Harvest for Sea of Marmara Species List Created 25 Dec 13:38

Stage: completed
Fetched: 25 Dec 13:38
Validated: 25 Dec 13:38
Deltas Created 25 Dec 13:38
Units Normalized: 25 Dec 13:39
Ancestry Built: 25 Dec 13:38
Nodes Matched: 25 Dec 13:39
Names Parsed: 25 Dec 13:38
New Models Stored: 25 Dec 13:38
Indexed: 25 Dec 13:39
Completed: 25 Dec 13:41
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 13:38:22 -0500 by logger.rb/56815
[START] [2019-12-25 13:38:22] logged process
[START] [2019-12-25 13:38:22] create_harvest_instance
[STOP] [2019-12-25 13:38:22] create_harvest_instance
[START] [2019-12-25 13:38:22] fetch_files
[STOP] [2019-12-25 13:38:22] fetch_files
[START] [2019-12-25 13:38:22] validate_each_file
[STOP] [2019-12-25 13:38:23] validate_each_file
[START] [2019-12-25 13:38:23] convert_to_csv
[CMD] [2019-12-25 13:38:23] /usr/bin/sort /app/public/converted_csv/sea_marmara_sp_l_refs_19634.csv > /app/public/converted_csv/sea_marmara_sp_l_refs_19634.csv_sorted
[CMD] [2019-12-25 13:38:23] /usr/bin/sort /app/public/converted_csv/sea_marmara_sp_l_nodes_19635.csv > /app/public/converted_csv/sea_marmara_sp_l_nodes_19635.csv_sorted
[CMD] [2019-12-25 13:38:24] /usr/bin/sort /app/public/converted_csv/sea_marmara_sp_l_occurrences_19636.csv > /app/public/converted_csv/sea_marmara_sp_l_occurrences_19636.csv_sorted
[CMD] [2019-12-25 13:38:24] /usr/bin/sort /app/public/converted_csv/sea_marmara_sp_l_measurements_19637.csv > /app/public/converted_csv/sea_marmara_sp_l_measurements_19637.csv_sorted
[STOP] [2019-12-25 13:38:25] convert_to_csv
[START] [2019-12-25 13:38:25] calculate_delta
[CMD] [2019-12-25 13:38:25] echo "0a" > /app/public/diff/sea_marmara_sp_l_refs_19634.diff
[CMD] [2019-12-25 13:38:26] tail -n +1 /app/public/converted_csv/sea_marmara_sp_l_refs_19634.csv >> /app/public/diff/sea_marmara_sp_l_refs_19634.diff
[CMD] [2019-12-25 13:38:26] echo "." >> /app/public/diff/sea_marmara_sp_l_refs_19634.diff
[CMD] [2019-12-25 13:38:27] echo "0a" > /app/public/diff/sea_marmara_sp_l_nodes_19635.diff
[CMD] [2019-12-25 13:38:28] tail -n +1 /app/public/converted_csv/sea_marmara_sp_l_nodes_19635.csv >> /app/public/diff/sea_marmara_sp_l_nodes_19635.diff
[CMD] [2019-12-25 13:38:28] echo "." >> /app/public/diff/sea_marmara_sp_l_nodes_19635.diff
[CMD] [2019-12-25 13:38:29] echo "0a" > /app/public/diff/sea_marmara_sp_l_occurrences_19636.diff
[CMD] [2019-12-25 13:38:30] tail -n +1 /app/public/converted_csv/sea_marmara_sp_l_occurrences_19636.csv >> /app/public/diff/sea_marmara_sp_l_occurrences_19636.diff
[CMD] [2019-12-25 13:38:30] echo "." >> /app/public/diff/sea_marmara_sp_l_occurrences_19636.diff
[CMD] [2019-12-25 13:38:31] echo "0a" > /app/public/diff/sea_marmara_sp_l_measurements_19637.diff
[CMD] [2019-12-25 13:38:32] tail -n +1 /app/public/converted_csv/sea_marmara_sp_l_measurements_19637.csv >> /app/public/diff/sea_marmara_sp_l_measurements_19637.diff
[CMD] [2019-12-25 13:38:32] echo "." >> /app/public/diff/sea_marmara_sp_l_measurements_19637.diff
[STOP] [2019-12-25 13:38:33] calculate_delta
[START] [2019-12-25 13:38:33] parse_diff_and_store
[INFO] [2019-12-25 13:38:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 13:38:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 13:38:35] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 13:38:36] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 13:38:37] Storing 2 References
[INFO] [2019-12-25 13:38:37] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 13:38:37] Average Time: 0.0
[INFO] [2019-12-25 13:38:37] Total Time: 1s
[INFO] [2019-12-25 13:38:37] Storing 588 ScientificNames
[INFO] [2019-12-25 13:38:37] Processing group of 588 in 1 groups of 1000
[INFO] [2019-12-25 13:38:37] Average Time: 0.28
[INFO] [2019-12-25 13:38:37] Total Time: 1s
[INFO] [2019-12-25 13:38:37] Storing 588 Nodes
[INFO] [2019-12-25 13:38:37] Processing group of 588 in 1 groups of 1000
[INFO] [2019-12-25 13:38:37] Average Time: 0.22
[INFO] [2019-12-25 13:38:37] Total Time: 1s
[INFO] [2019-12-25 13:38:37] Storing 222 Occurrences
[INFO] [2019-12-25 13:38:37] Processing group of 222 in 1 groups of 1000
[INFO] [2019-12-25 13:38:37] Average Time: 0.05
[INFO] [2019-12-25 13:38:37] Total Time: 1s
[INFO] [2019-12-25 13:38:37] Storing 444 TraitsReferences
[INFO] [2019-12-25 13:38:37] Processing group of 444 in 1 groups of 1000
[INFO] [2019-12-25 13:38:38] Average Time: 0.12
[INFO] [2019-12-25 13:38:38] Total Time: 1s
[INFO] [2019-12-25 13:38:38] Storing 444 Traits
[INFO] [2019-12-25 13:38:38] Processing group of 444 in 1 groups of 1000
[INFO] [2019-12-25 13:38:38] Average Time: 0.25
[INFO] [2019-12-25 13:38:38] Total Time: 1s
[INFO] [2019-12-25 13:38:38] Storing 444 MetaTraits
[INFO] [2019-12-25 13:38:38] Processing group of 444 in 1 groups of 1000
[INFO] [2019-12-25 13:38:38] Average Time: 0.09
[INFO] [2019-12-25 13:38:38] Total Time: 1s
[STOP] [2019-12-25 13:38:38] parse_diff_and_store
[START] [2019-12-25 13:38:38] resolve_keys
[INFO] [2019-12-25 13:38:43] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 13:38:43] traits to occurrences...
[INFO] [2019-12-25 13:38:44] traits to nodes (through occurrences)...
[INFO] [2019-12-25 13:38:44] Traits to sex term...
[INFO] [2019-12-25 13:38:44] Traits to lifestage term...
[INFO] [2019-12-25 13:38:44] MetaTraits to traits...
[INFO] [2019-12-25 13:38:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 13:38:44] Assocs to occurrences...
[INFO] [2019-12-25 13:38:44] Assocs to nodes...
[INFO] [2019-12-25 13:38:44] Assoc to sex term...
[INFO] [2019-12-25 13:38:44] Assoc to lifestage term...
[STOP] [2019-12-25 13:38:44] resolve_keys
[START] [2019-12-25 13:38:44] hold_for_later_1
[STOP] [2019-12-25 13:38:44] hold_for_later_1
[START] [2019-12-25 13:38:44] hold_for_later_2
[STOP] [2019-12-25 13:38:44] hold_for_later_2
[START] [2019-12-25 13:38:44] resolve_missing_parents
[STOP] [2019-12-25 13:38:44] resolve_missing_parents
[START] [2019-12-25 13:38:44] rebuild_nodes
[START] [2019-12-25 13:38:44] Flattener#flatten
[START] [2019-12-25 13:38:44] Flattener#study_resource
[START] [2019-12-25 13:38:44] Flattener#build_ancestry
[STOP] [2019-12-25 13:38:44] Flattener#build_ancestry
[INFO] [2019-12-25 13:38:44] 588 ancestry keys
[START] [2019-12-25 13:38:44] build_node_ancestors
[INFO] [2019-12-25 13:38:44] old ancestors deleted.
[STOP] [2019-12-25 13:38:45] build_node_ancestors
[START] [2019-12-25 13:38:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:38:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 13:38:45] Flattener#flatten
[STOP] [2019-12-25 13:38:45] rebuild_nodes
[START] [2019-12-25 13:38:45] resolve_missing_media_owners
[STOP] [2019-12-25 13:38:45] resolve_missing_media_owners
[START] [2019-12-25 13:38:45] sanitize_media_verbatims
[STOP] [2019-12-25 13:38:45] sanitize_media_verbatims
[START] [2019-12-25 13:38:45] queue_downloads
[STOP] [2019-12-25 13:38:45] queue_downloads
[START] [2019-12-25 13:38:45] parse_names
[WARN] [2019-12-25 13:38:45] I see 588 names which still need to be parsed.
[STOP] [2019-12-25 13:38:47] parse_names
[START] [2019-12-25 13:38:47] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 13:38:47] denormalize_canonical_names_to_nodes
[START] [2019-12-25 13:38:47] match_nodes
[START] [2019-12-25 13:38:47] map_all_nodes_to_pages
[STOP] [2019-12-25 13:39:39] map_all_nodes_to_pages
[INFO] [2019-12-25 13:39:39] 40 Unmatched nodes (of 588)! That's too many to output. First 10: Phalacrocorax pygmaeus (#62439838); Larus melanocephalus (#62439964); Anas querquedula (#62440051); Anas strepera (#62440238); Anas penelope (#62440309); Centracanthidae (#62440090); Scorpaeniformes (#62439935); Maxillopoda (#62439922); Diosaccidae (#62439920); Daptonema setosus (#62440009)
[START] [2019-12-25 13:39:39] update_nodes
[STOP] [2019-12-25 13:39:40] update_nodes
[STOP] [2019-12-25 13:39:40] match_nodes
[START] [2019-12-25 13:39:40] reindex_search
[STOP] [2019-12-25 13:39:40] reindex_search
[START] [2019-12-25 13:39:40] normalize_units
[STOP] [2019-12-25 13:39:40] normalize_units
[START] [2019-12-25 13:39:40] calculate_statistics
[STOP] [2019-12-25 13:39:40] calculate_statistics
[START] [2019-12-25 13:39:40] complete_harvest_instance
[START] [2019-12-25 13:39:40] overall_tsv_creation
[INFO] [2019-12-25 13:39:40] Processing group of 588 in 1 batches of 10000
[INFO] [2019-12-25 13:40:30] 222 Traits (unfiltered)...
[INFO] [2019-12-25 13:40:44] 222 Traits (filtered)...
[INFO] [2019-12-25 13:40:44] 0 Associations (filtered)...
[INFO] [2019-12-25 13:41:24] 1110 metadata added.
[INFO] [2019-12-25 13:41:24] 0 metadata added.
[INFO] [2019-12-25 13:41:24] Average Time: 80.06
[INFO] [2019-12-25 13:41:24] Total Time: 1m44s
[STOP] [2019-12-25 13:41:24] overall_tsv_creation
[INFO] [2019-12-25 13:41:24] Done. Check your files:
[INFO] [2019-12-25 13:41:25] (588 lines) /app/public/data/sea_marmara_sp_l/publish_nodes.tsv
[INFO] [2019-12-25 13:41:25] (2625 lines) /app/public/data/sea_marmara_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-25 13:41:26] (588 lines) /app/public/data/sea_marmara_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-25 13:41:27] (223 lines) /app/public/data/sea_marmara_sp_l/publish_traits.tsv
[INFO] [2019-12-25 13:41:27] (1111 lines) /app/public/data/sea_marmara_sp_l/publish_metadata.tsv
[STOP] [2019-12-25 13:41:27] complete_harvest_instance
[START] [2019-12-25 13:41:27] completed
[STOP] [2019-12-25 13:41:27] completed
[STOP] [2019-12-25 13:41:27] logged process, took 185.34
Latest Process

25 Dec 13:38 EXITED currently processing 0