Harvest for Adriatic Sea Species List Created 22 Dec 17:13

Stage: completed
Fetched: 22 Dec 17:13
Validated: 22 Dec 17:13
Deltas Created 22 Dec 17:13
Units Normalized: 22 Dec 17:29
Ancestry Built: 22 Dec 17:14
Nodes Matched: 22 Dec 17:29
Names Parsed: 22 Dec 17:14
New Models Stored: 22 Dec 17:13
Indexed: 22 Dec 17:29
Completed: 22 Dec 17:32
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 17:13:30 -0500 by logger.rb/56815
[START] [2019-12-22 17:13:30] logged process
[START] [2019-12-22 17:13:30] create_harvest_instance
[STOP] [2019-12-22 17:13:32] create_harvest_instance
[START] [2019-12-22 17:13:32] fetch_files
[STOP] [2019-12-22 17:13:32] fetch_files
[START] [2019-12-22 17:13:32] validate_each_file
[STOP] [2019-12-22 17:13:32] validate_each_file
[START] [2019-12-22 17:13:32] convert_to_csv
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv > /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv > /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv > /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv_sorted
[CMD] [2019-12-22 17:13:32] /usr/bin/sort /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv > /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv_sorted
[STOP] [2019-12-22 17:13:32] convert_to_csv
[START] [2019-12-22 17:13:32] calculate_delta
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_refs_18978.csv >> /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_refs_18978.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_nodes_18979.csv >> /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_nodes_18979.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_occurrences_18980.csv >> /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_occurrences_18980.diff
[CMD] [2019-12-22 17:13:32] echo "0a" > /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[CMD] [2019-12-22 17:13:32] tail -n +1 /app/public/converted_csv/adriatic_sea_sp2_measurements_18981.csv >> /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[CMD] [2019-12-22 17:13:32] echo "." >> /app/public/diff/adriatic_sea_sp2_measurements_18981.diff
[STOP] [2019-12-22 17:13:32] calculate_delta
[START] [2019-12-22 17:13:32] parse_diff_and_store
[INFO] [2019-12-22 17:13:32] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:46] Storing 2 References
[INFO] [2019-12-22 17:13:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 17:13:46] Average Time: 0.02
[INFO] [2019-12-22 17:13:46] Total Time: 1s
[INFO] [2019-12-22 17:13:46] Storing 4442 ScientificNames
[INFO] [2019-12-22 17:13:46] Processing group of 4442 in 5 groups of 1000
[INFO] [2019-12-22 17:13:48] Average Time: 0.376
[INFO] [2019-12-22 17:13:48] Total Time: 2s
[INFO] [2019-12-22 17:13:48] Storing 4442 Nodes
[INFO] [2019-12-22 17:13:48] Processing group of 4442 in 5 groups of 1000
[INFO] [2019-12-22 17:13:49] Average Time: 0.274
[INFO] [2019-12-22 17:13:49] Total Time: 2s
[INFO] [2019-12-22 17:13:49] Storing 2173 Occurrences
[INFO] [2019-12-22 17:13:49] Processing group of 2173 in 3 groups of 1000
[INFO] [2019-12-22 17:13:50] Average Time: 0.087
[INFO] [2019-12-22 17:13:50] Total Time: 1s
[INFO] [2019-12-22 17:13:50] Storing 4346 TraitsReferences
[INFO] [2019-12-22 17:13:50] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-12-22 17:13:50] Average Time: 0.122
[INFO] [2019-12-22 17:13:50] Total Time: 1s
[INFO] [2019-12-22 17:13:50] Storing 4346 Traits
[INFO] [2019-12-22 17:13:50] Processing group of 4346 in 5 groups of 1000
[INFO] [2019-12-22 17:13:52] Average Time: 0.388
[INFO] [2019-12-22 17:13:52] Total Time: 3s
[INFO] [2019-12-22 17:13:52] Storing 4345 MetaTraits
[INFO] [2019-12-22 17:13:52] Processing group of 4345 in 5 groups of 1000
[INFO] [2019-12-22 17:13:53] Average Time: 0.17
[INFO] [2019-12-22 17:13:53] Total Time: 1s
[STOP] [2019-12-22 17:13:53] parse_diff_and_store
[START] [2019-12-22 17:13:53] resolve_keys
[INFO] [2019-12-22 17:14:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 17:14:16] traits to occurrences...
[INFO] [2019-12-22 17:14:18] traits to nodes (through occurrences)...
[INFO] [2019-12-22 17:14:18] Traits to sex term...
[INFO] [2019-12-22 17:14:19] Traits to lifestage term...
[INFO] [2019-12-22 17:14:19] MetaTraits to traits...
[INFO] [2019-12-22 17:14:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 17:14:21] Assocs to occurrences...
[INFO] [2019-12-22 17:14:21] Assocs to nodes...
[INFO] [2019-12-22 17:14:21] Assoc to sex term...
[INFO] [2019-12-22 17:14:21] Assoc to lifestage term...
[STOP] [2019-12-22 17:14:21] resolve_keys
[START] [2019-12-22 17:14:21] hold_for_later_1
[STOP] [2019-12-22 17:14:21] hold_for_later_1
[START] [2019-12-22 17:14:21] hold_for_later_2
[STOP] [2019-12-22 17:14:21] hold_for_later_2
[START] [2019-12-22 17:14:21] resolve_missing_parents
[STOP] [2019-12-22 17:14:28] resolve_missing_parents
[START] [2019-12-22 17:14:28] rebuild_nodes
[START] [2019-12-22 17:14:28] Flattener#flatten
[START] [2019-12-22 17:14:28] Flattener#study_resource
[START] [2019-12-22 17:14:28] Flattener#build_ancestry
[STOP] [2019-12-22 17:14:28] Flattener#build_ancestry
[INFO] [2019-12-22 17:14:28] 4442 ancestry keys
[START] [2019-12-22 17:14:28] build_node_ancestors
[INFO] [2019-12-22 17:14:28] old ancestors deleted.
[STOP] [2019-12-22 17:14:30] build_node_ancestors
[START] [2019-12-22 17:14:32] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:14:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:14:33] Flattener#flatten
[STOP] [2019-12-22 17:14:33] rebuild_nodes
[START] [2019-12-22 17:14:33] resolve_missing_media_owners
[STOP] [2019-12-22 17:14:33] resolve_missing_media_owners
[START] [2019-12-22 17:14:33] sanitize_media_verbatims
[STOP] [2019-12-22 17:14:33] sanitize_media_verbatims
[START] [2019-12-22 17:14:33] queue_downloads
[STOP] [2019-12-22 17:14:33] queue_downloads
[START] [2019-12-22 17:14:33] parse_names
[WARN] [2019-12-22 17:14:33] I see 4442 names which still need to be parsed.
[STOP] [2019-12-22 17:14:37] parse_names
[START] [2019-12-22 17:14:37] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 17:14:39] denormalize_canonical_names_to_nodes
[START] [2019-12-22 17:14:39] match_nodes
[START] [2019-12-22 17:14:39] map_all_nodes_to_pages
[STOP] [2019-12-22 17:29:30] map_all_nodes_to_pages
[INFO] [2019-12-22 17:29:30] 293 Unmatched nodes (of 4442)! That's too many to output. First 10: Cassidulina crassa (#61647214); Globocassidulina oblonga (#61648424); Cassidulinoides bradyi (#61647365); Elphidium albiumbilicatum (#61647689); Elphidium poeyanum (#61648276); Bolivina subspinescens (#61647377); Cibicides lobatulus (#61647263); Gyroidinoides umbonatus (#61647255); Cancris auriculus (#61650971); Bigenerina nodosaria (#61647249)
[START] [2019-12-22 17:29:30] update_nodes
[STOP] [2019-12-22 17:29:32] update_nodes
[STOP] [2019-12-22 17:29:32] match_nodes
[START] [2019-12-22 17:29:32] reindex_search
[STOP] [2019-12-22 17:29:42] reindex_search
[START] [2019-12-22 17:29:42] normalize_units
[STOP] [2019-12-22 17:29:42] normalize_units
[START] [2019-12-22 17:29:42] calculate_statistics
[STOP] [2019-12-22 17:29:42] calculate_statistics
[START] [2019-12-22 17:29:42] complete_harvest_instance
[START] [2019-12-22 17:29:42] overall_tsv_creation
[INFO] [2019-12-22 17:29:42] Processing group of 4442 in 1 batches of 10000
[INFO] [2019-12-22 17:31:05] 2173 Traits (unfiltered)...
[INFO] [2019-12-22 17:31:18] 2173 Traits (filtered)...
[INFO] [2019-12-22 17:31:18] 0 Associations (filtered)...
[INFO] [2019-12-22 17:32:01] 10864 metadata added.
[INFO] [2019-12-22 17:32:01] 0 metadata added.
[INFO] [2019-12-22 17:32:01] Average Time: 99.12
[INFO] [2019-12-22 17:32:01] Total Time: 2m19s
[STOP] [2019-12-22 17:32:01] overall_tsv_creation
[INFO] [2019-12-22 17:32:01] Done. Check your files:
[INFO] [2019-12-22 17:32:01] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_nodes.tsv
[INFO] [2019-12-22 17:32:01] (21955 lines) /app/public/data/adriatic_sea_sp2/publish_node_ancestors.tsv
[INFO] [2019-12-22 17:32:01] (4442 lines) /app/public/data/adriatic_sea_sp2/publish_scientific_names.tsv
[INFO] [2019-12-22 17:32:01] (2174 lines) /app/public/data/adriatic_sea_sp2/publish_traits.tsv
[INFO] [2019-12-22 17:32:01] (10865 lines) /app/public/data/adriatic_sea_sp2/publish_metadata.tsv
[STOP] [2019-12-22 17:32:01] complete_harvest_instance
[START] [2019-12-22 17:32:01] completed
[STOP] [2019-12-22 17:32:01] completed
[STOP] [2019-12-22 17:32:01] logged process, took 1111.28

Latest Process