Harvest for Gibraltar Species List Created 13 Oct 04:27

Stage: completed
Fetched: 13 Oct 04:27
Validated: 13 Oct 04:27
Deltas Created 13 Oct 04:27
Units Normalized: 13 Oct 04:29
Ancestry Built: 13 Oct 04:28
Nodes Matched: 13 Oct 04:29
Names Parsed: 13 Oct 04:28
New Models Stored: 13 Oct 04:28
Indexed: 13 Oct 04:29
Completed: 13 Oct 04:30
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 04:27:57 -0400 by logger.rb/56815
[START] [2019-10-13 04:27:57] logged process
[START] [2019-10-13 04:27:57] create_harvest_instance
[STOP] [2019-10-13 04:27:58] create_harvest_instance
[START] [2019-10-13 04:27:58] fetch_files
[STOP] [2019-10-13 04:27:58] fetch_files
[START] [2019-10-13 04:27:58] validate_each_file
[STOP] [2019-10-13 04:27:58] validate_each_file
[START] [2019-10-13 04:27:58] convert_to_csv
[CMD] [2019-10-13 04:27:58] /usr/bin/sort /app/public/converted_csv/gibraltar_sp_lis_refs_15851.csv > /app/public/converted_csv/gibraltar_sp_lis_refs_15851.csv_sorted
[CMD] [2019-10-13 04:27:58] /usr/bin/sort /app/public/converted_csv/gibraltar_sp_lis_nodes_15852.csv > /app/public/converted_csv/gibraltar_sp_lis_nodes_15852.csv_sorted
[CMD] [2019-10-13 04:27:58] /usr/bin/sort /app/public/converted_csv/gibraltar_sp_lis_occurrences_15853.csv > /app/public/converted_csv/gibraltar_sp_lis_occurrences_15853.csv_sorted
[CMD] [2019-10-13 04:27:58] /usr/bin/sort /app/public/converted_csv/gibraltar_sp_lis_measurements_15854.csv > /app/public/converted_csv/gibraltar_sp_lis_measurements_15854.csv_sorted
[STOP] [2019-10-13 04:27:58] convert_to_csv
[START] [2019-10-13 04:27:58] calculate_delta
[CMD] [2019-10-13 04:27:58] echo "0a" > /app/public/diff/gibraltar_sp_lis_refs_15851.diff
[CMD] [2019-10-13 04:27:58] tail -n +1 /app/public/converted_csv/gibraltar_sp_lis_refs_15851.csv >> /app/public/diff/gibraltar_sp_lis_refs_15851.diff
[CMD] [2019-10-13 04:27:58] echo "." >> /app/public/diff/gibraltar_sp_lis_refs_15851.diff
[CMD] [2019-10-13 04:27:58] echo "0a" > /app/public/diff/gibraltar_sp_lis_nodes_15852.diff
[CMD] [2019-10-13 04:27:59] tail -n +1 /app/public/converted_csv/gibraltar_sp_lis_nodes_15852.csv >> /app/public/diff/gibraltar_sp_lis_nodes_15852.diff
[CMD] [2019-10-13 04:27:59] echo "." >> /app/public/diff/gibraltar_sp_lis_nodes_15852.diff
[CMD] [2019-10-13 04:27:59] echo "0a" > /app/public/diff/gibraltar_sp_lis_occurrences_15853.diff
[CMD] [2019-10-13 04:27:59] tail -n +1 /app/public/converted_csv/gibraltar_sp_lis_occurrences_15853.csv >> /app/public/diff/gibraltar_sp_lis_occurrences_15853.diff
[CMD] [2019-10-13 04:27:59] echo "." >> /app/public/diff/gibraltar_sp_lis_occurrences_15853.diff
[CMD] [2019-10-13 04:27:59] echo "0a" > /app/public/diff/gibraltar_sp_lis_measurements_15854.diff
[CMD] [2019-10-13 04:27:59] tail -n +1 /app/public/converted_csv/gibraltar_sp_lis_measurements_15854.csv >> /app/public/diff/gibraltar_sp_lis_measurements_15854.diff
[CMD] [2019-10-13 04:27:59] echo "." >> /app/public/diff/gibraltar_sp_lis_measurements_15854.diff
[STOP] [2019-10-13 04:27:59] calculate_delta
[START] [2019-10-13 04:27:59] parse_diff_and_store
[INFO] [2019-10-13 04:27:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 04:28:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 04:28:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 04:28:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 04:28:01] Storing 2 References
[INFO] [2019-10-13 04:28:01] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 04:28:01] Average Time: 0.0
[INFO] [2019-10-13 04:28:01] Total Time: 1s
[INFO] [2019-10-13 04:28:01] Storing 541 ScientificNames
[INFO] [2019-10-13 04:28:01] Processing group of 541 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.3
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[INFO] [2019-10-13 04:28:02] Storing 541 Nodes
[INFO] [2019-10-13 04:28:02] Processing group of 541 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.2
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[INFO] [2019-10-13 04:28:02] Storing 203 Occurrences
[INFO] [2019-10-13 04:28:02] Processing group of 203 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.04
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[INFO] [2019-10-13 04:28:02] Storing 406 TraitsReferences
[INFO] [2019-10-13 04:28:02] Processing group of 406 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.12
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[INFO] [2019-10-13 04:28:02] Storing 406 Traits
[INFO] [2019-10-13 04:28:02] Processing group of 406 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.22
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[INFO] [2019-10-13 04:28:02] Storing 406 MetaTraits
[INFO] [2019-10-13 04:28:02] Processing group of 406 in 1 groups of 1000
[INFO] [2019-10-13 04:28:02] Average Time: 0.08
[INFO] [2019-10-13 04:28:02] Total Time: 1s
[STOP] [2019-10-13 04:28:02] parse_diff_and_store
[START] [2019-10-13 04:28:02] resolve_keys
[INFO] [2019-10-13 04:28:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 04:28:09] traits to occurrences...
[INFO] [2019-10-13 04:28:09] traits to nodes (through occurrences)...
[INFO] [2019-10-13 04:28:09] Traits to sex term...
[INFO] [2019-10-13 04:28:09] Traits to lifestage term...
[INFO] [2019-10-13 04:28:09] MetaTraits to traits...
[INFO] [2019-10-13 04:28:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 04:28:09] Assocs to occurrences...
[INFO] [2019-10-13 04:28:09] Assocs to nodes...
[INFO] [2019-10-13 04:28:09] Assoc to sex term...
[INFO] [2019-10-13 04:28:09] Assoc to lifestage term...
[STOP] [2019-10-13 04:28:09] resolve_keys
[START] [2019-10-13 04:28:09] hold_for_later_1
[STOP] [2019-10-13 04:28:09] hold_for_later_1
[START] [2019-10-13 04:28:09] hold_for_later_2
[STOP] [2019-10-13 04:28:09] hold_for_later_2
[START] [2019-10-13 04:28:09] resolve_missing_parents
[STOP] [2019-10-13 04:28:09] resolve_missing_parents
[START] [2019-10-13 04:28:09] rebuild_nodes
[START] [2019-10-13 04:28:09] Flattener#flatten
[START] [2019-10-13 04:28:09] Flattener#study_resource
[START] [2019-10-13 04:28:09] Flattener#build_ancestry
[STOP] [2019-10-13 04:28:09] Flattener#build_ancestry
[INFO] [2019-10-13 04:28:09] 541 ancestry keys
[START] [2019-10-13 04:28:09] build_node_ancestors
[INFO] [2019-10-13 04:28:09] old ancestors deleted.
[STOP] [2019-10-13 04:28:09] build_node_ancestors
[START] [2019-10-13 04:28:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:28:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:28:10] Flattener#flatten
[STOP] [2019-10-13 04:28:10] rebuild_nodes
[START] [2019-10-13 04:28:10] resolve_missing_media_owners
[STOP] [2019-10-13 04:28:10] resolve_missing_media_owners
[START] [2019-10-13 04:28:10] sanitize_media_verbatims
[STOP] [2019-10-13 04:28:10] sanitize_media_verbatims
[START] [2019-10-13 04:28:10] queue_downloads
[STOP] [2019-10-13 04:28:10] queue_downloads
[START] [2019-10-13 04:28:10] parse_names
[WARN] [2019-10-13 04:28:10] I see 541 names which still need to be parsed.
[STOP] [2019-10-13 04:28:11] parse_names
[START] [2019-10-13 04:28:11] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 04:28:11] denormalize_canonical_names_to_nodes
[START] [2019-10-13 04:28:11] match_nodes
[START] [2019-10-13 04:28:11] map_all_nodes_to_pages
[STOP] [2019-10-13 04:29:02] map_all_nodes_to_pages
[INFO] [2019-10-13 04:29:02] 19 Unmatched nodes (of 541)! That's too many to output. First 10: Thalaseus (#49892513); Thalaseus sandvicensis (#49892512); Archaeogastropoda (#49892717); Neotaenioglossa (#49892777); Veneroida (#49892733); Carditoida (#49892741); Mytiloida (#49892751); Amara tingitanus (#49892906); Magnoliopsida (#49892469); Campanula erinoides (#49892796)
[START] [2019-10-13 04:29:02] update_nodes
[STOP] [2019-10-13 04:29:02] update_nodes
[STOP] [2019-10-13 04:29:02] match_nodes
[START] [2019-10-13 04:29:02] reindex_search
[STOP] [2019-10-13 04:29:03] reindex_search
[START] [2019-10-13 04:29:03] normalize_units
[STOP] [2019-10-13 04:29:03] normalize_units
[START] [2019-10-13 04:29:03] calculate_statistics
[STOP] [2019-10-13 04:29:03] calculate_statistics
[START] [2019-10-13 04:29:03] complete_harvest_instance
[START] [2019-10-13 04:29:03] overall_tsv_creation
[INFO] [2019-10-13 04:29:03] Processing group of 541 in 1 batches of 10000
[INFO] [2019-10-13 04:29:51] 203 Traits (unfiltered)...
[INFO] [2019-10-13 04:30:05] 203 Traits (filtered)...
[INFO] [2019-10-13 04:30:05] 0 Associations (filtered)...
[INFO] [2019-10-13 04:30:42] 1015 metadata added.
[INFO] [2019-10-13 04:30:42] 0 metadata added.
[INFO] [2019-10-13 04:30:42] Average Time: 76.5
[INFO] [2019-10-13 04:30:42] Total Time: 1m39s
[STOP] [2019-10-13 04:30:42] overall_tsv_creation
[INFO] [2019-10-13 04:30:42] Done. Check your files:
[INFO] [2019-10-13 04:30:42] (541 lines) /app/public/data/gibraltar_sp_lis/publish_nodes.tsv
[INFO] [2019-10-13 04:30:42] (2569 lines) /app/public/data/gibraltar_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-13 04:30:42] (541 lines) /app/public/data/gibraltar_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-13 04:30:42] (204 lines) /app/public/data/gibraltar_sp_lis/publish_traits.tsv
[INFO] [2019-10-13 04:30:42] (1016 lines) /app/public/data/gibraltar_sp_lis/publish_metadata.tsv
[STOP] [2019-10-13 04:30:42] complete_harvest_instance
[START] [2019-10-13 04:30:42] completed
[STOP] [2019-10-13 04:30:42] completed
[STOP] [2019-10-13 04:30:42] logged process, took 164.91
Latest Process

13 Oct 04:27 EXITED currently processing 0