Harvest for Cambodia Species List Created 11 Oct 23:39

Stage: completed
Fetched: 11 Oct 23:39
Validated: 11 Oct 23:39
Deltas Created 11 Oct 23:39
Units Normalized: 11 Oct 23:43
Ancestry Built: 11 Oct 23:40
Nodes Matched: 11 Oct 23:43
Names Parsed: 11 Oct 23:40
New Models Stored: 11 Oct 23:39
Indexed: 11 Oct 23:43
Completed: 11 Oct 23:45
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-11 23:39:17 -0400 by logger.rb/56815
[START] [2019-10-11 23:39:17] logged process
[START] [2019-10-11 23:39:17] create_harvest_instance
[STOP] [2019-10-11 23:39:17] create_harvest_instance
[START] [2019-10-11 23:39:17] fetch_files
[STOP] [2019-10-11 23:39:17] fetch_files
[START] [2019-10-11 23:39:17] validate_each_file
[STOP] [2019-10-11 23:39:18] validate_each_file
[START] [2019-10-11 23:39:18] convert_to_csv
[CMD] [2019-10-11 23:39:18] /usr/bin/sort /app/public/converted_csv/cambodia_sp_list_refs_15355.csv > /app/public/converted_csv/cambodia_sp_list_refs_15355.csv_sorted
[CMD] [2019-10-11 23:39:18] /usr/bin/sort /app/public/converted_csv/cambodia_sp_list_nodes_15356.csv > /app/public/converted_csv/cambodia_sp_list_nodes_15356.csv_sorted
[CMD] [2019-10-11 23:39:18] /usr/bin/sort /app/public/converted_csv/cambodia_sp_list_occurrences_15357.csv > /app/public/converted_csv/cambodia_sp_list_occurrences_15357.csv_sorted
[CMD] [2019-10-11 23:39:18] /usr/bin/sort /app/public/converted_csv/cambodia_sp_list_measurements_15358.csv > /app/public/converted_csv/cambodia_sp_list_measurements_15358.csv_sorted
[STOP] [2019-10-11 23:39:18] convert_to_csv
[START] [2019-10-11 23:39:18] calculate_delta
[CMD] [2019-10-11 23:39:18] echo "0a" > /app/public/diff/cambodia_sp_list_refs_15355.diff
[CMD] [2019-10-11 23:39:19] tail -n +1 /app/public/converted_csv/cambodia_sp_list_refs_15355.csv >> /app/public/diff/cambodia_sp_list_refs_15355.diff
[CMD] [2019-10-11 23:39:19] echo "." >> /app/public/diff/cambodia_sp_list_refs_15355.diff
[CMD] [2019-10-11 23:39:19] echo "0a" > /app/public/diff/cambodia_sp_list_nodes_15356.diff
[CMD] [2019-10-11 23:39:19] tail -n +1 /app/public/converted_csv/cambodia_sp_list_nodes_15356.csv >> /app/public/diff/cambodia_sp_list_nodes_15356.diff
[CMD] [2019-10-11 23:39:19] echo "." >> /app/public/diff/cambodia_sp_list_nodes_15356.diff
[CMD] [2019-10-11 23:39:19] echo "0a" > /app/public/diff/cambodia_sp_list_occurrences_15357.diff
[CMD] [2019-10-11 23:39:19] tail -n +1 /app/public/converted_csv/cambodia_sp_list_occurrences_15357.csv >> /app/public/diff/cambodia_sp_list_occurrences_15357.diff
[CMD] [2019-10-11 23:39:19] echo "." >> /app/public/diff/cambodia_sp_list_occurrences_15357.diff
[CMD] [2019-10-11 23:39:19] echo "0a" > /app/public/diff/cambodia_sp_list_measurements_15358.diff
[CMD] [2019-10-11 23:39:19] tail -n +1 /app/public/converted_csv/cambodia_sp_list_measurements_15358.csv >> /app/public/diff/cambodia_sp_list_measurements_15358.diff
[CMD] [2019-10-11 23:39:19] echo "." >> /app/public/diff/cambodia_sp_list_measurements_15358.diff
[STOP] [2019-10-11 23:39:20] calculate_delta
[START] [2019-10-11 23:39:20] parse_diff_and_store
[INFO] [2019-10-11 23:39:20] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 23:39:20] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 23:39:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 23:39:22] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 23:39:36] Storing 2 References
[INFO] [2019-10-11 23:39:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 23:39:36] Average Time: 0.0
[INFO] [2019-10-11 23:39:36] Total Time: 1s
[INFO] [2019-10-11 23:39:36] Storing 4487 ScientificNames
[INFO] [2019-10-11 23:39:36] Processing group of 4487 in 5 groups of 1000
[INFO] [2019-10-11 23:39:38] Average Time: 0.352
[INFO] [2019-10-11 23:39:38] Total Time: 2s
[INFO] [2019-10-11 23:39:38] Storing 4487 Nodes
[INFO] [2019-10-11 23:39:38] Processing group of 4487 in 5 groups of 1000
[INFO] [2019-10-11 23:39:40] Average Time: 0.28
[INFO] [2019-10-11 23:39:40] Total Time: 2s
[INFO] [2019-10-11 23:39:40] Storing 2410 Occurrences
[INFO] [2019-10-11 23:39:40] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-11 23:39:40] Average Time: 0.083
[INFO] [2019-10-11 23:39:40] Total Time: 1s
[INFO] [2019-10-11 23:39:40] Storing 5080 TraitsReferences
[INFO] [2019-10-11 23:39:40] Processing group of 5080 in 6 groups of 1000
[INFO] [2019-10-11 23:39:40] Average Time: 0.073
[INFO] [2019-10-11 23:39:40] Total Time: 1s
[INFO] [2019-10-11 23:39:40] Storing 5079 Traits
[INFO] [2019-10-11 23:39:40] Processing group of 5079 in 6 groups of 1000
[INFO] [2019-10-11 23:39:42] Average Time: 0.293
[INFO] [2019-10-11 23:39:42] Total Time: 2s
[INFO] [2019-10-11 23:39:42] Storing 5077 MetaTraits
[INFO] [2019-10-11 23:39:42] Processing group of 5077 in 6 groups of 1000
[INFO] [2019-10-11 23:39:43] Average Time: 0.123
[INFO] [2019-10-11 23:39:43] Total Time: 1s
[STOP] [2019-10-11 23:39:43] parse_diff_and_store
[START] [2019-10-11 23:39:43] resolve_keys
[INFO] [2019-10-11 23:40:03] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 23:40:05] traits to occurrences...
[INFO] [2019-10-11 23:40:07] traits to nodes (through occurrences)...
[INFO] [2019-10-11 23:40:07] Traits to sex term...
[INFO] [2019-10-11 23:40:09] Traits to lifestage term...
[INFO] [2019-10-11 23:40:11] MetaTraits to traits...
[INFO] [2019-10-11 23:40:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 23:40:12] Assocs to occurrences...
[INFO] [2019-10-11 23:40:12] Assocs to nodes...
[INFO] [2019-10-11 23:40:12] Assoc to sex term...
[INFO] [2019-10-11 23:40:12] Assoc to lifestage term...
[STOP] [2019-10-11 23:40:12] resolve_keys
[START] [2019-10-11 23:40:12] hold_for_later_1
[STOP] [2019-10-11 23:40:12] hold_for_later_1
[START] [2019-10-11 23:40:12] hold_for_later_2
[STOP] [2019-10-11 23:40:12] hold_for_later_2
[START] [2019-10-11 23:40:12] resolve_missing_parents
[STOP] [2019-10-11 23:40:21] resolve_missing_parents
[START] [2019-10-11 23:40:21] rebuild_nodes
[START] [2019-10-11 23:40:21] Flattener#flatten
[START] [2019-10-11 23:40:21] Flattener#study_resource
[START] [2019-10-11 23:40:21] Flattener#build_ancestry
[STOP] [2019-10-11 23:40:21] Flattener#build_ancestry
[INFO] [2019-10-11 23:40:21] 4487 ancestry keys
[START] [2019-10-11 23:40:21] build_node_ancestors
[INFO] [2019-10-11 23:40:21] old ancestors deleted.
[STOP] [2019-10-11 23:40:22] build_node_ancestors
[START] [2019-10-11 23:40:23] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:40:23] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:40:23] Flattener#flatten
[STOP] [2019-10-11 23:40:23] rebuild_nodes
[START] [2019-10-11 23:40:23] resolve_missing_media_owners
[STOP] [2019-10-11 23:40:23] resolve_missing_media_owners
[START] [2019-10-11 23:40:23] sanitize_media_verbatims
[STOP] [2019-10-11 23:40:23] sanitize_media_verbatims
[START] [2019-10-11 23:40:23] queue_downloads
[STOP] [2019-10-11 23:40:23] queue_downloads
[START] [2019-10-11 23:40:23] parse_names
[WARN] [2019-10-11 23:40:23] I see 4487 names which still need to be parsed.
[STOP] [2019-10-11 23:40:28] parse_names
[START] [2019-10-11 23:40:28] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 23:40:28] denormalize_canonical_names_to_nodes
[START] [2019-10-11 23:40:28] match_nodes
[START] [2019-10-11 23:40:28] map_all_nodes_to_pages
[STOP] [2019-10-11 23:43:04] map_all_nodes_to_pages
[INFO] [2019-10-11 23:43:04] 210 Unmatched nodes (of 4487)! That's too many to output. First 10: Sturnus sinensis (#48995703); Sturnus nigricollis (#48996207); Saxicola maura (#48996704); Muscicapa latirostris (#48992599); Luscinia cyane (#48993217); Eumyias thalassina (#48996807); Myiomela leucurum (#48994661); Brachypteryx leucophrys (#48993539); Cinclidium leucurum (#48995070); Dicrurus annectans (#48993615)
[START] [2019-10-11 23:43:04] update_nodes
[STOP] [2019-10-11 23:43:05] update_nodes
[STOP] [2019-10-11 23:43:05] match_nodes
[START] [2019-10-11 23:43:05] reindex_search
[STOP] [2019-10-11 23:43:13] reindex_search
[START] [2019-10-11 23:43:13] normalize_units
[STOP] [2019-10-11 23:43:13] normalize_units
[START] [2019-10-11 23:43:13] calculate_statistics
[STOP] [2019-10-11 23:43:13] calculate_statistics
[START] [2019-10-11 23:43:13] complete_harvest_instance
[START] [2019-10-11 23:43:13] overall_tsv_creation
[INFO] [2019-10-11 23:43:13] Processing group of 4487 in 1 batches of 10000
[INFO] [2019-10-11 23:44:19] 2410 Traits (unfiltered)...
[INFO] [2019-10-11 23:44:35] 2410 Traits (filtered)...
[INFO] [2019-10-11 23:44:35] 0 Associations (filtered)...
[INFO] [2019-10-11 23:45:16] 12047 metadata added.
[INFO] [2019-10-11 23:45:16] 0 metadata added.
[INFO] [2019-10-11 23:45:16] Average Time: 97.53
[INFO] [2019-10-11 23:45:16] Total Time: 2m3s
[STOP] [2019-10-11 23:45:16] overall_tsv_creation
[INFO] [2019-10-11 23:45:16] Done. Check your files:
[INFO] [2019-10-11 23:45:16] (4487 lines) /app/public/data/cambodia_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 23:45:16] (14083 lines) /app/public/data/cambodia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 23:45:16] (4487 lines) /app/public/data/cambodia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 23:45:16] (2411 lines) /app/public/data/cambodia_sp_list/publish_traits.tsv
[INFO] [2019-10-11 23:45:16] (12048 lines) /app/public/data/cambodia_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 23:45:16] complete_harvest_instance
[START] [2019-10-11 23:45:16] completed
[STOP] [2019-10-11 23:45:16] completed
[STOP] [2019-10-11 23:45:16] logged process, took 359.59
Latest Process

11 Oct 23:39 EXITED currently processing 0