Harvest for coraltraits Created 24 Mar 15:13

Stage: completed
Fetched: 24 Mar 15:13
Validated: 24 Mar 15:13
Deltas Created 24 Mar 15:13
Units Normalized: 24 Mar 15:28
Ancestry Built: 24 Mar 15:23
Nodes Matched: 24 Mar 15:26
Names Parsed: 24 Mar 15:23
New Models Stored: 24 Mar 15:23
Indexed: 24 Mar 15:26
Completed: 24 Mar 15:31
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-03-24 15:13:30 -0400 by logger.rb/56815
[INFO] [2020-03-24 15:13:30] ## HARVEST: type = -harvest
[START] [2020-03-24 15:13:30] logged process
[START] [2020-03-24 15:13:30] create_harvest_instance
[STOP] [2020-03-24 15:13:31] create_harvest_instance
[START] [2020-03-24 15:13:31] fetch_files
[STOP] [2020-03-24 15:13:31] fetch_files
[START] [2020-03-24 15:13:31] validate_each_file
[STOP] [2020-03-24 15:13:42] validate_each_file
[START] [2020-03-24 15:13:42] convert_to_csv
[CMD] [2020-03-24 15:13:42] /usr/bin/sort /app/public/converted_csv/coraltraits_tar__refs_20485.csv > /app/public/converted_csv/coraltraits_tar__refs_20485.csv_sorted
[CMD] [2020-03-24 15:13:43] /usr/bin/sort /app/public/converted_csv/coraltraits_tar__nodes_20486.csv > /app/public/converted_csv/coraltraits_tar__nodes_20486.csv_sorted
[CMD] [2020-03-24 15:13:44] /usr/bin/sort /app/public/converted_csv/coraltraits_tar__occurrences_20487.csv > /app/public/converted_csv/coraltraits_tar__occurrences_20487.csv_sorted
[CMD] [2020-03-24 15:13:44] /usr/bin/sort /app/public/converted_csv/coraltraits_tar__measurements_20488.csv > /app/public/converted_csv/coraltraits_tar__measurements_20488.csv_sorted
[STOP] [2020-03-24 15:13:45] convert_to_csv
[START] [2020-03-24 15:13:45] calculate_delta
[CMD] [2020-03-24 15:13:45] echo "0a" > /app/public/diff/coraltraits_tar__refs_20485.diff
[CMD] [2020-03-24 15:13:46] tail -n +1 /app/public/converted_csv/coraltraits_tar__refs_20485.csv >> /app/public/diff/coraltraits_tar__refs_20485.diff
[CMD] [2020-03-24 15:13:47] echo "." >> /app/public/diff/coraltraits_tar__refs_20485.diff
[CMD] [2020-03-24 15:13:47] echo "0a" > /app/public/diff/coraltraits_tar__nodes_20486.diff
[CMD] [2020-03-24 15:13:48] tail -n +1 /app/public/converted_csv/coraltraits_tar__nodes_20486.csv >> /app/public/diff/coraltraits_tar__nodes_20486.diff
[CMD] [2020-03-24 15:13:49] echo "." >> /app/public/diff/coraltraits_tar__nodes_20486.diff
[CMD] [2020-03-24 15:13:50] echo "0a" > /app/public/diff/coraltraits_tar__occurrences_20487.diff
[CMD] [2020-03-24 15:13:50] tail -n +1 /app/public/converted_csv/coraltraits_tar__occurrences_20487.csv >> /app/public/diff/coraltraits_tar__occurrences_20487.diff
[CMD] [2020-03-24 15:13:51] echo "." >> /app/public/diff/coraltraits_tar__occurrences_20487.diff
[CMD] [2020-03-24 15:13:52] echo "0a" > /app/public/diff/coraltraits_tar__measurements_20488.diff
[CMD] [2020-03-24 15:13:53] tail -n +1 /app/public/converted_csv/coraltraits_tar__measurements_20488.csv >> /app/public/diff/coraltraits_tar__measurements_20488.diff
[CMD] [2020-03-24 15:13:53] echo "." >> /app/public/diff/coraltraits_tar__measurements_20488.diff
[STOP] [2020-03-24 15:13:54] calculate_delta
[START] [2020-03-24 15:13:54] parse_diff_and_store
[INFO] [2020-03-24 15:13:55] Loading refs diff file into memory (true lines)...
[INFO] [2020-03-24 15:13:56] Loading nodes diff file into memory (true lines)...
[INFO] [2020-03-24 15:13:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-03-24 15:15:02] Loading measurements diff file into memory (true lines)...
[INFO] [2020-03-24 15:22:16] Storing 555 References
[INFO] [2020-03-24 15:22:16] Processing group of 555 in 1 groups of 1000
[INFO] [2020-03-24 15:22:16] Average Time: 0.12
[INFO] [2020-03-24 15:22:16] Total Time: 1s
[INFO] [2020-03-24 15:22:16] Storing 1551 ScientificNames
[INFO] [2020-03-24 15:22:16] Processing group of 1551 in 2 groups of 1000
[INFO] [2020-03-24 15:22:17] Average Time: 0.36
[INFO] [2020-03-24 15:22:17] Total Time: 1s
[INFO] [2020-03-24 15:22:17] Storing 1551 Nodes
[INFO] [2020-03-24 15:22:17] Processing group of 1551 in 2 groups of 1000
[INFO] [2020-03-24 15:22:17] Average Time: 0.25
[INFO] [2020-03-24 15:22:17] Total Time: 1s
[INFO] [2020-03-24 15:22:17] Storing 33475 Occurrences
[INFO] [2020-03-24 15:22:17] Processing group of 33475 in 34 groups of 1000
[INFO] [2020-03-24 15:22:21] Average Time: 0.102
[INFO] [2020-03-24 15:22:21] Total Time: 4s
[INFO] [2020-03-24 15:22:21] last 3 / first 3: 0.77
[INFO] [2020-03-24 15:22:21] Std.Dev: 0.0; Max: 0.18
[INFO] [2020-03-24 15:22:21] Storing 51859 OccurrenceMetadata
[INFO] [2020-03-24 15:22:21] Processing group of 51859 in 52 groups of 1000
[INFO] [2020-03-24 15:22:27] Average Time: 0.116
[INFO] [2020-03-24 15:22:27] Total Time: 7s
[INFO] [2020-03-24 15:22:27] last 3 / first 3: 0.71
[INFO] [2020-03-24 15:22:27] Std.Dev: 0.0; Max: 0.2
[INFO] [2020-03-24 15:22:27] Storing 42970 TraitsReferences
[INFO] [2020-03-24 15:22:27] Processing group of 42970 in 43 groups of 1000
[INFO] [2020-03-24 15:22:31] Average Time: 0.074
[INFO] [2020-03-24 15:22:31] Total Time: 4s
[INFO] [2020-03-24 15:22:31] last 3 / first 3: 0.7
[INFO] [2020-03-24 15:22:31] Std.Dev: 0.0; Max: 0.14
[INFO] [2020-03-24 15:22:31] Storing 56648 Traits
[INFO] [2020-03-24 15:22:31] Processing group of 56648 in 57 groups of 1000
[INFO] [2020-03-24 15:22:51] Average Time: 0.347
[INFO] [2020-03-24 15:22:51] Total Time: 21s
[INFO] [2020-03-24 15:22:51] last 3 / first 3: 0.75
[INFO] [2020-03-24 15:22:51] Std.Dev: 0.1224744871391589; Max: 0.9
[INFO] [2020-03-24 15:22:51] Storing 195103 MetaTraits
[INFO] [2020-03-24 15:22:51] Processing group of 195103 in 196 groups of 1000
[INFO] [2020-03-24 15:23:16] Average Time: 0.127
[INFO] [2020-03-24 15:23:16] Total Time: 26s
[INFO] [2020-03-24 15:23:16] last 3 / first 3: 1.31
[INFO] [2020-03-24 15:23:16] Std.Dev: 0.10954451150103323; Max: 1.59
[STOP] [2020-03-24 15:23:16] parse_diff_and_store
[START] [2020-03-24 15:23:16] resolve_keys
[INFO] [2020-03-24 15:23:25] Occurrences to nodes (through scientific_names)...
[INFO] [2020-03-24 15:23:27] traits to occurrences...
[INFO] [2020-03-24 15:23:30] traits to nodes (through occurrences)...
[INFO] [2020-03-24 15:23:31] Traits to sex term...
[INFO] [2020-03-24 15:23:32] Traits to lifestage term...
[INFO] [2020-03-24 15:23:32] MetaTraits to traits...
[INFO] [2020-03-24 15:23:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-03-24 15:23:51] Assocs to occurrences...
[INFO] [2020-03-24 15:23:51] Assocs to nodes...
[INFO] [2020-03-24 15:23:51] Assoc to sex term...
[INFO] [2020-03-24 15:23:51] Assoc to lifestage term...
[STOP] [2020-03-24 15:23:51] resolve_keys
[START] [2020-03-24 15:23:51] hold_for_later_1
[STOP] [2020-03-24 15:23:51] hold_for_later_1
[START] [2020-03-24 15:23:51] hold_for_later_2
[STOP] [2020-03-24 15:23:51] hold_for_later_2
[START] [2020-03-24 15:23:51] resolve_missing_parents
[STOP] [2020-03-24 15:23:52] resolve_missing_parents
[START] [2020-03-24 15:23:52] rebuild_nodes
[START] [2020-03-24 15:23:52] Flattener#flatten
[START] [2020-03-24 15:23:52] Flattener#study_resource
[START] [2020-03-24 15:23:52] Flattener#build_ancestry
[STOP] [2020-03-24 15:23:52] Flattener#build_ancestry
[INFO] [2020-03-24 15:23:52] 1551 ancestry keys
[START] [2020-03-24 15:23:52] build_node_ancestors
[INFO] [2020-03-24 15:23:52] old ancestors deleted.
[STOP] [2020-03-24 15:23:54] build_node_ancestors
[START] [2020-03-24 15:23:54] Flattener#propagate_ancestor_ids
[STOP] [2020-03-24 15:23:54] Flattener#propagate_ancestor_ids
[STOP] [2020-03-24 15:23:54] Flattener#flatten
[STOP] [2020-03-24 15:23:54] rebuild_nodes
[START] [2020-03-24 15:23:54] resolve_missing_media_owners
[STOP] [2020-03-24 15:23:54] resolve_missing_media_owners
[START] [2020-03-24 15:23:54] sanitize_media_verbatims
[STOP] [2020-03-24 15:23:54] sanitize_media_verbatims
[START] [2020-03-24 15:23:54] queue_downloads
[STOP] [2020-03-24 15:23:54] queue_downloads
[START] [2020-03-24 15:23:54] parse_names
[WARN] [2020-03-24 15:23:54] I see 1551 names which still need to be parsed.
[STOP] [2020-03-24 15:23:57] parse_names
[START] [2020-03-24 15:23:57] denormalize_canonical_names_to_nodes
[STOP] [2020-03-24 15:23:57] denormalize_canonical_names_to_nodes
[START] [2020-03-24 15:23:57] match_nodes
[START] [2020-03-24 15:23:57] map_all_nodes_to_pages
[STOP] [2020-03-24 15:26:35] map_all_nodes_to_pages
[INFO] [2020-03-24 15:26:35] 51 Unmatched nodes (of 1551)! That's too many to output. First 10: Acropora lutkeni (#67515084); Montipora granulosa (#67515093); Montipora hirsuta (#67515097); Oulangia stokesianamiltoni (#67515181); Oulangia stokesianastokesiana (#67515183); Acropora mirabilis (#67515193); Paracyathus indicusgracilis (#67515218); Paracyathus indicusindicus (#67515219); Phyllangia americanaamericana (#67515271); Phyllangia americanamouchezii (#67515272)
[START] [2020-03-24 15:26:35] update_nodes
[STOP] [2020-03-24 15:26:35] update_nodes
[STOP] [2020-03-24 15:26:35] match_nodes
[START] [2020-03-24 15:26:35] reindex_search
[STOP] [2020-03-24 15:26:40] reindex_search
[START] [2020-03-24 15:26:40] normalize_units
[STOP] [2020-03-24 15:28:13] normalize_units
[START] [2020-03-24 15:28:13] calculate_statistics
[STOP] [2020-03-24 15:28:13] calculate_statistics
[START] [2020-03-24 15:28:13] complete_harvest_instance
[START] [2020-03-24 15:28:13] overall_tsv_creation
[INFO] [2020-03-24 15:28:13] Processing group of 1551 in 1 batches of 10000
[INFO] [2020-03-24 15:29:12] 34185 Traits (unfiltered)...
[INFO] [2020-03-24 15:29:25] 34185 Traits (filtered)...
[INFO] [2020-03-24 15:29:25] 0 Associations (filtered)...
[INFO] [2020-03-24 15:31:23] 257118 metadata added.
[INFO] [2020-03-24 15:31:23] 0 metadata added.
[INFO] [2020-03-24 15:31:23] Average Time: 159.56
[INFO] [2020-03-24 15:31:23] Total Time: 3m11s
[STOP] [2020-03-24 15:31:23] overall_tsv_creation
[INFO] [2020-03-24 15:31:23] Done. Check your files:
[INFO] [2020-03-24 15:31:24] (1551 lines) /app/public/data/coraltraits_tar_/publish_nodes.tsv
[INFO] [2020-03-24 15:31:24] (6194 lines) /app/public/data/coraltraits_tar_/publish_node_ancestors.tsv
[INFO] [2020-03-24 15:31:25] (1551 lines) /app/public/data/coraltraits_tar_/publish_scientific_names.tsv
[INFO] [2020-03-24 15:31:26] (34186 lines) /app/public/data/coraltraits_tar_/publish_traits.tsv
[INFO] [2020-03-24 15:31:27] (257119 lines) /app/public/data/coraltraits_tar_/publish_metadata.tsv
[STOP] [2020-03-24 15:31:27] complete_harvest_instance
[START] [2020-03-24 15:31:27] completed
[STOP] [2020-03-24 15:31:27] completed
[STOP] [2020-03-24 15:31:27] logged process, took 1076.8

Latest Process