Harvest for Senegal Species List Created 15 Oct 17:33

Stage: completed
Fetched: 15 Oct 17:33
Validated: 15 Oct 17:33
Deltas Created 15 Oct 17:33
Units Normalized: 15 Oct 17:42
Ancestry Built: 15 Oct 17:35
Nodes Matched: 15 Oct 17:42
Names Parsed: 15 Oct 17:35
New Models Stored: 15 Oct 17:34
Indexed: 15 Oct 17:42
Completed: 15 Oct 17:44
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-15 17:33:51 -0400 by logger.rb/56815
[START] [2019-10-15 17:33:51] logged process
[START] [2019-10-15 17:33:51] create_harvest_instance
[STOP] [2019-10-15 17:33:52] create_harvest_instance
[START] [2019-10-15 17:33:52] fetch_files
[STOP] [2019-10-15 17:33:52] fetch_files
[START] [2019-10-15 17:33:52] validate_each_file
[STOP] [2019-10-15 17:33:52] validate_each_file
[START] [2019-10-15 17:33:52] convert_to_csv
[CMD] [2019-10-15 17:33:52] /usr/bin/sort /app/public/converted_csv/senegal_sp_list_refs_17149.csv > /app/public/converted_csv/senegal_sp_list_refs_17149.csv_sorted
[CMD] [2019-10-15 17:33:53] /usr/bin/sort /app/public/converted_csv/senegal_sp_list_nodes_17150.csv > /app/public/converted_csv/senegal_sp_list_nodes_17150.csv_sorted
[CMD] [2019-10-15 17:33:53] /usr/bin/sort /app/public/converted_csv/senegal_sp_list_occurrences_17151.csv > /app/public/converted_csv/senegal_sp_list_occurrences_17151.csv_sorted
[CMD] [2019-10-15 17:33:53] /usr/bin/sort /app/public/converted_csv/senegal_sp_list_measurements_17152.csv > /app/public/converted_csv/senegal_sp_list_measurements_17152.csv_sorted
[STOP] [2019-10-15 17:33:53] convert_to_csv
[START] [2019-10-15 17:33:53] calculate_delta
[CMD] [2019-10-15 17:33:53] echo "0a" > /app/public/diff/senegal_sp_list_refs_17149.diff
[CMD] [2019-10-15 17:33:54] tail -n +1 /app/public/converted_csv/senegal_sp_list_refs_17149.csv >> /app/public/diff/senegal_sp_list_refs_17149.diff
[CMD] [2019-10-15 17:33:54] echo "." >> /app/public/diff/senegal_sp_list_refs_17149.diff
[CMD] [2019-10-15 17:33:54] echo "0a" > /app/public/diff/senegal_sp_list_nodes_17150.diff
[CMD] [2019-10-15 17:33:54] tail -n +1 /app/public/converted_csv/senegal_sp_list_nodes_17150.csv >> /app/public/diff/senegal_sp_list_nodes_17150.diff
[CMD] [2019-10-15 17:33:55] echo "." >> /app/public/diff/senegal_sp_list_nodes_17150.diff
[CMD] [2019-10-15 17:33:55] echo "0a" > /app/public/diff/senegal_sp_list_occurrences_17151.diff
[CMD] [2019-10-15 17:33:55] tail -n +1 /app/public/converted_csv/senegal_sp_list_occurrences_17151.csv >> /app/public/diff/senegal_sp_list_occurrences_17151.diff
[CMD] [2019-10-15 17:33:56] echo "." >> /app/public/diff/senegal_sp_list_occurrences_17151.diff
[CMD] [2019-10-15 17:33:56] echo "0a" > /app/public/diff/senegal_sp_list_measurements_17152.diff
[CMD] [2019-10-15 17:33:56] tail -n +1 /app/public/converted_csv/senegal_sp_list_measurements_17152.csv >> /app/public/diff/senegal_sp_list_measurements_17152.diff
[CMD] [2019-10-15 17:33:56] echo "." >> /app/public/diff/senegal_sp_list_measurements_17152.diff
[STOP] [2019-10-15 17:33:57] calculate_delta
[START] [2019-10-15 17:33:57] parse_diff_and_store
[INFO] [2019-10-15 17:33:57] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 17:33:57] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 17:34:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 17:34:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 17:34:21] Storing 2 References
[INFO] [2019-10-15 17:34:21] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 17:34:21] Average Time: 0.0
[INFO] [2019-10-15 17:34:21] Total Time: 1s
[INFO] [2019-10-15 17:34:21] Storing 5955 ScientificNames
[INFO] [2019-10-15 17:34:21] Processing group of 5955 in 6 groups of 1000
[INFO] [2019-10-15 17:34:23] Average Time: 0.368
[INFO] [2019-10-15 17:34:23] Total Time: 3s
[INFO] [2019-10-15 17:34:23] Storing 5955 Nodes
[INFO] [2019-10-15 17:34:23] Processing group of 5955 in 6 groups of 1000
[INFO] [2019-10-15 17:34:25] Average Time: 0.31
[INFO] [2019-10-15 17:34:25] Total Time: 2s
[INFO] [2019-10-15 17:34:25] Storing 3374 Occurrences
[INFO] [2019-10-15 17:34:25] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-15 17:34:25] Average Time: 0.092
[INFO] [2019-10-15 17:34:25] Total Time: 1s
[INFO] [2019-10-15 17:34:25] Storing 7040 TraitsReferences
[INFO] [2019-10-15 17:34:25] Processing group of 7040 in 8 groups of 1000
[INFO] [2019-10-15 17:34:26] Average Time: 0.075
[INFO] [2019-10-15 17:34:26] Total Time: 1s
[INFO] [2019-10-15 17:34:26] last 3 / first 3: 0.44
[INFO] [2019-10-15 17:34:26] Std.Dev: 0.044721359549995794; Max: 0.15
[INFO] [2019-10-15 17:34:26] Storing 7039 Traits
[INFO] [2019-10-15 17:34:26] Processing group of 7039 in 8 groups of 1000
[INFO] [2019-10-15 17:34:28] Average Time: 0.281
[INFO] [2019-10-15 17:34:28] Total Time: 3s
[INFO] [2019-10-15 17:34:28] last 3 / first 3: 0.57
[INFO] [2019-10-15 17:34:28] Std.Dev: 0.11832159566199232; Max: 0.42
[INFO] [2019-10-15 17:34:28] Storing 7039 MetaTraits
[INFO] [2019-10-15 17:34:28] Processing group of 7039 in 8 groups of 1000
[INFO] [2019-10-15 17:34:29] Average Time: 0.115
[INFO] [2019-10-15 17:34:29] Total Time: 1s
[INFO] [2019-10-15 17:34:29] last 3 / first 3: 0.68
[INFO] [2019-10-15 17:34:29] Std.Dev: 0.044721359549995794; Max: 0.16
[STOP] [2019-10-15 17:34:29] parse_diff_and_store
[START] [2019-10-15 17:34:29] resolve_keys
[INFO] [2019-10-15 17:34:55] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 17:34:58] traits to occurrences...
[INFO] [2019-10-15 17:34:59] traits to nodes (through occurrences)...
[INFO] [2019-10-15 17:34:59] Traits to sex term...
[INFO] [2019-10-15 17:35:01] Traits to lifestage term...
[INFO] [2019-10-15 17:35:02] MetaTraits to traits...
[INFO] [2019-10-15 17:35:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 17:35:03] Assocs to occurrences...
[INFO] [2019-10-15 17:35:03] Assocs to nodes...
[INFO] [2019-10-15 17:35:03] Assoc to sex term...
[INFO] [2019-10-15 17:35:03] Assoc to lifestage term...
[STOP] [2019-10-15 17:35:03] resolve_keys
[START] [2019-10-15 17:35:03] hold_for_later_1
[STOP] [2019-10-15 17:35:03] hold_for_later_1
[START] [2019-10-15 17:35:03] hold_for_later_2
[STOP] [2019-10-15 17:35:03] hold_for_later_2
[START] [2019-10-15 17:35:03] resolve_missing_parents
[STOP] [2019-10-15 17:35:16] resolve_missing_parents
[START] [2019-10-15 17:35:16] rebuild_nodes
[START] [2019-10-15 17:35:16] Flattener#flatten
[START] [2019-10-15 17:35:16] Flattener#study_resource
[START] [2019-10-15 17:35:16] Flattener#build_ancestry
[STOP] [2019-10-15 17:35:16] Flattener#build_ancestry
[INFO] [2019-10-15 17:35:16] 5955 ancestry keys
[START] [2019-10-15 17:35:16] build_node_ancestors
[INFO] [2019-10-15 17:35:16] old ancestors deleted.
[STOP] [2019-10-15 17:35:17] build_node_ancestors
[START] [2019-10-15 17:35:18] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 17:35:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 17:35:19] Flattener#flatten
[STOP] [2019-10-15 17:35:19] rebuild_nodes
[START] [2019-10-15 17:35:19] resolve_missing_media_owners
[STOP] [2019-10-15 17:35:19] resolve_missing_media_owners
[START] [2019-10-15 17:35:19] sanitize_media_verbatims
[STOP] [2019-10-15 17:35:19] sanitize_media_verbatims
[START] [2019-10-15 17:35:19] queue_downloads
[STOP] [2019-10-15 17:35:19] queue_downloads
[START] [2019-10-15 17:35:19] parse_names
[WARN] [2019-10-15 17:35:19] I see 5955 names which still need to be parsed.
[STOP] [2019-10-15 17:35:24] parse_names
[START] [2019-10-15 17:35:24] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 17:35:24] denormalize_canonical_names_to_nodes
[START] [2019-10-15 17:35:24] match_nodes
[START] [2019-10-15 17:35:24] map_all_nodes_to_pages
[STOP] [2019-10-15 17:42:12] map_all_nodes_to_pages
[INFO] [2019-10-15 17:42:12] 305 Unmatched nodes (of 5955)! That's too many to output. First 10: Larus audouinii (#51780872); Thalaseus (#51780328); Thalaseus sandvicensis (#51780327); Thalaseus maxima (#51780606); Thalaseus maximus (#51781002); Thalaseus bengalensis (#51782034); Thalasseus maxima (#51780809); Philomachus pugnax (#51780844); Delichon urbica (#51785896); Hippolais pallida (#51780990)
[START] [2019-10-15 17:42:12] update_nodes
[STOP] [2019-10-15 17:42:15] update_nodes
[STOP] [2019-10-15 17:42:15] match_nodes
[START] [2019-10-15 17:42:15] reindex_search
[STOP] [2019-10-15 17:42:32] reindex_search
[START] [2019-10-15 17:42:32] normalize_units
[STOP] [2019-10-15 17:42:32] normalize_units
[START] [2019-10-15 17:42:32] calculate_statistics
[STOP] [2019-10-15 17:42:32] calculate_statistics
[START] [2019-10-15 17:42:32] complete_harvest_instance
[START] [2019-10-15 17:42:32] overall_tsv_creation
[INFO] [2019-10-15 17:42:32] Processing group of 5955 in 1 batches of 10000
[INFO] [2019-10-15 17:43:43] 3374 Traits (unfiltered)...
[INFO] [2019-10-15 17:43:57] 3374 Traits (filtered)...
[INFO] [2019-10-15 17:43:57] 0 Associations (filtered)...
[INFO] [2019-10-15 17:44:42] 16869 metadata added.
[INFO] [2019-10-15 17:44:42] 0 metadata added.
[INFO] [2019-10-15 17:44:42] Average Time: 105.61
[INFO] [2019-10-15 17:44:42] Total Time: 2m10s
[STOP] [2019-10-15 17:44:42] overall_tsv_creation
[INFO] [2019-10-15 17:44:42] Done. Check your files:
[INFO] [2019-10-15 17:44:42] (5955 lines) /app/public/data/senegal_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 17:44:43] (12725 lines) /app/public/data/senegal_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 17:44:43] (5955 lines) /app/public/data/senegal_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 17:44:43] (3375 lines) /app/public/data/senegal_sp_list/publish_traits.tsv
[INFO] [2019-10-15 17:44:43] (16870 lines) /app/public/data/senegal_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 17:44:44] complete_harvest_instance
[START] [2019-10-15 17:44:44] completed
[STOP] [2019-10-15 17:44:44] completed
[STOP] [2019-10-15 17:44:44] logged process, took 652.64
Latest Process

15 Oct 17:33 EXITED currently processing 0