Harvest for Mali Species List Created 14 Oct 04:50

Stage: completed
Fetched: 14 Oct 04:50
Validated: 14 Oct 04:50
Deltas Created 14 Oct 04:50
Units Normalized: 14 Oct 04:55
Ancestry Built: 14 Oct 04:51
Nodes Matched: 14 Oct 04:55
Names Parsed: 14 Oct 04:51
New Models Stored: 14 Oct 04:51
Indexed: 14 Oct 04:55
Completed: 14 Oct 04:57
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 04:50:37 -0400 by logger.rb/56815
[START] [2019-10-14 04:50:37] logged process
[START] [2019-10-14 04:50:37] create_harvest_instance
[STOP] [2019-10-14 04:50:37] create_harvest_instance
[START] [2019-10-14 04:50:37] fetch_files
[STOP] [2019-10-14 04:50:37] fetch_files
[START] [2019-10-14 04:50:37] validate_each_file
[STOP] [2019-10-14 04:50:38] validate_each_file
[START] [2019-10-14 04:50:38] convert_to_csv
[CMD] [2019-10-14 04:50:38] /usr/bin/sort /app/public/converted_csv/mali_sp_list_refs_16515.csv > /app/public/converted_csv/mali_sp_list_refs_16515.csv_sorted
[CMD] [2019-10-14 04:50:38] /usr/bin/sort /app/public/converted_csv/mali_sp_list_nodes_16516.csv > /app/public/converted_csv/mali_sp_list_nodes_16516.csv_sorted
[CMD] [2019-10-14 04:50:38] /usr/bin/sort /app/public/converted_csv/mali_sp_list_occurrences_16517.csv > /app/public/converted_csv/mali_sp_list_occurrences_16517.csv_sorted
[CMD] [2019-10-14 04:50:38] /usr/bin/sort /app/public/converted_csv/mali_sp_list_measurements_16518.csv > /app/public/converted_csv/mali_sp_list_measurements_16518.csv_sorted
[STOP] [2019-10-14 04:50:38] convert_to_csv
[START] [2019-10-14 04:50:38] calculate_delta
[CMD] [2019-10-14 04:50:38] echo "0a" > /app/public/diff/mali_sp_list_refs_16515.diff
[CMD] [2019-10-14 04:50:38] tail -n +1 /app/public/converted_csv/mali_sp_list_refs_16515.csv >> /app/public/diff/mali_sp_list_refs_16515.diff
[CMD] [2019-10-14 04:50:38] echo "." >> /app/public/diff/mali_sp_list_refs_16515.diff
[CMD] [2019-10-14 04:50:38] echo "0a" > /app/public/diff/mali_sp_list_nodes_16516.diff
[CMD] [2019-10-14 04:50:39] tail -n +1 /app/public/converted_csv/mali_sp_list_nodes_16516.csv >> /app/public/diff/mali_sp_list_nodes_16516.diff
[CMD] [2019-10-14 04:50:39] echo "." >> /app/public/diff/mali_sp_list_nodes_16516.diff
[CMD] [2019-10-14 04:50:39] echo "0a" > /app/public/diff/mali_sp_list_occurrences_16517.diff
[CMD] [2019-10-14 04:50:39] tail -n +1 /app/public/converted_csv/mali_sp_list_occurrences_16517.csv >> /app/public/diff/mali_sp_list_occurrences_16517.diff
[CMD] [2019-10-14 04:50:39] echo "." >> /app/public/diff/mali_sp_list_occurrences_16517.diff
[CMD] [2019-10-14 04:50:39] echo "0a" > /app/public/diff/mali_sp_list_measurements_16518.diff
[CMD] [2019-10-14 04:50:39] tail -n +1 /app/public/converted_csv/mali_sp_list_measurements_16518.csv >> /app/public/diff/mali_sp_list_measurements_16518.diff
[CMD] [2019-10-14 04:50:39] echo "." >> /app/public/diff/mali_sp_list_measurements_16518.diff
[STOP] [2019-10-14 04:50:39] calculate_delta
[START] [2019-10-14 04:50:39] parse_diff_and_store
[INFO] [2019-10-14 04:50:39] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 04:50:39] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 04:50:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 04:50:41] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 04:50:55] Storing 2 References
[INFO] [2019-10-14 04:50:55] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 04:50:55] Average Time: 0.0
[INFO] [2019-10-14 04:50:55] Total Time: 1s
[INFO] [2019-10-14 04:50:55] Storing 4011 ScientificNames
[INFO] [2019-10-14 04:50:55] Processing group of 4011 in 5 groups of 1000
[INFO] [2019-10-14 04:50:57] Average Time: 0.316
[INFO] [2019-10-14 04:50:57] Total Time: 2s
[INFO] [2019-10-14 04:50:57] Storing 4011 Nodes
[INFO] [2019-10-14 04:50:57] Processing group of 4011 in 5 groups of 1000
[INFO] [2019-10-14 04:50:58] Average Time: 0.246
[INFO] [2019-10-14 04:50:58] Total Time: 2s
[INFO] [2019-10-14 04:50:58] Storing 1928 Occurrences
[INFO] [2019-10-14 04:50:58] Processing group of 1928 in 2 groups of 1000
[INFO] [2019-10-14 04:50:58] Average Time: 0.115
[INFO] [2019-10-14 04:50:58] Total Time: 1s
[INFO] [2019-10-14 04:50:58] Storing 4810 TraitsReferences
[INFO] [2019-10-14 04:50:58] Processing group of 4810 in 5 groups of 1000
[INFO] [2019-10-14 04:50:59] Average Time: 0.092
[INFO] [2019-10-14 04:50:59] Total Time: 1s
[INFO] [2019-10-14 04:50:59] Storing 4809 Traits
[INFO] [2019-10-14 04:50:59] Processing group of 4809 in 5 groups of 1000
[INFO] [2019-10-14 04:51:00] Average Time: 0.31
[INFO] [2019-10-14 04:51:00] Total Time: 2s
[INFO] [2019-10-14 04:51:00] Storing 4807 MetaTraits
[INFO] [2019-10-14 04:51:00] Processing group of 4807 in 5 groups of 1000
[INFO] [2019-10-14 04:51:01] Average Time: 0.112
[INFO] [2019-10-14 04:51:01] Total Time: 1s
[STOP] [2019-10-14 04:51:01] parse_diff_and_store
[START] [2019-10-14 04:51:01] resolve_keys
[INFO] [2019-10-14 04:51:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 04:51:20] traits to occurrences...
[INFO] [2019-10-14 04:51:21] traits to nodes (through occurrences)...
[INFO] [2019-10-14 04:51:21] Traits to sex term...
[INFO] [2019-10-14 04:51:22] Traits to lifestage term...
[INFO] [2019-10-14 04:51:23] MetaTraits to traits...
[INFO] [2019-10-14 04:51:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 04:51:24] Assocs to occurrences...
[INFO] [2019-10-14 04:51:24] Assocs to nodes...
[INFO] [2019-10-14 04:51:24] Assoc to sex term...
[INFO] [2019-10-14 04:51:24] Assoc to lifestage term...
[STOP] [2019-10-14 04:51:24] resolve_keys
[START] [2019-10-14 04:51:24] hold_for_later_1
[STOP] [2019-10-14 04:51:24] hold_for_later_1
[START] [2019-10-14 04:51:24] hold_for_later_2
[STOP] [2019-10-14 04:51:24] hold_for_later_2
[START] [2019-10-14 04:51:24] resolve_missing_parents
[STOP] [2019-10-14 04:51:33] resolve_missing_parents
[START] [2019-10-14 04:51:33] rebuild_nodes
[START] [2019-10-14 04:51:33] Flattener#flatten
[START] [2019-10-14 04:51:33] Flattener#study_resource
[START] [2019-10-14 04:51:33] Flattener#build_ancestry
[STOP] [2019-10-14 04:51:33] Flattener#build_ancestry
[INFO] [2019-10-14 04:51:33] 4011 ancestry keys
[START] [2019-10-14 04:51:33] build_node_ancestors
[INFO] [2019-10-14 04:51:33] old ancestors deleted.
[STOP] [2019-10-14 04:51:34] build_node_ancestors
[START] [2019-10-14 04:51:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:51:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:51:35] Flattener#flatten
[STOP] [2019-10-14 04:51:35] rebuild_nodes
[START] [2019-10-14 04:51:35] resolve_missing_media_owners
[STOP] [2019-10-14 04:51:35] resolve_missing_media_owners
[START] [2019-10-14 04:51:35] sanitize_media_verbatims
[STOP] [2019-10-14 04:51:35] sanitize_media_verbatims
[START] [2019-10-14 04:51:35] queue_downloads
[STOP] [2019-10-14 04:51:35] queue_downloads
[START] [2019-10-14 04:51:35] parse_names
[WARN] [2019-10-14 04:51:35] I see 4011 names which still need to be parsed.
[STOP] [2019-10-14 04:51:39] parse_names
[START] [2019-10-14 04:51:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 04:51:39] denormalize_canonical_names_to_nodes
[START] [2019-10-14 04:51:39] match_nodes
[START] [2019-10-14 04:51:39] map_all_nodes_to_pages
[STOP] [2019-10-14 04:55:14] map_all_nodes_to_pages
[INFO] [2019-10-14 04:55:14] 184 Unmatched nodes (of 4011)! That's too many to output. First 10: Pennisetum polystachyon (#50650746); Pennisetum americanus (#50652276); Echinochloa colonum (#50651312); Cenchrus prieuri (#50649122); Cenchrus polystachyon (#50651335); Digitaria leptorrhachis (#50652294); Paspalum polystachyum (#50651345); Paspalidium (#50649522); Ischaemum fasciculatum (#50651050); Chrysopogon nigritana (#50650032)
[START] [2019-10-14 04:55:14] update_nodes
[STOP] [2019-10-14 04:55:16] update_nodes
[STOP] [2019-10-14 04:55:16] match_nodes
[START] [2019-10-14 04:55:16] reindex_search
[STOP] [2019-10-14 04:55:24] reindex_search
[START] [2019-10-14 04:55:24] normalize_units
[STOP] [2019-10-14 04:55:24] normalize_units
[START] [2019-10-14 04:55:24] calculate_statistics
[STOP] [2019-10-14 04:55:24] calculate_statistics
[START] [2019-10-14 04:55:24] complete_harvest_instance
[START] [2019-10-14 04:55:24] overall_tsv_creation
[INFO] [2019-10-14 04:55:24] Processing group of 4011 in 1 batches of 10000
[INFO] [2019-10-14 04:56:27] 1928 Traits (unfiltered)...
[INFO] [2019-10-14 04:56:41] 1928 Traits (filtered)...
[INFO] [2019-10-14 04:56:41] 0 Associations (filtered)...
[INFO] [2019-10-14 04:57:23] 9637 metadata added.
[INFO] [2019-10-14 04:57:23] 0 metadata added.
[INFO] [2019-10-14 04:57:23] Average Time: 94.9
[INFO] [2019-10-14 04:57:23] Total Time: 1m59s
[STOP] [2019-10-14 04:57:23] overall_tsv_creation
[INFO] [2019-10-14 04:57:23] Done. Check your files:
[INFO] [2019-10-14 04:57:23] (4011 lines) /app/public/data/mali_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 04:57:23] (9747 lines) /app/public/data/mali_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 04:57:23] (4011 lines) /app/public/data/mali_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 04:57:24] (1929 lines) /app/public/data/mali_sp_list/publish_traits.tsv
[INFO] [2019-10-14 04:57:24] (9638 lines) /app/public/data/mali_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 04:57:24] complete_harvest_instance
[START] [2019-10-14 04:57:24] completed
[STOP] [2019-10-14 04:57:24] completed
[STOP] [2019-10-14 04:57:24] logged process, took 407.31
Latest Process

14 Oct 04:50 EXITED currently processing 0