Harvest for Aegean 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 17:33
Ancestry Built: 22 Dec 17:15
Nodes Matched: 22 Dec 17:33
Names Parsed: 22 Dec 17:15
New Models Stored: 22 Dec 17:14
Indexed: 22 Dec 17:33
Completed: 22 Dec 17:35
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 17:13:42 -0500 by logger.rb/56815
[START] [2019-12-22 17:13:42] logged process
[START] [2019-12-22 17:13:42] create_harvest_instance
[STOP] [2019-12-22 17:13:43] create_harvest_instance
[START] [2019-12-22 17:13:43] fetch_files
[STOP] [2019-12-22 17:13:43] fetch_files
[START] [2019-12-22 17:13:43] validate_each_file
[STOP] [2019-12-22 17:13:44] validate_each_file
[START] [2019-12-22 17:13:44] convert_to_csv
[CMD] [2019-12-22 17:13:44] /usr/bin/sort /app/public/converted_csv/aegean_sea_sp_l2_refs_18986.csv > /app/public/converted_csv/aegean_sea_sp_l2_refs_18986.csv_sorted
[CMD] [2019-12-22 17:13:44] /usr/bin/sort /app/public/converted_csv/aegean_sea_sp_l2_nodes_18987.csv > /app/public/converted_csv/aegean_sea_sp_l2_nodes_18987.csv_sorted
[CMD] [2019-12-22 17:13:45] /usr/bin/sort /app/public/converted_csv/aegean_sea_sp_l2_occurrences_18988.csv > /app/public/converted_csv/aegean_sea_sp_l2_occurrences_18988.csv_sorted
[CMD] [2019-12-22 17:13:46] /usr/bin/sort /app/public/converted_csv/aegean_sea_sp_l2_measurements_18989.csv > /app/public/converted_csv/aegean_sea_sp_l2_measurements_18989.csv_sorted
[STOP] [2019-12-22 17:13:46] convert_to_csv
[START] [2019-12-22 17:13:47] calculate_delta
[CMD] [2019-12-22 17:13:47] echo "0a" > /app/public/diff/aegean_sea_sp_l2_refs_18986.diff
[CMD] [2019-12-22 17:13:47] tail -n +1 /app/public/converted_csv/aegean_sea_sp_l2_refs_18986.csv >> /app/public/diff/aegean_sea_sp_l2_refs_18986.diff
[CMD] [2019-12-22 17:13:48] echo "." >> /app/public/diff/aegean_sea_sp_l2_refs_18986.diff
[CMD] [2019-12-22 17:13:48] echo "0a" > /app/public/diff/aegean_sea_sp_l2_nodes_18987.diff
[CMD] [2019-12-22 17:13:49] tail -n +1 /app/public/converted_csv/aegean_sea_sp_l2_nodes_18987.csv >> /app/public/diff/aegean_sea_sp_l2_nodes_18987.diff
[CMD] [2019-12-22 17:13:50] echo "." >> /app/public/diff/aegean_sea_sp_l2_nodes_18987.diff
[CMD] [2019-12-22 17:13:50] echo "0a" > /app/public/diff/aegean_sea_sp_l2_occurrences_18988.diff
[CMD] [2019-12-22 17:13:51] tail -n +1 /app/public/converted_csv/aegean_sea_sp_l2_occurrences_18988.csv >> /app/public/diff/aegean_sea_sp_l2_occurrences_18988.diff
[CMD] [2019-12-22 17:13:52] echo "." >> /app/public/diff/aegean_sea_sp_l2_occurrences_18988.diff
[CMD] [2019-12-22 17:13:52] echo "0a" > /app/public/diff/aegean_sea_sp_l2_measurements_18989.diff
[CMD] [2019-12-22 17:13:53] tail -n +1 /app/public/converted_csv/aegean_sea_sp_l2_measurements_18989.csv >> /app/public/diff/aegean_sea_sp_l2_measurements_18989.diff
[CMD] [2019-12-22 17:13:53] echo "." >> /app/public/diff/aegean_sea_sp_l2_measurements_18989.diff
[STOP] [2019-12-22 17:13:54] calculate_delta
[START] [2019-12-22 17:13:54] parse_diff_and_store
[INFO] [2019-12-22 17:13:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:55] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 17:13:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 17:14:15] Storing 2 References
[INFO] [2019-12-22 17:14:15] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 17:14:15] Average Time: 0.0
[INFO] [2019-12-22 17:14:15] Total Time: 1s
[INFO] [2019-12-22 17:14:15] Storing 5937 ScientificNames
[INFO] [2019-12-22 17:14:15] Processing group of 5937 in 6 groups of 1000
[INFO] [2019-12-22 17:14:18] Average Time: 0.622
[INFO] [2019-12-22 17:14:18] Total Time: 4s
[INFO] [2019-12-22 17:14:18] Storing 5937 Nodes
[INFO] [2019-12-22 17:14:18] Processing group of 5937 in 6 groups of 1000
[INFO] [2019-12-22 17:14:20] Average Time: 0.318
[INFO] [2019-12-22 17:14:20] Total Time: 2s
[INFO] [2019-12-22 17:14:20] Storing 3104 Occurrences
[INFO] [2019-12-22 17:14:20] Processing group of 3104 in 4 groups of 1000
[INFO] [2019-12-22 17:14:21] Average Time: 0.095
[INFO] [2019-12-22 17:14:21] Total Time: 1s
[INFO] [2019-12-22 17:14:21] Storing 6208 TraitsReferences
[INFO] [2019-12-22 17:14:21] Processing group of 6208 in 7 groups of 1000
[INFO] [2019-12-22 17:14:21] Average Time: 0.07
[INFO] [2019-12-22 17:14:21] Total Time: 1s
[INFO] [2019-12-22 17:14:21] last 3 / first 3: 0.73
[INFO] [2019-12-22 17:14:21] Std.Dev: 0.03162277660168379; Max: 0.11
[INFO] [2019-12-22 17:14:21] Storing 6208 Traits
[INFO] [2019-12-22 17:14:21] Processing group of 6208 in 7 groups of 1000
[INFO] [2019-12-22 17:14:24] Average Time: 0.363
[INFO] [2019-12-22 17:14:24] Total Time: 3s
[INFO] [2019-12-22 17:14:24] last 3 / first 3: 0.76
[INFO] [2019-12-22 17:14:24] Std.Dev: 0.17029386365926402; Max: 0.57
[INFO] [2019-12-22 17:14:24] Storing 6207 MetaTraits
[INFO] [2019-12-22 17:14:24] Processing group of 6207 in 7 groups of 1000
[INFO] [2019-12-22 17:14:25] Average Time: 0.14
[INFO] [2019-12-22 17:14:25] Total Time: 2s
[INFO] [2019-12-22 17:14:25] last 3 / first 3: 0.65
[INFO] [2019-12-22 17:14:25] Std.Dev: 0.05477225575051661; Max: 0.22
[STOP] [2019-12-22 17:14:25] parse_diff_and_store
[START] [2019-12-22 17:14:25] resolve_keys
[INFO] [2019-12-22 17:14:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 17:14:55] traits to occurrences...
[INFO] [2019-12-22 17:14:57] traits to nodes (through occurrences)...
[INFO] [2019-12-22 17:14:57] Traits to sex term...
[INFO] [2019-12-22 17:14:58] Traits to lifestage term...
[INFO] [2019-12-22 17:14:59] MetaTraits to traits...
[INFO] [2019-12-22 17:15:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 17:15:01] Assocs to occurrences...
[INFO] [2019-12-22 17:15:01] Assocs to nodes...
[INFO] [2019-12-22 17:15:01] Assoc to sex term...
[INFO] [2019-12-22 17:15:01] Assoc to lifestage term...
[STOP] [2019-12-22 17:15:01] resolve_keys
[START] [2019-12-22 17:15:01] hold_for_later_1
[STOP] [2019-12-22 17:15:01] hold_for_later_1
[START] [2019-12-22 17:15:01] hold_for_later_2
[STOP] [2019-12-22 17:15:01] hold_for_later_2
[START] [2019-12-22 17:15:01] resolve_missing_parents
[STOP] [2019-12-22 17:15:13] resolve_missing_parents
[START] [2019-12-22 17:15:13] rebuild_nodes
[START] [2019-12-22 17:15:13] Flattener#flatten
[START] [2019-12-22 17:15:13] Flattener#study_resource
[START] [2019-12-22 17:15:13] Flattener#build_ancestry
[STOP] [2019-12-22 17:15:13] Flattener#build_ancestry
[INFO] [2019-12-22 17:15:13] 5937 ancestry keys
[START] [2019-12-22 17:15:13] build_node_ancestors
[INFO] [2019-12-22 17:15:13] old ancestors deleted.
[STOP] [2019-12-22 17:15:15] build_node_ancestors
[START] [2019-12-22 17:15:18] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:15:19] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:15:19] Flattener#flatten
[STOP] [2019-12-22 17:15:19] rebuild_nodes
[START] [2019-12-22 17:15:19] resolve_missing_media_owners
[STOP] [2019-12-22 17:15:19] resolve_missing_media_owners
[START] [2019-12-22 17:15:19] sanitize_media_verbatims
[STOP] [2019-12-22 17:15:19] sanitize_media_verbatims
[START] [2019-12-22 17:15:19] queue_downloads
[STOP] [2019-12-22 17:15:19] queue_downloads
[START] [2019-12-22 17:15:19] parse_names
[WARN] [2019-12-22 17:15:19] I see 5937 names which still need to be parsed.
[STOP] [2019-12-22 17:15:25] parse_names
[START] [2019-12-22 17:15:25] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 17:15:25] denormalize_canonical_names_to_nodes
[START] [2019-12-22 17:15:25] match_nodes
[START] [2019-12-22 17:15:25] map_all_nodes_to_pages
[STOP] [2019-12-22 17:33:18] map_all_nodes_to_pages
[INFO] [2019-12-22 17:33:18] 278 Unmatched nodes (of 5937)! That's too many to output. First 10: Granuloreticulosea (#61651572); Globigerinoides sacculifer (#61651722); Globigerinoides triloba (#61652285); Globigerinoides trilobus (#61652295); Globigerina digitata (#61651881); Globigerina calida (#61653150); Globoturborotalita tenella (#61651751); Globigerinella aequilateralis (#61652421); Globorotalia inflata (#61651752); Dentagloborotalia (#61654193)
[START] [2019-12-22 17:33:18] update_nodes
[STOP] [2019-12-22 17:33:21] update_nodes
[STOP] [2019-12-22 17:33:21] match_nodes
[START] [2019-12-22 17:33:21] reindex_search
[STOP] [2019-12-22 17:33:35] reindex_search
[START] [2019-12-22 17:33:35] normalize_units
[STOP] [2019-12-22 17:33:35] normalize_units
[START] [2019-12-22 17:33:35] calculate_statistics
[STOP] [2019-12-22 17:33:35] calculate_statistics
[START] [2019-12-22 17:33:35] complete_harvest_instance
[START] [2019-12-22 17:33:35] overall_tsv_creation
[INFO] [2019-12-22 17:33:35] Processing group of 5937 in 1 batches of 10000
[INFO] [2019-12-22 17:34:52] 3104 Traits (unfiltered)...
[INFO] [2019-12-22 17:35:05] 3104 Traits (filtered)...
[INFO] [2019-12-22 17:35:05] 0 Associations (filtered)...
[INFO] [2019-12-22 17:35:49] 15519 metadata added.
[INFO] [2019-12-22 17:35:49] 0 metadata added.
[INFO] [2019-12-22 17:35:50] Average Time: 104.27
[INFO] [2019-12-22 17:35:50] Total Time: 2m15s
[STOP] [2019-12-22 17:35:50] overall_tsv_creation
[INFO] [2019-12-22 17:35:50] Done. Check your files:
[INFO] [2019-12-22 17:35:50] (5937 lines) /app/public/data/aegean_sea_sp_l2/publish_nodes.tsv
[INFO] [2019-12-22 17:35:51] (30032 lines) /app/public/data/aegean_sea_sp_l2/publish_node_ancestors.tsv
[INFO] [2019-12-22 17:35:52] (5937 lines) /app/public/data/aegean_sea_sp_l2/publish_scientific_names.tsv
[INFO] [2019-12-22 17:35:52] (3105 lines) /app/public/data/aegean_sea_sp_l2/publish_traits.tsv
[INFO] [2019-12-22 17:35:53] (15520 lines) /app/public/data/aegean_sea_sp_l2/publish_metadata.tsv
[STOP] [2019-12-22 17:35:53] complete_harvest_instance
[START] [2019-12-22 17:35:53] completed
[STOP] [2019-12-22 17:35:53] completed
[STOP] [2019-12-22 17:35:53] logged process, took 1330.79

Latest Process