Harvest for San Marino Species List Created 15 Oct 16:39

Stage: completed
Fetched: 15 Oct 16:39
Validated: 15 Oct 16:39
Deltas Created 15 Oct 16:39
Units Normalized: 15 Oct 16:39
Ancestry Built: 15 Oct 16:39
Nodes Matched: 15 Oct 16:39
Names Parsed: 15 Oct 16:39
New Models Stored: 15 Oct 16:39
Indexed: 15 Oct 16:39
Completed: 15 Oct 16:41
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:39:26 -0400 by logger.rb/56815
[START] [2019-10-15 16:39:26] logged process
[START] [2019-10-15 16:39:26] create_harvest_instance
[STOP] [2019-10-15 16:39:26] create_harvest_instance
[START] [2019-10-15 16:39:26] fetch_files
[STOP] [2019-10-15 16:39:26] fetch_files
[START] [2019-10-15 16:39:26] validate_each_file
[STOP] [2019-10-15 16:39:26] validate_each_file
[START] [2019-10-15 16:39:26] convert_to_csv
[CMD] [2019-10-15 16:39:26] /usr/bin/sort /app/public/converted_csv/san_marino_sp_li_refs_17085.csv > /app/public/converted_csv/san_marino_sp_li_refs_17085.csv_sorted
[CMD] [2019-10-15 16:39:26] /usr/bin/sort /app/public/converted_csv/san_marino_sp_li_nodes_17086.csv > /app/public/converted_csv/san_marino_sp_li_nodes_17086.csv_sorted
[CMD] [2019-10-15 16:39:27] /usr/bin/sort /app/public/converted_csv/san_marino_sp_li_occurrences_17087.csv > /app/public/converted_csv/san_marino_sp_li_occurrences_17087.csv_sorted
[CMD] [2019-10-15 16:39:27] /usr/bin/sort /app/public/converted_csv/san_marino_sp_li_measurements_17088.csv > /app/public/converted_csv/san_marino_sp_li_measurements_17088.csv_sorted
[STOP] [2019-10-15 16:39:27] convert_to_csv
[START] [2019-10-15 16:39:27] calculate_delta
[CMD] [2019-10-15 16:39:27] echo "0a" > /app/public/diff/san_marino_sp_li_refs_17085.diff
[CMD] [2019-10-15 16:39:28] tail -n +1 /app/public/converted_csv/san_marino_sp_li_refs_17085.csv >> /app/public/diff/san_marino_sp_li_refs_17085.diff
[CMD] [2019-10-15 16:39:28] echo "." >> /app/public/diff/san_marino_sp_li_refs_17085.diff
[CMD] [2019-10-15 16:39:28] echo "0a" > /app/public/diff/san_marino_sp_li_nodes_17086.diff
[CMD] [2019-10-15 16:39:28] tail -n +1 /app/public/converted_csv/san_marino_sp_li_nodes_17086.csv >> /app/public/diff/san_marino_sp_li_nodes_17086.diff
[CMD] [2019-10-15 16:39:29] echo "." >> /app/public/diff/san_marino_sp_li_nodes_17086.diff
[CMD] [2019-10-15 16:39:29] echo "0a" > /app/public/diff/san_marino_sp_li_occurrences_17087.diff
[CMD] [2019-10-15 16:39:29] tail -n +1 /app/public/converted_csv/san_marino_sp_li_occurrences_17087.csv >> /app/public/diff/san_marino_sp_li_occurrences_17087.diff
[CMD] [2019-10-15 16:39:30] echo "." >> /app/public/diff/san_marino_sp_li_occurrences_17087.diff
[CMD] [2019-10-15 16:39:30] echo "0a" > /app/public/diff/san_marino_sp_li_measurements_17088.diff
[CMD] [2019-10-15 16:39:30] tail -n +1 /app/public/converted_csv/san_marino_sp_li_measurements_17088.csv >> /app/public/diff/san_marino_sp_li_measurements_17088.diff
[CMD] [2019-10-15 16:39:30] echo "." >> /app/public/diff/san_marino_sp_li_measurements_17088.diff
[STOP] [2019-10-15 16:39:31] calculate_delta
[START] [2019-10-15 16:39:31] parse_diff_and_store
[INFO] [2019-10-15 16:39:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:39:31] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:39:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:39:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:39:32] Storing 2 References
[INFO] [2019-10-15 16:39:32] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.0
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 157 ScientificNames
[INFO] [2019-10-15 16:39:32] Processing group of 157 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.11
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 157 Nodes
[INFO] [2019-10-15 16:39:32] Processing group of 157 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.05
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 46 Occurrences
[INFO] [2019-10-15 16:39:32] Processing group of 46 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.01
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 92 TraitsReferences
[INFO] [2019-10-15 16:39:32] Processing group of 92 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.03
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 92 Traits
[INFO] [2019-10-15 16:39:32] Processing group of 92 in 1 groups of 1000
[INFO] [2019-10-15 16:39:32] Average Time: 0.06
[INFO] [2019-10-15 16:39:32] Total Time: 1s
[INFO] [2019-10-15 16:39:32] Storing 92 MetaTraits
[INFO] [2019-10-15 16:39:32] Processing group of 92 in 1 groups of 1000
[INFO] [2019-10-15 16:39:33] Average Time: 0.02
[INFO] [2019-10-15 16:39:33] Total Time: 1s
[STOP] [2019-10-15 16:39:33] parse_diff_and_store
[START] [2019-10-15 16:39:33] resolve_keys
[INFO] [2019-10-15 16:39:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:39:36] traits to occurrences...
[INFO] [2019-10-15 16:39:36] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:39:36] Traits to sex term...
[INFO] [2019-10-15 16:39:36] Traits to lifestage term...
[INFO] [2019-10-15 16:39:36] MetaTraits to traits...
[INFO] [2019-10-15 16:39:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:39:36] Assocs to occurrences...
[INFO] [2019-10-15 16:39:36] Assocs to nodes...
[INFO] [2019-10-15 16:39:36] Assoc to sex term...
[INFO] [2019-10-15 16:39:36] Assoc to lifestage term...
[STOP] [2019-10-15 16:39:36] resolve_keys
[START] [2019-10-15 16:39:36] hold_for_later_1
[STOP] [2019-10-15 16:39:36] hold_for_later_1
[START] [2019-10-15 16:39:36] hold_for_later_2
[STOP] [2019-10-15 16:39:36] hold_for_later_2
[START] [2019-10-15 16:39:36] resolve_missing_parents
[STOP] [2019-10-15 16:39:36] resolve_missing_parents
[START] [2019-10-15 16:39:36] rebuild_nodes
[START] [2019-10-15 16:39:36] Flattener#flatten
[START] [2019-10-15 16:39:36] Flattener#study_resource
[START] [2019-10-15 16:39:36] Flattener#build_ancestry
[STOP] [2019-10-15 16:39:36] Flattener#build_ancestry
[INFO] [2019-10-15 16:39:36] 157 ancestry keys
[START] [2019-10-15 16:39:36] build_node_ancestors
[INFO] [2019-10-15 16:39:36] old ancestors deleted.
[STOP] [2019-10-15 16:39:37] build_node_ancestors
[START] [2019-10-15 16:39:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:39:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:39:37] Flattener#flatten
[STOP] [2019-10-15 16:39:37] rebuild_nodes
[START] [2019-10-15 16:39:37] resolve_missing_media_owners
[STOP] [2019-10-15 16:39:37] resolve_missing_media_owners
[START] [2019-10-15 16:39:37] sanitize_media_verbatims
[STOP] [2019-10-15 16:39:37] sanitize_media_verbatims
[START] [2019-10-15 16:39:37] queue_downloads
[STOP] [2019-10-15 16:39:37] queue_downloads
[START] [2019-10-15 16:39:37] parse_names
[WARN] [2019-10-15 16:39:37] I see 157 names which still need to be parsed.
[STOP] [2019-10-15 16:39:38] parse_names
[START] [2019-10-15 16:39:38] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:39:38] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:39:38] match_nodes
[START] [2019-10-15 16:39:38] map_all_nodes_to_pages
[STOP] [2019-10-15 16:39:51] map_all_nodes_to_pages
[INFO] [2019-10-15 16:39:51] Unmatched nodes (4 of 157): Titanocetus sammariensis (#51759736); Fuscoporia torulosus (#51759703); Magnoliophyta (#51759682); Magnoliopsida (#51759647)
[START] [2019-10-15 16:39:51] update_nodes
[STOP] [2019-10-15 16:39:51] update_nodes
[STOP] [2019-10-15 16:39:51] match_nodes
[START] [2019-10-15 16:39:51] reindex_search
[STOP] [2019-10-15 16:39:52] reindex_search
[START] [2019-10-15 16:39:52] normalize_units
[STOP] [2019-10-15 16:39:52] normalize_units
[START] [2019-10-15 16:39:52] calculate_statistics
[STOP] [2019-10-15 16:39:52] calculate_statistics
[START] [2019-10-15 16:39:52] complete_harvest_instance
[START] [2019-10-15 16:39:52] overall_tsv_creation
[INFO] [2019-10-15 16:39:52] Processing group of 157 in 1 batches of 10000
[INFO] [2019-10-15 16:40:36] 46 Traits (unfiltered)...
[INFO] [2019-10-15 16:40:50] 46 Traits (filtered)...
[INFO] [2019-10-15 16:40:50] 0 Associations (filtered)...
[INFO] [2019-10-15 16:41:28] 230 metadata added.
[INFO] [2019-10-15 16:41:28] 0 metadata added.
[INFO] [2019-10-15 16:41:28] Average Time: 75.61
[INFO] [2019-10-15 16:41:28] Total Time: 1m37s
[STOP] [2019-10-15 16:41:28] overall_tsv_creation
[INFO] [2019-10-15 16:41:28] Done. Check your files:
[INFO] [2019-10-15 16:41:28] (157 lines) /app/public/data/san_marino_sp_li/publish_nodes.tsv
[INFO] [2019-10-15 16:41:29] (681 lines) /app/public/data/san_marino_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:41:29] (157 lines) /app/public/data/san_marino_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-15 16:41:29] (47 lines) /app/public/data/san_marino_sp_li/publish_traits.tsv
[INFO] [2019-10-15 16:41:29] (231 lines) /app/public/data/san_marino_sp_li/publish_metadata.tsv
[STOP] [2019-10-15 16:41:29] complete_harvest_instance
[START] [2019-10-15 16:41:29] completed
[STOP] [2019-10-15 16:41:29] completed
[STOP] [2019-10-15 16:41:29] logged process, took 123.88
Latest Process

15 Oct 16:39 EXITED currently processing 0