Harvest for Republic of the Congo Species List Created 15 Oct 14:06

Stage: completed
Fetched: 15 Oct 14:06
Validated: 15 Oct 14:06
Deltas Created 15 Oct 14:06
Units Normalized: 15 Oct 14:13
Ancestry Built: 15 Oct 14:08
Nodes Matched: 15 Oct 14:13
Names Parsed: 15 Oct 14:08
New Models Stored: 15 Oct 14:07
Indexed: 15 Oct 14:13
Completed: 15 Oct 14:15
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-15 14:06:41 -0400 by logger.rb/56815
[START] [2019-10-15 14:06:41] logged process
[START] [2019-10-15 14:06:41] create_harvest_instance
[STOP] [2019-10-15 14:06:42] create_harvest_instance
[START] [2019-10-15 14:06:42] fetch_files
[STOP] [2019-10-15 14:06:42] fetch_files
[START] [2019-10-15 14:06:42] validate_each_file
[STOP] [2019-10-15 14:06:42] validate_each_file
[START] [2019-10-15 14:06:43] convert_to_csv
[CMD] [2019-10-15 14:06:43] /usr/bin/sort /app/public/converted_csv/republic_congo_refs_16973.csv > /app/public/converted_csv/republic_congo_refs_16973.csv_sorted
[CMD] [2019-10-15 14:06:43] /usr/bin/sort /app/public/converted_csv/republic_congo_nodes_16974.csv > /app/public/converted_csv/republic_congo_nodes_16974.csv_sorted
[CMD] [2019-10-15 14:06:43] /usr/bin/sort /app/public/converted_csv/republic_congo_occurrences_16975.csv > /app/public/converted_csv/republic_congo_occurrences_16975.csv_sorted
[CMD] [2019-10-15 14:06:43] /usr/bin/sort /app/public/converted_csv/republic_congo_measurements_16976.csv > /app/public/converted_csv/republic_congo_measurements_16976.csv_sorted
[STOP] [2019-10-15 14:06:44] convert_to_csv
[START] [2019-10-15 14:06:44] calculate_delta
[CMD] [2019-10-15 14:06:44] echo "0a" > /app/public/diff/republic_congo_refs_16973.diff
[CMD] [2019-10-15 14:06:44] tail -n +1 /app/public/converted_csv/republic_congo_refs_16973.csv >> /app/public/diff/republic_congo_refs_16973.diff
[CMD] [2019-10-15 14:06:44] echo "." >> /app/public/diff/republic_congo_refs_16973.diff
[CMD] [2019-10-15 14:06:44] echo "0a" > /app/public/diff/republic_congo_nodes_16974.diff
[CMD] [2019-10-15 14:06:45] tail -n +1 /app/public/converted_csv/republic_congo_nodes_16974.csv >> /app/public/diff/republic_congo_nodes_16974.diff
[CMD] [2019-10-15 14:06:45] echo "." >> /app/public/diff/republic_congo_nodes_16974.diff
[CMD] [2019-10-15 14:06:45] echo "0a" > /app/public/diff/republic_congo_occurrences_16975.diff
[CMD] [2019-10-15 14:06:46] tail -n +1 /app/public/converted_csv/republic_congo_occurrences_16975.csv >> /app/public/diff/republic_congo_occurrences_16975.diff
[CMD] [2019-10-15 14:06:46] echo "." >> /app/public/diff/republic_congo_occurrences_16975.diff
[CMD] [2019-10-15 14:06:46] echo "0a" > /app/public/diff/republic_congo_measurements_16976.diff
[CMD] [2019-10-15 14:06:46] tail -n +1 /app/public/converted_csv/republic_congo_measurements_16976.csv >> /app/public/diff/republic_congo_measurements_16976.diff
[CMD] [2019-10-15 14:06:47] echo "." >> /app/public/diff/republic_congo_measurements_16976.diff
[STOP] [2019-10-15 14:06:47] calculate_delta
[START] [2019-10-15 14:06:47] parse_diff_and_store
[INFO] [2019-10-15 14:06:47] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 14:06:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 14:06:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 14:06:51] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 14:07:12] Storing 2 References
[INFO] [2019-10-15 14:07:12] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 14:07:12] Average Time: 0.0
[INFO] [2019-10-15 14:07:12] Total Time: 1s
[INFO] [2019-10-15 14:07:12] Storing 5778 ScientificNames
[INFO] [2019-10-15 14:07:12] Processing group of 5778 in 6 groups of 1000
[INFO] [2019-10-15 14:07:15] Average Time: 0.362
[INFO] [2019-10-15 14:07:15] Total Time: 3s
[INFO] [2019-10-15 14:07:15] Storing 5778 Nodes
[INFO] [2019-10-15 14:07:15] Processing group of 5778 in 6 groups of 1000
[INFO] [2019-10-15 14:07:16] Average Time: 0.308
[INFO] [2019-10-15 14:07:16] Total Time: 2s
[INFO] [2019-10-15 14:07:16] Storing 3374 Occurrences
[INFO] [2019-10-15 14:07:16] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-15 14:07:17] Average Time: 0.088
[INFO] [2019-10-15 14:07:17] Total Time: 1s
[INFO] [2019-10-15 14:07:17] Storing 7270 TraitsReferences
[INFO] [2019-10-15 14:07:17] Processing group of 7270 in 8 groups of 1000
[INFO] [2019-10-15 14:07:17] Average Time: 0.073
[INFO] [2019-10-15 14:07:17] Total Time: 1s
[INFO] [2019-10-15 14:07:17] last 3 / first 3: 0.52
[INFO] [2019-10-15 14:07:17] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-15 14:07:17] Storing 7269 Traits
[INFO] [2019-10-15 14:07:17] Processing group of 7269 in 8 groups of 1000
[INFO] [2019-10-15 14:07:20] Average Time: 0.29
[INFO] [2019-10-15 14:07:20] Total Time: 3s
[INFO] [2019-10-15 14:07:20] last 3 / first 3: 0.7
[INFO] [2019-10-15 14:07:20] Std.Dev: 0.09486832980505137; Max: 0.38
[INFO] [2019-10-15 14:07:20] Storing 7261 MetaTraits
[INFO] [2019-10-15 14:07:20] Processing group of 7261 in 8 groups of 1000
[INFO] [2019-10-15 14:07:21] Average Time: 0.105
[INFO] [2019-10-15 14:07:21] Total Time: 1s
[INFO] [2019-10-15 14:07:21] last 3 / first 3: 0.68
[INFO] [2019-10-15 14:07:21] Std.Dev: 0.03162277660168379; Max: 0.15
[STOP] [2019-10-15 14:07:21] parse_diff_and_store
[START] [2019-10-15 14:07:21] resolve_keys
[INFO] [2019-10-15 14:07:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 14:07:47] traits to occurrences...
[INFO] [2019-10-15 14:07:49] traits to nodes (through occurrences)...
[INFO] [2019-10-15 14:07:49] Traits to sex term...
[INFO] [2019-10-15 14:07:50] Traits to lifestage term...
[INFO] [2019-10-15 14:07:52] MetaTraits to traits...
[INFO] [2019-10-15 14:07:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 14:07:53] Assocs to occurrences...
[INFO] [2019-10-15 14:07:53] Assocs to nodes...
[INFO] [2019-10-15 14:07:53] Assoc to sex term...
[INFO] [2019-10-15 14:07:53] Assoc to lifestage term...
[STOP] [2019-10-15 14:07:53] resolve_keys
[START] [2019-10-15 14:07:53] hold_for_later_1
[STOP] [2019-10-15 14:07:53] hold_for_later_1
[START] [2019-10-15 14:07:53] hold_for_later_2
[STOP] [2019-10-15 14:07:53] hold_for_later_2
[START] [2019-10-15 14:07:53] resolve_missing_parents
[STOP] [2019-10-15 14:08:06] resolve_missing_parents
[START] [2019-10-15 14:08:06] rebuild_nodes
[START] [2019-10-15 14:08:06] Flattener#flatten
[START] [2019-10-15 14:08:06] Flattener#study_resource
[START] [2019-10-15 14:08:06] Flattener#build_ancestry
[STOP] [2019-10-15 14:08:06] Flattener#build_ancestry
[INFO] [2019-10-15 14:08:06] 5778 ancestry keys
[START] [2019-10-15 14:08:06] build_node_ancestors
[INFO] [2019-10-15 14:08:06] old ancestors deleted.
[STOP] [2019-10-15 14:08:08] build_node_ancestors
[START] [2019-10-15 14:08:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 14:08:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 14:08:09] Flattener#flatten
[STOP] [2019-10-15 14:08:09] rebuild_nodes
[START] [2019-10-15 14:08:09] resolve_missing_media_owners
[STOP] [2019-10-15 14:08:09] resolve_missing_media_owners
[START] [2019-10-15 14:08:09] sanitize_media_verbatims
[STOP] [2019-10-15 14:08:09] sanitize_media_verbatims
[START] [2019-10-15 14:08:09] queue_downloads
[STOP] [2019-10-15 14:08:09] queue_downloads
[START] [2019-10-15 14:08:09] parse_names
[WARN] [2019-10-15 14:08:09] I see 5778 names which still need to be parsed.
[STOP] [2019-10-15 14:08:14] parse_names
[START] [2019-10-15 14:08:14] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 14:08:14] denormalize_canonical_names_to_nodes
[START] [2019-10-15 14:08:14] match_nodes
[START] [2019-10-15 14:08:14] map_all_nodes_to_pages
[STOP] [2019-10-15 14:13:00] map_all_nodes_to_pages
[INFO] [2019-10-15 14:13:00] 202 Unmatched nodes (of 5778)! That's too many to output. First 10: Oreochromis flavomarginata (#51691913); Sarotherodon flavomarginata (#51691952); Sicydium (#51692527); Barbus miolepis (#51688812); Varicorhinus (#51688892); Anthonotha obanense (#51693485); Anthonotha graciliflorum (#51693737); Albizia altissimum (#51688787); Albizia rhombifolium (#51692240); Baphia obanense (#51693403)
[START] [2019-10-15 14:13:00] update_nodes
[STOP] [2019-10-15 14:13:01] update_nodes
[STOP] [2019-10-15 14:13:01] match_nodes
[START] [2019-10-15 14:13:01] reindex_search
[STOP] [2019-10-15 14:13:14] reindex_search
[START] [2019-10-15 14:13:14] normalize_units
[STOP] [2019-10-15 14:13:14] normalize_units
[START] [2019-10-15 14:13:14] calculate_statistics
[STOP] [2019-10-15 14:13:14] calculate_statistics
[START] [2019-10-15 14:13:14] complete_harvest_instance
[START] [2019-10-15 14:13:14] overall_tsv_creation
[INFO] [2019-10-15 14:13:14] Processing group of 5778 in 1 batches of 10000
[INFO] [2019-10-15 14:14:24] 3374 Traits (unfiltered)...
[INFO] [2019-10-15 14:14:38] 3374 Traits (filtered)...
[INFO] [2019-10-15 14:14:38] 0 Associations (filtered)...
[INFO] [2019-10-15 14:15:23] 16862 metadata added.
[INFO] [2019-10-15 14:15:23] 0 metadata added.
[INFO] [2019-10-15 14:15:23] Average Time: 103.33
[INFO] [2019-10-15 14:15:23] Total Time: 2m9s
[STOP] [2019-10-15 14:15:23] overall_tsv_creation
[INFO] [2019-10-15 14:15:23] Done. Check your files:
[INFO] [2019-10-15 14:15:23] (5778 lines) /app/public/data/republic_congo/publish_nodes.tsv
[INFO] [2019-10-15 14:15:23] (14350 lines) /app/public/data/republic_congo/publish_node_ancestors.tsv
[INFO] [2019-10-15 14:15:23] (5778 lines) /app/public/data/republic_congo/publish_scientific_names.tsv
[INFO] [2019-10-15 14:15:24] (3375 lines) /app/public/data/republic_congo/publish_traits.tsv
[INFO] [2019-10-15 14:15:24] (16863 lines) /app/public/data/republic_congo/publish_metadata.tsv
[STOP] [2019-10-15 14:15:24] complete_harvest_instance
[START] [2019-10-15 14:15:24] completed
[STOP] [2019-10-15 14:15:24] completed
[STOP] [2019-10-15 14:15:24] logged process, took 523.04
Latest Process

15 Oct 14:06 EXITED currently processing 0