Harvest for English Channel Species List Created 23 Dec 01:22

Stage: completed
Fetched: 23 Dec 01:22
Validated: 23 Dec 01:22
Deltas Created 23 Dec 01:22
Units Normalized: 23 Dec 01:59
Ancestry Built: 23 Dec 01:24
Nodes Matched: 23 Dec 01:59
Names Parsed: 23 Dec 01:24
New Models Stored: 23 Dec 01:23
Indexed: 23 Dec 01:59
Completed: 23 Dec 02:02
Time to Harvest: 1 minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-23 01:22:55 -0500 by logger.rb/56815
[START] [2019-12-23 01:22:55] logged process
[START] [2019-12-23 01:22:55] create_harvest_instance
[STOP] [2019-12-23 01:22:56] create_harvest_instance
[START] [2019-12-23 01:22:56] fetch_files
[STOP] [2019-12-23 01:22:56] fetch_files
[START] [2019-12-23 01:22:56] validate_each_file
[STOP] [2019-12-23 01:22:57] validate_each_file
[START] [2019-12-23 01:22:57] convert_to_csv
[CMD] [2019-12-23 01:22:57] /usr/bin/sort /app/public/converted_csv/english_channel__refs_19226.csv > /app/public/converted_csv/english_channel__refs_19226.csv_sorted
[CMD] [2019-12-23 01:22:57] /usr/bin/sort /app/public/converted_csv/english_channel__nodes_19227.csv > /app/public/converted_csv/english_channel__nodes_19227.csv_sorted
[CMD] [2019-12-23 01:22:57] /usr/bin/sort /app/public/converted_csv/english_channel__occurrences_19228.csv > /app/public/converted_csv/english_channel__occurrences_19228.csv_sorted
[CMD] [2019-12-23 01:22:57] /usr/bin/sort /app/public/converted_csv/english_channel__measurements_19229.csv > /app/public/converted_csv/english_channel__measurements_19229.csv_sorted
[STOP] [2019-12-23 01:22:57] convert_to_csv
[START] [2019-12-23 01:22:58] calculate_delta
[CMD] [2019-12-23 01:22:58] echo "0a" > /app/public/diff/english_channel__refs_19226.diff
[CMD] [2019-12-23 01:22:58] tail -n +1 /app/public/converted_csv/english_channel__refs_19226.csv >> /app/public/diff/english_channel__refs_19226.diff
[CMD] [2019-12-23 01:22:58] echo "." >> /app/public/diff/english_channel__refs_19226.diff
[CMD] [2019-12-23 01:22:58] echo "0a" > /app/public/diff/english_channel__nodes_19227.diff
[CMD] [2019-12-23 01:22:58] tail -n +1 /app/public/converted_csv/english_channel__nodes_19227.csv >> /app/public/diff/english_channel__nodes_19227.diff
[CMD] [2019-12-23 01:22:58] echo "." >> /app/public/diff/english_channel__nodes_19227.diff
[CMD] [2019-12-23 01:22:58] echo "0a" > /app/public/diff/english_channel__occurrences_19228.diff
[CMD] [2019-12-23 01:22:58] tail -n +1 /app/public/converted_csv/english_channel__occurrences_19228.csv >> /app/public/diff/english_channel__occurrences_19228.diff
[CMD] [2019-12-23 01:22:58] echo "." >> /app/public/diff/english_channel__occurrences_19228.diff
[CMD] [2019-12-23 01:22:58] echo "0a" > /app/public/diff/english_channel__measurements_19229.diff
[CMD] [2019-12-23 01:22:58] tail -n +1 /app/public/converted_csv/english_channel__measurements_19229.csv >> /app/public/diff/english_channel__measurements_19229.diff
[CMD] [2019-12-23 01:22:58] echo "." >> /app/public/diff/english_channel__measurements_19229.diff
[STOP] [2019-12-23 01:22:58] calculate_delta
[START] [2019-12-23 01:22:58] parse_diff_and_store
[INFO] [2019-12-23 01:22:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 01:22:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 01:23:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 01:23:03] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 01:23:28] Storing 2 References
[INFO] [2019-12-23 01:23:28] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 01:23:28] Average Time: 0.0
[INFO] [2019-12-23 01:23:28] Total Time: 1s
[INFO] [2019-12-23 01:23:28] Storing 8449 ScientificNames
[INFO] [2019-12-23 01:23:28] Processing group of 8449 in 9 groups of 1000
[INFO] [2019-12-23 01:23:32] Average Time: 0.374
[INFO] [2019-12-23 01:23:32] Total Time: 4s
[INFO] [2019-12-23 01:23:32] last 3 / first 3: 0.73
[INFO] [2019-12-23 01:23:32] Std.Dev: 0.08944271909999159; Max: 0.49
[INFO] [2019-12-23 01:23:32] Storing 8449 Nodes
[INFO] [2019-12-23 01:23:32] Processing group of 8449 in 9 groups of 1000
[INFO] [2019-12-23 01:23:35] Average Time: 0.306
[INFO] [2019-12-23 01:23:35] Total Time: 3s
[INFO] [2019-12-23 01:23:35] last 3 / first 3: 0.76
[INFO] [2019-12-23 01:23:35] Std.Dev: 0.07071067811865475; Max: 0.37
[INFO] [2019-12-23 01:23:35] Storing 4410 Occurrences
[INFO] [2019-12-23 01:23:35] Processing group of 4410 in 5 groups of 1000
[INFO] [2019-12-23 01:23:35] Average Time: 0.104
[INFO] [2019-12-23 01:23:35] Total Time: 1s
[INFO] [2019-12-23 01:23:35] Storing 8820 TraitsReferences
[INFO] [2019-12-23 01:23:35] Processing group of 8820 in 9 groups of 1000
[INFO] [2019-12-23 01:23:36] Average Time: 0.086
[INFO] [2019-12-23 01:23:36] Total Time: 1s
[INFO] [2019-12-23 01:23:36] last 3 / first 3: 0.71
[INFO] [2019-12-23 01:23:36] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-23 01:23:36] Storing 8820 Traits
[INFO] [2019-12-23 01:23:36] Processing group of 8820 in 9 groups of 1000
[INFO] [2019-12-23 01:23:40] Average Time: 0.407
[INFO] [2019-12-23 01:23:40] Total Time: 4s
[INFO] [2019-12-23 01:23:40] last 3 / first 3: 0.75
[INFO] [2019-12-23 01:23:40] Std.Dev: 0.130384048104053; Max: 0.69
[INFO] [2019-12-23 01:23:40] Storing 8812 MetaTraits
[INFO] [2019-12-23 01:23:40] Processing group of 8812 in 9 groups of 1000
[INFO] [2019-12-23 01:23:41] Average Time: 0.139
[INFO] [2019-12-23 01:23:41] Total Time: 2s
[INFO] [2019-12-23 01:23:41] last 3 / first 3: 0.86
[INFO] [2019-12-23 01:23:41] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-12-23 01:23:41] parse_diff_and_store
[START] [2019-12-23 01:23:41] resolve_keys
[INFO] [2019-12-23 01:24:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 01:24:17] traits to occurrences...
[INFO] [2019-12-23 01:24:19] traits to nodes (through occurrences)...
[INFO] [2019-12-23 01:24:19] Traits to sex term...
[INFO] [2019-12-23 01:24:21] Traits to lifestage term...
[INFO] [2019-12-23 01:24:23] MetaTraits to traits...
[INFO] [2019-12-23 01:24:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 01:24:25] Assocs to occurrences...
[INFO] [2019-12-23 01:24:25] Assocs to nodes...
[INFO] [2019-12-23 01:24:25] Assoc to sex term...
[INFO] [2019-12-23 01:24:25] Assoc to lifestage term...
[STOP] [2019-12-23 01:24:25] resolve_keys
[START] [2019-12-23 01:24:25] hold_for_later_1
[STOP] [2019-12-23 01:24:25] hold_for_later_1
[START] [2019-12-23 01:24:25] hold_for_later_2
[STOP] [2019-12-23 01:24:25] hold_for_later_2
[START] [2019-12-23 01:24:25] resolve_missing_parents
[STOP] [2019-12-23 01:24:41] resolve_missing_parents
[START] [2019-12-23 01:24:41] rebuild_nodes
[START] [2019-12-23 01:24:41] Flattener#flatten
[START] [2019-12-23 01:24:41] Flattener#study_resource
[START] [2019-12-23 01:24:41] Flattener#build_ancestry
[STOP] [2019-12-23 01:24:41] Flattener#build_ancestry
[INFO] [2019-12-23 01:24:41] 8449 ancestry keys
[START] [2019-12-23 01:24:41] build_node_ancestors
[INFO] [2019-12-23 01:24:41] old ancestors deleted.
[STOP] [2019-12-23 01:24:45] build_node_ancestors
[START] [2019-12-23 01:24:49] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 01:24:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 01:24:50] Flattener#flatten
[STOP] [2019-12-23 01:24:50] rebuild_nodes
[START] [2019-12-23 01:24:50] resolve_missing_media_owners
[STOP] [2019-12-23 01:24:50] resolve_missing_media_owners
[START] [2019-12-23 01:24:50] sanitize_media_verbatims
[STOP] [2019-12-23 01:24:50] sanitize_media_verbatims
[START] [2019-12-23 01:24:50] queue_downloads
[STOP] [2019-12-23 01:24:50] queue_downloads
[START] [2019-12-23 01:24:50] parse_names
[WARN] [2019-12-23 01:24:50] I see 8449 names which still need to be parsed.
[STOP] [2019-12-23 01:24:57] parse_names
[START] [2019-12-23 01:24:57] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 01:24:58] denormalize_canonical_names_to_nodes
[START] [2019-12-23 01:24:58] match_nodes
[START] [2019-12-23 01:24:58] map_all_nodes_to_pages
[STOP] [2019-12-23 01:59:17] map_all_nodes_to_pages
[INFO] [2019-12-23 01:59:17] 499 Unmatched nodes (of 8449)! That's too many to output. First 10: Maxillopoda (#61867613); Metridia lucens (#61867927); Mecynoceridae (#61874160); Solidobalanus fallax (#61872692); Pedunculata (#61869709); Lepas hilli (#61875636); Tigriopus fulvus (#61873162); Euterpinidae (#61871451); Diosaccidae (#61876050); Poecilostomatoida (#61873638)
[START] [2019-12-23 01:59:17] update_nodes
[STOP] [2019-12-23 01:59:20] update_nodes
[STOP] [2019-12-23 01:59:21] match_nodes
[START] [2019-12-23 01:59:21] reindex_search
[STOP] [2019-12-23 01:59:46] reindex_search
[START] [2019-12-23 01:59:46] normalize_units
[STOP] [2019-12-23 01:59:46] normalize_units
[START] [2019-12-23 01:59:46] calculate_statistics
[STOP] [2019-12-23 01:59:47] calculate_statistics
[START] [2019-12-23 01:59:47] complete_harvest_instance
[START] [2019-12-23 01:59:47] overall_tsv_creation
[INFO] [2019-12-23 01:59:47] Processing group of 8449 in 1 batches of 10000
[INFO] [2019-12-23 02:01:13] 4410 Traits (unfiltered)...
[INFO] [2019-12-23 02:01:26] 4410 Traits (filtered)...
[INFO] [2019-12-23 02:01:26] 0 Associations (filtered)...
[INFO] [2019-12-23 02:02:13] 22042 metadata added.
[INFO] [2019-12-23 02:02:13] 0 metadata added.
[INFO] [2019-12-23 02:02:13] Average Time: 118.0
[INFO] [2019-12-23 02:02:13] Total Time: 2m27s
[STOP] [2019-12-23 02:02:13] overall_tsv_creation
[INFO] [2019-12-23 02:02:13] Done. Check your files:
[INFO] [2019-12-23 02:02:13] (8449 lines) /app/public/data/english_channel_/publish_nodes.tsv
[INFO] [2019-12-23 02:02:13] (42560 lines) /app/public/data/english_channel_/publish_node_ancestors.tsv
[INFO] [2019-12-23 02:02:13] (8449 lines) /app/public/data/english_channel_/publish_scientific_names.tsv
[INFO] [2019-12-23 02:02:13] (4411 lines) /app/public/data/english_channel_/publish_traits.tsv
[INFO] [2019-12-23 02:02:13] (22043 lines) /app/public/data/english_channel_/publish_metadata.tsv
[STOP] [2019-12-23 02:02:14] complete_harvest_instance
[START] [2019-12-23 02:02:14] completed
[STOP] [2019-12-23 02:02:14] completed
[STOP] [2019-12-23 02:02:14] logged process, took 2358.23
Latest Process

23 Dec 01:22 EXITED currently processing 0