Harvest for Alaskan Arthropods Created 13 Nov 15:24

Stage: completed
Fetched: 13 Nov 15:24
Validated: 13 Nov 15:24
Deltas Created 13 Nov 15:24
Units Normalized: 13 Nov 15:35
Ancestry Built: 13 Nov 15:25
Nodes Matched: 13 Nov 15:34
Names Parsed: 13 Nov 15:26
New Models Stored: 13 Nov 15:25
Indexed: 13 Nov 15:35
Completed: 13 Nov 15:39
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-11-13 15:24:31 -0500 by logger.rb/56815
[START] [2019-11-13 15:24:31] logged process
[START] [2019-11-13 15:24:31] create_harvest_instance
[STOP] [2019-11-13 15:24:35] create_harvest_instance
[START] [2019-11-13 15:24:35] fetch_files
[STOP] [2019-11-13 15:24:35] fetch_files
[START] [2019-11-13 15:24:35] validate_each_file
[STOP] [2019-11-13 15:24:38] validate_each_file
[START] [2019-11-13 15:24:38] convert_to_csv
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_agents_18504.csv > /app/public/converted_csv/Alaskan_Arthropo_agents_18504.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_refs_18505.csv > /app/public/converted_csv/Alaskan_Arthropo_refs_18505.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_nodes_18506.csv > /app/public/converted_csv/Alaskan_Arthropo_nodes_18506.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_media_18507.csv > /app/public/converted_csv/Alaskan_Arthropo_media_18507.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_vernaculars_18508.csv > /app/public/converted_csv/Alaskan_Arthropo_vernaculars_18508.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_occurrences_18509.csv > /app/public/converted_csv/Alaskan_Arthropo_occurrences_18509.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_assocs_18510.csv > /app/public/converted_csv/Alaskan_Arthropo_assocs_18510.csv_sorted
[CMD] [2019-11-13 15:24:38] /usr/bin/sort /app/public/converted_csv/Alaskan_Arthropo_measurements_18511.csv > /app/public/converted_csv/Alaskan_Arthropo_measurements_18511.csv_sorted
[STOP] [2019-11-13 15:24:38] convert_to_csv
[START] [2019-11-13 15:24:38] calculate_delta
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_agents_18504.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_agents_18504.csv >> /app/public/diff/Alaskan_Arthropo_agents_18504.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_agents_18504.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_refs_18505.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_refs_18505.csv >> /app/public/diff/Alaskan_Arthropo_refs_18505.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_refs_18505.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_nodes_18506.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_nodes_18506.csv >> /app/public/diff/Alaskan_Arthropo_nodes_18506.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_nodes_18506.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_media_18507.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_media_18507.csv >> /app/public/diff/Alaskan_Arthropo_media_18507.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_media_18507.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_vernaculars_18508.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_vernaculars_18508.csv >> /app/public/diff/Alaskan_Arthropo_vernaculars_18508.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_vernaculars_18508.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_occurrences_18509.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_occurrences_18509.csv >> /app/public/diff/Alaskan_Arthropo_occurrences_18509.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_occurrences_18509.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_assocs_18510.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_assocs_18510.csv >> /app/public/diff/Alaskan_Arthropo_assocs_18510.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_assocs_18510.diff
[CMD] [2019-11-13 15:24:38] echo "0a" > /app/public/diff/Alaskan_Arthropo_measurements_18511.diff
[CMD] [2019-11-13 15:24:38] tail -n +1 /app/public/converted_csv/Alaskan_Arthropo_measurements_18511.csv >> /app/public/diff/Alaskan_Arthropo_measurements_18511.diff
[CMD] [2019-11-13 15:24:38] echo "." >> /app/public/diff/Alaskan_Arthropo_measurements_18511.diff
[STOP] [2019-11-13 15:24:38] calculate_delta
[START] [2019-11-13 15:24:38] parse_diff_and_store
[INFO] [2019-11-13 15:24:38] Loading agents diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:39] Loading nodes diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:43] Loading media diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:43] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:43] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:44] Loading assocs diff file into memory (true lines)...
[INFO] [2019-11-13 15:24:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-13 15:25:23] Storing 443 References
[INFO] [2019-11-13 15:25:23] Processing group of 443 in 1 groups of 1000
[INFO] [2019-11-13 15:25:23] Average Time: 0.11
[INFO] [2019-11-13 15:25:23] Total Time: 1s
[INFO] [2019-11-13 15:25:23] Storing 11116 ScientificNames
[INFO] [2019-11-13 15:25:23] Processing group of 11116 in 12 groups of 1000
[INFO] [2019-11-13 15:25:27] Average Time: 0.343
[INFO] [2019-11-13 15:25:27] Total Time: 5s
[INFO] [2019-11-13 15:25:27] last 3 / first 3: 0.64
[INFO] [2019-11-13 15:25:27] Std.Dev: 0.10488088481701516; Max: 0.5
[INFO] [2019-11-13 15:25:27] Storing 11116 Nodes
[INFO] [2019-11-13 15:25:27] Processing group of 11116 in 12 groups of 1000
[INFO] [2019-11-13 15:25:31] Average Time: 0.306
[INFO] [2019-11-13 15:25:31] Total Time: 4s
[INFO] [2019-11-13 15:25:31] last 3 / first 3: 0.49
[INFO] [2019-11-13 15:25:31] Std.Dev: 0.10488088481701516; Max: 0.46
[INFO] [2019-11-13 15:25:31] Storing 7682 Occurrences
[INFO] [2019-11-13 15:25:31] Processing group of 7682 in 8 groups of 1000
[INFO] [2019-11-13 15:25:32] Average Time: 0.112
[INFO] [2019-11-13 15:25:32] Total Time: 1s
[INFO] [2019-11-13 15:25:32] last 3 / first 3: 0.94
[INFO] [2019-11-13 15:25:32] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-11-13 15:25:32] Storing 8258 TraitsReferences
[INFO] [2019-11-13 15:25:32] Processing group of 8258 in 9 groups of 1000
[INFO] [2019-11-13 15:25:33] Average Time: 0.078
[INFO] [2019-11-13 15:25:33] Total Time: 1s
[INFO] [2019-11-13 15:25:33] last 3 / first 3: 0.48
[INFO] [2019-11-13 15:25:33] Std.Dev: 0.044721359549995794; Max: 0.18
[INFO] [2019-11-13 15:25:33] Storing 7880 Traits
[INFO] [2019-11-13 15:25:33] Processing group of 7880 in 8 groups of 1000
[INFO] [2019-11-13 15:25:35] Average Time: 0.315
[INFO] [2019-11-13 15:25:35] Total Time: 3s
[INFO] [2019-11-13 15:25:35] last 3 / first 3: 0.84
[INFO] [2019-11-13 15:25:35] Std.Dev: 0.05477225575051661; Max: 0.44
[INFO] [2019-11-13 15:25:35] Storing 14991 MetaTraits
[INFO] [2019-11-13 15:25:35] Processing group of 14991 in 15 groups of 1000
[INFO] [2019-11-13 15:25:37] Average Time: 0.114
[INFO] [2019-11-13 15:25:37] Total Time: 2s
[INFO] [2019-11-13 15:25:37] last 3 / first 3: 1.0
[INFO] [2019-11-13 15:25:37] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-11-13 15:25:37] parse_diff_and_store
[START] [2019-11-13 15:25:37] resolve_keys
[INFO] [2019-11-13 15:25:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-13 15:25:46] traits to occurrences...
[INFO] [2019-11-13 15:25:46] traits to nodes (through occurrences)...
[INFO] [2019-11-13 15:25:47] Traits to sex term...
[INFO] [2019-11-13 15:25:47] Traits to lifestage term...
[INFO] [2019-11-13 15:25:47] MetaTraits to traits...
[INFO] [2019-11-13 15:25:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-13 15:25:49] Assocs to occurrences...
[INFO] [2019-11-13 15:25:49] Assocs to nodes...
[INFO] [2019-11-13 15:25:49] Assoc to sex term...
[INFO] [2019-11-13 15:25:49] Assoc to lifestage term...
[STOP] [2019-11-13 15:25:49] resolve_keys
[START] [2019-11-13 15:25:49] hold_for_later_1
[STOP] [2019-11-13 15:25:49] hold_for_later_1
[START] [2019-11-13 15:25:49] hold_for_later_2
[STOP] [2019-11-13 15:25:49] hold_for_later_2
[START] [2019-11-13 15:25:49] resolve_missing_parents
[STOP] [2019-11-13 15:25:50] resolve_missing_parents
[START] [2019-11-13 15:25:50] rebuild_nodes
[START] [2019-11-13 15:25:50] Flattener#flatten
[START] [2019-11-13 15:25:50] Flattener#study_resource
[START] [2019-11-13 15:25:50] Flattener#build_ancestry
[STOP] [2019-11-13 15:25:51] Flattener#build_ancestry
[INFO] [2019-11-13 15:25:51] 11116 ancestry keys
[START] [2019-11-13 15:25:51] build_node_ancestors
[INFO] [2019-11-13 15:25:51] old ancestors deleted.
[STOP] [2019-11-13 15:25:54] build_node_ancestors
[START] [2019-11-13 15:25:58] Flattener#propagate_ancestor_ids
[STOP] [2019-11-13 15:25:59] Flattener#propagate_ancestor_ids
[STOP] [2019-11-13 15:25:59] Flattener#flatten
[STOP] [2019-11-13 15:25:59] rebuild_nodes
[START] [2019-11-13 15:25:59] resolve_missing_media_owners
[STOP] [2019-11-13 15:25:59] resolve_missing_media_owners
[START] [2019-11-13 15:25:59] sanitize_media_verbatims
[STOP] [2019-11-13 15:25:59] sanitize_media_verbatims
[START] [2019-11-13 15:25:59] queue_downloads
[STOP] [2019-11-13 15:25:59] queue_downloads
[START] [2019-11-13 15:25:59] parse_names
[WARN] [2019-11-13 15:25:59] I see 11116 names which still need to be parsed.
[WARN] [2019-11-13 15:26:08] I see 54 names which still need to be parsed.
[STOP] [2019-11-13 15:26:09] parse_names
[START] [2019-11-13 15:26:09] denormalize_canonical_names_to_nodes
[STOP] [2019-11-13 15:26:09] denormalize_canonical_names_to_nodes
[START] [2019-11-13 15:26:09] match_nodes
[START] [2019-11-13 15:26:09] map_all_nodes_to_pages
[STOP] [2019-11-13 15:34:37] map_all_nodes_to_pages
[INFO] [2019-11-13 15:34:37] 1062 Unmatched nodes (of 11116)! That's too many to output. First 10: Acronicta lupini (#54775070); Acronicta vulpina (#54775072); Actebia balanitis (#54775098); Alypia langtoni (#54775488); Anarta nigrolunata (#54775637); Anarta trifolii (#54775638); Androloma (#54775689); Androloma maccullochii (#54775690); Apamea amputatrix (#54775834); Apamea cogitata (#54775836)
[START] [2019-11-13 15:34:37] update_nodes
[STOP] [2019-11-13 15:34:41] update_nodes
[STOP] [2019-11-13 15:34:41] match_nodes
[START] [2019-11-13 15:34:41] reindex_search
[STOP] [2019-11-13 15:35:00] reindex_search
[START] [2019-11-13 15:35:00] normalize_units
[STOP] [2019-11-13 15:35:06] normalize_units
[START] [2019-11-13 15:35:06] calculate_statistics
[STOP] [2019-11-13 15:35:06] calculate_statistics
[START] [2019-11-13 15:35:06] complete_harvest_instance
[START] [2019-11-13 15:35:06] overall_tsv_creation
[INFO] [2019-11-13 15:35:06] Processing group of 11116 in 2 batches of 10000
[INFO] [2019-11-13 15:36:39] 7145 Traits (unfiltered)...
[INFO] [2019-11-13 15:36:52] 7145 Traits (filtered)...
[INFO] [2019-11-13 15:36:52] 0 Associations (filtered)...
[INFO] [2019-11-13 15:37:40] 20721 metadata added.
[INFO] [2019-11-13 15:37:40] 0 metadata added.
[INFO] [2019-11-13 15:38:28] 735 Traits (unfiltered)...
[INFO] [2019-11-13 15:38:41] 735 Traits (filtered)...
[INFO] [2019-11-13 15:38:41] 0 Associations (filtered)...
[INFO] [2019-11-13 15:39:20] 1853 metadata added.
[INFO] [2019-11-13 15:39:20] 0 metadata added.
[INFO] [2019-11-13 15:39:20] Average Time: 99.365
[INFO] [2019-11-13 15:39:20] Total Time: 4m14s
[STOP] [2019-11-13 15:39:20] overall_tsv_creation
[INFO] [2019-11-13 15:39:20] Done. Check your files:
[INFO] [2019-11-13 15:39:20] (11063 lines) /app/public/data/Alaskan_Arthropo/publish_nodes.tsv
[INFO] [2019-11-13 15:39:20] (50687 lines) /app/public/data/Alaskan_Arthropo/publish_node_ancestors.tsv
[INFO] [2019-11-13 15:39:20] (11116 lines) /app/public/data/Alaskan_Arthropo/publish_scientific_names.tsv
[INFO] [2019-11-13 15:39:20] (7881 lines) /app/public/data/Alaskan_Arthropo/publish_traits.tsv
[INFO] [2019-11-13 15:39:20] (22575 lines) /app/public/data/Alaskan_Arthropo/publish_metadata.tsv
[STOP] [2019-11-13 15:39:20] complete_harvest_instance
[START] [2019-11-13 15:39:20] completed
[STOP] [2019-11-13 15:39:20] completed
[STOP] [2019-11-13 15:39:20] logged process, took 888.99

Latest Process