Harvest for Territory of the French Southern and Antarctic Lands Created 16 Oct 12:06

Stage: completed
Fetched: 16 Oct 12:06
Validated: 16 Oct 12:06
Deltas Created 16 Oct 12:06
Units Normalized: 16 Oct 12:08
Ancestry Built: 16 Oct 12:07
Nodes Matched: 16 Oct 12:08
Names Parsed: 16 Oct 12:07
New Models Stored: 16 Oct 12:06
Indexed: 16 Oct 12:08
Completed: 16 Oct 12:09
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 12:06:47 -0400 by logger.rb/56815
[START] [2019-10-16 12:06:47] logged process
[START] [2019-10-16 12:06:47] create_harvest_instance
[STOP] [2019-10-16 12:06:48] create_harvest_instance
[START] [2019-10-16 12:06:48] fetch_files
[STOP] [2019-10-16 12:06:48] fetch_files
[START] [2019-10-16 12:06:48] validate_each_file
[STOP] [2019-10-16 12:06:48] validate_each_file
[START] [2019-10-16 12:06:48] convert_to_csv
[CMD] [2019-10-16 12:06:48] /usr/bin/sort /app/public/converted_csv/territory_french_refs_17417.csv > /app/public/converted_csv/territory_french_refs_17417.csv_sorted
[CMD] [2019-10-16 12:06:48] /usr/bin/sort /app/public/converted_csv/territory_french_nodes_17418.csv > /app/public/converted_csv/territory_french_nodes_17418.csv_sorted
[CMD] [2019-10-16 12:06:49] /usr/bin/sort /app/public/converted_csv/territory_french_occurrences_17419.csv > /app/public/converted_csv/territory_french_occurrences_17419.csv_sorted
[CMD] [2019-10-16 12:06:49] /usr/bin/sort /app/public/converted_csv/territory_french_measurements_17420.csv > /app/public/converted_csv/territory_french_measurements_17420.csv_sorted
[STOP] [2019-10-16 12:06:49] convert_to_csv
[START] [2019-10-16 12:06:49] calculate_delta
[CMD] [2019-10-16 12:06:49] echo "0a" > /app/public/diff/territory_french_refs_17417.diff
[CMD] [2019-10-16 12:06:49] tail -n +1 /app/public/converted_csv/territory_french_refs_17417.csv >> /app/public/diff/territory_french_refs_17417.diff
[CMD] [2019-10-16 12:06:50] echo "." >> /app/public/diff/territory_french_refs_17417.diff
[CMD] [2019-10-16 12:06:50] echo "0a" > /app/public/diff/territory_french_nodes_17418.diff
[CMD] [2019-10-16 12:06:50] tail -n +1 /app/public/converted_csv/territory_french_nodes_17418.csv >> /app/public/diff/territory_french_nodes_17418.diff
[CMD] [2019-10-16 12:06:51] echo "." >> /app/public/diff/territory_french_nodes_17418.diff
[CMD] [2019-10-16 12:06:51] echo "0a" > /app/public/diff/territory_french_occurrences_17419.diff
[CMD] [2019-10-16 12:06:51] tail -n +1 /app/public/converted_csv/territory_french_occurrences_17419.csv >> /app/public/diff/territory_french_occurrences_17419.diff
[CMD] [2019-10-16 12:06:51] echo "." >> /app/public/diff/territory_french_occurrences_17419.diff
[CMD] [2019-10-16 12:06:52] echo "0a" > /app/public/diff/territory_french_measurements_17420.diff
[CMD] [2019-10-16 12:06:52] tail -n +1 /app/public/converted_csv/territory_french_measurements_17420.csv >> /app/public/diff/territory_french_measurements_17420.diff
[CMD] [2019-10-16 12:06:52] echo "." >> /app/public/diff/territory_french_measurements_17420.diff
[STOP] [2019-10-16 12:06:52] calculate_delta
[START] [2019-10-16 12:06:53] parse_diff_and_store
[INFO] [2019-10-16 12:06:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 12:06:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 12:06:54] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 12:06:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 12:06:57] Storing 2 References
[INFO] [2019-10-16 12:06:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 12:06:57] Average Time: 0.0
[INFO] [2019-10-16 12:06:57] Total Time: 1s
[INFO] [2019-10-16 12:06:57] Storing 1101 ScientificNames
[INFO] [2019-10-16 12:06:57] Processing group of 1101 in 2 groups of 1000
[INFO] [2019-10-16 12:06:58] Average Time: 0.265
[INFO] [2019-10-16 12:06:58] Total Time: 1s
[INFO] [2019-10-16 12:06:58] Storing 1101 Nodes
[INFO] [2019-10-16 12:06:58] Processing group of 1101 in 2 groups of 1000
[INFO] [2019-10-16 12:06:58] Average Time: 0.205
[INFO] [2019-10-16 12:06:58] Total Time: 1s
[INFO] [2019-10-16 12:06:58] Storing 482 Occurrences
[INFO] [2019-10-16 12:06:58] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-16 12:06:58] Average Time: 0.07
[INFO] [2019-10-16 12:06:58] Total Time: 1s
[INFO] [2019-10-16 12:06:58] Storing 970 TraitsReferences
[INFO] [2019-10-16 12:06:58] Processing group of 970 in 1 groups of 1000
[INFO] [2019-10-16 12:06:58] Average Time: 0.15
[INFO] [2019-10-16 12:06:58] Total Time: 1s
[INFO] [2019-10-16 12:06:58] Storing 969 Traits
[INFO] [2019-10-16 12:06:58] Processing group of 969 in 1 groups of 1000
[INFO] [2019-10-16 12:06:59] Average Time: 0.41
[INFO] [2019-10-16 12:06:59] Total Time: 1s
[INFO] [2019-10-16 12:06:59] Storing 970 MetaTraits
[INFO] [2019-10-16 12:06:59] Processing group of 970 in 1 groups of 1000
[INFO] [2019-10-16 12:06:59] Average Time: 0.14
[INFO] [2019-10-16 12:06:59] Total Time: 1s
[STOP] [2019-10-16 12:06:59] parse_diff_and_store
[START] [2019-10-16 12:06:59] resolve_keys
[INFO] [2019-10-16 12:07:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 12:07:06] traits to occurrences...
[INFO] [2019-10-16 12:07:07] traits to nodes (through occurrences)...
[INFO] [2019-10-16 12:07:07] Traits to sex term...
[INFO] [2019-10-16 12:07:07] Traits to lifestage term...
[INFO] [2019-10-16 12:07:08] MetaTraits to traits...
[INFO] [2019-10-16 12:07:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 12:07:08] Assocs to occurrences...
[INFO] [2019-10-16 12:07:08] Assocs to nodes...
[INFO] [2019-10-16 12:07:08] Assoc to sex term...
[INFO] [2019-10-16 12:07:08] Assoc to lifestage term...
[STOP] [2019-10-16 12:07:08] resolve_keys
[START] [2019-10-16 12:07:08] hold_for_later_1
[STOP] [2019-10-16 12:07:08] hold_for_later_1
[START] [2019-10-16 12:07:08] hold_for_later_2
[STOP] [2019-10-16 12:07:08] hold_for_later_2
[START] [2019-10-16 12:07:08] resolve_missing_parents
[STOP] [2019-10-16 12:07:09] resolve_missing_parents
[START] [2019-10-16 12:07:09] rebuild_nodes
[START] [2019-10-16 12:07:09] Flattener#flatten
[START] [2019-10-16 12:07:09] Flattener#study_resource
[START] [2019-10-16 12:07:09] Flattener#build_ancestry
[STOP] [2019-10-16 12:07:09] Flattener#build_ancestry
[INFO] [2019-10-16 12:07:09] 1101 ancestry keys
[START] [2019-10-16 12:07:09] build_node_ancestors
[INFO] [2019-10-16 12:07:09] old ancestors deleted.
[STOP] [2019-10-16 12:07:09] build_node_ancestors
[START] [2019-10-16 12:07:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 12:07:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 12:07:09] Flattener#flatten
[STOP] [2019-10-16 12:07:09] rebuild_nodes
[START] [2019-10-16 12:07:09] resolve_missing_media_owners
[STOP] [2019-10-16 12:07:09] resolve_missing_media_owners
[START] [2019-10-16 12:07:09] sanitize_media_verbatims
[STOP] [2019-10-16 12:07:09] sanitize_media_verbatims
[START] [2019-10-16 12:07:09] queue_downloads
[STOP] [2019-10-16 12:07:09] queue_downloads
[START] [2019-10-16 12:07:09] parse_names
[WARN] [2019-10-16 12:07:09] I see 1101 names which still need to be parsed.
[STOP] [2019-10-16 12:07:11] parse_names
[START] [2019-10-16 12:07:11] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 12:07:11] denormalize_canonical_names_to_nodes
[START] [2019-10-16 12:07:11] match_nodes
[START] [2019-10-16 12:07:11] map_all_nodes_to_pages
[STOP] [2019-10-16 12:08:11] map_all_nodes_to_pages
[INFO] [2019-10-16 12:08:11] 36 Unmatched nodes (of 1101)! That's too many to output. First 10: Pelecanoididae (#52368059); Eudyptes crestatus (#52367785); Bromus erecta (#52367795); Orchomene plebs (#52368288); Phippsiella kergueleni (#52368253); Cardenioidae (#52367950); Blechnum penna-marina (#52367619); Tortula princeps (#52368562); Limoida (#52367638); Racomitrium didyma (#52367683)
[START] [2019-10-16 12:08:11] update_nodes
[STOP] [2019-10-16 12:08:11] update_nodes
[STOP] [2019-10-16 12:08:11] match_nodes
[START] [2019-10-16 12:08:11] reindex_search
[STOP] [2019-10-16 12:08:14] reindex_search
[START] [2019-10-16 12:08:14] normalize_units
[STOP] [2019-10-16 12:08:14] normalize_units
[START] [2019-10-16 12:08:14] calculate_statistics
[STOP] [2019-10-16 12:08:14] calculate_statistics
[START] [2019-10-16 12:08:14] complete_harvest_instance
[START] [2019-10-16 12:08:14] overall_tsv_creation
[INFO] [2019-10-16 12:08:14] Processing group of 1101 in 1 batches of 10000
[INFO] [2019-10-16 12:09:02] 482 Traits (unfiltered)...
[INFO] [2019-10-16 12:09:16] 482 Traits (filtered)...
[INFO] [2019-10-16 12:09:16] 0 Associations (filtered)...
[INFO] [2019-10-16 12:09:54] 2410 metadata added.
[INFO] [2019-10-16 12:09:54] 0 metadata added.
[INFO] [2019-10-16 12:09:54] Average Time: 78.71
[INFO] [2019-10-16 12:09:54] Total Time: 1m40s
[STOP] [2019-10-16 12:09:54] overall_tsv_creation
[INFO] [2019-10-16 12:09:54] Done. Check your files:
[INFO] [2019-10-16 12:09:54] (1101 lines) /app/public/data/territory_french/publish_nodes.tsv
[INFO] [2019-10-16 12:09:54] (1727 lines) /app/public/data/territory_french/publish_node_ancestors.tsv
[INFO] [2019-10-16 12:09:55] (1101 lines) /app/public/data/territory_french/publish_scientific_names.tsv
[INFO] [2019-10-16 12:09:55] (483 lines) /app/public/data/territory_french/publish_traits.tsv
[INFO] [2019-10-16 12:09:55] (2411 lines) /app/public/data/territory_french/publish_metadata.tsv
[STOP] [2019-10-16 12:09:55] complete_harvest_instance
[START] [2019-10-16 12:09:55] completed
[STOP] [2019-10-16 12:09:55] completed
[STOP] [2019-10-16 12:09:55] logged process, took 187.7
Latest Process

16 Oct 12:06 EXITED currently processing 0