Harvest for Macau Species List Created 14 Oct 02:54

Stage: completed
Fetched: 14 Oct 02:54
Validated: 14 Oct 02:54
Deltas Created 14 Oct 02:54
Units Normalized: 14 Oct 02:55
Ancestry Built: 14 Oct 02:54
Nodes Matched: 14 Oct 02:55
Names Parsed: 14 Oct 02:54
New Models Stored: 14 Oct 02:54
Indexed: 14 Oct 02:55
Completed: 14 Oct 02:56
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 02:54:41 -0400 by logger.rb/56815
[START] [2019-10-14 02:54:41] logged process
[START] [2019-10-14 02:54:41] create_harvest_instance
[STOP] [2019-10-14 02:54:41] create_harvest_instance
[START] [2019-10-14 02:54:41] fetch_files
[STOP] [2019-10-14 02:54:42] fetch_files
[START] [2019-10-14 02:54:42] validate_each_file
[STOP] [2019-10-14 02:54:42] validate_each_file
[START] [2019-10-14 02:54:42] convert_to_csv
[CMD] [2019-10-14 02:54:42] /usr/bin/sort /app/public/converted_csv/macau_sp_list_refs_16451.csv > /app/public/converted_csv/macau_sp_list_refs_16451.csv_sorted
[CMD] [2019-10-14 02:54:42] /usr/bin/sort /app/public/converted_csv/macau_sp_list_nodes_16452.csv > /app/public/converted_csv/macau_sp_list_nodes_16452.csv_sorted
[CMD] [2019-10-14 02:54:42] /usr/bin/sort /app/public/converted_csv/macau_sp_list_occurrences_16453.csv > /app/public/converted_csv/macau_sp_list_occurrences_16453.csv_sorted
[CMD] [2019-10-14 02:54:42] /usr/bin/sort /app/public/converted_csv/macau_sp_list_measurements_16454.csv > /app/public/converted_csv/macau_sp_list_measurements_16454.csv_sorted
[STOP] [2019-10-14 02:54:42] convert_to_csv
[START] [2019-10-14 02:54:42] calculate_delta
[CMD] [2019-10-14 02:54:42] echo "0a" > /app/public/diff/macau_sp_list_refs_16451.diff
[CMD] [2019-10-14 02:54:42] tail -n +1 /app/public/converted_csv/macau_sp_list_refs_16451.csv >> /app/public/diff/macau_sp_list_refs_16451.diff
[CMD] [2019-10-14 02:54:42] echo "." >> /app/public/diff/macau_sp_list_refs_16451.diff
[CMD] [2019-10-14 02:54:42] echo "0a" > /app/public/diff/macau_sp_list_nodes_16452.diff
[CMD] [2019-10-14 02:54:42] tail -n +1 /app/public/converted_csv/macau_sp_list_nodes_16452.csv >> /app/public/diff/macau_sp_list_nodes_16452.diff
[CMD] [2019-10-14 02:54:42] echo "." >> /app/public/diff/macau_sp_list_nodes_16452.diff
[CMD] [2019-10-14 02:54:43] echo "0a" > /app/public/diff/macau_sp_list_occurrences_16453.diff
[CMD] [2019-10-14 02:54:43] tail -n +1 /app/public/converted_csv/macau_sp_list_occurrences_16453.csv >> /app/public/diff/macau_sp_list_occurrences_16453.diff
[CMD] [2019-10-14 02:54:43] echo "." >> /app/public/diff/macau_sp_list_occurrences_16453.diff
[CMD] [2019-10-14 02:54:43] echo "0a" > /app/public/diff/macau_sp_list_measurements_16454.diff
[CMD] [2019-10-14 02:54:43] tail -n +1 /app/public/converted_csv/macau_sp_list_measurements_16454.csv >> /app/public/diff/macau_sp_list_measurements_16454.diff
[CMD] [2019-10-14 02:54:43] echo "." >> /app/public/diff/macau_sp_list_measurements_16454.diff
[STOP] [2019-10-14 02:54:43] calculate_delta
[START] [2019-10-14 02:54:43] parse_diff_and_store
[INFO] [2019-10-14 02:54:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 02:54:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 02:54:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 02:54:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 02:54:44] Storing 2 References
[INFO] [2019-10-14 02:54:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 02:54:44] Average Time: 0.0
[INFO] [2019-10-14 02:54:44] Total Time: 1s
[INFO] [2019-10-14 02:54:44] Storing 311 ScientificNames
[INFO] [2019-10-14 02:54:44] Processing group of 311 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.2
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[INFO] [2019-10-14 02:54:45] Storing 311 Nodes
[INFO] [2019-10-14 02:54:45] Processing group of 311 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.25
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[INFO] [2019-10-14 02:54:45] Storing 121 Occurrences
[INFO] [2019-10-14 02:54:45] Processing group of 121 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.03
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[INFO] [2019-10-14 02:54:45] Storing 242 TraitsReferences
[INFO] [2019-10-14 02:54:45] Processing group of 242 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.1
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[INFO] [2019-10-14 02:54:45] Storing 242 Traits
[INFO] [2019-10-14 02:54:45] Processing group of 242 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.17
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[INFO] [2019-10-14 02:54:45] Storing 242 MetaTraits
[INFO] [2019-10-14 02:54:45] Processing group of 242 in 1 groups of 1000
[INFO] [2019-10-14 02:54:45] Average Time: 0.06
[INFO] [2019-10-14 02:54:45] Total Time: 1s
[STOP] [2019-10-14 02:54:45] parse_diff_and_store
[START] [2019-10-14 02:54:45] resolve_keys
[INFO] [2019-10-14 02:54:49] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 02:54:49] traits to occurrences...
[INFO] [2019-10-14 02:54:50] traits to nodes (through occurrences)...
[INFO] [2019-10-14 02:54:50] Traits to sex term...
[INFO] [2019-10-14 02:54:50] Traits to lifestage term...
[INFO] [2019-10-14 02:54:50] MetaTraits to traits...
[INFO] [2019-10-14 02:54:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 02:54:50] Assocs to occurrences...
[INFO] [2019-10-14 02:54:50] Assocs to nodes...
[INFO] [2019-10-14 02:54:50] Assoc to sex term...
[INFO] [2019-10-14 02:54:50] Assoc to lifestage term...
[STOP] [2019-10-14 02:54:50] resolve_keys
[START] [2019-10-14 02:54:50] hold_for_later_1
[STOP] [2019-10-14 02:54:50] hold_for_later_1
[START] [2019-10-14 02:54:50] hold_for_later_2
[STOP] [2019-10-14 02:54:50] hold_for_later_2
[START] [2019-10-14 02:54:50] resolve_missing_parents
[STOP] [2019-10-14 02:54:50] resolve_missing_parents
[START] [2019-10-14 02:54:50] rebuild_nodes
[START] [2019-10-14 02:54:50] Flattener#flatten
[START] [2019-10-14 02:54:50] Flattener#study_resource
[START] [2019-10-14 02:54:50] Flattener#build_ancestry
[STOP] [2019-10-14 02:54:50] Flattener#build_ancestry
[INFO] [2019-10-14 02:54:50] 311 ancestry keys
[START] [2019-10-14 02:54:50] build_node_ancestors
[INFO] [2019-10-14 02:54:50] old ancestors deleted.
[STOP] [2019-10-14 02:54:50] build_node_ancestors
[START] [2019-10-14 02:54:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:54:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:54:50] Flattener#flatten
[STOP] [2019-10-14 02:54:50] rebuild_nodes
[START] [2019-10-14 02:54:50] resolve_missing_media_owners
[STOP] [2019-10-14 02:54:50] resolve_missing_media_owners
[START] [2019-10-14 02:54:50] sanitize_media_verbatims
[STOP] [2019-10-14 02:54:50] sanitize_media_verbatims
[START] [2019-10-14 02:54:50] queue_downloads
[STOP] [2019-10-14 02:54:50] queue_downloads
[START] [2019-10-14 02:54:50] parse_names
[WARN] [2019-10-14 02:54:50] I see 311 names which still need to be parsed.
[STOP] [2019-10-14 02:54:52] parse_names
[START] [2019-10-14 02:54:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 02:54:52] denormalize_canonical_names_to_nodes
[START] [2019-10-14 02:54:52] match_nodes
[START] [2019-10-14 02:54:52] map_all_nodes_to_pages
[STOP] [2019-10-14 02:55:21] map_all_nodes_to_pages
[INFO] [2019-10-14 02:55:21] Unmatched nodes (9 of 311): Streptopelia chinensis (#50576979); Muscicapa latirostris (#50577122); Urocissa erythrorhyncha (#50577073); Ianthocincla chinensis (#50577149); Egretta intermedia (#50577237); Garrulax perspicillatus (#50577078); Magnoliopsida (#50577099); Cheilanthes tenuifolia (#50577199); Cheilanthes hirsuta (#50577275)
[START] [2019-10-14 02:55:21] update_nodes
[STOP] [2019-10-14 02:55:21] update_nodes
[STOP] [2019-10-14 02:55:21] match_nodes
[START] [2019-10-14 02:55:21] reindex_search
[STOP] [2019-10-14 02:55:22] reindex_search
[START] [2019-10-14 02:55:22] normalize_units
[STOP] [2019-10-14 02:55:22] normalize_units
[START] [2019-10-14 02:55:22] calculate_statistics
[STOP] [2019-10-14 02:55:22] calculate_statistics
[START] [2019-10-14 02:55:22] complete_harvest_instance
[START] [2019-10-14 02:55:22] overall_tsv_creation
[INFO] [2019-10-14 02:55:22] Processing group of 311 in 1 batches of 10000
[INFO] [2019-10-14 02:56:07] 121 Traits (unfiltered)...
[INFO] [2019-10-14 02:56:21] 121 Traits (filtered)...
[INFO] [2019-10-14 02:56:21] 0 Associations (filtered)...
[INFO] [2019-10-14 02:56:58] 605 metadata added.
[INFO] [2019-10-14 02:56:58] 0 metadata added.
[INFO] [2019-10-14 02:56:58] Average Time: 75.59
[INFO] [2019-10-14 02:56:58] Total Time: 1m37s
[STOP] [2019-10-14 02:56:58] overall_tsv_creation
[INFO] [2019-10-14 02:56:58] Done. Check your files:
[INFO] [2019-10-14 02:56:58] (311 lines) /app/public/data/macau_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 02:56:58] (1492 lines) /app/public/data/macau_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 02:56:58] (311 lines) /app/public/data/macau_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 02:56:58] (122 lines) /app/public/data/macau_sp_list/publish_traits.tsv
[INFO] [2019-10-14 02:56:59] (606 lines) /app/public/data/macau_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 02:56:59] complete_harvest_instance
[START] [2019-10-14 02:56:59] completed
[STOP] [2019-10-14 02:56:59] completed
[STOP] [2019-10-14 02:56:59] logged process, took 137.61
Latest Process

14 Oct 02:54 EXITED currently processing 0