Harvest for Eritrea Species List Created 12 Oct 17:36

Stage: completed
Fetched: 12 Oct 17:36
Validated: 12 Oct 17:36
Deltas Created 12 Oct 17:36
Units Normalized: 12 Oct 17:41
Ancestry Built: 12 Oct 17:37
Nodes Matched: 12 Oct 17:41
Names Parsed: 12 Oct 17:37
New Models Stored: 12 Oct 17:36
Indexed: 12 Oct 17:41
Completed: 12 Oct 17:43
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 17:36:40 -0400 by logger.rb/56815
[START] [2019-10-12 17:36:40] logged process
[START] [2019-10-12 17:36:40] create_harvest_instance
[STOP] [2019-10-12 17:36:41] create_harvest_instance
[START] [2019-10-12 17:36:41] fetch_files
[STOP] [2019-10-12 17:36:41] fetch_files
[START] [2019-10-12 17:36:41] validate_each_file
[STOP] [2019-10-12 17:36:41] validate_each_file
[START] [2019-10-12 17:36:41] convert_to_csv
[CMD] [2019-10-12 17:36:41] /usr/bin/sort /app/public/converted_csv/eritrea_sp_list_refs_15675.csv > /app/public/converted_csv/eritrea_sp_list_refs_15675.csv_sorted
[CMD] [2019-10-12 17:36:41] /usr/bin/sort /app/public/converted_csv/eritrea_sp_list_nodes_15676.csv > /app/public/converted_csv/eritrea_sp_list_nodes_15676.csv_sorted
[CMD] [2019-10-12 17:36:41] /usr/bin/sort /app/public/converted_csv/eritrea_sp_list_occurrences_15677.csv > /app/public/converted_csv/eritrea_sp_list_occurrences_15677.csv_sorted
[CMD] [2019-10-12 17:36:41] /usr/bin/sort /app/public/converted_csv/eritrea_sp_list_measurements_15678.csv > /app/public/converted_csv/eritrea_sp_list_measurements_15678.csv_sorted
[STOP] [2019-10-12 17:36:42] convert_to_csv
[START] [2019-10-12 17:36:42] calculate_delta
[CMD] [2019-10-12 17:36:42] echo "0a" > /app/public/diff/eritrea_sp_list_refs_15675.diff
[CMD] [2019-10-12 17:36:42] tail -n +1 /app/public/converted_csv/eritrea_sp_list_refs_15675.csv >> /app/public/diff/eritrea_sp_list_refs_15675.diff
[CMD] [2019-10-12 17:36:42] echo "." >> /app/public/diff/eritrea_sp_list_refs_15675.diff
[CMD] [2019-10-12 17:36:42] echo "0a" > /app/public/diff/eritrea_sp_list_nodes_15676.diff
[CMD] [2019-10-12 17:36:42] tail -n +1 /app/public/converted_csv/eritrea_sp_list_nodes_15676.csv >> /app/public/diff/eritrea_sp_list_nodes_15676.diff
[CMD] [2019-10-12 17:36:42] echo "." >> /app/public/diff/eritrea_sp_list_nodes_15676.diff
[CMD] [2019-10-12 17:36:42] echo "0a" > /app/public/diff/eritrea_sp_list_occurrences_15677.diff
[CMD] [2019-10-12 17:36:42] tail -n +1 /app/public/converted_csv/eritrea_sp_list_occurrences_15677.csv >> /app/public/diff/eritrea_sp_list_occurrences_15677.diff
[CMD] [2019-10-12 17:36:42] echo "." >> /app/public/diff/eritrea_sp_list_occurrences_15677.diff
[CMD] [2019-10-12 17:36:42] echo "0a" > /app/public/diff/eritrea_sp_list_measurements_15678.diff
[CMD] [2019-10-12 17:36:42] tail -n +1 /app/public/converted_csv/eritrea_sp_list_measurements_15678.csv >> /app/public/diff/eritrea_sp_list_measurements_15678.diff
[CMD] [2019-10-12 17:36:43] echo "." >> /app/public/diff/eritrea_sp_list_measurements_15678.diff
[STOP] [2019-10-12 17:36:43] calculate_delta
[START] [2019-10-12 17:36:43] parse_diff_and_store
[INFO] [2019-10-12 17:36:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 17:36:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 17:36:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 17:36:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 17:36:51] Storing 2 References
[INFO] [2019-10-12 17:36:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 17:36:51] Average Time: 0.0
[INFO] [2019-10-12 17:36:51] Total Time: 1s
[INFO] [2019-10-12 17:36:51] Storing 2488 ScientificNames
[INFO] [2019-10-12 17:36:51] Processing group of 2488 in 3 groups of 1000
[INFO] [2019-10-12 17:36:52] Average Time: 0.347
[INFO] [2019-10-12 17:36:52] Total Time: 2s
[INFO] [2019-10-12 17:36:52] Storing 2488 Nodes
[INFO] [2019-10-12 17:36:52] Processing group of 2488 in 3 groups of 1000
[INFO] [2019-10-12 17:36:53] Average Time: 0.25
[INFO] [2019-10-12 17:36:53] Total Time: 1s
[INFO] [2019-10-12 17:36:53] Storing 1219 Occurrences
[INFO] [2019-10-12 17:36:53] Processing group of 1219 in 2 groups of 1000
[INFO] [2019-10-12 17:36:53] Average Time: 0.065
[INFO] [2019-10-12 17:36:53] Total Time: 1s
[INFO] [2019-10-12 17:36:53] Storing 2438 TraitsReferences
[INFO] [2019-10-12 17:36:53] Processing group of 2438 in 3 groups of 1000
[INFO] [2019-10-12 17:36:53] Average Time: 0.077
[INFO] [2019-10-12 17:36:53] Total Time: 1s
[INFO] [2019-10-12 17:36:53] Storing 2438 Traits
[INFO] [2019-10-12 17:36:53] Processing group of 2438 in 3 groups of 1000
[INFO] [2019-10-12 17:36:54] Average Time: 0.32
[INFO] [2019-10-12 17:36:54] Total Time: 1s
[INFO] [2019-10-12 17:36:54] Storing 2437 MetaTraits
[INFO] [2019-10-12 17:36:54] Processing group of 2437 in 3 groups of 1000
[INFO] [2019-10-12 17:36:55] Average Time: 0.17
[INFO] [2019-10-12 17:36:55] Total Time: 1s
[STOP] [2019-10-12 17:36:55] parse_diff_and_store
[START] [2019-10-12 17:36:55] resolve_keys
[INFO] [2019-10-12 17:37:07] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 17:37:08] traits to occurrences...
[INFO] [2019-10-12 17:37:09] traits to nodes (through occurrences)...
[INFO] [2019-10-12 17:37:09] Traits to sex term...
[INFO] [2019-10-12 17:37:09] Traits to lifestage term...
[INFO] [2019-10-12 17:37:09] MetaTraits to traits...
[INFO] [2019-10-12 17:37:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 17:37:10] Assocs to occurrences...
[INFO] [2019-10-12 17:37:10] Assocs to nodes...
[INFO] [2019-10-12 17:37:10] Assoc to sex term...
[INFO] [2019-10-12 17:37:10] Assoc to lifestage term...
[STOP] [2019-10-12 17:37:10] resolve_keys
[START] [2019-10-12 17:37:10] hold_for_later_1
[STOP] [2019-10-12 17:37:10] hold_for_later_1
[START] [2019-10-12 17:37:10] hold_for_later_2
[STOP] [2019-10-12 17:37:10] hold_for_later_2
[START] [2019-10-12 17:37:10] resolve_missing_parents
[STOP] [2019-10-12 17:37:14] resolve_missing_parents
[START] [2019-10-12 17:37:14] rebuild_nodes
[START] [2019-10-12 17:37:14] Flattener#flatten
[START] [2019-10-12 17:37:14] Flattener#study_resource
[START] [2019-10-12 17:37:14] Flattener#build_ancestry
[STOP] [2019-10-12 17:37:15] Flattener#build_ancestry
[INFO] [2019-10-12 17:37:15] 2488 ancestry keys
[START] [2019-10-12 17:37:15] build_node_ancestors
[INFO] [2019-10-12 17:37:15] old ancestors deleted.
[STOP] [2019-10-12 17:37:16] build_node_ancestors
[START] [2019-10-12 17:37:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 17:37:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 17:37:17] Flattener#flatten
[STOP] [2019-10-12 17:37:17] rebuild_nodes
[START] [2019-10-12 17:37:17] resolve_missing_media_owners
[STOP] [2019-10-12 17:37:17] resolve_missing_media_owners
[START] [2019-10-12 17:37:17] sanitize_media_verbatims
[STOP] [2019-10-12 17:37:17] sanitize_media_verbatims
[START] [2019-10-12 17:37:17] queue_downloads
[STOP] [2019-10-12 17:37:17] queue_downloads
[START] [2019-10-12 17:37:17] parse_names
[WARN] [2019-10-12 17:37:17] I see 2488 names which still need to be parsed.
[STOP] [2019-10-12 17:37:20] parse_names
[START] [2019-10-12 17:37:20] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 17:37:20] denormalize_canonical_names_to_nodes
[START] [2019-10-12 17:37:20] match_nodes
[START] [2019-10-12 17:37:20] map_all_nodes_to_pages
[STOP] [2019-10-12 17:41:05] map_all_nodes_to_pages
[INFO] [2019-10-12 17:41:05] 115 Unmatched nodes (of 2488)! That's too many to output. First 10: Magnoliophyta (#49554805); Pennisetum (#49555669); Setaria rhachitrichum (#49555860); Cenchrus setigerus (#49557006); Kylinga (#49556898); Kylinga controversa (#49556897); Xanthorrhoeaceae (#49554876); Stuckenia pectinatus (#49555559); Magnoliopsida (#49554860); Euphorbia scordifolia (#49556608)
[START] [2019-10-12 17:41:05] update_nodes
[STOP] [2019-10-12 17:41:06] update_nodes
[STOP] [2019-10-12 17:41:06] match_nodes
[START] [2019-10-12 17:41:06] reindex_search
[STOP] [2019-10-12 17:41:12] reindex_search
[START] [2019-10-12 17:41:12] normalize_units
[STOP] [2019-10-12 17:41:13] normalize_units
[START] [2019-10-12 17:41:13] calculate_statistics
[STOP] [2019-10-12 17:41:13] calculate_statistics
[START] [2019-10-12 17:41:13] complete_harvest_instance
[START] [2019-10-12 17:41:13] overall_tsv_creation
[INFO] [2019-10-12 17:41:13] Processing group of 2488 in 1 batches of 10000
[INFO] [2019-10-12 17:42:08] 1219 Traits (unfiltered)...
[INFO] [2019-10-12 17:42:22] 1219 Traits (filtered)...
[INFO] [2019-10-12 17:42:22] 0 Associations (filtered)...
[INFO] [2019-10-12 17:43:01] 6094 metadata added.
[INFO] [2019-10-12 17:43:01] 0 metadata added.
[INFO] [2019-10-12 17:43:01] Average Time: 86.33
[INFO] [2019-10-12 17:43:01] Total Time: 1m49s
[STOP] [2019-10-12 17:43:01] overall_tsv_creation
[INFO] [2019-10-12 17:43:01] Done. Check your files:
[INFO] [2019-10-12 17:43:01] (2488 lines) /app/public/data/eritrea_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 17:43:01] (12740 lines) /app/public/data/eritrea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 17:43:01] (2488 lines) /app/public/data/eritrea_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 17:43:01] (1220 lines) /app/public/data/eritrea_sp_list/publish_traits.tsv
[INFO] [2019-10-12 17:43:01] (6095 lines) /app/public/data/eritrea_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 17:43:01] complete_harvest_instance
[START] [2019-10-12 17:43:01] completed
[STOP] [2019-10-12 17:43:01] completed
[STOP] [2019-10-12 17:43:01] logged process, took 381.11
Latest Process

12 Oct 17:36 EXITED currently processing 0