Harvest for Saint Pierre et Miquelon Species List Created 15 Oct 16:28

Stage: completed
Fetched: 15 Oct 16:28
Validated: 15 Oct 16:28
Deltas Created 15 Oct 16:28
Units Normalized: 15 Oct 16:29
Ancestry Built: 15 Oct 16:28
Nodes Matched: 15 Oct 16:29
Names Parsed: 15 Oct 16:28
New Models Stored: 15 Oct 16:28
Indexed: 15 Oct 16:29
Completed: 15 Oct 16:30
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:28:37 -0400 by logger.rb/56815
[START] [2019-10-15 16:28:37] logged process
[START] [2019-10-15 16:28:37] create_harvest_instance
[STOP] [2019-10-15 16:28:37] create_harvest_instance
[START] [2019-10-15 16:28:37] fetch_files
[STOP] [2019-10-15 16:28:37] fetch_files
[START] [2019-10-15 16:28:37] validate_each_file
[STOP] [2019-10-15 16:28:37] validate_each_file
[START] [2019-10-15 16:28:37] convert_to_csv
[CMD] [2019-10-15 16:28:37] /usr/bin/sort /app/public/converted_csv/spemsl_refs_17061.csv > /app/public/converted_csv/spemsl_refs_17061.csv_sorted
[CMD] [2019-10-15 16:28:38] /usr/bin/sort /app/public/converted_csv/spemsl_nodes_17062.csv > /app/public/converted_csv/spemsl_nodes_17062.csv_sorted
[CMD] [2019-10-15 16:28:38] /usr/bin/sort /app/public/converted_csv/spemsl_occurrences_17063.csv > /app/public/converted_csv/spemsl_occurrences_17063.csv_sorted
[CMD] [2019-10-15 16:28:38] /usr/bin/sort /app/public/converted_csv/spemsl_measurements_17064.csv > /app/public/converted_csv/spemsl_measurements_17064.csv_sorted
[STOP] [2019-10-15 16:28:38] convert_to_csv
[START] [2019-10-15 16:28:39] calculate_delta
[CMD] [2019-10-15 16:28:39] echo "0a" > /app/public/diff/spemsl_refs_17061.diff
[CMD] [2019-10-15 16:28:39] tail -n +1 /app/public/converted_csv/spemsl_refs_17061.csv >> /app/public/diff/spemsl_refs_17061.diff
[CMD] [2019-10-15 16:28:39] echo "." >> /app/public/diff/spemsl_refs_17061.diff
[CMD] [2019-10-15 16:28:39] echo "0a" > /app/public/diff/spemsl_nodes_17062.diff
[CMD] [2019-10-15 16:28:40] tail -n +1 /app/public/converted_csv/spemsl_nodes_17062.csv >> /app/public/diff/spemsl_nodes_17062.diff
[CMD] [2019-10-15 16:28:40] echo "." >> /app/public/diff/spemsl_nodes_17062.diff
[CMD] [2019-10-15 16:28:40] echo "0a" > /app/public/diff/spemsl_occurrences_17063.diff
[CMD] [2019-10-15 16:28:40] tail -n +1 /app/public/converted_csv/spemsl_occurrences_17063.csv >> /app/public/diff/spemsl_occurrences_17063.diff
[CMD] [2019-10-15 16:28:41] echo "." >> /app/public/diff/spemsl_occurrences_17063.diff
[CMD] [2019-10-15 16:28:41] echo "0a" > /app/public/diff/spemsl_measurements_17064.diff
[CMD] [2019-10-15 16:28:41] tail -n +1 /app/public/converted_csv/spemsl_measurements_17064.csv >> /app/public/diff/spemsl_measurements_17064.diff
[CMD] [2019-10-15 16:28:42] echo "." >> /app/public/diff/spemsl_measurements_17064.diff
[STOP] [2019-10-15 16:28:42] calculate_delta
[START] [2019-10-15 16:28:42] parse_diff_and_store
[INFO] [2019-10-15 16:28:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:28:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:28:43] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:28:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:28:43] Storing 2 References
[INFO] [2019-10-15 16:28:43] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:28:43] Average Time: 0.0
[INFO] [2019-10-15 16:28:43] Total Time: 1s
[INFO] [2019-10-15 16:28:43] Storing 172 ScientificNames
[INFO] [2019-10-15 16:28:43] Processing group of 172 in 1 groups of 1000
[INFO] [2019-10-15 16:28:43] Average Time: 0.13
[INFO] [2019-10-15 16:28:43] Total Time: 1s
[INFO] [2019-10-15 16:28:43] Storing 172 Nodes
[INFO] [2019-10-15 16:28:43] Processing group of 172 in 1 groups of 1000
[INFO] [2019-10-15 16:28:44] Average Time: 0.06
[INFO] [2019-10-15 16:28:44] Total Time: 1s
[INFO] [2019-10-15 16:28:44] Storing 52 Occurrences
[INFO] [2019-10-15 16:28:44] Processing group of 52 in 1 groups of 1000
[INFO] [2019-10-15 16:28:44] Average Time: 0.01
[INFO] [2019-10-15 16:28:44] Total Time: 1s
[INFO] [2019-10-15 16:28:44] Storing 104 TraitsReferences
[INFO] [2019-10-15 16:28:44] Processing group of 104 in 1 groups of 1000
[INFO] [2019-10-15 16:28:44] Average Time: 0.04
[INFO] [2019-10-15 16:28:44] Total Time: 1s
[INFO] [2019-10-15 16:28:44] Storing 104 Traits
[INFO] [2019-10-15 16:28:44] Processing group of 104 in 1 groups of 1000
[INFO] [2019-10-15 16:28:44] Average Time: 0.08
[INFO] [2019-10-15 16:28:44] Total Time: 1s
[INFO] [2019-10-15 16:28:44] Storing 104 MetaTraits
[INFO] [2019-10-15 16:28:44] Processing group of 104 in 1 groups of 1000
[INFO] [2019-10-15 16:28:44] Average Time: 0.03
[INFO] [2019-10-15 16:28:44] Total Time: 1s
[STOP] [2019-10-15 16:28:44] parse_diff_and_store
[START] [2019-10-15 16:28:44] resolve_keys
[INFO] [2019-10-15 16:28:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:28:48] traits to occurrences...
[INFO] [2019-10-15 16:28:48] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:28:48] Traits to sex term...
[INFO] [2019-10-15 16:28:48] Traits to lifestage term...
[INFO] [2019-10-15 16:28:48] MetaTraits to traits...
[INFO] [2019-10-15 16:28:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:28:48] Assocs to occurrences...
[INFO] [2019-10-15 16:28:48] Assocs to nodes...
[INFO] [2019-10-15 16:28:48] Assoc to sex term...
[INFO] [2019-10-15 16:28:48] Assoc to lifestage term...
[STOP] [2019-10-15 16:28:48] resolve_keys
[START] [2019-10-15 16:28:48] hold_for_later_1
[STOP] [2019-10-15 16:28:48] hold_for_later_1
[START] [2019-10-15 16:28:48] hold_for_later_2
[STOP] [2019-10-15 16:28:48] hold_for_later_2
[START] [2019-10-15 16:28:48] resolve_missing_parents
[STOP] [2019-10-15 16:28:48] resolve_missing_parents
[START] [2019-10-15 16:28:48] rebuild_nodes
[START] [2019-10-15 16:28:48] Flattener#flatten
[START] [2019-10-15 16:28:48] Flattener#study_resource
[START] [2019-10-15 16:28:48] Flattener#build_ancestry
[STOP] [2019-10-15 16:28:48] Flattener#build_ancestry
[INFO] [2019-10-15 16:28:48] 172 ancestry keys
[START] [2019-10-15 16:28:48] build_node_ancestors
[INFO] [2019-10-15 16:28:48] old ancestors deleted.
[STOP] [2019-10-15 16:28:48] build_node_ancestors
[START] [2019-10-15 16:28:48] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:28:48] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:28:48] Flattener#flatten
[STOP] [2019-10-15 16:28:48] rebuild_nodes
[START] [2019-10-15 16:28:48] resolve_missing_media_owners
[STOP] [2019-10-15 16:28:48] resolve_missing_media_owners
[START] [2019-10-15 16:28:48] sanitize_media_verbatims
[STOP] [2019-10-15 16:28:48] sanitize_media_verbatims
[START] [2019-10-15 16:28:48] queue_downloads
[STOP] [2019-10-15 16:28:48] queue_downloads
[START] [2019-10-15 16:28:48] parse_names
[WARN] [2019-10-15 16:28:48] I see 172 names which still need to be parsed.
[STOP] [2019-10-15 16:28:50] parse_names
[START] [2019-10-15 16:28:50] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:28:50] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:28:50] match_nodes
[START] [2019-10-15 16:28:50] map_all_nodes_to_pages
[STOP] [2019-10-15 16:29:05] map_all_nodes_to_pages
[INFO] [2019-10-15 16:29:05] Unmatched nodes (5 of 172): Scytosiphonales (#51755981); Magnoliophyta (#51756036); Magnoliopsida (#51756035); Psilotopsida (#51756116); Plectocarpon lichenum (#51756093)
[START] [2019-10-15 16:29:05] update_nodes
[STOP] [2019-10-15 16:29:05] update_nodes
[STOP] [2019-10-15 16:29:05] match_nodes
[START] [2019-10-15 16:29:05] reindex_search
[STOP] [2019-10-15 16:29:06] reindex_search
[START] [2019-10-15 16:29:06] normalize_units
[STOP] [2019-10-15 16:29:06] normalize_units
[START] [2019-10-15 16:29:06] calculate_statistics
[STOP] [2019-10-15 16:29:06] calculate_statistics
[START] [2019-10-15 16:29:06] complete_harvest_instance
[START] [2019-10-15 16:29:06] overall_tsv_creation
[INFO] [2019-10-15 16:29:06] Processing group of 172 in 1 batches of 10000
[INFO] [2019-10-15 16:29:50] 52 Traits (unfiltered)...
[INFO] [2019-10-15 16:30:04] 52 Traits (filtered)...
[INFO] [2019-10-15 16:30:04] 0 Associations (filtered)...
[INFO] [2019-10-15 16:30:42] 260 metadata added.
[INFO] [2019-10-15 16:30:42] 0 metadata added.
[INFO] [2019-10-15 16:30:42] Average Time: 75.16
[INFO] [2019-10-15 16:30:42] Total Time: 1m36s
[STOP] [2019-10-15 16:30:42] overall_tsv_creation
[INFO] [2019-10-15 16:30:42] Done. Check your files:
[INFO] [2019-10-15 16:30:42] (172 lines) /app/public/data/spemsl/publish_nodes.tsv
[INFO] [2019-10-15 16:30:42] (740 lines) /app/public/data/spemsl/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:30:43] (172 lines) /app/public/data/spemsl/publish_scientific_names.tsv
[INFO] [2019-10-15 16:30:43] (53 lines) /app/public/data/spemsl/publish_traits.tsv
[INFO] [2019-10-15 16:30:43] (261 lines) /app/public/data/spemsl/publish_metadata.tsv
[STOP] [2019-10-15 16:30:43] complete_harvest_instance
[START] [2019-10-15 16:30:43] completed
[STOP] [2019-10-15 16:30:43] completed
[STOP] [2019-10-15 16:30:43] logged process, took 126.35
Latest Process

15 Oct 16:28 EXITED currently processing 0