Harvest for Ghana Species List Created 13 Oct 04:09

Stage: completed
Fetched: 13 Oct 04:09
Validated: 13 Oct 04:09
Deltas Created 13 Oct 04:09
Units Normalized: 13 Oct 04:23
Ancestry Built: 13 Oct 04:12
Nodes Matched: 13 Oct 04:23
Names Parsed: 13 Oct 04:12
New Models Stored: 13 Oct 04:11
Indexed: 13 Oct 04:23
Completed: 13 Oct 04:27
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-13 04:09:48 -0400 by logger.rb/56815
[START] [2019-10-13 04:09:48] logged process
[START] [2019-10-13 04:09:48] create_harvest_instance
[STOP] [2019-10-13 04:09:48] create_harvest_instance
[START] [2019-10-13 04:09:48] fetch_files
[STOP] [2019-10-13 04:09:48] fetch_files
[START] [2019-10-13 04:09:48] validate_each_file
[STOP] [2019-10-13 04:09:52] validate_each_file
[START] [2019-10-13 04:09:52] convert_to_csv
[CMD] [2019-10-13 04:09:52] /usr/bin/sort /app/public/converted_csv/ghana_sp_list_refs_15843.csv > /app/public/converted_csv/ghana_sp_list_refs_15843.csv_sorted
[CMD] [2019-10-13 04:09:52] /usr/bin/sort /app/public/converted_csv/ghana_sp_list_nodes_15844.csv > /app/public/converted_csv/ghana_sp_list_nodes_15844.csv_sorted
[CMD] [2019-10-13 04:09:52] /usr/bin/sort /app/public/converted_csv/ghana_sp_list_occurrences_15845.csv > /app/public/converted_csv/ghana_sp_list_occurrences_15845.csv_sorted
[CMD] [2019-10-13 04:09:52] /usr/bin/sort /app/public/converted_csv/ghana_sp_list_measurements_15846.csv > /app/public/converted_csv/ghana_sp_list_measurements_15846.csv_sorted
[STOP] [2019-10-13 04:09:52] convert_to_csv
[START] [2019-10-13 04:09:52] calculate_delta
[CMD] [2019-10-13 04:09:52] echo "0a" > /app/public/diff/ghana_sp_list_refs_15843.diff
[CMD] [2019-10-13 04:09:52] tail -n +1 /app/public/converted_csv/ghana_sp_list_refs_15843.csv >> /app/public/diff/ghana_sp_list_refs_15843.diff
[CMD] [2019-10-13 04:09:52] echo "." >> /app/public/diff/ghana_sp_list_refs_15843.diff
[CMD] [2019-10-13 04:09:52] echo "0a" > /app/public/diff/ghana_sp_list_nodes_15844.diff
[CMD] [2019-10-13 04:09:53] tail -n +1 /app/public/converted_csv/ghana_sp_list_nodes_15844.csv >> /app/public/diff/ghana_sp_list_nodes_15844.diff
[CMD] [2019-10-13 04:09:53] echo "." >> /app/public/diff/ghana_sp_list_nodes_15844.diff
[CMD] [2019-10-13 04:09:53] echo "0a" > /app/public/diff/ghana_sp_list_occurrences_15845.diff
[CMD] [2019-10-13 04:09:53] tail -n +1 /app/public/converted_csv/ghana_sp_list_occurrences_15845.csv >> /app/public/diff/ghana_sp_list_occurrences_15845.diff
[CMD] [2019-10-13 04:09:53] echo "." >> /app/public/diff/ghana_sp_list_occurrences_15845.diff
[CMD] [2019-10-13 04:09:53] echo "0a" > /app/public/diff/ghana_sp_list_measurements_15846.diff
[CMD] [2019-10-13 04:09:53] tail -n +1 /app/public/converted_csv/ghana_sp_list_measurements_15846.csv >> /app/public/diff/ghana_sp_list_measurements_15846.diff
[CMD] [2019-10-13 04:09:53] echo "." >> /app/public/diff/ghana_sp_list_measurements_15846.diff
[STOP] [2019-10-13 04:09:53] calculate_delta
[START] [2019-10-13 04:09:53] parse_diff_and_store
[INFO] [2019-10-13 04:09:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 04:09:54] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 04:09:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 04:10:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 04:10:46] Storing 2 References
[INFO] [2019-10-13 04:10:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 04:10:46] Average Time: 0.0
[INFO] [2019-10-13 04:10:46] Total Time: 1s
[INFO] [2019-10-13 04:10:46] Storing 12366 ScientificNames
[INFO] [2019-10-13 04:10:46] Processing group of 12366 in 13 groups of 1000
[INFO] [2019-10-13 04:10:51] Average Time: 0.381
[INFO] [2019-10-13 04:10:51] Total Time: 6s
[INFO] [2019-10-13 04:10:51] last 3 / first 3: 1.04
[INFO] [2019-10-13 04:10:51] Std.Dev: 0.06324555320336758; Max: 0.56
[INFO] [2019-10-13 04:10:51] Storing 12366 Nodes
[INFO] [2019-10-13 04:10:51] Processing group of 12366 in 13 groups of 1000
[INFO] [2019-10-13 04:10:56] Average Time: 0.337
[INFO] [2019-10-13 04:10:56] Total Time: 5s
[INFO] [2019-10-13 04:10:56] last 3 / first 3: 0.42
[INFO] [2019-10-13 04:10:56] Std.Dev: 0.18439088914585774; Max: 0.91
[INFO] [2019-10-13 04:10:56] Storing 7712 Occurrences
[INFO] [2019-10-13 04:10:56] Processing group of 7712 in 8 groups of 1000
[INFO] [2019-10-13 04:10:57] Average Time: 0.101
[INFO] [2019-10-13 04:10:57] Total Time: 1s
[INFO] [2019-10-13 04:10:57] last 3 / first 3: 0.81
[INFO] [2019-10-13 04:10:57] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-13 04:10:57] Storing 16200 TraitsReferences
[INFO] [2019-10-13 04:10:57] Processing group of 16200 in 17 groups of 1000
[INFO] [2019-10-13 04:10:58] Average Time: 0.072
[INFO] [2019-10-13 04:10:58] Total Time: 2s
[INFO] [2019-10-13 04:10:58] last 3 / first 3: 0.54
[INFO] [2019-10-13 04:10:58] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-13 04:10:58] Storing 16199 Traits
[INFO] [2019-10-13 04:10:58] Processing group of 16199 in 17 groups of 1000
[INFO] [2019-10-13 04:11:03] Average Time: 0.309
[INFO] [2019-10-13 04:11:03] Total Time: 6s
[INFO] [2019-10-13 04:11:03] last 3 / first 3: 0.65
[INFO] [2019-10-13 04:11:03] Std.Dev: 0.07745966692414834; Max: 0.46
[INFO] [2019-10-13 04:11:03] Storing 16192 MetaTraits
[INFO] [2019-10-13 04:11:03] Processing group of 16192 in 17 groups of 1000
[INFO] [2019-10-13 04:11:06] Average Time: 0.131
[INFO] [2019-10-13 04:11:06] Total Time: 3s
[INFO] [2019-10-13 04:11:06] last 3 / first 3: 0.74
[INFO] [2019-10-13 04:11:06] Std.Dev: 0.03162277660168379; Max: 0.16
[STOP] [2019-10-13 04:11:06] parse_diff_and_store
[START] [2019-10-13 04:11:06] resolve_keys
[INFO] [2019-10-13 04:11:51] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 04:11:55] traits to occurrences...
[INFO] [2019-10-13 04:12:00] traits to nodes (through occurrences)...
[INFO] [2019-10-13 04:12:01] Traits to sex term...
[INFO] [2019-10-13 04:12:05] Traits to lifestage term...
[INFO] [2019-10-13 04:12:10] MetaTraits to traits...
[INFO] [2019-10-13 04:12:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 04:12:13] Assocs to occurrences...
[INFO] [2019-10-13 04:12:13] Assocs to nodes...
[INFO] [2019-10-13 04:12:13] Assoc to sex term...
[INFO] [2019-10-13 04:12:13] Assoc to lifestage term...
[STOP] [2019-10-13 04:12:13] resolve_keys
[START] [2019-10-13 04:12:13] hold_for_later_1
[STOP] [2019-10-13 04:12:13] hold_for_later_1
[START] [2019-10-13 04:12:13] hold_for_later_2
[STOP] [2019-10-13 04:12:13] hold_for_later_2
[START] [2019-10-13 04:12:13] resolve_missing_parents
[STOP] [2019-10-13 04:12:37] resolve_missing_parents
[START] [2019-10-13 04:12:37] rebuild_nodes
[START] [2019-10-13 04:12:37] Flattener#flatten
[START] [2019-10-13 04:12:37] Flattener#study_resource
[START] [2019-10-13 04:12:37] Flattener#build_ancestry
[STOP] [2019-10-13 04:12:38] Flattener#build_ancestry
[INFO] [2019-10-13 04:12:38] 12366 ancestry keys
[START] [2019-10-13 04:12:38] build_node_ancestors
[INFO] [2019-10-13 04:12:38] old ancestors deleted.
[STOP] [2019-10-13 04:12:40] build_node_ancestors
[START] [2019-10-13 04:12:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:12:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 04:12:43] Flattener#flatten
[STOP] [2019-10-13 04:12:43] rebuild_nodes
[START] [2019-10-13 04:12:43] resolve_missing_media_owners
[STOP] [2019-10-13 04:12:43] resolve_missing_media_owners
[START] [2019-10-13 04:12:43] sanitize_media_verbatims
[STOP] [2019-10-13 04:12:43] sanitize_media_verbatims
[START] [2019-10-13 04:12:43] queue_downloads
[STOP] [2019-10-13 04:12:43] queue_downloads
[START] [2019-10-13 04:12:43] parse_names
[WARN] [2019-10-13 04:12:43] I see 12366 names which still need to be parsed.
[STOP] [2019-10-13 04:12:54] parse_names
[START] [2019-10-13 04:12:54] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 04:12:54] denormalize_canonical_names_to_nodes
[START] [2019-10-13 04:12:54] match_nodes
[START] [2019-10-13 04:12:54] map_all_nodes_to_pages
[STOP] [2019-10-13 04:22:56] map_all_nodes_to_pages
[INFO] [2019-10-13 04:22:56] 716 Unmatched nodes (of 12366)! That's too many to output. First 10: Tadarida leucogaster (#49881464); Tadarida brachyptera (#49890685); Bleda canicapilla (#49884213); Bleda syndactyla (#49884976); Bleda eximia (#49886412); Andropadus virens (#49883317); Andropadus latirostris (#49886760); Andropadus curvirostris (#49887068); Andropadus gracilirostris (#49888229); Andropadus gracilis (#49890322)
[START] [2019-10-13 04:22:56] update_nodes
[STOP] [2019-10-13 04:23:01] update_nodes
[STOP] [2019-10-13 04:23:01] match_nodes
[START] [2019-10-13 04:23:01] reindex_search
[STOP] [2019-10-13 04:23:28] reindex_search
[START] [2019-10-13 04:23:28] normalize_units
[STOP] [2019-10-13 04:23:28] normalize_units
[START] [2019-10-13 04:23:28] calculate_statistics
[STOP] [2019-10-13 04:23:28] calculate_statistics
[START] [2019-10-13 04:23:28] complete_harvest_instance
[START] [2019-10-13 04:23:28] overall_tsv_creation
[INFO] [2019-10-13 04:23:28] Processing group of 12366 in 2 batches of 10000
[INFO] [2019-10-13 04:24:59] 6382 Traits (unfiltered)...
[INFO] [2019-10-13 04:25:13] 6382 Traits (filtered)...
[INFO] [2019-10-13 04:25:13] 0 Associations (filtered)...
[INFO] [2019-10-13 04:26:04] 31902 metadata added.
[INFO] [2019-10-13 04:26:04] 0 metadata added.
[INFO] [2019-10-13 04:26:58] 1330 Traits (unfiltered)...
[INFO] [2019-10-13 04:27:12] 1330 Traits (filtered)...
[INFO] [2019-10-13 04:27:12] 0 Associations (filtered)...
[INFO] [2019-10-13 04:27:54] 6650 metadata added.
[INFO] [2019-10-13 04:27:54] 0 metadata added.
[INFO] [2019-10-13 04:27:54] Average Time: 108.005
[INFO] [2019-10-13 04:27:54] Total Time: 4m26s
[STOP] [2019-10-13 04:27:54] overall_tsv_creation
[INFO] [2019-10-13 04:27:54] Done. Check your files:
[INFO] [2019-10-13 04:27:54] (12366 lines) /app/public/data/ghana_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 04:27:54] (31217 lines) /app/public/data/ghana_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 04:27:54] (12366 lines) /app/public/data/ghana_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 04:27:54] (7713 lines) /app/public/data/ghana_sp_list/publish_traits.tsv
[INFO] [2019-10-13 04:27:54] (38553 lines) /app/public/data/ghana_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 04:27:55] complete_harvest_instance
[START] [2019-10-13 04:27:55] completed
[STOP] [2019-10-13 04:27:55] completed
[STOP] [2019-10-13 04:27:55] logged process, took 1086.96
Latest Process

13 Oct 04:09 EXITED currently processing 0