Harvest for Djibouti Species List Created 12 Oct 14:23

Stage: completed
Fetched: 12 Oct 14:23
Validated: 12 Oct 14:23
Deltas Created 12 Oct 14:23
Units Normalized: 12 Oct 14:25
Ancestry Built: 12 Oct 14:23
Nodes Matched: 12 Oct 14:25
Names Parsed: 12 Oct 14:23
New Models Stored: 12 Oct 14:23
Indexed: 12 Oct 14:25
Completed: 12 Oct 14:26
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 14:23:12 -0400 by logger.rb/56815
[START] [2019-10-12 14:23:12] logged process
[START] [2019-10-12 14:23:12] create_harvest_instance
[STOP] [2019-10-12 14:23:12] create_harvest_instance
[START] [2019-10-12 14:23:12] fetch_files
[STOP] [2019-10-12 14:23:12] fetch_files
[START] [2019-10-12 14:23:12] validate_each_file
[STOP] [2019-10-12 14:23:13] validate_each_file
[START] [2019-10-12 14:23:13] convert_to_csv
[CMD] [2019-10-12 14:23:13] /usr/bin/sort /app/public/converted_csv/djibouti_sp_list_refs_15595.csv > /app/public/converted_csv/djibouti_sp_list_refs_15595.csv_sorted
[CMD] [2019-10-12 14:23:13] /usr/bin/sort /app/public/converted_csv/djibouti_sp_list_nodes_15596.csv > /app/public/converted_csv/djibouti_sp_list_nodes_15596.csv_sorted
[CMD] [2019-10-12 14:23:13] /usr/bin/sort /app/public/converted_csv/djibouti_sp_list_occurrences_15597.csv > /app/public/converted_csv/djibouti_sp_list_occurrences_15597.csv_sorted
[CMD] [2019-10-12 14:23:13] /usr/bin/sort /app/public/converted_csv/djibouti_sp_list_measurements_15598.csv > /app/public/converted_csv/djibouti_sp_list_measurements_15598.csv_sorted
[STOP] [2019-10-12 14:23:13] convert_to_csv
[START] [2019-10-12 14:23:13] calculate_delta
[CMD] [2019-10-12 14:23:13] echo "0a" > /app/public/diff/djibouti_sp_list_refs_15595.diff
[CMD] [2019-10-12 14:23:13] tail -n +1 /app/public/converted_csv/djibouti_sp_list_refs_15595.csv >> /app/public/diff/djibouti_sp_list_refs_15595.diff
[CMD] [2019-10-12 14:23:13] echo "." >> /app/public/diff/djibouti_sp_list_refs_15595.diff
[CMD] [2019-10-12 14:23:13] echo "0a" > /app/public/diff/djibouti_sp_list_nodes_15596.diff
[CMD] [2019-10-12 14:23:13] tail -n +1 /app/public/converted_csv/djibouti_sp_list_nodes_15596.csv >> /app/public/diff/djibouti_sp_list_nodes_15596.diff
[CMD] [2019-10-12 14:23:13] echo "." >> /app/public/diff/djibouti_sp_list_nodes_15596.diff
[CMD] [2019-10-12 14:23:14] echo "0a" > /app/public/diff/djibouti_sp_list_occurrences_15597.diff
[CMD] [2019-10-12 14:23:14] tail -n +1 /app/public/converted_csv/djibouti_sp_list_occurrences_15597.csv >> /app/public/diff/djibouti_sp_list_occurrences_15597.diff
[CMD] [2019-10-12 14:23:14] echo "." >> /app/public/diff/djibouti_sp_list_occurrences_15597.diff
[CMD] [2019-10-12 14:23:14] echo "0a" > /app/public/diff/djibouti_sp_list_measurements_15598.diff
[CMD] [2019-10-12 14:23:14] tail -n +1 /app/public/converted_csv/djibouti_sp_list_measurements_15598.csv >> /app/public/diff/djibouti_sp_list_measurements_15598.diff
[CMD] [2019-10-12 14:23:14] echo "." >> /app/public/diff/djibouti_sp_list_measurements_15598.diff
[STOP] [2019-10-12 14:23:14] calculate_delta
[START] [2019-10-12 14:23:14] parse_diff_and_store
[INFO] [2019-10-12 14:23:14] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 14:23:14] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 14:23:15] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 14:23:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 14:23:17] Storing 2 References
[INFO] [2019-10-12 14:23:17] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 14:23:17] Average Time: 0.0
[INFO] [2019-10-12 14:23:17] Total Time: 1s
[INFO] [2019-10-12 14:23:17] Storing 948 ScientificNames
[INFO] [2019-10-12 14:23:17] Processing group of 948 in 1 groups of 1000
[INFO] [2019-10-12 14:23:18] Average Time: 0.41
[INFO] [2019-10-12 14:23:18] Total Time: 1s
[INFO] [2019-10-12 14:23:18] Storing 948 Nodes
[INFO] [2019-10-12 14:23:18] Processing group of 948 in 1 groups of 1000
[INFO] [2019-10-12 14:23:18] Average Time: 0.31
[INFO] [2019-10-12 14:23:18] Total Time: 1s
[INFO] [2019-10-12 14:23:18] Storing 383 Occurrences
[INFO] [2019-10-12 14:23:18] Processing group of 383 in 1 groups of 1000
[INFO] [2019-10-12 14:23:18] Average Time: 0.06
[INFO] [2019-10-12 14:23:18] Total Time: 1s
[INFO] [2019-10-12 14:23:18] Storing 766 TraitsReferences
[INFO] [2019-10-12 14:23:18] Processing group of 766 in 1 groups of 1000
[INFO] [2019-10-12 14:23:18] Average Time: 0.14
[INFO] [2019-10-12 14:23:18] Total Time: 1s
[INFO] [2019-10-12 14:23:18] Storing 766 Traits
[INFO] [2019-10-12 14:23:18] Processing group of 766 in 1 groups of 1000
[INFO] [2019-10-12 14:23:18] Average Time: 0.34
[INFO] [2019-10-12 14:23:18] Total Time: 1s
[INFO] [2019-10-12 14:23:18] Storing 766 MetaTraits
[INFO] [2019-10-12 14:23:18] Processing group of 766 in 1 groups of 1000
[INFO] [2019-10-12 14:23:19] Average Time: 0.11
[INFO] [2019-10-12 14:23:19] Total Time: 1s
[STOP] [2019-10-12 14:23:19] parse_diff_and_store
[START] [2019-10-12 14:23:19] resolve_keys
[INFO] [2019-10-12 14:23:25] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 14:23:25] traits to occurrences...
[INFO] [2019-10-12 14:23:25] traits to nodes (through occurrences)...
[INFO] [2019-10-12 14:23:25] Traits to sex term...
[INFO] [2019-10-12 14:23:25] Traits to lifestage term...
[INFO] [2019-10-12 14:23:25] MetaTraits to traits...
[INFO] [2019-10-12 14:23:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 14:23:25] Assocs to occurrences...
[INFO] [2019-10-12 14:23:25] Assocs to nodes...
[INFO] [2019-10-12 14:23:25] Assoc to sex term...
[INFO] [2019-10-12 14:23:25] Assoc to lifestage term...
[STOP] [2019-10-12 14:23:25] resolve_keys
[START] [2019-10-12 14:23:25] hold_for_later_1
[STOP] [2019-10-12 14:23:25] hold_for_later_1
[START] [2019-10-12 14:23:25] hold_for_later_2
[STOP] [2019-10-12 14:23:25] hold_for_later_2
[START] [2019-10-12 14:23:25] resolve_missing_parents
[STOP] [2019-10-12 14:23:26] resolve_missing_parents
[START] [2019-10-12 14:23:26] rebuild_nodes
[START] [2019-10-12 14:23:26] Flattener#flatten
[START] [2019-10-12 14:23:26] Flattener#study_resource
[START] [2019-10-12 14:23:26] Flattener#build_ancestry
[STOP] [2019-10-12 14:23:26] Flattener#build_ancestry
[INFO] [2019-10-12 14:23:26] 948 ancestry keys
[START] [2019-10-12 14:23:26] build_node_ancestors
[INFO] [2019-10-12 14:23:26] old ancestors deleted.
[STOP] [2019-10-12 14:23:26] build_node_ancestors
[START] [2019-10-12 14:23:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:23:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:23:27] Flattener#flatten
[STOP] [2019-10-12 14:23:27] rebuild_nodes
[START] [2019-10-12 14:23:27] resolve_missing_media_owners
[STOP] [2019-10-12 14:23:27] resolve_missing_media_owners
[START] [2019-10-12 14:23:27] sanitize_media_verbatims
[STOP] [2019-10-12 14:23:27] sanitize_media_verbatims
[START] [2019-10-12 14:23:27] queue_downloads
[STOP] [2019-10-12 14:23:27] queue_downloads
[START] [2019-10-12 14:23:27] parse_names
[WARN] [2019-10-12 14:23:27] I see 948 names which still need to be parsed.
[STOP] [2019-10-12 14:23:29] parse_names
[START] [2019-10-12 14:23:29] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 14:23:29] denormalize_canonical_names_to_nodes
[START] [2019-10-12 14:23:29] match_nodes
[START] [2019-10-12 14:23:29] map_all_nodes_to_pages
[STOP] [2019-10-12 14:25:01] map_all_nodes_to_pages
[INFO] [2019-10-12 14:25:01] 43 Unmatched nodes (of 948)! That's too many to output. First 10: Coluber rhodorachis (#49451971); Rhodophoneus (#49451588); Rhodophoneus cruentus (#49451587); Cercotrichas minor (#49451853); Cercomela (#49451705); Cercomela melanura (#49451704); Cercomela dubia (#49451963); Erythropygia (#49451739); Erythropygia galactotes (#49451738); Serinus xanthopygius (#49451732)
[START] [2019-10-12 14:25:01] update_nodes
[STOP] [2019-10-12 14:25:01] update_nodes
[STOP] [2019-10-12 14:25:01] match_nodes
[START] [2019-10-12 14:25:01] reindex_search
[STOP] [2019-10-12 14:25:03] reindex_search
[START] [2019-10-12 14:25:03] normalize_units
[STOP] [2019-10-12 14:25:03] normalize_units
[START] [2019-10-12 14:25:03] calculate_statistics
[STOP] [2019-10-12 14:25:03] calculate_statistics
[START] [2019-10-12 14:25:03] complete_harvest_instance
[START] [2019-10-12 14:25:03] overall_tsv_creation
[INFO] [2019-10-12 14:25:03] Processing group of 948 in 1 batches of 10000
[INFO] [2019-10-12 14:25:54] 383 Traits (unfiltered)...
[INFO] [2019-10-12 14:26:08] 383 Traits (filtered)...
[INFO] [2019-10-12 14:26:08] 0 Associations (filtered)...
[INFO] [2019-10-12 14:26:47] 1915 metadata added.
[INFO] [2019-10-12 14:26:47] 0 metadata added.
[INFO] [2019-10-12 14:26:47] Average Time: 81.18
[INFO] [2019-10-12 14:26:47] Total Time: 1m45s
[STOP] [2019-10-12 14:26:47] overall_tsv_creation
[INFO] [2019-10-12 14:26:47] Done. Check your files:
[INFO] [2019-10-12 14:26:47] (948 lines) /app/public/data/djibouti_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 14:26:48] (4600 lines) /app/public/data/djibouti_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 14:26:48] (948 lines) /app/public/data/djibouti_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 14:26:48] (384 lines) /app/public/data/djibouti_sp_list/publish_traits.tsv
[INFO] [2019-10-12 14:26:48] (1916 lines) /app/public/data/djibouti_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 14:26:48] complete_harvest_instance
[START] [2019-10-12 14:26:48] completed
[STOP] [2019-10-12 14:26:48] completed
[STOP] [2019-10-12 14:26:48] logged process, took 215.95
Latest Process

12 Oct 14:23 EXITED currently processing 0