Harvest for Ceram Sea Species List- duplicate Created 23 Dec 00:09

Stage: completed
Fetched: 23 Dec 00:09
Validated: 23 Dec 00:09
Deltas Created 23 Dec 00:09
Units Normalized: 23 Dec 00:24
Ancestry Built: 23 Dec 00:09
Nodes Matched: 23 Dec 00:24
Names Parsed: 23 Dec 00:09
New Models Stored: 23 Dec 00:09
Indexed: 23 Dec 00:24
Completed: 23 Dec 00:26
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 00:09:07 -0500 by logger.rb/56815
[START] [2019-12-23 00:09:07] logged process
[START] [2019-12-23 00:09:07] create_harvest_instance
[STOP] [2019-12-23 00:09:08] create_harvest_instance
[START] [2019-12-23 00:09:08] fetch_files
[STOP] [2019-12-23 00:09:08] fetch_files
[START] [2019-12-23 00:09:08] validate_each_file
[STOP] [2019-12-23 00:09:08] validate_each_file
[START] [2019-12-23 00:09:08] convert_to_csv
[CMD] [2019-12-23 00:09:08] /usr/bin/sort /app/public/converted_csv/ceram_sea_sp_li2_refs_19178.csv > /app/public/converted_csv/ceram_sea_sp_li2_refs_19178.csv_sorted
[CMD] [2019-12-23 00:09:08] /usr/bin/sort /app/public/converted_csv/ceram_sea_sp_li2_nodes_19179.csv > /app/public/converted_csv/ceram_sea_sp_li2_nodes_19179.csv_sorted
[CMD] [2019-12-23 00:09:08] /usr/bin/sort /app/public/converted_csv/ceram_sea_sp_li2_occurrences_19180.csv > /app/public/converted_csv/ceram_sea_sp_li2_occurrences_19180.csv_sorted
[CMD] [2019-12-23 00:09:08] /usr/bin/sort /app/public/converted_csv/ceram_sea_sp_li2_measurements_19181.csv > /app/public/converted_csv/ceram_sea_sp_li2_measurements_19181.csv_sorted
[STOP] [2019-12-23 00:09:08] convert_to_csv
[START] [2019-12-23 00:09:08] calculate_delta
[CMD] [2019-12-23 00:09:08] echo "0a" > /app/public/diff/ceram_sea_sp_li2_refs_19178.diff
[CMD] [2019-12-23 00:09:08] tail -n +1 /app/public/converted_csv/ceram_sea_sp_li2_refs_19178.csv >> /app/public/diff/ceram_sea_sp_li2_refs_19178.diff
[CMD] [2019-12-23 00:09:08] echo "." >> /app/public/diff/ceram_sea_sp_li2_refs_19178.diff
[CMD] [2019-12-23 00:09:09] echo "0a" > /app/public/diff/ceram_sea_sp_li2_nodes_19179.diff
[CMD] [2019-12-23 00:09:09] tail -n +1 /app/public/converted_csv/ceram_sea_sp_li2_nodes_19179.csv >> /app/public/diff/ceram_sea_sp_li2_nodes_19179.diff
[CMD] [2019-12-23 00:09:09] echo "." >> /app/public/diff/ceram_sea_sp_li2_nodes_19179.diff
[CMD] [2019-12-23 00:09:09] echo "0a" > /app/public/diff/ceram_sea_sp_li2_occurrences_19180.diff
[CMD] [2019-12-23 00:09:09] tail -n +1 /app/public/converted_csv/ceram_sea_sp_li2_occurrences_19180.csv >> /app/public/diff/ceram_sea_sp_li2_occurrences_19180.diff
[CMD] [2019-12-23 00:09:09] echo "." >> /app/public/diff/ceram_sea_sp_li2_occurrences_19180.diff
[CMD] [2019-12-23 00:09:09] echo "0a" > /app/public/diff/ceram_sea_sp_li2_measurements_19181.diff
[CMD] [2019-12-23 00:09:09] tail -n +1 /app/public/converted_csv/ceram_sea_sp_li2_measurements_19181.csv >> /app/public/diff/ceram_sea_sp_li2_measurements_19181.diff
[CMD] [2019-12-23 00:09:09] echo "." >> /app/public/diff/ceram_sea_sp_li2_measurements_19181.diff
[STOP] [2019-12-23 00:09:09] calculate_delta
[START] [2019-12-23 00:09:09] parse_diff_and_store
[INFO] [2019-12-23 00:09:09] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:09:09] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:09:10] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:09:11] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:09:20] Storing 2 References
[INFO] [2019-12-23 00:09:20] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:09:20] Average Time: 0.0
[INFO] [2019-12-23 00:09:20] Total Time: 1s
[INFO] [2019-12-23 00:09:20] Storing 3500 ScientificNames
[INFO] [2019-12-23 00:09:20] Processing group of 3500 in 4 groups of 1000
[INFO] [2019-12-23 00:09:22] Average Time: 0.378
[INFO] [2019-12-23 00:09:22] Total Time: 2s
[INFO] [2019-12-23 00:09:22] Storing 3500 Nodes
[INFO] [2019-12-23 00:09:22] Processing group of 3500 in 4 groups of 1000
[INFO] [2019-12-23 00:09:23] Average Time: 0.295
[INFO] [2019-12-23 00:09:23] Total Time: 2s
[INFO] [2019-12-23 00:09:23] Storing 1709 Occurrences
[INFO] [2019-12-23 00:09:23] Processing group of 1709 in 2 groups of 1000
[INFO] [2019-12-23 00:09:23] Average Time: 0.11
[INFO] [2019-12-23 00:09:23] Total Time: 1s
[INFO] [2019-12-23 00:09:23] Storing 3418 TraitsReferences
[INFO] [2019-12-23 00:09:23] Processing group of 3418 in 4 groups of 1000
[INFO] [2019-12-23 00:09:24] Average Time: 0.118
[INFO] [2019-12-23 00:09:24] Total Time: 1s
[INFO] [2019-12-23 00:09:24] Storing 3418 Traits
[INFO] [2019-12-23 00:09:24] Processing group of 3418 in 4 groups of 1000
[INFO] [2019-12-23 00:09:25] Average Time: 0.285
[INFO] [2019-12-23 00:09:25] Total Time: 2s
[INFO] [2019-12-23 00:09:25] Storing 3417 MetaTraits
[INFO] [2019-12-23 00:09:25] Processing group of 3417 in 4 groups of 1000
[INFO] [2019-12-23 00:09:25] Average Time: 0.115
[INFO] [2019-12-23 00:09:25] Total Time: 1s
[STOP] [2019-12-23 00:09:25] parse_diff_and_store
[START] [2019-12-23 00:09:25] resolve_keys
[INFO] [2019-12-23 00:09:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:09:43] traits to occurrences...
[INFO] [2019-12-23 00:09:44] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:09:44] Traits to sex term...
[INFO] [2019-12-23 00:09:45] Traits to lifestage term...
[INFO] [2019-12-23 00:09:45] MetaTraits to traits...
[INFO] [2019-12-23 00:09:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:09:46] Assocs to occurrences...
[INFO] [2019-12-23 00:09:46] Assocs to nodes...
[INFO] [2019-12-23 00:09:46] Assoc to sex term...
[INFO] [2019-12-23 00:09:46] Assoc to lifestage term...
[STOP] [2019-12-23 00:09:46] resolve_keys
[START] [2019-12-23 00:09:46] hold_for_later_1
[STOP] [2019-12-23 00:09:46] hold_for_later_1
[START] [2019-12-23 00:09:46] hold_for_later_2
[STOP] [2019-12-23 00:09:46] hold_for_later_2
[START] [2019-12-23 00:09:46] resolve_missing_parents
[STOP] [2019-12-23 00:09:52] resolve_missing_parents
[START] [2019-12-23 00:09:52] rebuild_nodes
[START] [2019-12-23 00:09:52] Flattener#flatten
[START] [2019-12-23 00:09:52] Flattener#study_resource
[START] [2019-12-23 00:09:52] Flattener#build_ancestry
[STOP] [2019-12-23 00:09:52] Flattener#build_ancestry
[INFO] [2019-12-23 00:09:52] 3500 ancestry keys
[START] [2019-12-23 00:09:52] build_node_ancestors
[INFO] [2019-12-23 00:09:52] old ancestors deleted.
[STOP] [2019-12-23 00:09:53] build_node_ancestors
[START] [2019-12-23 00:09:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:09:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:09:55] Flattener#flatten
[STOP] [2019-12-23 00:09:55] rebuild_nodes
[START] [2019-12-23 00:09:55] resolve_missing_media_owners
[STOP] [2019-12-23 00:09:55] resolve_missing_media_owners
[START] [2019-12-23 00:09:55] sanitize_media_verbatims
[STOP] [2019-12-23 00:09:55] sanitize_media_verbatims
[START] [2019-12-23 00:09:55] queue_downloads
[STOP] [2019-12-23 00:09:55] queue_downloads
[START] [2019-12-23 00:09:55] parse_names
[WARN] [2019-12-23 00:09:55] I see 3500 names which still need to be parsed.
[STOP] [2019-12-23 00:09:59] parse_names
[START] [2019-12-23 00:09:59] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:09:59] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:09:59] match_nodes
[START] [2019-12-23 00:09:59] map_all_nodes_to_pages
[STOP] [2019-12-23 00:24:33] map_all_nodes_to_pages
[INFO] [2019-12-23 00:24:33] 117 Unmatched nodes (of 3500)! That's too many to output. First 10: Siphamia papuensis (#61815435); Ptereleotridae (#61815286); Scorpaeniformes (#61815248); Stephanoberyciformes (#61815456); Cetomimiformes (#61816464); Hydrophiidae (#61814828); Lapemis (#61814827); Manta (#61815270); Pleurogona (#61815955); Enterogona (#61816081)
[START] [2019-12-23 00:24:33] update_nodes
[STOP] [2019-12-23 00:24:34] update_nodes
[STOP] [2019-12-23 00:24:34] match_nodes
[START] [2019-12-23 00:24:34] reindex_search
[STOP] [2019-12-23 00:24:41] reindex_search
[START] [2019-12-23 00:24:41] normalize_units
[STOP] [2019-12-23 00:24:41] normalize_units
[START] [2019-12-23 00:24:41] calculate_statistics
[STOP] [2019-12-23 00:24:41] calculate_statistics
[START] [2019-12-23 00:24:41] complete_harvest_instance
[START] [2019-12-23 00:24:41] overall_tsv_creation
[INFO] [2019-12-23 00:24:41] Processing group of 3500 in 1 batches of 10000
[INFO] [2019-12-23 00:25:46] 1709 Traits (unfiltered)...
[INFO] [2019-12-23 00:26:01] 1709 Traits (filtered)...
[INFO] [2019-12-23 00:26:01] 0 Associations (filtered)...
[INFO] [2019-12-23 00:26:45] 8544 metadata added.
[INFO] [2019-12-23 00:26:45] 0 metadata added.
[INFO] [2019-12-23 00:26:45] Average Time: 95.26
[INFO] [2019-12-23 00:26:45] Total Time: 2m4s
[STOP] [2019-12-23 00:26:45] overall_tsv_creation
[INFO] [2019-12-23 00:26:45] Done. Check your files:
[INFO] [2019-12-23 00:26:45] (3500 lines) /app/public/data/ceram_sea_sp_li2/publish_nodes.tsv
[INFO] [2019-12-23 00:26:45] (17904 lines) /app/public/data/ceram_sea_sp_li2/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:26:45] (3500 lines) /app/public/data/ceram_sea_sp_li2/publish_scientific_names.tsv
[INFO] [2019-12-23 00:26:45] (1710 lines) /app/public/data/ceram_sea_sp_li2/publish_traits.tsv
[INFO] [2019-12-23 00:26:45] (8545 lines) /app/public/data/ceram_sea_sp_li2/publish_metadata.tsv
[STOP] [2019-12-23 00:26:45] complete_harvest_instance
[START] [2019-12-23 00:26:45] completed
[STOP] [2019-12-23 00:26:45] completed
[STOP] [2019-12-23 00:26:45] logged process, took 1058.16
Latest Process

23 Dec 00:09 EXITED currently processing 0