Harvest for Guernsey Species List Created 13 Oct 06:40

Stage: completed
Fetched: 13 Oct 06:40
Validated: 13 Oct 06:40
Deltas Created 13 Oct 06:40
Units Normalized: 13 Oct 06:42
Ancestry Built: 13 Oct 06:40
Nodes Matched: 13 Oct 06:42
Names Parsed: 13 Oct 06:40
New Models Stored: 13 Oct 06:40
Indexed: 13 Oct 06:42
Completed: 13 Oct 06:44
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-13 06:40:24 -0400 by logger.rb/56815
[START] [2019-10-13 06:40:24] logged process
[START] [2019-10-13 06:40:24] create_harvest_instance
[STOP] [2019-10-13 06:40:24] create_harvest_instance
[START] [2019-10-13 06:40:24] fetch_files
[STOP] [2019-10-13 06:40:24] fetch_files
[START] [2019-10-13 06:40:24] validate_each_file
[STOP] [2019-10-13 06:40:25] validate_each_file
[START] [2019-10-13 06:40:25] convert_to_csv
[CMD] [2019-10-13 06:40:25] /usr/bin/sort /app/public/converted_csv/guernsey_sp_list_refs_15923.csv > /app/public/converted_csv/guernsey_sp_list_refs_15923.csv_sorted
[CMD] [2019-10-13 06:40:25] /usr/bin/sort /app/public/converted_csv/guernsey_sp_list_nodes_15924.csv > /app/public/converted_csv/guernsey_sp_list_nodes_15924.csv_sorted
[CMD] [2019-10-13 06:40:25] /usr/bin/sort /app/public/converted_csv/guernsey_sp_list_occurrences_15925.csv > /app/public/converted_csv/guernsey_sp_list_occurrences_15925.csv_sorted
[CMD] [2019-10-13 06:40:25] /usr/bin/sort /app/public/converted_csv/guernsey_sp_list_measurements_15926.csv > /app/public/converted_csv/guernsey_sp_list_measurements_15926.csv_sorted
[STOP] [2019-10-13 06:40:25] convert_to_csv
[START] [2019-10-13 06:40:25] calculate_delta
[CMD] [2019-10-13 06:40:25] echo "0a" > /app/public/diff/guernsey_sp_list_refs_15923.diff
[CMD] [2019-10-13 06:40:25] tail -n +1 /app/public/converted_csv/guernsey_sp_list_refs_15923.csv >> /app/public/diff/guernsey_sp_list_refs_15923.diff
[CMD] [2019-10-13 06:40:25] echo "." >> /app/public/diff/guernsey_sp_list_refs_15923.diff
[CMD] [2019-10-13 06:40:26] echo "0a" > /app/public/diff/guernsey_sp_list_nodes_15924.diff
[CMD] [2019-10-13 06:40:26] tail -n +1 /app/public/converted_csv/guernsey_sp_list_nodes_15924.csv >> /app/public/diff/guernsey_sp_list_nodes_15924.diff
[CMD] [2019-10-13 06:40:26] echo "." >> /app/public/diff/guernsey_sp_list_nodes_15924.diff
[CMD] [2019-10-13 06:40:26] echo "0a" > /app/public/diff/guernsey_sp_list_occurrences_15925.diff
[CMD] [2019-10-13 06:40:26] tail -n +1 /app/public/converted_csv/guernsey_sp_list_occurrences_15925.csv >> /app/public/diff/guernsey_sp_list_occurrences_15925.diff
[CMD] [2019-10-13 06:40:26] echo "." >> /app/public/diff/guernsey_sp_list_occurrences_15925.diff
[CMD] [2019-10-13 06:40:26] echo "0a" > /app/public/diff/guernsey_sp_list_measurements_15926.diff
[CMD] [2019-10-13 06:40:26] tail -n +1 /app/public/converted_csv/guernsey_sp_list_measurements_15926.csv >> /app/public/diff/guernsey_sp_list_measurements_15926.diff
[CMD] [2019-10-13 06:40:26] echo "." >> /app/public/diff/guernsey_sp_list_measurements_15926.diff
[STOP] [2019-10-13 06:40:26] calculate_delta
[START] [2019-10-13 06:40:26] parse_diff_and_store
[INFO] [2019-10-13 06:40:26] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 06:40:27] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 06:40:27] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 06:40:27] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 06:40:32] Storing 2 References
[INFO] [2019-10-13 06:40:32] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 06:40:32] Average Time: 0.0
[INFO] [2019-10-13 06:40:32] Total Time: 1s
[INFO] [2019-10-13 06:40:32] Storing 1597 ScientificNames
[INFO] [2019-10-13 06:40:32] Processing group of 1597 in 2 groups of 1000
[INFO] [2019-10-13 06:40:32] Average Time: 0.295
[INFO] [2019-10-13 06:40:32] Total Time: 1s
[INFO] [2019-10-13 06:40:32] Storing 1597 Nodes
[INFO] [2019-10-13 06:40:32] Processing group of 1597 in 2 groups of 1000
[INFO] [2019-10-13 06:40:33] Average Time: 0.36
[INFO] [2019-10-13 06:40:33] Total Time: 1s
[INFO] [2019-10-13 06:40:33] Storing 482 Occurrences
[INFO] [2019-10-13 06:40:33] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-13 06:40:33] Average Time: 0.07
[INFO] [2019-10-13 06:40:33] Total Time: 1s
[INFO] [2019-10-13 06:40:33] Storing 1370 TraitsReferences
[INFO] [2019-10-13 06:40:33] Processing group of 1370 in 2 groups of 1000
[INFO] [2019-10-13 06:40:33] Average Time: 0.085
[INFO] [2019-10-13 06:40:33] Total Time: 1s
[INFO] [2019-10-13 06:40:33] Storing 1369 Traits
[INFO] [2019-10-13 06:40:33] Processing group of 1369 in 2 groups of 1000
[INFO] [2019-10-13 06:40:34] Average Time: 0.255
[INFO] [2019-10-13 06:40:34] Total Time: 1s
[INFO] [2019-10-13 06:40:34] Storing 1370 MetaTraits
[INFO] [2019-10-13 06:40:34] Processing group of 1370 in 2 groups of 1000
[INFO] [2019-10-13 06:40:34] Average Time: 0.09
[INFO] [2019-10-13 06:40:34] Total Time: 1s
[STOP] [2019-10-13 06:40:34] parse_diff_and_store
[START] [2019-10-13 06:40:34] resolve_keys
[INFO] [2019-10-13 06:40:42] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 06:40:43] traits to occurrences...
[INFO] [2019-10-13 06:40:43] traits to nodes (through occurrences)...
[INFO] [2019-10-13 06:40:43] Traits to sex term...
[INFO] [2019-10-13 06:40:43] Traits to lifestage term...
[INFO] [2019-10-13 06:40:43] MetaTraits to traits...
[INFO] [2019-10-13 06:40:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 06:40:44] Assocs to occurrences...
[INFO] [2019-10-13 06:40:44] Assocs to nodes...
[INFO] [2019-10-13 06:40:44] Assoc to sex term...
[INFO] [2019-10-13 06:40:44] Assoc to lifestage term...
[STOP] [2019-10-13 06:40:44] resolve_keys
[START] [2019-10-13 06:40:44] hold_for_later_1
[STOP] [2019-10-13 06:40:44] hold_for_later_1
[START] [2019-10-13 06:40:44] hold_for_later_2
[STOP] [2019-10-13 06:40:44] hold_for_later_2
[START] [2019-10-13 06:40:44] resolve_missing_parents
[STOP] [2019-10-13 06:40:45] resolve_missing_parents
[START] [2019-10-13 06:40:45] rebuild_nodes
[START] [2019-10-13 06:40:45] Flattener#flatten
[START] [2019-10-13 06:40:45] Flattener#study_resource
[START] [2019-10-13 06:40:45] Flattener#build_ancestry
[STOP] [2019-10-13 06:40:45] Flattener#build_ancestry
[INFO] [2019-10-13 06:40:45] 1597 ancestry keys
[START] [2019-10-13 06:40:45] build_node_ancestors
[INFO] [2019-10-13 06:40:45] old ancestors deleted.
[STOP] [2019-10-13 06:40:46] build_node_ancestors
[START] [2019-10-13 06:40:46] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:40:46] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:40:46] Flattener#flatten
[STOP] [2019-10-13 06:40:46] rebuild_nodes
[START] [2019-10-13 06:40:46] resolve_missing_media_owners
[STOP] [2019-10-13 06:40:46] resolve_missing_media_owners
[START] [2019-10-13 06:40:46] sanitize_media_verbatims
[STOP] [2019-10-13 06:40:46] sanitize_media_verbatims
[START] [2019-10-13 06:40:46] queue_downloads
[STOP] [2019-10-13 06:40:46] queue_downloads
[START] [2019-10-13 06:40:46] parse_names
[WARN] [2019-10-13 06:40:46] I see 1597 names which still need to be parsed.
[STOP] [2019-10-13 06:40:48] parse_names
[START] [2019-10-13 06:40:48] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 06:40:48] denormalize_canonical_names_to_nodes
[START] [2019-10-13 06:40:48] match_nodes
[START] [2019-10-13 06:40:48] map_all_nodes_to_pages
[STOP] [2019-10-13 06:42:20] map_all_nodes_to_pages
[INFO] [2019-10-13 06:42:20] 79 Unmatched nodes (of 1597)! That's too many to output. First 10: Thalaseus (#49964938); Thalaseus sandvicensis (#49964937); Carduelis cannabina (#49965163); Phylloscopus sibillatrix (#49966119); Archaeogastropoda (#49964870); Haliotididae (#49964948); Tricoliidae (#49965150); Patina (#49964998); Patina pellucidum (#49964997); Nassarius reticulata (#49965095)
[START] [2019-10-13 06:42:20] update_nodes
[STOP] [2019-10-13 06:42:21] update_nodes
[STOP] [2019-10-13 06:42:21] match_nodes
[START] [2019-10-13 06:42:21] reindex_search
[STOP] [2019-10-13 06:42:23] reindex_search
[START] [2019-10-13 06:42:23] normalize_units
[STOP] [2019-10-13 06:42:24] normalize_units
[START] [2019-10-13 06:42:24] calculate_statistics
[STOP] [2019-10-13 06:42:24] calculate_statistics
[START] [2019-10-13 06:42:24] complete_harvest_instance
[START] [2019-10-13 06:42:24] overall_tsv_creation
[INFO] [2019-10-13 06:42:24] Processing group of 1597 in 1 batches of 10000
[INFO] [2019-10-13 06:43:15] 482 Traits (unfiltered)...
[INFO] [2019-10-13 06:43:29] 482 Traits (filtered)...
[INFO] [2019-10-13 06:43:29] 0 Associations (filtered)...
[INFO] [2019-10-13 06:44:09] 2410 metadata added.
[INFO] [2019-10-13 06:44:09] 0 metadata added.
[INFO] [2019-10-13 06:44:09] Average Time: 83.54
[INFO] [2019-10-13 06:44:09] Total Time: 1m46s
[STOP] [2019-10-13 06:44:09] overall_tsv_creation
[INFO] [2019-10-13 06:44:09] Done. Check your files:
[INFO] [2019-10-13 06:44:09] (1597 lines) /app/public/data/guernsey_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 06:44:09] (3077 lines) /app/public/data/guernsey_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 06:44:09] (1597 lines) /app/public/data/guernsey_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 06:44:09] (483 lines) /app/public/data/guernsey_sp_list/publish_traits.tsv
[INFO] [2019-10-13 06:44:09] (2411 lines) /app/public/data/guernsey_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 06:44:09] complete_harvest_instance
[START] [2019-10-13 06:44:09] completed
[STOP] [2019-10-13 06:44:09] completed
[STOP] [2019-10-13 06:44:09] logged process, took 225.47

Latest Process