Harvest for Parasitic Plants Database Created 07 Nov 18:38

Harvesting Log

# Logfile created on 2019-11-07 18:38:00 -0500 by logger.rb/56815
[START] [2019-11-07 18:38:00] logged process
[START] [2019-11-07 18:38:00] create_harvest_instance
[STOP] [2019-11-07 18:38:01] create_harvest_instance
[START] [2019-11-07 18:38:01] fetch_files
[STOP] [2019-11-07 18:38:01] fetch_files
[START] [2019-11-07 18:38:01] validate_each_file
[STOP] [2019-11-07 18:38:01] validate_each_file
[START] [2019-11-07 18:38:01] convert_to_csv
[CMD] [2019-11-07 18:38:01] /usr/bin/sort /app/public/converted_csv/parasitic_pl_db_refs_18386.csv > /app/public/converted_csv/parasitic_pl_db_refs_18386.csv_sorted
[CMD] [2019-11-07 18:38:01] /usr/bin/sort /app/public/converted_csv/parasitic_pl_db_nodes_18387.csv > /app/public/converted_csv/parasitic_pl_db_nodes_18387.csv_sorted
[CMD] [2019-11-07 18:38:01] /usr/bin/sort /app/public/converted_csv/parasitic_pl_db_occurrences_18388.csv > /app/public/converted_csv/parasitic_pl_db_occurrences_18388.csv_sorted
[CMD] [2019-11-07 18:38:01] /usr/bin/sort /app/public/converted_csv/parasitic_pl_db_measurements_18389.csv > /app/public/converted_csv/parasitic_pl_db_measurements_18389.csv_sorted
[STOP] [2019-11-07 18:38:01] convert_to_csv
[START] [2019-11-07 18:38:01] calculate_delta
[CMD] [2019-11-07 18:38:01] echo "0a" > /app/public/diff/parasitic_pl_db_refs_18386.diff
[CMD] [2019-11-07 18:38:01] tail -n +1 /app/public/converted_csv/parasitic_pl_db_refs_18386.csv >> /app/public/diff/parasitic_pl_db_refs_18386.diff
[CMD] [2019-11-07 18:38:01] echo "." >> /app/public/diff/parasitic_pl_db_refs_18386.diff
[CMD] [2019-11-07 18:38:01] echo "0a" > /app/public/diff/parasitic_pl_db_nodes_18387.diff
[CMD] [2019-11-07 18:38:01] tail -n +1 /app/public/converted_csv/parasitic_pl_db_nodes_18387.csv >> /app/public/diff/parasitic_pl_db_nodes_18387.diff
[CMD] [2019-11-07 18:38:01] echo "." >> /app/public/diff/parasitic_pl_db_nodes_18387.diff
[CMD] [2019-11-07 18:38:01] echo "0a" > /app/public/diff/parasitic_pl_db_occurrences_18388.diff
[CMD] [2019-11-07 18:38:01] tail -n +1 /app/public/converted_csv/parasitic_pl_db_occurrences_18388.csv >> /app/public/diff/parasitic_pl_db_occurrences_18388.diff
[CMD] [2019-11-07 18:38:01] echo "." >> /app/public/diff/parasitic_pl_db_occurrences_18388.diff
[CMD] [2019-11-07 18:38:01] echo "0a" > /app/public/diff/parasitic_pl_db_measurements_18389.diff
[CMD] [2019-11-07 18:38:01] tail -n +1 /app/public/converted_csv/parasitic_pl_db_measurements_18389.csv >> /app/public/diff/parasitic_pl_db_measurements_18389.diff
[CMD] [2019-11-07 18:38:01] echo "." >> /app/public/diff/parasitic_pl_db_measurements_18389.diff
[STOP] [2019-11-07 18:38:01] calculate_delta
[START] [2019-11-07 18:38:01] parse_diff_and_store
[INFO] [2019-11-07 18:38:01] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-07 18:38:02] Loading nodes diff file into memory (true lines)...
[INFO] [2019-11-07 18:38:02] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-07 18:38:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-07 18:38:20] Storing 1307 References
[INFO] [2019-11-07 18:38:20] Processing group of 1307 in 2 groups of 1000
[INFO] [2019-11-07 18:38:20] Average Time: 0.12
[INFO] [2019-11-07 18:38:20] Total Time: 1s
[INFO] [2019-11-07 18:38:20] Storing 1315 ScientificNames
[INFO] [2019-11-07 18:38:20] Processing group of 1315 in 2 groups of 1000
[INFO] [2019-11-07 18:38:20] Average Time: 0.25
[INFO] [2019-11-07 18:38:20] Total Time: 1s
[INFO] [2019-11-07 18:38:20] Storing 1315 Nodes
[INFO] [2019-11-07 18:38:20] Processing group of 1315 in 2 groups of 1000
[INFO] [2019-11-07 18:38:21] Average Time: 0.205
[INFO] [2019-11-07 18:38:21] Total Time: 1s
[INFO] [2019-11-07 18:38:21] Storing 6769 Occurrences
[INFO] [2019-11-07 18:38:21] Processing group of 6769 in 7 groups of 1000
[INFO] [2019-11-07 18:38:22] Average Time: 0.101
[INFO] [2019-11-07 18:38:22] Total Time: 1s
[INFO] [2019-11-07 18:38:22] last 3 / first 3: 0.85
[INFO] [2019-11-07 18:38:22] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-11-07 18:38:22] Storing 9072 OccurrenceMetadata
[INFO] [2019-11-07 18:38:22] Processing group of 9072 in 10 groups of 1000
[INFO] [2019-11-07 18:38:23] Average Time: 0.111
[INFO] [2019-11-07 18:38:23] Total Time: 2s
[INFO] [2019-11-07 18:38:23] last 3 / first 3: 0.66
[INFO] [2019-11-07 18:38:23] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-11-07 18:38:23] Storing 1478 Traits
[INFO] [2019-11-07 18:38:23] Processing group of 1478 in 2 groups of 1000
[INFO] [2019-11-07 18:38:23] Average Time: 0.29
[INFO] [2019-11-07 18:38:23] Total Time: 1s
[INFO] [2019-11-07 18:38:23] Storing 3029 MetaTraits
[INFO] [2019-11-07 18:38:23] Processing group of 3029 in 4 groups of 1000
[INFO] [2019-11-07 18:38:24] Average Time: 0.105
[INFO] [2019-11-07 18:38:24] Total Time: 1s
[STOP] [2019-11-07 18:38:24] parse_diff_and_store
[START] [2019-11-07 18:38:24] resolve_keys
[INFO] [2019-11-07 18:38:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-07 18:38:29] traits to occurrences...
[INFO] [2019-11-07 18:38:29] traits to nodes (through occurrences)...
[INFO] [2019-11-07 18:38:29] Traits to sex term...
[INFO] [2019-11-07 18:38:29] Traits to lifestage term...
[INFO] [2019-11-07 18:38:29] MetaTraits to traits...
[INFO] [2019-11-07 18:38:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-07 18:38:29] Assocs to occurrences...
[INFO] [2019-11-07 18:38:29] Assocs to nodes...
[INFO] [2019-11-07 18:38:29] Assoc to sex term...
[INFO] [2019-11-07 18:38:29] Assoc to lifestage term...
[STOP] [2019-11-07 18:38:29] resolve_keys
[START] [2019-11-07 18:38:29] hold_for_later_1
[STOP] [2019-11-07 18:38:29] hold_for_later_1
[START] [2019-11-07 18:38:29] hold_for_later_2
[STOP] [2019-11-07 18:38:29] hold_for_later_2
[START] [2019-11-07 18:38:29] resolve_missing_parents
[STOP] [2019-11-07 18:38:29] resolve_missing_parents
[START] [2019-11-07 18:38:29] rebuild_nodes
[START] [2019-11-07 18:38:29] Flattener#flatten
[START] [2019-11-07 18:38:29] Flattener#study_resource
[START] [2019-11-07 18:38:29] Flattener#build_ancestry
[STOP] [2019-11-07 18:38:29] Flattener#build_ancestry
[INFO] [2019-11-07 18:38:29] 1315 ancestry keys
[START] [2019-11-07 18:38:29] build_node_ancestors
[INFO] [2019-11-07 18:38:29] old ancestors deleted.
[STOP] [2019-11-07 18:38:29] build_node_ancestors
[START] [2019-11-07 18:38:30] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 18:38:30] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 18:38:30] Flattener#flatten
[STOP] [2019-11-07 18:38:30] rebuild_nodes
[START] [2019-11-07 18:38:30] resolve_missing_media_owners
[STOP] [2019-11-07 18:38:30] resolve_missing_media_owners
[START] [2019-11-07 18:38:30] sanitize_media_verbatims
[STOP] [2019-11-07 18:38:30] sanitize_media_verbatims
[START] [2019-11-07 18:38:30] queue_downloads
[STOP] [2019-11-07 18:38:30] queue_downloads
[START] [2019-11-07 18:38:30] parse_names
[WARN] [2019-11-07 18:38:30] I see 1315 names which still need to be parsed.
[WARN] [2019-11-07 18:38:32] I see 97 names which still need to be parsed.
[WARN] [2019-11-07 18:38:33] I see 31 names which still need to be parsed.
[WARN] [2019-11-07 18:38:34] I see 11 names which still need to be parsed.
[WARN] [2019-11-07 18:38:35] I see 2 names which still need to be parsed.
[STOP] [2019-11-07 18:38:36] parse_names
[START] [2019-11-07 18:38:36] denormalize_canonical_names_to_nodes
[STOP] [2019-11-07 18:38:37] denormalize_canonical_names_to_nodes
[START] [2019-11-07 18:38:37] match_nodes
[START] [2019-11-07 18:38:37] map_all_nodes_to_pages
[STOP] [2019-11-07 18:39:42] map_all_nodes_to_pages
[INFO] [2019-11-07 18:39:42] 233 Unmatched nodes (of 1315)! That's too many to output. First 10: Grammica obtusiflora (#54745777); Grammica scandens cesatiana (#54745793); Lepidanche compositarum helianthi (#54745815); Lepidanche compositarum solidaginis (#54745816); Lepidanche squarrosa (#54745817); Nemepis africana (#54745837); Nemepis prolifera (#54745840); Schrebera schinoides (#54745844); Chlamydophyton aphyllum (#54746160); Lophophytum leandroi (#54746223)
[START] [2019-11-07 18:39:42] update_nodes
[STOP] [2019-11-07 18:39:42] update_nodes
[STOP] [2019-11-07 18:39:42] match_nodes
[START] [2019-11-07 18:39:42] reindex_search
[STOP] [2019-11-07 18:39:44] reindex_search
[START] [2019-11-07 18:39:44] normalize_units
[STOP] [2019-11-07 18:39:44] normalize_units
[START] [2019-11-07 18:39:44] calculate_statistics
[STOP] [2019-11-07 18:39:44] calculate_statistics
[START] [2019-11-07 18:39:44] complete_harvest_instance
[START] [2019-11-07 18:39:44] overall_tsv_creation
[INFO] [2019-11-07 18:39:44] Processing group of 1315 in 1 batches of 10000
[INFO] [2019-11-07 18:40:32] 1478 Traits (unfiltered)...
[INFO] [2019-11-07 18:40:45] 1478 Traits (filtered)...
[INFO] [2019-11-07 18:40:45] 0 Associations (filtered)...
[INFO] [2019-11-07 18:41:24] 4718 metadata added.
[INFO] [2019-11-07 18:41:24] 0 metadata added.
[INFO] [2019-11-07 18:41:24] Average Time: 78.45
[INFO] [2019-11-07 18:41:24] Total Time: 1m41s
[STOP] [2019-11-07 18:41:24] overall_tsv_creation
[INFO] [2019-11-07 18:41:24] Done. Check your files:
[INFO] [2019-11-07 18:41:24] (1315 lines) /app/public/data/parasitic_pl_db/publish_nodes.tsv
[INFO] [2019-11-07 18:41:24] (2984 lines) /app/public/data/parasitic_pl_db/publish_node_ancestors.tsv
[INFO] [2019-11-07 18:41:24] (1315 lines) /app/public/data/parasitic_pl_db/publish_scientific_names.tsv
[INFO] [2019-11-07 18:41:24] (1479 lines) /app/public/data/parasitic_pl_db/publish_traits.tsv
[INFO] [2019-11-07 18:41:24] (4719 lines) /app/public/data/parasitic_pl_db/publish_metadata.tsv
[STOP] [2019-11-07 18:41:24] complete_harvest_instance
[START] [2019-11-07 18:41:24] completed
[STOP] [2019-11-07 18:41:24] completed
[STOP] [2019-11-07 18:41:24] logged process, took 204.31

Latest Process

07 Nov 18:38 EXITED currently processing 0