing 5478 MetaTraits
[INFO] [2019-10-15 06:20:58] Processing group of 5478 in 6 groups of 1000
[INFO] [2019-10-15 06:20:59] Average Time: 0.105
[INFO] [2019-10-15 06:20:59] Total Time: 1s
[STOP] [2019-10-15 06:20:59] parse_diff_and_store
[START] [2019-10-15 06:20:59] resolve_keys
[INFO] [2019-10-15 06:21:18] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 06:21:20] traits to occurrences...
[INFO] [2019-10-15 06:21:22] traits to nodes (through occurrences)...
[INFO] [2019-10-15 06:21:22] Traits to sex term...
[INFO] [2019-10-15 06:21:24] Traits to lifestage term...
[INFO] [2019-10-15 06:21:25] MetaTraits to traits...
[INFO] [2019-10-15 06:21:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 06:21:27] Assocs to occurrences...
[INFO] [2019-10-15 06:21:27] Assocs to nodes...
[INFO] [2019-10-15 06:21:27] Assoc to sex term...
[INFO] [2019-10-15 06:21:27] Assoc to lifestage term...
[STOP] [2019-10-15 06:21:27] resolve_keys
[START] [2019-10-15 06:21:27] hold_for_later_1
[STOP] [2019-10-15 06:21:27] hold_for_later_1
[START] [2019-10-15 06:21:27] hold_for_later_2
[STOP] [2019-10-15 06:21:27] hold_for_later_2
[START] [2019-10-15 06:21:27] resolve_missing_parents
[STOP] [2019-10-15 06:21:35] resolve_missing_parents
[START] [2019-10-15 06:21:35] rebuild_nodes
[START] [2019-10-15 06:21:35] Flattener#flatten
[START] [2019-10-15 06:21:35] Flattener#study_resource
[START] [2019-10-15 06:21:35] Flattener#build_ancestry
[STOP] [2019-10-15 06:21:35] Flattener#build_ancestry
[INFO] [2019-10-15 06:21:35] 4244 ancestry keys
[START] [2019-10-15 06:21:35] build_node_ancestors
[INFO] [2019-10-15 06:21:35] old ancestors deleted.
[STOP] [2019-10-15 06:21:36] build_node_ancestors
[START] [2019-10-15 06:21:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 06:21:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 06:21:37] Flattener#flatten
[STOP] [2019-10-15 06:21:37] rebuild_nodes
[START] [2019-10-15 06:21:37] resolve_missing_media_owners
[STOP] [2019-10-15 06:21:37] resolve_missing_media_owners
[START] [2019-10-15 06:21:37] sanitize_media_verbatims
[STOP] [2019-10-15 06:21:37] sanitize_media_verbatims
[START] [2019-10-15 06:21:37] queue_downloads
[STOP] [2019-10-15 06:21:37] queue_downloads
[START] [2019-10-15 06:21:37] parse_names
[WARN] [2019-10-15 06:21:37] I see 4244 names which still need to be parsed.
[STOP] [2019-10-15 06:21:41] parse_names
[START] [2019-10-15 06:21:41] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 06:21:41] denormalize_canonical_names_to_nodes
[START] [2019-10-15 06:21:41] match_nodes
[START] [2019-10-15 06:21:41] map_all_nodes_to_pages
[STOP] [2019-10-15 06:25:27] map_all_nodes_to_pages
[INFO] [2019-10-15 06:25:27] 233 Unmatched nodes (of 4244)! That's too many to output. First 10: Crataegus aronia (#51417717); Prunus communis (#51418695); Parietaria diffusa (#51421568); Anthemis eliezrae (#51421741); Centaurea benedictus (#51420579); Centaurea araneosa (#51420861); Echinops adenocaulis (#51417834); Leontodon tuberosa (#51417843); Sonchus bulbosa (#51420112); Tripleurospermum factorovskyi (#51418208)
[START] [2019-10-15 06:25:27] update_nodes
[STOP] [2019-10-15 06:25:29] update_nodes
[STOP] [2019-10-15 06:25:29] match_nodes
[START] [2019-10-15 06:25:29] reindex_search
[STOP] [2019-10-15 06:25:38] reindex_search
[START] [2019-10-15 06:25:38] normalize_units
[STOP] [2019-10-15 06:25:38] normalize_units
[START] [2019-10-15 06:25:38] calculate_statistics
[STOP] [2019-10-15 06:25:38] calculate_statistics
[START] [2019-10-15 06:25:38] complete_harvest_instance
[START] [2019-10-15 06:25:38] overall_tsv_creation
[INFO] [2019-10-15 06:25:38] Processing group of 4244 in 1 batches of 10000
[INFO] [2019-10-15 06:26:44] 2410 Traits (unfiltered)...
[INFO] [2019-10-15 06:26:58] 2410 Traits (filtered)...
[INFO] [2019-10-15 06:26:58] 0 Associations (filtered)...
[INFO] [2019-10-15 06:27:43] 12049 metadata added.
[INFO] [2019-10-15 06:27:43] 0 metadata added.
[INFO] [2019-10-15 06:27:43] Average Time: 100.58
[INFO] [2019-10-15 06:27:43] Total Time: 2m5s
[STOP] [2019-10-15 06:27:43] overall_tsv_creation
[INFO] [2019-10-15 06:27:43] Done. Check your files:
[INFO] [2019-10-15 06:27:44] (4244 lines) /app/public/data/palestine_sp_lis/publish_nodes.tsv
[INFO] [2019-10-15 06:27:44] (10077 lines) /app/public/data/palestine_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-15 06:27:44] (4244 lines) /app/public/data/palestine_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-15 06:27:44] (2411 lines) /app/public/data/palestine_sp_lis/publish_traits.tsv
[INFO] [2019-10-15 06:27:45] (12050 lines) /app/public/data/palestine_sp_lis/publish_metadata.tsv
[STOP] [2019-10-15 06:27:45] complete_harvest_instance
[START] [2019-10-15 06:27:45] completed
[STOP] [2019-10-15 06:27:45] completed
[STOP] [2019-10-15 06:27:45] logged process, took 437.17
Latest Process

15 Oct 06:20 EXITED currently processing 0