Harvest for Croatia Species List Created 12 Oct 12:09

Stage: completed
Fetched: 12 Oct 12:09
Validated: 12 Oct 12:09
Deltas Created 12 Oct 12:09
Units Normalized: 12 Oct 12:19
Ancestry Built: 12 Oct 12:12
Nodes Matched: 12 Oct 12:19
Names Parsed: 12 Oct 12:12
New Models Stored: 12 Oct 12:10
Indexed: 12 Oct 12:19
Completed: 12 Oct 12:22
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-12 12:09:50 -0400 by logger.rb/56815
[START] [2019-10-12 12:09:50] logged process
[START] [2019-10-12 12:09:50] create_harvest_instance
[STOP] [2019-10-12 12:09:50] create_harvest_instance
[START] [2019-10-12 12:09:50] fetch_files
[STOP] [2019-10-12 12:09:50] fetch_files
[START] [2019-10-12 12:09:50] validate_each_file
[STOP] [2019-10-12 12:09:52] validate_each_file
[START] [2019-10-12 12:09:52] convert_to_csv
[CMD] [2019-10-12 12:09:52] /usr/bin/sort /app/public/converted_csv/croatia_sp_list_refs_15531.csv > /app/public/converted_csv/croatia_sp_list_refs_15531.csv_sorted
[CMD] [2019-10-12 12:09:52] /usr/bin/sort /app/public/converted_csv/croatia_sp_list_nodes_15532.csv > /app/public/converted_csv/croatia_sp_list_nodes_15532.csv_sorted
[CMD] [2019-10-12 12:09:52] /usr/bin/sort /app/public/converted_csv/croatia_sp_list_occurrences_15533.csv > /app/public/converted_csv/croatia_sp_list_occurrences_15533.csv_sorted
[CMD] [2019-10-12 12:09:52] /usr/bin/sort /app/public/converted_csv/croatia_sp_list_measurements_15534.csv > /app/public/converted_csv/croatia_sp_list_measurements_15534.csv_sorted
[STOP] [2019-10-12 12:09:52] convert_to_csv
[START] [2019-10-12 12:09:52] calculate_delta
[CMD] [2019-10-12 12:09:52] echo "0a" > /app/public/diff/croatia_sp_list_refs_15531.diff
[CMD] [2019-10-12 12:09:52] tail -n +1 /app/public/converted_csv/croatia_sp_list_refs_15531.csv >> /app/public/diff/croatia_sp_list_refs_15531.diff
[CMD] [2019-10-12 12:09:52] echo "." >> /app/public/diff/croatia_sp_list_refs_15531.diff
[CMD] [2019-10-12 12:09:52] echo "0a" > /app/public/diff/croatia_sp_list_nodes_15532.diff
[CMD] [2019-10-12 12:09:52] tail -n +1 /app/public/converted_csv/croatia_sp_list_nodes_15532.csv >> /app/public/diff/croatia_sp_list_nodes_15532.diff
[CMD] [2019-10-12 12:09:52] echo "." >> /app/public/diff/croatia_sp_list_nodes_15532.diff
[CMD] [2019-10-12 12:09:53] echo "0a" > /app/public/diff/croatia_sp_list_occurrences_15533.diff
[CMD] [2019-10-12 12:09:53] tail -n +1 /app/public/converted_csv/croatia_sp_list_occurrences_15533.csv >> /app/public/diff/croatia_sp_list_occurrences_15533.diff
[CMD] [2019-10-12 12:09:53] echo "." >> /app/public/diff/croatia_sp_list_occurrences_15533.diff
[CMD] [2019-10-12 12:09:53] echo "0a" > /app/public/diff/croatia_sp_list_measurements_15534.diff
[CMD] [2019-10-12 12:09:53] tail -n +1 /app/public/converted_csv/croatia_sp_list_measurements_15534.csv >> /app/public/diff/croatia_sp_list_measurements_15534.diff
[CMD] [2019-10-12 12:09:53] echo "." >> /app/public/diff/croatia_sp_list_measurements_15534.diff
[STOP] [2019-10-12 12:09:53] calculate_delta
[START] [2019-10-12 12:09:53] parse_diff_and_store
[INFO] [2019-10-12 12:09:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 12:09:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 12:09:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 12:09:58] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 12:10:31] Storing 2 References
[INFO] [2019-10-12 12:10:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 12:10:31] Average Time: 0.0
[INFO] [2019-10-12 12:10:31] Total Time: 1s
[INFO] [2019-10-12 12:10:31] Storing 9710 ScientificNames
[INFO] [2019-10-12 12:10:31] Processing group of 9710 in 10 groups of 1000
[INFO] [2019-10-12 12:10:35] Average Time: 0.397
[INFO] [2019-10-12 12:10:35] Total Time: 5s
[INFO] [2019-10-12 12:10:35] last 3 / first 3: 1.11
[INFO] [2019-10-12 12:10:35] Std.Dev: 0.09486832980505137; Max: 0.64
[INFO] [2019-10-12 12:10:35] Storing 9710 Nodes
[INFO] [2019-10-12 12:10:35] Processing group of 9710 in 10 groups of 1000
[INFO] [2019-10-12 12:10:38] Average Time: 0.287
[INFO] [2019-10-12 12:10:38] Total Time: 3s
[INFO] [2019-10-12 12:10:38] last 3 / first 3: 0.84
[INFO] [2019-10-12 12:10:38] Std.Dev: 0.03162277660168379; Max: 0.33
[INFO] [2019-10-12 12:10:38] Storing 5302 Occurrences
[INFO] [2019-10-12 12:10:38] Processing group of 5302 in 6 groups of 1000
[INFO] [2019-10-12 12:10:38] Average Time: 0.1
[INFO] [2019-10-12 12:10:38] Total Time: 1s
[INFO] [2019-10-12 12:10:38] Storing 10854 TraitsReferences
[INFO] [2019-10-12 12:10:38] Processing group of 10854 in 11 groups of 1000
[INFO] [2019-10-12 12:10:39] Average Time: 0.076
[INFO] [2019-10-12 12:10:39] Total Time: 1s
[INFO] [2019-10-12 12:10:39] last 3 / first 3: 0.69
[INFO] [2019-10-12 12:10:39] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-12 12:10:39] Storing 10853 Traits
[INFO] [2019-10-12 12:10:39] Processing group of 10853 in 11 groups of 1000
[INFO] [2019-10-12 12:10:43] Average Time: 0.313
[INFO] [2019-10-12 12:10:43] Total Time: 4s
[INFO] [2019-10-12 12:10:43] last 3 / first 3: 0.82
[INFO] [2019-10-12 12:10:43] Std.Dev: 0.05477225575051661; Max: 0.45
[INFO] [2019-10-12 12:10:43] Storing 10847 MetaTraits
[INFO] [2019-10-12 12:10:43] Processing group of 10847 in 11 groups of 1000
[INFO] [2019-10-12 12:10:44] Average Time: 0.134
[INFO] [2019-10-12 12:10:44] Total Time: 2s
[INFO] [2019-10-12 12:10:44] last 3 / first 3: 0.95
[INFO] [2019-10-12 12:10:44] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-10-12 12:10:44] parse_diff_and_store
[START] [2019-10-12 12:10:44] resolve_keys
[INFO] [2019-10-12 12:11:24] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 12:11:27] traits to occurrences...
[INFO] [2019-10-12 12:11:29] traits to nodes (through occurrences)...
[INFO] [2019-10-12 12:11:29] Traits to sex term...
[INFO] [2019-10-12 12:11:31] Traits to lifestage term...
[INFO] [2019-10-12 12:11:33] MetaTraits to traits...
[INFO] [2019-10-12 12:11:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 12:11:36] Assocs to occurrences...
[INFO] [2019-10-12 12:11:36] Assocs to nodes...
[INFO] [2019-10-12 12:11:36] Assoc to sex term...
[INFO] [2019-10-12 12:11:36] Assoc to lifestage term...
[STOP] [2019-10-12 12:11:36] resolve_keys
[START] [2019-10-12 12:11:36] hold_for_later_1
[STOP] [2019-10-12 12:11:36] hold_for_later_1
[START] [2019-10-12 12:11:36] hold_for_later_2
[STOP] [2019-10-12 12:11:36] hold_for_later_2
[START] [2019-10-12 12:11:36] resolve_missing_parents
[STOP] [2019-10-12 12:11:55] resolve_missing_parents
[START] [2019-10-12 12:11:55] rebuild_nodes
[START] [2019-10-12 12:11:55] Flattener#flatten
[START] [2019-10-12 12:11:55] Flattener#study_resource
[START] [2019-10-12 12:11:55] Flattener#build_ancestry
[STOP] [2019-10-12 12:11:56] Flattener#build_ancestry
[INFO] [2019-10-12 12:11:56] 9710 ancestry keys
[START] [2019-10-12 12:11:56] build_node_ancestors
[INFO] [2019-10-12 12:11:56] old ancestors deleted.
[STOP] [2019-10-12 12:11:58] build_node_ancestors
[START] [2019-10-12 12:11:59] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:12:00] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:12:00] Flattener#flatten
[STOP] [2019-10-12 12:12:00] rebuild_nodes
[START] [2019-10-12 12:12:00] resolve_missing_media_owners
[STOP] [2019-10-12 12:12:00] resolve_missing_media_owners
[START] [2019-10-12 12:12:00] sanitize_media_verbatims
[STOP] [2019-10-12 12:12:00] sanitize_media_verbatims
[START] [2019-10-12 12:12:00] queue_downloads
[STOP] [2019-10-12 12:12:00] queue_downloads
[START] [2019-10-12 12:12:00] parse_names
[WARN] [2019-10-12 12:12:00] I see 9710 names which still need to be parsed.
[STOP] [2019-10-12 12:12:08] parse_names
[START] [2019-10-12 12:12:08] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 12:12:08] denormalize_canonical_names_to_nodes
[START] [2019-10-12 12:12:08] match_nodes
[START] [2019-10-12 12:12:08] map_all_nodes_to_pages
[STOP] [2019-10-12 12:19:28] map_all_nodes_to_pages
[INFO] [2019-10-12 12:19:28] 863 Unmatched nodes (of 9710)! That's too many to output. First 10: Clethrionomys (#49364034); Ctenophthalmidae (#49361224); Homo neanderthalensis (#49360973); Larus melanocephalus (#49368799); Thalaseus (#49363647); Thalaseus sandvicensis (#49363646); Philomachus pugnax (#49361914); Hirundo rupestris (#49362785); Delichon urbica (#49361620); Corvus monedula (#49361905)
[START] [2019-10-12 12:19:28] update_nodes
[STOP] [2019-10-12 12:19:31] update_nodes
[STOP] [2019-10-12 12:19:31] match_nodes
[START] [2019-10-12 12:19:31] reindex_search
[STOP] [2019-10-12 12:19:52] reindex_search
[START] [2019-10-12 12:19:52] normalize_units
[STOP] [2019-10-12 12:19:52] normalize_units
[START] [2019-10-12 12:19:52] calculate_statistics
[STOP] [2019-10-12 12:19:52] calculate_statistics
[START] [2019-10-12 12:19:52] complete_harvest_instance
[START] [2019-10-12 12:19:52] overall_tsv_creation
[INFO] [2019-10-12 12:19:52] Processing group of 9710 in 1 batches of 10000
[INFO] [2019-10-12 12:21:19] 5302 Traits (unfiltered)...
[INFO] [2019-10-12 12:21:33] 5302 Traits (filtered)...
[INFO] [2019-10-12 12:21:33] 0 Associations (filtered)...
[INFO] [2019-10-12 12:22:21] 26504 metadata added.
[INFO] [2019-10-12 12:22:21] 0 metadata added.
[INFO] [2019-10-12 12:22:21] Average Time: 121.77
[INFO] [2019-10-12 12:22:21] Total Time: 2m29s
[STOP] [2019-10-12 12:22:21] overall_tsv_creation
[INFO] [2019-10-12 12:22:21] Done. Check your files:
[INFO] [2019-10-12 12:22:21] (9710 lines) /app/public/data/croatia_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 12:22:21] (22408 lines) /app/public/data/croatia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 12:22:21] (9710 lines) /app/public/data/croatia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 12:22:21] (5303 lines) /app/public/data/croatia_sp_list/publish_traits.tsv
[INFO] [2019-10-12 12:22:21] (26505 lines) /app/public/data/croatia_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 12:22:21] complete_harvest_instance
[START] [2019-10-12 12:22:21] completed
[STOP] [2019-10-12 12:22:21] completed
[STOP] [2019-10-12 12:22:21] logged process, took 751.58
Latest Process

12 Oct 12:09 EXITED currently processing 0